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"Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/75.outputCTF_GRID_01_DATA_Images-Disc1_GridSquare_3271608_Data_FoilHole_3276325_Data_3274746_3274748_20210205_072544_Fractions_aligned_mic_DW_ctf.jpg" }, { "_defocusU": "11425.76", "_defocusV": "11039.13", "_defocusAngle": "159.79000000000002", "_defocusRatio": "1.0350235933447656", "_psdFile": "Runs/000075_ProtGctf/extra/GRID_01_DATA_Images-Disc1_GridSquare_3271608_Data_FoilHole_3276326_Data_3274746_3274748_20210205_072716_Fractions_aligned_mic_DW_ctf.mrc", "_micObj": "Micrograph (4096 x 4096, 0.85 \u212b/px)", "_resolution": "3.49", "_fitQuality": "0.013628", "item_id": 3, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/75.outputCTF_GRID_01_DATA_Images-Disc1_GridSquare_3271608_Data_FoilHole_3276326_Data_3274746_3274748_20210205_072716_Fractions_aligned_mic_DW_ctf.jpg" } ] } ], "summary": "CTF estimation of 4841 micrographs.Input: SetOfMicrographs (4841 items, 4096 x 4096, 0.85 \u212b/px) \nOutput: SetOfCTF (4841 items)", "log": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/75_ProtGctf.log", "plugin": "gctf", "pluginVersion": "3.0.12" }, { "object.className": "CistemProtCTFFind", "object.id": "149", "object.label": "cistem - ctffind4", "object.comment": "", "_useQueue": false, "_prerequisites": "", "_queueParams": null, "runName": null, "runMode": 0, "recalculate": false, "sqliteFile": null, "inputType": 1, "avgFrames": 3, "usePowerSpectra": false, "windowSize": 1024, "lowRes": 20.0, "highRes": 2.13, "minDefocus": 4000.0, "maxDefocus": 50000.0, "stepDefocus": 50.0, "slowSearch": false, "fixAstig": false, "astigmatism": 100.0, "findPhaseShift": false, "minPhaseShift": 0.0, "maxPhaseShift": 180.0, "stepPhaseShift": 10.0, "hostName": "localhost", "numberOfThreads": 30, "numberOfMpi": 1, "streamingWarning": null, "streamingSleepOnWait": 0, "streamingBatchSize": 1, "inputMicrographs": "2.outputMicrographs", "output": [ { "outputName": "149.outputCTF", "outputType": "SetOfCTF", "outputSize": 4841, "outputItems": [ { "_defocusU": "13699.841797", "_defocusV": "13305.478516", "_defocusAngle": "166.467176", "_defocusRatio": "1.0296391655907582", "_psdFile": "Runs/000149_CistemProtCTFFind/extra/GRID_01_DATA_Images-Disc1_GridSquare_3271608_Data_FoilHole_3276324_Data_3274746_3274748_20210205_072410_Fractions_aligned_mic_DW_ctf.mrc", "_micObj": "Micrograph (4096 x 4096, 0.85 \u212b/px)", "_resolution": "7.137762", "_fitQuality": "0.013702", "item_id": 1, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/149.outputCTF_GRID_01_DATA_Images-Disc1_GridSquare_3271608_Data_FoilHole_3276324_Data_3274746_3274748_20210205_072410_Fractions_aligned_mic_DW_ctf.jpg" }, { "_defocusU": "12371.224609", "_defocusV": "11987.53418", "_defocusAngle": "161.187397", "_defocusRatio": "1.0320074523449658", "_psdFile": 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"item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/149.outputCTF_GRID_01_DATA_Images-Disc1_GridSquare_3271608_Data_FoilHole_3276326_Data_3274746_3274748_20210205_072716_Fractions_aligned_mic_DW_ctf.jpg" } ] } ], "summary": "CTF estimation of 4841 micrographs.Input: SetOfMicrographs (4841 items, 4096 x 4096, 0.85 \u212b/px) \nOutput: SetOfCTF (4841 items)", "log": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/149_CistemProtCTFFind.log", "plugin": "cistem", "pluginVersion": "3.1.0" }, { "object.className": "XmippProtCTFConsensus", "object.id": "212", "object.label": "xmipp3 - ctf consensus", "object.comment": "", "_useQueue": false, "_prerequisites": "", "_queueParams": null, "runName": null, "runMode": 0, "useDefocus": true, "minDefocus": 3000.0, "maxDefocus": 40000.0, "useAstigmatism": true, "astigmatism": 1000.0, "useResolution": true, "resolution": 5.0, "useCritXmipp": false, "critFirstZero": 5.0, 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"Runs/000149_CistemProtCTFFind/extra/GRID_01_DATA_Images-Disc1_GridSquare_3271608_Data_FoilHole_3276339_Data_3274746_3274748_20210205_074730_Fractions_aligned_mic_DW_ctf.mrc", "_astigmatism": "401.6708395000005", "item_id": 16, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/212.outputCTFDiscarded_GRID_01_DATA_Images-Disc1_GridSquare_3271608_Data_FoilHole_3276339_Data_3274746_3274748_20210205_074730_Fractions_aligned_mic_DW_ctf.jpg" }, { "_defocusU": "11245.5368065", "_defocusV": "11167.6606835", "_defocusAngle": "59.08814149999999", "_defocusRatio": "1.0069733604205096", "_psdFile": "Runs/000075_ProtGctf/extra/GRID_01_DATA_Images-Disc1_GridSquare_3271608_Data_FoilHole_3276354_Data_3274746_3274748_20210205_081049_Fractions_aligned_mic_DW_ctf.mrc", "_micObj": "Micrograph (4096 x 4096, 0.85 \u212b/px)", "_resolution": "13.794", "_fitQuality": "0.077606", "_consensus_resolution": "167.38814320785423", "_ctf2_defocus_diff": "6711.666387000001", "_ctf2_defocusAngle_diff": "74.016283", "_ctf2_resolution": "1434.690063", "_ctf2_fitQuality": "0.022572", "_ctf2_psdFile": "Runs/000149_CistemProtCTFFind/extra/GRID_01_DATA_Images-Disc1_GridSquare_3271608_Data_FoilHole_3276354_Data_3274746_3274748_20210205_081049_Fractions_aligned_mic_DW_ctf.mrc", "_astigmatism": "77.876123", "item_id": 31, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/212.outputCTFDiscarded_GRID_01_DATA_Images-Disc1_GridSquare_3271608_Data_FoilHole_3276354_Data_3274746_3274748_20210205_081049_Fractions_aligned_mic_DW_ctf.jpg" }, { "_defocusU": "17310.334961", "_defocusV": "16950.166796999998", "_defocusAngle": "158.287641", "_defocusRatio": "1.0212486501350386", "_psdFile": "Runs/000075_ProtGctf/extra/GRID_01_DATA_Images-Disc1_GridSquare_3271608_Data_FoilHole_3276380_Data_3274746_3274748_20210205_085222_Fractions_aligned_mic_DW_ctf.mrc", "_micObj": "Micrograph (4096 x 4096, 0.85 \u212b/px)", "_resolution": "2.969", "_fitQuality": "0.007333", "_consensus_resolution": "4.83326485153436", "_ctf2_defocus_diff": "284.66992200000095", "_ctf2_defocusAngle_diff": "28.535281999999995", "_ctf2_resolution": "8.80178", "_ctf2_fitQuality": "0.023412", "_ctf2_psdFile": "Runs/000149_CistemProtCTFFind/extra/GRID_01_DATA_Images-Disc1_GridSquare_3271608_Data_FoilHole_3276380_Data_3274746_3274748_20210205_085222_Fractions_aligned_mic_DW_ctf.mrc", "_astigmatism": "360.16816400000243", "item_id": 57, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/212.outputCTFDiscarded_GRID_01_DATA_Images-Disc1_GridSquare_3271608_Data_FoilHole_3276380_Data_3274746_3274748_20210205_085222_Fractions_aligned_mic_DW_ctf.jpg" } ] }, { "outputName": "212.outputMicrographsDiscarded", "outputType": "SetOfMicrographs", "outputSize": 511, "outputItems": [ { "_index": "0", "_filename": "Runs/000002_ProtImportMicrographs/extra/GRID_01_DATA_Images-Disc1_GridSquare_3271608_Data_FoilHole_3276339_Data_3274746_3274748_20210205_074730_Fractions_aligned_mic_DW.mrc", "_samplingRate": "0.855", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_micName": "GRID_01_DATA_Images-Disc1_GridSquare_3271608_Data_FoilHole_3276339_Data_3274746_3274748_20210205_074730_Fractions_aligned_mic_DW.mrc", "item_id": 16, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/212.outputMicrographsDiscarded_0_GRID_01_DATA_Images-Disc1_GridSquare_3271608_Data_FoilHole_3276339_Data_3274746_3274748_20210205_074730_Fractions_aligned_mic_DW.jpg" }, { "_index": "0", "_filename": "Runs/000002_ProtImportMicrographs/extra/GRID_01_DATA_Images-Disc1_GridSquare_3271608_Data_FoilHole_3276354_Data_3274746_3274748_20210205_081049_Fractions_aligned_mic_DW.mrc", "_samplingRate": "0.855", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_micName": "GRID_01_DATA_Images-Disc1_GridSquare_3271608_Data_FoilHole_3276354_Data_3274746_3274748_20210205_081049_Fractions_aligned_mic_DW.mrc", "item_id": 31, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/212.outputMicrographsDiscarded_0_GRID_01_DATA_Images-Disc1_GridSquare_3271608_Data_FoilHole_3276354_Data_3274746_3274748_20210205_081049_Fractions_aligned_mic_DW.jpg" }, { "_index": "0", "_filename": "Runs/000002_ProtImportMicrographs/extra/GRID_01_DATA_Images-Disc1_GridSquare_3271608_Data_FoilHole_3276380_Data_3274746_3274748_20210205_085222_Fractions_aligned_mic_DW.mrc", "_samplingRate": "0.855", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_micName": "GRID_01_DATA_Images-Disc1_GridSquare_3271608_Data_FoilHole_3276380_Data_3274746_3274748_20210205_085222_Fractions_aligned_mic_DW.mrc", "item_id": 57, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/212.outputMicrographsDiscarded_0_GRID_01_DATA_Images-Disc1_GridSquare_3271608_Data_FoilHole_3276380_Data_3274746_3274748_20210205_085222_Fractions_aligned_mic_DW.jpg" } ] } ], "summary": "4841/4841 CTF processed (4330 accepted and 511 discarded).*General Criteria*: - _Defocus_. Range: 3000 - 40000 (72 discarded) - _Astigmatism_. Threshold: 1000 (181 discarded) - _Resolution_. Threshold: 5 (452 discarded)*CTF consensus*: - _Consensus resolution. Threshold_: 4 (381 discarded) > _Primary CTF_: gctf - ctf estimation > _Reference CTF_: cistem - ctffind4Input: SetOfCTF (4841 items) \nInput: SetOfCTF (4841 items) \nOutput: SetOfCTF (4330 items)SetOfMicrographs (4330 items, 4096 x 4096, 0.85 \u212b/px)SetOfCTF (511 items)SetOfMicrographs (511 items, 4096 x 4096, 0.85 \u212b/px)", "log": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/212_XmippProtCTFConsensus.log", "plugin": "xmipp3" }, { "object.className": "SphireProtCRYOLOPicking", "object.id": "326", "object.label": "sphire - cryolo picking", "object.comment": "", "_useQueue": false, "_prerequisites": "", "_queueParams": null, "runName": null, "runMode": 0, "inputModelFrom": 0, "conservPickVar": 0.3, "lowPassFilter": true, "absCutOffFreq": 0.1, "numCpus": 4, "input_size": 1024, "boxSize": 0, "max_box_per_image": 600, "useGpu": true, "gpuList": "1", "hostName": "localhost", "numberOfThreads": 1, "numberOfMpi": 1, "streamingWarning": null, "streamingSleepOnWait": 0, "streamingBatchSize": 16, "inputMicrographs": "212.outputMicrographs", "output": [ { "outputName": "326.outputCoordinates", "outputType": "SetOfCoordinates", "outputSize": 879303, "outputItems": [ { "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/326.outputCoordinates_GRID_01_DATA_Images-Disc1_GridSquare_3271608_Data_FoilHole_3276324_Data_3274746_3274748_20210205_072410_Fractions_aligned_mic_DW.jpg" }, { "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/326.outputCoordinates_GRID_01_DATA_Images-Disc1_GridSquare_3271608_Data_FoilHole_3276325_Data_3274746_3274748_20210205_072544_Fractions_aligned_mic_DW.jpg" }, { "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/326.outputCoordinates_GRID_01_DATA_Images-Disc1_GridSquare_3271608_Data_FoilHole_3276326_Data_3274746_3274748_20210205_072716_Fractions_aligned_mic_DW.jpg" } ] }, { "outputName": "326.boxsize", "outputType": "Integer", "outputItems": [ { "item_id": 577 } ] } ], "summary": "Picking using (GENERAL) model: \n/home/spa/scipion/software/em/cryolo_model-202005_N63_c17/gmodel_phosnet_202005_N63_c17.h5Input: SetOfMicrographs (4330 items, 4096 x 4096, 0.85 \u212b/px) \nOutput: SetOfCoordinates (879303 items, 198 x 198)198", "log": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/326_SphireProtCRYOLOPicking.log", "plugin": "sphire", "pluginVersion": "3.0.6" }, { "object.className": "ProtImportAverages", "object.id": "379", "object.label": "pwem - import averages_2refs", "object.comment": "", "_useQueue": false, "_prerequisites": "", "_queueParams": null, "runName": null, "runMode": 0, "importFrom": 0, "filesPath": "/home/spa/ScipionUserData/projects/2021_05_25_daniel-luque_000036/Runs/000649_ProtUserSubSet/averages_export_2refs.stk", "filesPattern": null, "copyFiles": false, "emxFile": null, "alignType": 0, "mdFile": null, "starFile": null, "ignoreIdColumn": false, "sqliteFile": null, "frealignLabel": null, "stackFile": null, "parFile": null, "lstFile": null, "samplingRate": 0.74, "haveDataBeenPhaseFlipped": false, "acquisitionWizard": null, "voltage": 300.0, "sphericalAberration": 2.7, "amplitudeContrast": 0.1, "magnification": 50000, "dataStreaming": false, "timeout": 43200, "fileTimeout": 30, "output": [ { "outputName": "379.outputAverages", "outputType": "SetOfAverages", "outputSize": 2, "outputItems": [ { "_index": "1", "_filename": "Runs/000379_ProtImportAverages/extra/averages_export_2refs.stk", "_samplingRate": "0.74", "_acquisition": "\n mag=50000.0\n volt= 300.0\n Cs=2.7\n Q0=0.1\n\n", "_micId": "None", "_classId": "None", "item_id": 1, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/379.outputAverages_1_averages_export_2refs.jpg" }, { "_index": "2", "_filename": "Runs/000379_ProtImportAverages/extra/averages_export_2refs.stk", "_samplingRate": "0.74", "_acquisition": "\n mag=50000.0\n volt= 300.0\n Cs=2.7\n Q0=0.1\n\n", "_micId": "None", "_classId": "None", "item_id": 2, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/379.outputAverages_2_averages_export_2refs.jpg" } ] } ], "summary": "*2* Averages imported from /home/spa/ScipionUserData/projects/2021_05_25_daniel-luque_000036/Runs/000649_ProtUserSubSet/averages_export_2refs.stkIs the data phase flipped : FalseSampling rate : *0.74* \u212b/pxOutput: SetOfAverages (2 items, 564 x 564, 0.74 \u212b/px)", "log": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/379_ProtImportAverages.log", "plugin": "pwem", "pluginVersion": "3.0.10" }, { "object.className": "ProtGautomatch", "object.id": "452", "object.label": "gautomatch - auto-picking", "object.comment": "", "_useQueue": false, "_prerequisites": "", "_queueParams": null, "runName": null, "runMode": 0, "invertTemplatesContrast": true, "angStep": 5, "micrographsSelection": 0, "micrographsNumber": 10, "threshold": 0.1, "particleSize": 85, "gpuList": "3", "advanced": true, "boxSize": -1, "minDist": 300, "speed": 2, "advLabel": null, "localSigmaCutoff": 1.2, "localSigmaDiam": 100, "localAvgMin": -1.0, "localAvgMax": 1.0, "localAvgDiam": 100, "lowPass": 30, "highPass": 1000, "preFilt": false, "prelowPass": 8, "prehighPass": 1000, "detectIce": true, "templateNorm": 1, "doBandpass": true, "exclusive": false, "writeCC": false, "writeFilt": false, "writeBg": false, "writeBgSub": false, "writeSigma": false, "writeMsk": false, "streamingWarning": null, "streamingSleepOnWait": 0, "streamingBatchSize": 1, "hostName": "localhost", "numberOfThreads": 1, "numberOfMpi": 1, "inputMicrographs": "212.outputMicrographs", "inputReferences": "379.outputAverages", "output": [ { "outputName": "452.outputCoordinates", "outputType": "SetOfCoordinates", "outputSize": 1016357, "outputItems": [ { "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/452.outputCoordinates_GRID_01_DATA_Images-Disc1_GridSquare_3271608_Data_FoilHole_3276324_Data_3274746_3274748_20210205_072410_Fractions_aligned_mic_DW.jpg" }, { "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/452.outputCoordinates_GRID_01_DATA_Images-Disc1_GridSquare_3271608_Data_FoilHole_3276325_Data_3274746_3274748_20210205_072544_Fractions_aligned_mic_DW.jpg" }, { "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/452.outputCoordinates_GRID_01_DATA_Images-Disc1_GridSquare_3271608_Data_FoilHole_3276326_Data_3274746_3274748_20210205_072716_Fractions_aligned_mic_DW.jpg" } ] } ], "summary": "Number of input micrographs: 4330Number of particles picked: 1016357Particle size: 564 pxThreshold min: 0.10Input: SetOfMicrographs (4330 items, 4096 x 4096, 0.85 \u212b/px) \nInput: SetOfAverages (2 items, 564 x 564, 0.74 \u212b/px) \nOutput: SetOfCoordinates (1016357 items, 564 x 564)", "log": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/452_ProtGautomatch.log", "plugin": "gautomatch", "pluginVersion": "3.0.13" }, { "object.className": "XmippProtConsensusPicking", "object.id": "533", "object.label": "xmipp3 - picking consensus", "object.comment": "", "_useQueue": false, "_prerequisites": "", "_queueParams": null, "runName": null, "runMode": 0, "inputCoordinates": [ "452.outputCoordinates", "326.outputCoordinates" ], "consensusRadius": 50, "consensus": -1, "mode": 0, "output": [ { "outputName": "533.consensusCoordinates", "outputType": "SetOfCoordinates", "outputSize": 509466, "outputItems": [ { "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/533.consensusCoordinates_GRID_01_DATA_Images-Disc1_GridSquare_3271608_Data_FoilHole_3276324_Data_3274746_3274748_20210205_072410_Fractions_aligned_mic_DW.jpg" }, { "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/533.consensusCoordinates_GRID_01_DATA_Images-Disc1_GridSquare_3271608_Data_FoilHole_3276325_Data_3274746_3274748_20210205_072544_Fractions_aligned_mic_DW.jpg" }, { "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/533.consensusCoordinates_GRID_01_DATA_Images-Disc1_GridSquare_3271608_Data_FoilHole_3276326_Data_3274746_3274748_20210205_072716_Fractions_aligned_mic_DW.jpg" } ] } ], "summary": "Method 1 gautomatch - auto-pickingMethod 2 sphire - cryolo pickingRadius = 50Consensus = -1Input: SetOfCoordinates (1016357 items, 564 x 564) \nInput: SetOfCoordinates (879303 items, 198 x 198) \nOutput: SetOfCoordinates (509466 items, 564 x 564)", "log": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/533_XmippProtConsensusPicking.log", "plugin": "xmipp3" }, { "object.className": "ProtRelionExtractParticles", "object.id": "720", "object.label": "relion - particles extraction_consensus_bin1", "object.comment": "", "_useQueue": false, "_prerequisites": "", "_queueParams": null, "runName": null, "runMode": 0, "downsampleType": 0, "boxSize": 492, "doRescale": false, "rescaledSize": 300, "doInvert": true, "doNormalize": true, "backDiameter": 490, "stddevWhiteDust": -1.0, "stddevBlackDust": -1.0, "streamingWarning": null, "streamingSleepOnWait": 0, "streamingBatchSize": 0, "hostName": "localhost", "numberOfMpi": 30, "ctfRelations": "212.outputCTF", "inputCoordinates": "533.consensusCoordinates", "output": [ { "outputName": "720.outputParticles", "outputType": "SetOfParticles", "outputSize": 509466, "outputItems": [ { "_index": "1", "_filename": "Runs/000720_ProtRelionExtractParticles/extra/mic_000021.mrcs", "_samplingRate": "0.855", "_ctfModel": "defU=25831.73, defV=25543.44, ast=288.28, psh=None, res=4.20, fit=0.04", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_coordinate": "Coordinate", "_micId": "21", "_classId": "None", "_rlnOpticsGroup": "1", "item_id": 1, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/720.outputParticles_1_mic_000021.jpg" }, { "_index": "2", "_filename": "Runs/000720_ProtRelionExtractParticles/extra/mic_000021.mrcs", "_samplingRate": "0.855", "_ctfModel": "defU=25831.73, defV=25543.44, ast=288.28, psh=None, res=4.20, fit=0.04", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_coordinate": "Coordinate", "_micId": "21", "_classId": "None", "_rlnOpticsGroup": "1", "item_id": 2, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/720.outputParticles_2_mic_000021.jpg" }, { "_index": "3", "_filename": "Runs/000720_ProtRelionExtractParticles/extra/mic_000021.mrcs", "_samplingRate": "0.855", "_ctfModel": "defU=25831.73, defV=25543.44, ast=288.28, psh=None, res=4.20, fit=0.04", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_coordinate": "Coordinate", "_micId": "21", "_classId": "None", "_rlnOpticsGroup": "1", "item_id": 3, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/720.outputParticles_3_mic_000021.jpg" }, { "_index": "4", "_filename": "Runs/000720_ProtRelionExtractParticles/extra/mic_000021.mrcs", "_samplingRate": "0.855", "_ctfModel": "defU=25831.73, defV=25543.44, ast=288.28, psh=None, res=4.20, fit=0.04", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_coordinate": "Coordinate", "_micId": "21", "_classId": "None", "_rlnOpticsGroup": "1", "item_id": 4, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/720.outputParticles_4_mic_000021.jpg" }, { "_index": "5", "_filename": "Runs/000720_ProtRelionExtractParticles/extra/mic_000021.mrcs", "_samplingRate": "0.855", "_ctfModel": "defU=25831.73, defV=25543.44, ast=288.28, psh=None, res=4.20, fit=0.04", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_coordinate": "Coordinate", "_micId": "21", "_classId": "None", "_rlnOpticsGroup": "1", "item_id": 5, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/720.outputParticles_5_mic_000021.jpg" }, { "_index": "6", "_filename": "Runs/000720_ProtRelionExtractParticles/extra/mic_000021.mrcs", "_samplingRate": "0.855", "_ctfModel": "defU=25831.73, defV=25543.44, ast=288.28, psh=None, res=4.20, fit=0.04", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_coordinate": "Coordinate", "_micId": "21", "_classId": "None", "_rlnOpticsGroup": "1", "item_id": 6, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/720.outputParticles_6_mic_000021.jpg" }, { "_index": "7", "_filename": "Runs/000720_ProtRelionExtractParticles/extra/mic_000021.mrcs", "_samplingRate": "0.855", "_ctfModel": "defU=25831.73, defV=25543.44, ast=288.28, psh=None, res=4.20, fit=0.04", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_coordinate": "Coordinate", "_micId": "21", "_classId": "None", "_rlnOpticsGroup": "1", "item_id": 7, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/720.outputParticles_7_mic_000021.jpg" }, { "_index": "8", "_filename": "Runs/000720_ProtRelionExtractParticles/extra/mic_000021.mrcs", "_samplingRate": "0.855", "_ctfModel": "defU=25831.73, defV=25543.44, ast=288.28, psh=None, res=4.20, fit=0.04", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_coordinate": "Coordinate", "_micId": "21", "_classId": "None", "_rlnOpticsGroup": "1", "item_id": 8, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/720.outputParticles_8_mic_000021.jpg" }, { "_index": "9", "_filename": "Runs/000720_ProtRelionExtractParticles/extra/mic_000021.mrcs", "_samplingRate": "0.855", "_ctfModel": "defU=25831.73, defV=25543.44, ast=288.28, psh=None, res=4.20, fit=0.04", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_coordinate": "Coordinate", "_micId": "21", "_classId": "None", "_rlnOpticsGroup": "1", "item_id": 9, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/720.outputParticles_9_mic_000021.jpg" }, { "_index": "10", "_filename": "Runs/000720_ProtRelionExtractParticles/extra/mic_000021.mrcs", "_samplingRate": "0.855", "_ctfModel": "defU=25831.73, defV=25543.44, ast=288.28, psh=None, res=4.20, fit=0.04", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_coordinate": "Coordinate", "_micId": "21", "_classId": "None", "_rlnOpticsGroup": "1", "item_id": 10, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/720.outputParticles_10_mic_000021.jpg" }, { "_index": "11", "_filename": "Runs/000720_ProtRelionExtractParticles/extra/mic_000021.mrcs", "_samplingRate": "0.855", "_ctfModel": "defU=25831.73, defV=25543.44, ast=288.28, psh=None, res=4.20, fit=0.04", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_coordinate": "Coordinate", "_micId": "21", "_classId": "None", "_rlnOpticsGroup": "1", "item_id": 11, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/720.outputParticles_11_mic_000021.jpg" }, { "_index": "12", "_filename": "Runs/000720_ProtRelionExtractParticles/extra/mic_000021.mrcs", "_samplingRate": "0.855", "_ctfModel": "defU=25831.73, defV=25543.44, ast=288.28, psh=None, res=4.20, fit=0.04", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_coordinate": "Coordinate", "_micId": "21", "_classId": "None", "_rlnOpticsGroup": "1", "item_id": 12, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/720.outputParticles_12_mic_000021.jpg" }, { "_index": "13", "_filename": "Runs/000720_ProtRelionExtractParticles/extra/mic_000021.mrcs", "_samplingRate": "0.855", "_ctfModel": "defU=25831.73, defV=25543.44, ast=288.28, psh=None, res=4.20, fit=0.04", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_coordinate": "Coordinate", "_micId": "21", "_classId": "None", "_rlnOpticsGroup": "1", "item_id": 13, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/720.outputParticles_13_mic_000021.jpg" }, { "_index": "14", "_filename": "Runs/000720_ProtRelionExtractParticles/extra/mic_000021.mrcs", "_samplingRate": "0.855", "_ctfModel": "defU=25831.73, defV=25543.44, ast=288.28, psh=None, res=4.20, fit=0.04", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_coordinate": "Coordinate", "_micId": "21", "_classId": "None", "_rlnOpticsGroup": "1", "item_id": 14, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/720.outputParticles_14_mic_000021.jpg" }, { "_index": "15", "_filename": "Runs/000720_ProtRelionExtractParticles/extra/mic_000021.mrcs", "_samplingRate": "0.855", "_ctfModel": "defU=25831.73, defV=25543.44, ast=288.28, psh=None, res=4.20, fit=0.04", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_coordinate": "Coordinate", "_micId": "21", "_classId": "None", "_rlnOpticsGroup": "1", "item_id": 15, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/720.outputParticles_15_mic_000021.jpg" } ] } ], "summary": "Micrographs source: same as pickingParticle box size: 492Particles extracted: 509466Input: SetOfCoordinates (509466 items, 564 x 564) \nInput: SetOfCTF (4330 items) \nOutput: SetOfParticles (509466 items, 492 x 492, 0.85 \u212b/px)", "log": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/720_ProtRelionExtractParticles.log", "plugin": "relion", "pluginVersion": "3.0.0" }, { "object.className": "XmippProtCropResizeParticles", "object.id": "787", "object.label": "xmipp3 - crop/resize particles_consensus_1.4Apx", "object.comment": "", "_useQueue": false, "_prerequisites": "", "_queueParams": null, "runName": null, "runMode": 0, "doResize": true, "resizeOption": 0, "resizeSamplingRate": 1.4, "doFourier": false, "resizeDim": 0, "resizeFactor": 0.5, "resizeLevel": 0, "hugeFile": false, "doWindow": false, "windowOperation": 1, "cropSize": 0, "windowSize": 0, "hostName": "localhost", "numberOfMpi": 60, "inputParticles": "720.outputParticles", "output": [ { "outputName": "787.outputParticles", "outputType": "SetOfParticles", "outputSize": 509466, "outputItems": [ { "_index": "1", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=25831.73, defV=25543.44, ast=288.28, psh=None, res=4.20, fit=0.04", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_coordinate": "Coordinate", "_micId": "21", "_classId": "None", "_rlnOpticsGroup": "1", "item_id": 1, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/787.outputParticles_1_output_images.jpg" }, { "_index": "2", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=25831.73, defV=25543.44, ast=288.28, psh=None, res=4.20, fit=0.04", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_coordinate": "Coordinate", "_micId": "21", "_classId": "None", "_rlnOpticsGroup": "1", "item_id": 2, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/787.outputParticles_2_output_images.jpg" }, { "_index": "3", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=25831.73, defV=25543.44, ast=288.28, psh=None, res=4.20, fit=0.04", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_coordinate": "Coordinate", "_micId": "21", "_classId": "None", "_rlnOpticsGroup": "1", "item_id": 3, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/787.outputParticles_3_output_images.jpg" }, { "_index": "4", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=25831.73, defV=25543.44, ast=288.28, psh=None, res=4.20, fit=0.04", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_coordinate": "Coordinate", "_micId": "21", "_classId": "None", "_rlnOpticsGroup": "1", "item_id": 4, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/787.outputParticles_4_output_images.jpg" }, { "_index": "5", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=25831.73, defV=25543.44, ast=288.28, psh=None, res=4.20, fit=0.04", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_coordinate": "Coordinate", "_micId": "21", "_classId": "None", "_rlnOpticsGroup": "1", "item_id": 5, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/787.outputParticles_5_output_images.jpg" }, { "_index": "6", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=25831.73, defV=25543.44, ast=288.28, psh=None, res=4.20, fit=0.04", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_coordinate": "Coordinate", "_micId": "21", "_classId": "None", "_rlnOpticsGroup": "1", "item_id": 6, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/787.outputParticles_6_output_images.jpg" }, { "_index": "7", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=25831.73, defV=25543.44, ast=288.28, psh=None, res=4.20, fit=0.04", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_coordinate": "Coordinate", "_micId": "21", "_classId": "None", "_rlnOpticsGroup": "1", "item_id": 7, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/787.outputParticles_7_output_images.jpg" }, { "_index": "8", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=25831.73, defV=25543.44, ast=288.28, psh=None, res=4.20, fit=0.04", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_coordinate": "Coordinate", "_micId": "21", "_classId": "None", "_rlnOpticsGroup": "1", "item_id": 8, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/787.outputParticles_8_output_images.jpg" }, { "_index": "9", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=25831.73, defV=25543.44, ast=288.28, psh=None, res=4.20, fit=0.04", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_coordinate": "Coordinate", "_micId": "21", "_classId": "None", "_rlnOpticsGroup": "1", "item_id": 9, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/787.outputParticles_9_output_images.jpg" }, { "_index": "10", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=25831.73, defV=25543.44, ast=288.28, psh=None, res=4.20, fit=0.04", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_coordinate": "Coordinate", "_micId": "21", "_classId": "None", "_rlnOpticsGroup": "1", "item_id": 10, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/787.outputParticles_10_output_images.jpg" }, { "_index": "11", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=25831.73, defV=25543.44, ast=288.28, psh=None, res=4.20, fit=0.04", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_coordinate": "Coordinate", "_micId": "21", "_classId": "None", "_rlnOpticsGroup": "1", "item_id": 11, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/787.outputParticles_11_output_images.jpg" }, { "_index": "12", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=25831.73, defV=25543.44, ast=288.28, psh=None, res=4.20, fit=0.04", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_coordinate": "Coordinate", "_micId": "21", "_classId": "None", "_rlnOpticsGroup": "1", "item_id": 12, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/787.outputParticles_12_output_images.jpg" }, { "_index": "13", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=25831.73, defV=25543.44, ast=288.28, psh=None, res=4.20, fit=0.04", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_coordinate": "Coordinate", "_micId": "21", "_classId": "None", "_rlnOpticsGroup": "1", "item_id": 13, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/787.outputParticles_13_output_images.jpg" }, { "_index": "14", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=25831.73, defV=25543.44, ast=288.28, psh=None, res=4.20, fit=0.04", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_coordinate": "Coordinate", "_micId": "21", "_classId": "None", "_rlnOpticsGroup": "1", "item_id": 14, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/787.outputParticles_14_output_images.jpg" }, { "_index": "15", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=25831.73, defV=25543.44, ast=288.28, psh=None, res=4.20, fit=0.04", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_coordinate": "Coordinate", "_micId": "21", "_classId": "None", "_rlnOpticsGroup": "1", "item_id": 15, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/787.outputParticles_15_output_images.jpg" } ] } ], "summary": "Output particles have a different sampling rate (pixel size): *1.400* \u212b/pxResizing method: *Sampling Rate*Input: SetOfParticles (509466 items, 492 x 492, 0.85 \u212b/px) \nOutput: SetOfParticles (509466 items, 300 x 300, 1.40 \u212b/px)", "log": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/787_XmippProtCropResizeParticles.log", "plugin": "xmipp3" }, { "object.className": "ProtCryo2D", "object.id": "850", "object.label": "cryosparc2 - 2d classification_consensus_1.40Apx", "object.comment": "", "_useQueue": false, "_prerequisites": "", "_queueParams": null, "runName": null, "runMode": 0, "numberOfClasses": 100, "maximunResolution": 6, "initialClassification": 2.0, "useCircular2D": true, "class2D_window_inner_A": null, "class2D_window_outer_A": null, "reCenter2D": true, "reCenterMask": 0.2, "reCenterMaskBinary": false, "forceMaxover": true, "ctfFlipPhases": false, "numberFinalIterator": 1, "numberOnlineEMIterator": 20, "batchSizeClass": 100, "initialScale2D": 1, "zeropadFactor": 2, "useFRCRegularized": true, "useFullFRC": true, "iterationToStartAnneling": 2, "iterationToStartAnneal": 15, "useWhiteNoiseModel": false, "compute_use_ssd": false, "gpuList": "2,3", "compute_lane": "default", "inputParticles": "787.outputParticles", "output": [ { "outputName": "850.outputClasses", "outputType": "SetOfClasses2D", "outputSize": 100, "outputItems": [ { "_size": "355", "_streamState": "2", "_mapperPath": "['Runs/000850_ProtCryo2D/classes2D.sqlite', 'Class001']", "_representative": "Particle (300 x 300, 1.40 \u212b/px)", "_samplingRate": "1.4", "_hasCtf": "True", "_alignment": "2D", "_isPhaseFlipped": "False", "_isAmplitudeCorrected": "False", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_firstDim": "300 x 300", "item_id": 1, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/850.outputClasses_1_cryosparc_P13_J4_020_class_averages_scaled.jpg" }, { "_size": "3442", "_streamState": "2", "_mapperPath": "['Runs/000850_ProtCryo2D/classes2D.sqlite', 'Class002']", "_representative": "Particle (300 x 300, 1.40 \u212b/px)", "_samplingRate": "1.4", "_hasCtf": "True", "_alignment": "2D", "_isPhaseFlipped": "False", "_isAmplitudeCorrected": "False", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_firstDim": "300 x 300", "item_id": 2, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/850.outputClasses_2_cryosparc_P13_J4_020_class_averages_scaled.jpg" }, { "_size": "3672", "_streamState": "2", "_mapperPath": "['Runs/000850_ProtCryo2D/classes2D.sqlite', 'Class003']", "_representative": "Particle (300 x 300, 1.40 \u212b/px)", "_samplingRate": "1.4", "_hasCtf": "True", "_alignment": "2D", "_isPhaseFlipped": "False", "_isAmplitudeCorrected": "False", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_firstDim": "300 x 300", "item_id": 3, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/850.outputClasses_3_cryosparc_P13_J4_020_class_averages_scaled.jpg" }, { "_size": "3226", "_streamState": "2", "_mapperPath": "['Runs/000850_ProtCryo2D/classes2D.sqlite', 'Class004']", "_representative": "Particle (300 x 300, 1.40 \u212b/px)", "_samplingRate": "1.4", "_hasCtf": "True", "_alignment": "2D", "_isPhaseFlipped": "False", "_isAmplitudeCorrected": "False", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_firstDim": "300 x 300", "item_id": 4, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/850.outputClasses_4_cryosparc_P13_J4_020_class_averages_scaled.jpg" }, { "_size": "11303", "_streamState": "2", "_mapperPath": "['Runs/000850_ProtCryo2D/classes2D.sqlite', 'Class005']", "_representative": "Particle (300 x 300, 1.40 \u212b/px)", "_samplingRate": "1.4", "_hasCtf": "True", "_alignment": "2D", "_isPhaseFlipped": "False", "_isAmplitudeCorrected": "False", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_firstDim": "300 x 300", "item_id": 5, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/850.outputClasses_5_cryosparc_P13_J4_020_class_averages_scaled.jpg" }, { "_size": "15709", "_streamState": "2", "_mapperPath": "['Runs/000850_ProtCryo2D/classes2D.sqlite', 'Class006']", "_representative": "Particle (300 x 300, 1.40 \u212b/px)", "_samplingRate": "1.4", "_hasCtf": "True", "_alignment": "2D", "_isPhaseFlipped": "False", "_isAmplitudeCorrected": "False", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_firstDim": "300 x 300", "item_id": 6, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/850.outputClasses_6_cryosparc_P13_J4_020_class_averages_scaled.jpg" }, { "_size": "4470", "_streamState": "2", "_mapperPath": "['Runs/000850_ProtCryo2D/classes2D.sqlite', 'Class007']", "_representative": "Particle (300 x 300, 1.40 \u212b/px)", "_samplingRate": "1.4", "_hasCtf": "True", "_alignment": "2D", "_isPhaseFlipped": "False", "_isAmplitudeCorrected": "False", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_firstDim": "300 x 300", "item_id": 7, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/850.outputClasses_7_cryosparc_P13_J4_020_class_averages_scaled.jpg" }, { "_size": "7074", "_streamState": "2", "_mapperPath": "['Runs/000850_ProtCryo2D/classes2D.sqlite', 'Class008']", "_representative": "Particle (300 x 300, 1.40 \u212b/px)", "_samplingRate": "1.4", "_hasCtf": "True", "_alignment": "2D", "_isPhaseFlipped": "False", "_isAmplitudeCorrected": "False", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_firstDim": "300 x 300", "item_id": 8, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/850.outputClasses_8_cryosparc_P13_J4_020_class_averages_scaled.jpg" }, { "_size": "4192", "_streamState": "2", "_mapperPath": "['Runs/000850_ProtCryo2D/classes2D.sqlite', 'Class009']", "_representative": "Particle (300 x 300, 1.40 \u212b/px)", "_samplingRate": "1.4", "_hasCtf": "True", "_alignment": "2D", "_isPhaseFlipped": "False", "_isAmplitudeCorrected": "False", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_firstDim": "300 x 300", "item_id": 9, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/850.outputClasses_9_cryosparc_P13_J4_020_class_averages_scaled.jpg" }, { "_size": "2776", "_streamState": "2", "_mapperPath": "['Runs/000850_ProtCryo2D/classes2D.sqlite', 'Class010']", "_representative": "Particle (300 x 300, 1.40 \u212b/px)", "_samplingRate": "1.4", "_hasCtf": "True", "_alignment": "2D", "_isPhaseFlipped": "False", 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"Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/850.outputClasses_73_cryosparc_P13_J4_020_class_averages_scaled.jpg" }, { "_size": "4615", "_streamState": "2", "_mapperPath": "['Runs/000850_ProtCryo2D/classes2D.sqlite', 'Class074']", "_representative": "Particle (300 x 300, 1.40 \u212b/px)", "_samplingRate": "1.4", "_hasCtf": "True", "_alignment": "2D", "_isPhaseFlipped": "False", "_isAmplitudeCorrected": "False", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_firstDim": "300 x 300", "item_id": 74, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/850.outputClasses_74_cryosparc_P13_J4_020_class_averages_scaled.jpg" }, { "_size": "2328", "_streamState": "2", "_mapperPath": "['Runs/000850_ProtCryo2D/classes2D.sqlite', 'Class075']", "_representative": "Particle (300 x 300, 1.40 \u212b/px)", "_samplingRate": "1.4", "_hasCtf": "True", "_alignment": "2D", "_isPhaseFlipped": "False", "_isAmplitudeCorrected": "False", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_firstDim": "300 x 300", "item_id": 75, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/850.outputClasses_75_cryosparc_P13_J4_020_class_averages_scaled.jpg" }, { "_size": "6894", "_streamState": "2", "_mapperPath": "['Runs/000850_ProtCryo2D/classes2D.sqlite', 'Class076']", "_representative": "Particle (300 x 300, 1.40 \u212b/px)", "_samplingRate": "1.4", "_hasCtf": "True", "_alignment": "2D", "_isPhaseFlipped": "False", "_isAmplitudeCorrected": "False", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_firstDim": "300 x 300", "item_id": 76, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/850.outputClasses_76_cryosparc_P13_J4_020_class_averages_scaled.jpg" }, { "_size": "797", "_streamState": "2", "_mapperPath": "['Runs/000850_ProtCryo2D/classes2D.sqlite', 'Class077']", "_representative": "Particle (300 x 300, 1.40 \u212b/px)", "_samplingRate": "1.4", "_hasCtf": "True", "_alignment": "2D", "_isPhaseFlipped": "False", "_isAmplitudeCorrected": "False", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_firstDim": "300 x 300", "item_id": 77, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/850.outputClasses_77_cryosparc_P13_J4_020_class_averages_scaled.jpg" }, { "_size": "3962", "_streamState": "2", "_mapperPath": "['Runs/000850_ProtCryo2D/classes2D.sqlite', 'Class078']", "_representative": "Particle (300 x 300, 1.40 \u212b/px)", "_samplingRate": "1.4", "_hasCtf": "True", "_alignment": "2D", "_isPhaseFlipped": "False", "_isAmplitudeCorrected": "False", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_firstDim": "300 x 300", "item_id": 78, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/850.outputClasses_78_cryosparc_P13_J4_020_class_averages_scaled.jpg" }, { "_size": "1351", "_streamState": "2", "_mapperPath": "['Runs/000850_ProtCryo2D/classes2D.sqlite', 'Class079']", "_representative": "Particle (300 x 300, 1.40 \u212b/px)", "_samplingRate": "1.4", "_hasCtf": "True", "_alignment": "2D", "_isPhaseFlipped": "False", "_isAmplitudeCorrected": "False", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_firstDim": "300 x 300", "item_id": 79, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/850.outputClasses_79_cryosparc_P13_J4_020_class_averages_scaled.jpg" }, { "_size": "6744", "_streamState": "2", "_mapperPath": "['Runs/000850_ProtCryo2D/classes2D.sqlite', 'Class080']", "_representative": "Particle (300 x 300, 1.40 \u212b/px)", "_samplingRate": "1.4", "_hasCtf": "True", "_alignment": "2D", "_isPhaseFlipped": "False", "_isAmplitudeCorrected": "False", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_firstDim": "300 x 300", "item_id": 80, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/850.outputClasses_80_cryosparc_P13_J4_020_class_averages_scaled.jpg" }, { "_size": "10711", "_streamState": "2", "_mapperPath": "['Runs/000850_ProtCryo2D/classes2D.sqlite', 'Class081']", "_representative": "Particle (300 x 300, 1.40 \u212b/px)", "_samplingRate": "1.4", "_hasCtf": "True", "_alignment": "2D", "_isPhaseFlipped": "False", "_isAmplitudeCorrected": "False", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_firstDim": "300 x 300", "item_id": 81, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/850.outputClasses_81_cryosparc_P13_J4_020_class_averages_scaled.jpg" }, { "_size": "3772", "_streamState": "2", "_mapperPath": "['Runs/000850_ProtCryo2D/classes2D.sqlite', 'Class082']", "_representative": "Particle (300 x 300, 1.40 \u212b/px)", "_samplingRate": "1.4", "_hasCtf": "True", "_alignment": "2D", "_isPhaseFlipped": "False", "_isAmplitudeCorrected": "False", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_firstDim": "300 x 300", "item_id": 82, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/850.outputClasses_82_cryosparc_P13_J4_020_class_averages_scaled.jpg" }, { "_size": "3018", "_streamState": "2", "_mapperPath": "['Runs/000850_ProtCryo2D/classes2D.sqlite', 'Class083']", "_representative": "Particle (300 x 300, 1.40 \u212b/px)", "_samplingRate": "1.4", "_hasCtf": "True", "_alignment": "2D", "_isPhaseFlipped": "False", "_isAmplitudeCorrected": "False", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_firstDim": "300 x 300", "item_id": 83, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/850.outputClasses_83_cryosparc_P13_J4_020_class_averages_scaled.jpg" }, { "_size": "4209", "_streamState": "2", "_mapperPath": "['Runs/000850_ProtCryo2D/classes2D.sqlite', 'Class084']", "_representative": "Particle (300 x 300, 1.40 \u212b/px)", "_samplingRate": "1.4", "_hasCtf": "True", "_alignment": "2D", "_isPhaseFlipped": "False", "_isAmplitudeCorrected": "False", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_firstDim": "300 x 300", "item_id": 84, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/850.outputClasses_84_cryosparc_P13_J4_020_class_averages_scaled.jpg" }, { "_size": "2282", "_streamState": "2", "_mapperPath": "['Runs/000850_ProtCryo2D/classes2D.sqlite', 'Class085']", "_representative": "Particle (300 x 300, 1.40 \u212b/px)", "_samplingRate": "1.4", "_hasCtf": "True", "_alignment": "2D", "_isPhaseFlipped": "False", "_isAmplitudeCorrected": "False", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_firstDim": "300 x 300", "item_id": 85, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/850.outputClasses_85_cryosparc_P13_J4_020_class_averages_scaled.jpg" }, { "_size": "13855", "_streamState": "2", "_mapperPath": "['Runs/000850_ProtCryo2D/classes2D.sqlite', 'Class086']", "_representative": "Particle (300 x 300, 1.40 \u212b/px)", "_samplingRate": "1.4", "_hasCtf": "True", "_alignment": "2D", "_isPhaseFlipped": "False", "_isAmplitudeCorrected": "False", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_firstDim": "300 x 300", "item_id": 86, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/850.outputClasses_86_cryosparc_P13_J4_020_class_averages_scaled.jpg" }, { "_size": "3358", "_streamState": "2", "_mapperPath": "['Runs/000850_ProtCryo2D/classes2D.sqlite', 'Class087']", "_representative": "Particle (300 x 300, 1.40 \u212b/px)", "_samplingRate": "1.4", "_hasCtf": "True", "_alignment": "2D", "_isPhaseFlipped": "False", "_isAmplitudeCorrected": "False", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_firstDim": "300 x 300", "item_id": 87, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/850.outputClasses_87_cryosparc_P13_J4_020_class_averages_scaled.jpg" }, { "_size": "178", "_streamState": "2", "_mapperPath": "['Runs/000850_ProtCryo2D/classes2D.sqlite', 'Class088']", "_representative": "Particle (300 x 300, 1.40 \u212b/px)", "_samplingRate": "1.4", "_hasCtf": "True", "_alignment": "2D", "_isPhaseFlipped": "False", "_isAmplitudeCorrected": "False", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_firstDim": "300 x 300", "item_id": 88, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/850.outputClasses_88_cryosparc_P13_J4_020_class_averages_scaled.jpg" }, { "_size": "2142", "_streamState": "2", "_mapperPath": "['Runs/000850_ProtCryo2D/classes2D.sqlite', 'Class089']", "_representative": "Particle (300 x 300, 1.40 \u212b/px)", "_samplingRate": "1.4", "_hasCtf": "True", "_alignment": "2D", "_isPhaseFlipped": "False", "_isAmplitudeCorrected": "False", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_firstDim": "300 x 300", "item_id": 89, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/850.outputClasses_89_cryosparc_P13_J4_020_class_averages_scaled.jpg" }, { "_size": "13110", "_streamState": "2", "_mapperPath": "['Runs/000850_ProtCryo2D/classes2D.sqlite', 'Class090']", "_representative": "Particle (300 x 300, 1.40 \u212b/px)", "_samplingRate": "1.4", "_hasCtf": "True", "_alignment": "2D", "_isPhaseFlipped": "False", "_isAmplitudeCorrected": "False", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_firstDim": "300 x 300", "item_id": 90, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/850.outputClasses_90_cryosparc_P13_J4_020_class_averages_scaled.jpg" }, { "_size": "3532", "_streamState": "2", "_mapperPath": "['Runs/000850_ProtCryo2D/classes2D.sqlite', 'Class091']", "_representative": "Particle (300 x 300, 1.40 \u212b/px)", "_samplingRate": "1.4", "_hasCtf": "True", "_alignment": "2D", "_isPhaseFlipped": "False", "_isAmplitudeCorrected": "False", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_firstDim": "300 x 300", "item_id": 91, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/850.outputClasses_91_cryosparc_P13_J4_020_class_averages_scaled.jpg" }, { "_size": "1117", "_streamState": "2", "_mapperPath": "['Runs/000850_ProtCryo2D/classes2D.sqlite', 'Class092']", "_representative": "Particle (300 x 300, 1.40 \u212b/px)", "_samplingRate": "1.4", "_hasCtf": "True", "_alignment": "2D", "_isPhaseFlipped": "False", "_isAmplitudeCorrected": "False", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_firstDim": "300 x 300", "item_id": 92, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/850.outputClasses_92_cryosparc_P13_J4_020_class_averages_scaled.jpg" }, { "_size": "2380", "_streamState": "2", "_mapperPath": "['Runs/000850_ProtCryo2D/classes2D.sqlite', 'Class093']", "_representative": "Particle (300 x 300, 1.40 \u212b/px)", "_samplingRate": "1.4", "_hasCtf": "True", "_alignment": "2D", "_isPhaseFlipped": "False", "_isAmplitudeCorrected": "False", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_firstDim": "300 x 300", "item_id": 93, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/850.outputClasses_93_cryosparc_P13_J4_020_class_averages_scaled.jpg" }, { "_size": "1211", "_streamState": "2", "_mapperPath": "['Runs/000850_ProtCryo2D/classes2D.sqlite', 'Class094']", "_representative": "Particle (300 x 300, 1.40 \u212b/px)", "_samplingRate": "1.4", "_hasCtf": "True", "_alignment": "2D", "_isPhaseFlipped": "False", "_isAmplitudeCorrected": "False", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_firstDim": "300 x 300", "item_id": 94, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/850.outputClasses_94_cryosparc_P13_J4_020_class_averages_scaled.jpg" }, { "_size": "8780", "_streamState": "2", "_mapperPath": "['Runs/000850_ProtCryo2D/classes2D.sqlite', 'Class095']", "_representative": "Particle (300 x 300, 1.40 \u212b/px)", "_samplingRate": "1.4", "_hasCtf": "True", "_alignment": "2D", "_isPhaseFlipped": "False", "_isAmplitudeCorrected": "False", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_firstDim": "300 x 300", "item_id": 95, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/850.outputClasses_95_cryosparc_P13_J4_020_class_averages_scaled.jpg" }, { "_size": "18187", "_streamState": "2", "_mapperPath": "['Runs/000850_ProtCryo2D/classes2D.sqlite', 'Class096']", "_representative": "Particle (300 x 300, 1.40 \u212b/px)", "_samplingRate": "1.4", "_hasCtf": "True", "_alignment": "2D", "_isPhaseFlipped": "False", "_isAmplitudeCorrected": "False", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_firstDim": "300 x 300", "item_id": 96, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/850.outputClasses_96_cryosparc_P13_J4_020_class_averages_scaled.jpg" }, { "_size": "2725", "_streamState": "2", "_mapperPath": "['Runs/000850_ProtCryo2D/classes2D.sqlite', 'Class097']", "_representative": "Particle (300 x 300, 1.40 \u212b/px)", "_samplingRate": "1.4", "_hasCtf": "True", "_alignment": "2D", "_isPhaseFlipped": "False", "_isAmplitudeCorrected": "False", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_firstDim": "300 x 300", "item_id": 97, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/850.outputClasses_97_cryosparc_P13_J4_020_class_averages_scaled.jpg" }, { "_size": "3820", "_streamState": "2", "_mapperPath": "['Runs/000850_ProtCryo2D/classes2D.sqlite', 'Class098']", "_representative": "Particle (300 x 300, 1.40 \u212b/px)", "_samplingRate": "1.4", "_hasCtf": "True", "_alignment": "2D", "_isPhaseFlipped": "False", "_isAmplitudeCorrected": "False", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_firstDim": "300 x 300", "item_id": 98, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/850.outputClasses_98_cryosparc_P13_J4_020_class_averages_scaled.jpg" }, { "_size": "5697", "_streamState": "2", "_mapperPath": "['Runs/000850_ProtCryo2D/classes2D.sqlite', 'Class099']", "_representative": "Particle (300 x 300, 1.40 \u212b/px)", "_samplingRate": "1.4", "_hasCtf": "True", "_alignment": "2D", "_isPhaseFlipped": "False", "_isAmplitudeCorrected": "False", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_firstDim": "300 x 300", "item_id": 99, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/850.outputClasses_99_cryosparc_P13_J4_020_class_averages_scaled.jpg" }, { "_size": "3625", "_streamState": "2", "_mapperPath": "['Runs/000850_ProtCryo2D/classes2D.sqlite', 'Class100']", "_representative": "Particle (300 x 300, 1.40 \u212b/px)", "_samplingRate": "1.4", "_hasCtf": "True", "_alignment": "2D", "_isPhaseFlipped": "False", "_isAmplitudeCorrected": "False", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_firstDim": "300 x 300", "item_id": 100, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/850.outputClasses_100_cryosparc_P13_J4_020_class_averages_scaled.jpg" } ] } ], "summary": "Input Particles: [[sci-open:830][787.outputParticles.830]]Classified into *100* classes.Output set: [[sci-open:911][850.outputClasses.911]]Input: SetOfParticles (509466 items, 300 x 300, 1.40 \u212b/px) \nOutput: SetOfClasses2D (100 items)", "log": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/850_ProtCryo2D.log", "plugin": "cryosparc2", "pluginVersion": "3.2.10" }, { "object.className": "ProtUserSubSet", "object.id": "918", "object.label": "create subset_2D_310162particles", "object.comment": "", "_useQueue": false, "_prerequisites": "", "_queueParams": null, "runName": null, "runMode": 0, "other": null, "sqliteFile": "Runs/000850_ProtCryo2D/classes2D_state.sqlite,", "outputClassName": "SetOfParticles", "inputObject": "850.outputClasses", "output": [ { "outputName": "918.outputParticles", "outputType": "SetOfParticles", "outputSize": 310162, "outputItems": [ { "_index": "2", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=25831.73, defV=25543.44, ast=288.28, psh=None, res=4.20, fit=0.04", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[ 0.93281242 -0.3603623 -0. 0.65 ]\n [ 0.3603623 0.93281242 -0. -9.75 ]\n [ 0. 0. 1. 0. ]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "21", "_classId": "14", "_rlnOpticsGroup": "1", "item_id": 2, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/918.outputParticles_2_output_images.jpg" }, { "_index": "4", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=25831.73, defV=25543.44, ast=288.28, psh=None, res=4.20, fit=0.04", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[-0.63594114 0.77173756 0. 3.25 ]\n [-0.77173756 -0.63594114 0. 20.15 ]\n [ 0. 0. 1. 0. ]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "21", "_classId": "49", "_rlnOpticsGroup": "1", "item_id": 4, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/918.outputParticles_4_output_images.jpg" }, { "_index": "5", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=25831.73, defV=25543.44, ast=288.28, psh=None, res=4.20, fit=0.04", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[-0.63594074 -0.7717379 0. 9.75 ]\n [ 0.7717379 -0.63594074 -0. -9.75 ]\n [ 0. 0. 1. 0. ]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "21", "_classId": "86", "_rlnOpticsGroup": "1", "item_id": 5, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/918.outputParticles_5_output_images.jpg" }, { "_index": "6", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=25831.73, defV=25543.44, ast=288.28, psh=None, res=4.20, fit=0.04", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[ 0.23811787 0.97123626 -0. 1.95 ]\n [-0.97123626 0.23811787 0. -3.25 ]\n [ 0. 0. 1. 0. ]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "21", "_classId": "44", "_rlnOpticsGroup": "1", "item_id": 6, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/918.outputParticles_6_output_images.jpg" }, { "_index": "7", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=25831.73, defV=25543.44, ast=288.28, psh=None, res=4.20, fit=0.04", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[ -0.50461975 -0.86334171 0. -1.95 ]\n [ 0.86334171 -0.50461975 -0. -12.35 ]\n [ 0. 0. 1. 0. ]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "21", "_classId": "5", "_rlnOpticsGroup": "1", "item_id": 7, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/918.outputParticles_7_output_images.jpg" }, { "_index": "8", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=25831.73, defV=25543.44, ast=288.28, psh=None, res=4.20, fit=0.04", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[ 0.750958 0.66034997 -0. 14.95 ]\n [-0.66034997 0.750958 0. 9.75 ]\n [ 0. 0. 1. 0. ]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "21", "_classId": "5", "_rlnOpticsGroup": "1", "item_id": 8, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/918.outputParticles_8_output_images.jpg" }, { "_index": "9", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=25831.73, defV=25543.44, ast=288.28, psh=None, res=4.20, fit=0.04", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[ 0.66034917 0.7509587 -0. 0.65 ]\n [-0.7509587 0.66034917 0. 7.15 ]\n [ 0. 0. 1. 0. ]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "21", "_classId": "11", "_rlnOpticsGroup": "1", "item_id": 9, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/918.outputParticles_9_output_images.jpg" }, { "_index": "10", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=25831.73, defV=25543.44, ast=288.28, psh=None, res=4.20, fit=0.04", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[ -0.23811839 0.97123614 0. 16.25 ]\n [ -0.97123614 -0.23811839 0. -16.25 ]\n [ 0. 0. 1. 0. ]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "21", "_classId": "90", "_rlnOpticsGroup": "1", "item_id": 10, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/918.outputParticles_10_output_images.jpg" }, { "_index": "14", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=25831.73, defV=25543.44, ast=288.28, psh=None, res=4.20, fit=0.04", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[ 0.72940742 -0.68407954 -0. 4.55 ]\n [ 0.68407954 0.72940742 -0. -0.65 ]\n [ 0. 0. 1. 0. ]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "21", "_classId": "86", "_rlnOpticsGroup": "1", "item_id": 14, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/918.outputParticles_14_output_images.jpg" }, { "_index": "15", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=25831.73, defV=25543.44, ast=288.28, psh=None, res=4.20, fit=0.04", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[ 0.29985634 0.95398437 -0. 0.65 ]\n [-0.95398437 0.29985634 0. -5.85 ]\n [ 0. 0. 1. 0. ]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "21", "_classId": "11", "_rlnOpticsGroup": "1", "item_id": 15, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/918.outputParticles_15_output_images.jpg" }, { "_index": "16", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=25831.73, defV=25543.44, ast=288.28, psh=None, res=4.20, fit=0.04", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[ 0.8467242 -0.53203207 -0. -8.45 ]\n [ 0.53203207 0.8467242 -0. 5.85 ]\n [ 0. 0. 1. 0. ]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "21", "_classId": "22", "_rlnOpticsGroup": "1", "item_id": 16, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/918.outputParticles_16_output_images.jpg" }, { "_index": "17", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=25831.73, defV=25543.44, ast=288.28, psh=None, res=4.20, fit=0.04", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[ -0.90780728 -0.41938758 0. -12.35 ]\n [ 0.41938758 -0.90780728 -0. 14.95 ]\n [ 0. 0. 1. 0. ]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "21", "_classId": "42", "_rlnOpticsGroup": "1", "item_id": 17, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/918.outputParticles_17_output_images.jpg" }, { "_index": "19", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=25831.73, defV=25543.44, ast=288.28, psh=None, res=4.20, fit=0.04", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[-0.81089722 0.5851886 0. 3.25 ]\n [-0.5851886 -0.81089722 0. 0.65 ]\n [ 0. 0. 1. 0. ]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "21", "_classId": "96", "_rlnOpticsGroup": "1", "item_id": 19, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/918.outputParticles_19_output_images.jpg" }, { "_index": "21", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=25831.73, defV=25543.44, ast=288.28, psh=None, res=4.20, fit=0.04", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[ -0.81089722 0.5851886 0. -22.75 ]\n [ -0.5851886 -0.81089722 0. -3.25 ]\n [ 0. 0. 1. 0. ]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "21", "_classId": "11", "_rlnOpticsGroup": "1", "item_id": 21, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/918.outputParticles_21_output_images.jpg" }, { "_index": "22", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=25831.73, defV=25543.44, ast=288.28, psh=None, res=4.20, fit=0.04", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[-0.98961302 -0.14375698 0. 4.55 ]\n [ 0.14375698 -0.98961302 -0. 1.95 ]\n [ 0. 0. 1. 0. ]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "21", "_classId": "96", "_rlnOpticsGroup": "1", "item_id": 22, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/918.outputParticles_22_output_images.jpg" } ] } ], "summary": "From input SetOfClasses2D of size 100 we selected 35 items to create output SetOfParticles of size 310162Input: SetOfClasses2D (100 items) \nOutput: SetOfParticles (310162 items, 300 x 300, 1.40 \u212b/px)", "log": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/918_ProtUserSubSet.log", "plugin": "pwem", "pluginVersion": "3.0.10" }, { "object.className": "ProtCryoSparcInitialModel", "object.id": "972", "object.label": "cryosparc2 - initial model_x6_C1", "object.comment": "", "_useQueue": false, "_prerequisites": "", "_queueParams": null, "runName": null, "runMode": 0, "abinit_K": 6, "abinit_max_res": 12.0, "abinit_init_res": 35.0, "abinit_num_init_iters": 200, "abinit_num_final_iters": 300, "abinit_radwn_step": 0.04, "abinit_window": true, "abinit_center": true, "abinit_scale_mg_correct": false, "abinit_scale_compute": false, "abinit_mom": 0.0, "abinit_sparsity": 0.0, "abinit_minisize_init": 90, "abinit_minisize": 300, "abinit_minisize_epsilon": 0.05, "abinit_minisize_minp": 0.01, "abinit_minisize_num_init_iters": 300, "abinit_noise_model": 0, "abinit_noise_priorw": 50, "abinit_noise_initw": 5000, "abinit_class_anneal_beta": 0.1, "abinit_class_anneal_start": 300, "abinit_class_anneal_end": 350, "abinit_target_initial_ess_fraction": 0.011, "symmetryGroup": 0, "symmetryOrder": 1, "abinit_r_grid": 25.0, "abinit_high_lr_duration": 100.0, "abinit_high_lr": 0.4, "abinit_nonneg": true, "abinit_ignore_dc": true, "abinit_init_radwn_cutoff": 7, "abinit_search_start_iter": 200, "abinit_use_engine": true, "intermediate_plots": true, "compute_use_ssd": false, "gpuList": "1", "compute_lane": "default", "inputParticles": "918.outputParticles", "output": [ { "outputName": "972.outputClasses", "outputType": "SetOfClasses3D", "outputSize": 6, "outputItems": [ { "_size": "32846", "_streamState": "2", "_mapperPath": "['Runs/000972_ProtCryoSparcInitialModel/classes3D.sqlite', 'Class001']", "_representative": "Volume (300 x 300 x 300, 1.40 \u212b/px)", "_samplingRate": "1.4", "_hasCtf": "True", "_alignment": "Projection", "_isPhaseFlipped": "False", "_isAmplitudeCorrected": "False", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_firstDim": "300 x 300", "item_id": 1, "item_representation": "['Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/972.outputClasses_cryosparc_P13_J8_class_00_final_volume_scaled/slicesX_0000.jpg', 'Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/972.outputClasses_cryosparc_P13_J8_class_00_final_volume_scaled/slicesX_0001.jpg', 'Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/972.outputClasses_cryosparc_P13_J8_class_00_final_volume_scaled/slicesX_0002.jpg', 'Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/972.outputClasses_cryosparc_P13_J8_class_00_final_volume_scaled/slicesX_0003.jpg', 'Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/972.outputClasses_cryosparc_P13_J8_class_00_final_volume_scaled/slicesX_0004.jpg', 'Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/972.outputClasses_cryosparc_P13_J8_class_00_final_volume_scaled/slicesX_0005.jpg', 'Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/972.outputClasses_cryosparc_P13_J8_class_00_final_volume_scaled/slicesX_0006.jpg', 'Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/972.outputClasses_cryosparc_P13_J8_class_00_final_volume_scaled/slicesX_0007.jpg', 'Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/972.outputClasses_cryosparc_P13_J8_class_00_final_volume_scaled/slicesX_0008.jpg', 'Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/972.outputClasses_cryosparc_P13_J8_class_00_final_volume_scaled/slicesX_0009.jpg', 'Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/972.outputClasses_cryosparc_P13_J8_class_00_final_volume_scaled/slicesX_0010.jpg', 'Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/972.outputClasses_cryosparc_P13_J8_class_00_final_volume_scaled/slicesX_0011.jpg', 'Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/972.outputClasses_cryosparc_P13_J8_class_00_final_volume_scaled/slicesX_0012.jpg', 'Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/972.outputClasses_cryosparc_P13_J8_class_00_final_volume_scaled/slicesX_0013.jpg', 'Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/972.outputClasses_cryosparc_P13_J8_class_00_final_volume_scaled/slicesX_0014.jpg', 'Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/972.outputClasses_cryosparc_P13_J8_class_00_final_volume_scaled/slicesX_0015.jpg', 'Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/972.outputClasses_cryosparc_P13_J8_class_00_final_volume_scaled/slicesX_0016.jpg', 'Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/972.outputClasses_cryosparc_P13_J8_class_00_final_volume_scaled/slicesX_0017.jpg', 'Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/972.outputClasses_cryosparc_P13_J8_class_00_final_volume_scaled/slicesX_0018.jpg', 'Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/972.outputClasses_cryosparc_P13_J8_class_00_final_volume_scaled/slicesX_0019.jpg', 'Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/972.outputClasses_cryosparc_P13_J8_class_00_final_volume_scaled/slicesX_0020.jpg', 'Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/972.outputClasses_cryosparc_P13_J8_class_00_final_volume_scaled/slicesX_0021.jpg', 'Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/972.outputClasses_cryosparc_P13_J8_class_00_final_volume_scaled/slicesX_0022.jpg', 'Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/972.outputClasses_cryosparc_P13_J8_class_00_final_volume_scaled/slicesX_0023.jpg', 'Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/972.outputClasses_cryosparc_P13_J8_class_00_final_volume_scaled/slicesX_0024.jpg', 'Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/972.outputClasses_cryosparc_P13_J8_class_00_final_volume_scaled/slicesX_0025.jpg', 'Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/972.outputClasses_cryosparc_P13_J8_class_00_final_volume_scaled/slicesX_0026.jpg', 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[[sci-open:952][918.outputParticles.952]]Number of Ab-Initio classes: 6Symmetry: C1------------------------------------------Output volume [[sci-open:1329][972.outputVolumes.1329]]Output classes [[sci-open:1322][972.outputClasses.1322]]Input: SetOfParticles (310162 items, 300 x 300, 1.40 \u212b/px) \nOutput: SetOfClasses3D (6 items)SetOfVolumes (6 items, 300 x 300 x 300, 1.40 \u212b/px)", "log": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/972_ProtCryoSparcInitialModel.log", "label": [ "C1" ], "labelColor": [ "#0ec3dc" ], "plugin": "cryosparc2", "pluginVersion": "3.2.10" }, { "object.className": "ProtCryoSparcInitialModel", "object.id": "1043", "object.label": "cryosparc2 - initial model_x6_C3", "object.comment": "", "_useQueue": false, "_prerequisites": "", "_queueParams": null, "runName": null, "runMode": 0, "abinit_K": 6, "abinit_max_res": 12.0, "abinit_init_res": 35.0, "abinit_num_init_iters": 200, "abinit_num_final_iters": 300, "abinit_radwn_step": 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[[sci-open:952][918.outputParticles.952]]Number of Ab-Initio classes: 6Symmetry: C3------------------------------------------Output volume [[sci-open:1354][1043.outputVolumes.1354]]Output classes [[sci-open:1347][1043.outputClasses.1347]]Input: SetOfParticles (310162 items, 300 x 300, 1.40 \u212b/px) \nOutput: SetOfClasses3D (6 items)SetOfVolumes (6 items, 300 x 300 x 300, 1.40 \u212b/px)", "log": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/1043_ProtCryoSparcInitialModel.log", "label": [ "C3" ], "labelColor": [ "#21d173" ], "plugin": "cryosparc2", "pluginVersion": "3.2.10" }, { "object.className": "ProtCryoSparcInitialModel", "object.id": "1122", "object.label": "cryosparc2 - initial model_x1_C1", "object.comment": "", "_useQueue": false, "_prerequisites": "", "_queueParams": null, "runName": null, "runMode": 0, "abinit_K": 1, "abinit_max_res": 12.0, "abinit_init_res": 35.0, "abinit_num_init_iters": 200, "abinit_num_final_iters": 300, "abinit_radwn_step": 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'Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/1122.outputVolumes_cryosparc_P13_J11_class_00_final_volume_scaled/slicesZ_0294.jpg', 'Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/1122.outputVolumes_cryosparc_P13_J11_class_00_final_volume_scaled/slicesZ_0295.jpg', 'Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/1122.outputVolumes_cryosparc_P13_J11_class_00_final_volume_scaled/slicesZ_0296.jpg', 'Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/1122.outputVolumes_cryosparc_P13_J11_class_00_final_volume_scaled/slicesZ_0297.jpg', 'Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/1122.outputVolumes_cryosparc_P13_J11_class_00_final_volume_scaled/slicesZ_0298.jpg', 'Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/1122.outputVolumes_cryosparc_P13_J11_class_00_final_volume_scaled/slicesZ_0299.jpg']" } ] } ], "summary": "Input Particles: [[sci-open:952][918.outputParticles.952]]Number of Ab-Initio classes: 1Symmetry: C1------------------------------------------Output volume [[sci-open:1279][1122.outputVolumes.1279]]Output classes [[sci-open:1272][1122.outputClasses.1272]]Input: SetOfParticles (310162 items, 300 x 300, 1.40 \u212b/px) \nOutput: SetOfClasses3D (1 items)SetOfVolumes (1 items, 300 x 300 x 300, 1.40 \u212b/px)", "log": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/1122_ProtCryoSparcInitialModel.log", "label": [ "C1" ], "labelColor": [ "#0ec3dc" ], "plugin": "cryosparc2", "pluginVersion": "3.2.10" }, { "object.className": "ProtCryoSparcInitialModel", "object.id": "1193", "object.label": "cryosparc2 - initial model_x1_C3", "object.comment": "", "_useQueue": false, "_prerequisites": "", "_queueParams": null, "runName": null, "runMode": 0, "abinit_K": 1, "abinit_max_res": 12.0, "abinit_init_res": 35.0, "abinit_num_init_iters": 200, "abinit_num_final_iters": 300, "abinit_radwn_step": 0.04, "abinit_window": true, "abinit_center": true, "abinit_scale_mg_correct": false, "abinit_scale_compute": false, "abinit_mom": 0.0, "abinit_sparsity": 0.0, "abinit_minisize_init": 90, "abinit_minisize": 300, "abinit_minisize_epsilon": 0.05, "abinit_minisize_minp": 0.01, "abinit_minisize_num_init_iters": 300, "abinit_noise_model": 0, "abinit_noise_priorw": 50, "abinit_noise_initw": 5000, "abinit_class_anneal_beta": 0.1, "abinit_class_anneal_start": 300, "abinit_class_anneal_end": 350, "abinit_target_initial_ess_fraction": 0.011, "symmetryGroup": 0, "symmetryOrder": 3, "abinit_r_grid": 25.0, "abinit_high_lr_duration": 100.0, "abinit_high_lr": 0.4, "abinit_nonneg": true, "abinit_ignore_dc": true, "abinit_init_radwn_cutoff": 7, "abinit_search_start_iter": 200, "abinit_use_engine": true, "intermediate_plots": true, "compute_use_ssd": false, "gpuList": "3", "compute_lane": "default", "inputParticles": "918.outputParticles", "output": [ { "outputName": "1193.outputClasses", "outputType": "SetOfClasses3D", "outputSize": 2, "outputItems": [ { "_size": "310152", "_streamState": "2", "_mapperPath": "['Runs/001193_ProtCryoSparcInitialModel/classes3D.sqlite', 'Class000']", "_representative": "Volume (No-Dim, 99999.00 \u212b/px)", "_samplingRate": "1.4", "_hasCtf": "True", "_alignment": "2D", "_isPhaseFlipped": "False", "_isAmplitudeCorrected": "False", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_firstDim": "300 x 300", "item_id": 0 }, { "_size": "10", "_streamState": "2", "_mapperPath": "['Runs/001193_ProtCryoSparcInitialModel/classes3D.sqlite', 'Class001']", "_representative": "Volume (300 x 300 x 300, 1.40 \u212b/px)", "_samplingRate": "1.4", "_hasCtf": "True", "_alignment": "Projection", "_isPhaseFlipped": "False", "_isAmplitudeCorrected": "False", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_firstDim": "300 x 300", "item_id": 1, "item_representation": 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'Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/1193.outputVolumes_cryosparc_P13_J12_class_00_final_volume_scaled/slicesZ_0296.jpg', 'Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/1193.outputVolumes_cryosparc_P13_J12_class_00_final_volume_scaled/slicesZ_0297.jpg', 'Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/1193.outputVolumes_cryosparc_P13_J12_class_00_final_volume_scaled/slicesZ_0298.jpg', 'Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/1193.outputVolumes_cryosparc_P13_J12_class_00_final_volume_scaled/slicesZ_0299.jpg']" } ] } ], "summary": "Input Particles: [[sci-open:952][918.outputParticles.952]]Number of Ab-Initio classes: 1Symmetry: C3------------------------------------------Output volume [[sci-open:1304][1193.outputVolumes.1304]]Output classes [[sci-open:1297][1193.outputClasses.1297]]Input: SetOfParticles (310162 items, 300 x 300, 1.40 \u212b/px) \nOutput: SetOfClasses3D (2 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[[sci-open:1834][1455.outputVolume.1834]]\nMap Resolution: 3.206\u00c5\nEstimated Bfactor: -158.9Input: SetOfParticles (310162 items, 300 x 300, 1.40 \u212b/px) \nInput: Volume (300 x 300 x 300, 1.40 \u212b/px) \nOutput: Volume (300 x 300 x 300, 1.40 \u212b/px) - w/halvesSetOfParticles (310162 items, 300 x 300, 1.40 \u212b/px)FSC", "log": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/1455_ProtCryoSparcNewNonUniformRefine3D.log", "label": [ "C3" ], "labelColor": [ "#21d173" ], "plugin": "cryosparc2", "pluginVersion": "3.2.10" }, { "object.className": "ProtUserSubSet", "object.id": "1548", "object.label": "create subset_classes01_02_03_211836particles", "object.comment": "", "_useQueue": false, "_prerequisites": "", "_queueParams": null, "runName": null, "runMode": 0, "other": null, "sqliteFile": "Runs/000972_ProtCryoSparcInitialModel/classes3D_state.sqlite,", "outputClassName": "SetOfParticles", "inputObject": "972.outputClasses", "output": [ { "outputName": "1548.outputParticles", "outputType": "SetOfParticles", "outputSize": 211836, "outputItems": [ { "_index": "2", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=25831.73, defV=25543.44, ast=288.28, psh=None, res=4.20, fit=0.04", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[ 0.50873144 -0.41989786 0.75158374 2.22677523]\n [-0.38072621 -0.89271851 -0.24104193 4.02133196]\n [ 0.7721657 -0.16352202 -0.61402009 1.14702828]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "21", "_classId": "4", "_rlnOpticsGroup": "1", "item_id": 2, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/1548.outputParticles_2_output_images.jpg" }, { "_index": "4", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=25831.73, defV=25543.44, ast=288.28, psh=None, res=4.20, fit=0.04", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[ 0.87156891 0.47654739 0.11519643 5.86596598]\n [-0.15363213 0.48859877 -0.85887625 2.78095012]\n [-0.46558007 0.73087196 0.49906049 3.43195601]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "21", "_classId": "3", "_rlnOpticsGroup": "1", "item_id": 4, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/1548.outputParticles_4_output_images.jpg" }, { "_index": "5", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=25831.73, defV=25543.44, ast=288.28, psh=None, res=4.20, fit=0.04", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[ 0.06665568 -0.06591163 0.99559664 0.56021777]\n [-0.78003146 0.61876248 0.09318751 -5.93611062]\n [-0.62217999 -0.78280818 -0.01016911 0.45034352]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "21", "_classId": "3", "_rlnOpticsGroup": "1", "item_id": 5, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/1548.outputParticles_5_output_images.jpg" }, { "_index": "6", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=25831.73, defV=25543.44, ast=288.28, psh=None, res=4.20, fit=0.04", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[-0.39048657 -0.63862253 -0.66308484 0.90491162]\n [ 0.71801827 -0.66205294 0.21479217 2.21533261]\n [-0.57616838 -0.39223357 0.71706543 0.17320188]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "21", "_classId": "2", "_rlnOpticsGroup": "1", "item_id": 6, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/1548.outputParticles_6_output_images.jpg" }, { "_index": "7", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=25831.73, defV=25543.44, ast=288.28, psh=None, res=4.20, fit=0.04", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[-1.34746356e-01 -3.39495396e-03 -9.90874308e-01 8.61010094e-02]\n [ 9.47709530e-01 2.91511679e-01 -1.29875277e-01 -2.21472237e+00]\n [ 2.89292354e-01 -9.56561245e-01 -3.60627064e-02 5.61029446e+00]\n [ 0.00000000e+00 0.00000000e+00 0.00000000e+00 1.00000000e+00]]", "_coordinate": "Coordinate", "_micId": "21", "_classId": "2", "_rlnOpticsGroup": "1", "item_id": 7, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/1548.outputParticles_7_output_images.jpg" }, { "_index": "8", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=25831.73, defV=25543.44, ast=288.28, psh=None, res=4.20, fit=0.04", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[-0.25240144 0.79752048 -0.54795492 1.65343561]\n [ 0.96754667 0.2009201 -0.15324669 7.95672198]\n [-0.01212222 -0.56885165 -0.82235081 -2.5844803 ]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "21", "_classId": "3", "_rlnOpticsGroup": "1", "item_id": 8, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/1548.outputParticles_8_output_images.jpg" }, { "_index": "9", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=25831.73, defV=25543.44, ast=288.28, psh=None, res=4.20, fit=0.04", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[ 0.88696973 0.44217175 0.13329982 1.50848432]\n [-0.02050405 0.3260542 -0.94512869 1.22195949]\n [-0.46137217 0.83556735 0.29826652 3.19790596]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "21", "_classId": "3", "_rlnOpticsGroup": "1", "item_id": 9, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/1548.outputParticles_9_output_images.jpg" }, { "_index": "14", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=25831.73, defV=25543.44, ast=288.28, psh=None, res=4.20, fit=0.04", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[ 0.48254376 -0.1996139 0.85282226 1.18155999]\n [-0.62495438 -0.76066261 0.17556883 -0.70217775]\n [ 0.61366403 -0.61769465 -0.49180258 1.79824217]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "21", "_classId": "3", "_rlnOpticsGroup": "1", "item_id": 14, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/1548.outputParticles_14_output_images.jpg" }, { "_index": "15", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=25831.73, defV=25543.44, ast=288.28, psh=None, res=4.20, fit=0.04", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[ 0.65248847 0.75649474 0.04443539 -2.26345018]\n [-0.22564676 0.24993225 -0.94160364 -0.96289659]\n [-0.72342404 0.60435881 0.3337785 -2.41504367]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "21", "_classId": "3", "_rlnOpticsGroup": "1", "item_id": 15, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/1548.outputParticles_15_output_images.jpg" }, { "_index": "16", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=25831.73, defV=25543.44, ast=288.28, psh=None, res=4.20, fit=0.04", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[-0.4924697 0.19603696 -0.8479641 3.73247179]\n [ 0.71334007 -0.46726697 -0.5223098 -4.78092834]\n [-0.49861764 -0.86210852 0.0902738 7.39834043]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "21", "_classId": "3", "_rlnOpticsGroup": "1", "item_id": 16, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/1548.outputParticles_16_output_images.jpg" }, { "_index": "17", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=25831.73, defV=25543.44, ast=288.28, psh=None, res=4.20, fit=0.04", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[ 0.82576267 -0.42120066 -0.375108 -9.38138467]\n [-0.2707309 -0.87944164 0.39151906 -3.70358519]\n [-0.49479369 -0.2217485 -0.84024211 2.46239535]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "21", "_classId": "3", "_rlnOpticsGroup": "1", "item_id": 17, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/1548.outputParticles_17_output_images.jpg" }, { "_index": "21", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=25831.73, defV=25543.44, ast=288.28, psh=None, res=4.20, fit=0.04", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[-0.50248268 -0.2071003 -0.83941683 5.58166582]\n [ 0.57313428 -0.80670023 -0.144055 -4.16330797]\n [-0.64732392 -0.55348371 0.52404917 7.79621292]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "21", "_classId": "4", "_rlnOpticsGroup": "1", "item_id": 21, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/1548.outputParticles_21_output_images.jpg" }, { "_index": "22", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=25831.73, defV=25543.44, ast=288.28, psh=None, res=4.20, fit=0.04", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[-0.887534 -0.38544453 0.25242009 -1.61119216]\n [ 0.28130305 -0.01942836 0.95942229 0.39562016]\n [-0.36489997 0.92252645 0.12567005 0.21588654]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "21", "_classId": "4", "_rlnOpticsGroup": "1", "item_id": 22, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/1548.outputParticles_22_output_images.jpg" }, { "_index": "23", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=25831.73, defV=25543.44, ast=288.28, psh=None, res=4.20, fit=0.04", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[ 0.35885146 -0.34078583 0.86895952 1.56445401]\n [-0.65177725 0.57491471 0.49463065 -2.39053385]\n [-0.66814073 -0.74386698 -0.01580747 11.1982429 ]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "21", "_classId": "4", "_rlnOpticsGroup": "1", "item_id": 23, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/1548.outputParticles_23_output_images.jpg" }, { "_index": "26", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=25831.73, defV=25543.44, ast=288.28, psh=None, res=4.20, fit=0.04", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[-0.66345753 -0.70959605 -0.23727105 0.06747758]\n [-0.19121667 -0.1457812 0.97066164 -0.06644939]\n [-0.72336732 0.68936296 -0.03896696 -2.06611804]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "21", "_classId": "3", "_rlnOpticsGroup": "1", "item_id": 26, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/1548.outputParticles_26_output_images.jpg" } ] } ], "summary": "From input SetOfClasses3D of size 6 we selected 3 items to create output SetOfParticles of size 211836Input: SetOfClasses3D (6 items) \nOutput: SetOfParticles (211836 items, 300 x 300, 1.40 \u212b/px)", "log": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/1548_ProtUserSubSet.log", "label": [ "C1" ], "labelColor": [ "#0ec3dc" ], "plugin": "pwem", "pluginVersion": "3.0.10" }, { "object.className": "ProtUserSubSet", "object.id": "1602", "object.label": "create subset_classes00_01_218011particles", "object.comment": "", "_useQueue": false, "_prerequisites": "", "_queueParams": null, "runName": null, "runMode": 0, "other": null, "sqliteFile": "Runs/001043_ProtCryoSparcInitialModel/classes3D_state.sqlite,", "outputClassName": "SetOfParticles", "inputObject": "1043.outputClasses", "output": [ { "outputName": "1602.outputParticles", "outputType": "SetOfParticles", "outputSize": 218011, "outputItems": [ { "_index": "2", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=25831.73, defV=25543.44, ast=288.28, psh=None, res=4.20, fit=0.04", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[ 0.28337754 -0.77268539 0.56802682 3.68732873]\n [-0.53789919 -0.61842748 -0.57289782 2.82693087]\n [ 0.79395316 -0.14319479 -0.5908753 0.80382286]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "21", "_classId": "2", "_rlnOpticsGroup": "1", "item_id": 2, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/1602.outputParticles_2_output_images.jpg" }, { "_index": "4", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=25831.73, defV=25543.44, ast=288.28, psh=None, res=4.20, fit=0.04", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[-0.48177625 0.39622906 -0.7815972 1.56651809]\n [-0.73817745 -0.66414878 0.1183235 -6.89580318]\n [-0.47221362 0.63396287 0.61245846 3.33136339]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "21", "_classId": "2", "_rlnOpticsGroup": "1", "item_id": 4, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/1602.outputParticles_4_output_images.jpg" }, { "_index": "5", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=25831.73, defV=25543.44, ast=288.28, psh=None, res=4.20, fit=0.04", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[-0.82076784 0.5480547 0.16117134 -5.29409201]\n [ 0.04613969 -0.21761166 0.97494425 1.05649446]\n [ 0.56939554 0.80763929 0.15332157 -1.15291878]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "21", "_classId": "1", "_rlnOpticsGroup": "1", "item_id": 5, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/1602.outputParticles_5_output_images.jpg" }, { "_index": "6", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=25831.73, defV=25543.44, ast=288.28, psh=None, res=4.20, fit=0.04", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[-0.93067173 -0.00556204 -0.36581306 -2.55923084]\n [ 0.07725239 -0.98032711 -0.18163376 2.28435076]\n [-0.35760621 -0.19730134 0.91279241 -0.57108807]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "21", "_classId": "1", "_rlnOpticsGroup": "1", "item_id": 6, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/1602.outputParticles_6_output_images.jpg" }, { "_index": "7", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=25831.73, defV=25543.44, ast=288.28, psh=None, res=4.20, fit=0.04", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[-0.19095367 0.8411085 0.50603675 -4.62865472]\n [-0.96282457 -0.26083848 0.07022923 2.26581379]\n [ 0.19106426 -0.47381408 0.85964799 2.53957789]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "21", "_classId": "1", "_rlnOpticsGroup": "1", "item_id": 7, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/1602.outputParticles_7_output_images.jpg" }, { "_index": "8", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=25831.73, defV=25543.44, ast=288.28, psh=None, res=4.20, fit=0.04", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[-0.33573897 0.81622175 -0.47017167 1.39135378]\n [ 0.93508041 0.22860624 -0.27085754 7.91508244]\n [-0.11359564 -0.53058575 -0.83998499 -3.33105347]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "21", "_classId": "2", "_rlnOpticsGroup": "1", "item_id": 8, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/1602.outputParticles_8_output_images.jpg" }, { "_index": "9", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=25831.73, defV=25543.44, ast=288.28, psh=None, res=4.20, fit=0.04", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[-0.86451373 -0.50204447 0.02381921 -1.85371024]\n [-0.18718044 0.27761621 -0.9422806 0.9169485 ]\n [ 0.46645417 -0.819073 -0.33397593 -2.71928783]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "21", "_classId": "1", "_rlnOpticsGroup": "1", "item_id": 9, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/1602.outputParticles_9_output_images.jpg" }, { "_index": "10", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=25831.73, defV=25543.44, ast=288.28, psh=None, res=4.20, fit=0.04", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[-8.65431387e-01 4.46997836e-01 2.26321559e-01 -1.03235102e+01]\n [ 2.03985124e-01 -9.82321649e-02 9.74033116e-01 2.36959119e+00]\n [ 4.57622752e-01 8.89125062e-01 -6.16771013e-03 -4.60018887e+00]\n [ 0.00000000e+00 0.00000000e+00 0.00000000e+00 1.00000000e+00]]", "_coordinate": "Coordinate", "_micId": "21", "_classId": "2", "_rlnOpticsGroup": "1", "item_id": 10, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/1602.outputParticles_10_output_images.jpg" }, { "_index": "14", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=25831.73, defV=25543.44, ast=288.28, psh=None, res=4.20, fit=0.04", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[ 0.17725899 0.72080424 -0.67008992 -0.4454552 ]\n [ 0.74468664 0.34691834 0.57016618 1.17853091]\n [ 0.64344468 -0.60007409 -0.47527889 2.04186117]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "21", "_classId": "2", "_rlnOpticsGroup": "1", "item_id": 14, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/1602.outputParticles_14_output_images.jpg" }, { "_index": "15", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=25831.73, defV=25543.44, ast=288.28, psh=None, res=4.20, fit=0.04", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[ 0.64220915 0.31613648 0.6983016 -0.97445676]\n [-0.27993475 -0.7513415 0.59759725 2.51846349]\n [ 0.71358527 -0.57926131 -0.3940208 2.09268683]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "21", "_classId": "1", "_rlnOpticsGroup": "1", "item_id": 15, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/1602.outputParticles_15_output_images.jpg" }, { "_index": "16", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=25831.73, defV=25543.44, ast=288.28, psh=None, res=4.20, fit=0.04", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[-0.56242195 0.25108867 -0.78780457 3.98701892]\n [ 0.65955743 -0.43837421 -0.61058337 -4.18448634]\n [-0.49866377 -0.86300784 0.08094388 7.23975598]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "21", "_classId": "2", "_rlnOpticsGroup": "1", "item_id": 16, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/1602.outputParticles_16_output_images.jpg" }, { "_index": "17", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=25831.73, defV=25543.44, ast=288.28, psh=None, res=4.20, fit=0.04", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[-0.27525638 0.96074544 0.03467167 9.21717997]\n [ 0.83991182 0.25787104 -0.47754649 -4.80211591]\n [-0.46774144 -0.10232657 -0.8779221 2.97612813]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "21", "_classId": "2", "_rlnOpticsGroup": "1", "item_id": 17, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/1602.outputParticles_17_output_images.jpg" }, { "_index": "23", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=25831.73, defV=25543.44, ast=288.28, psh=None, res=4.20, fit=0.04", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[ -0.69374687 0.63160378 0.34610974 -2.74582612]\n [ 0.23115923 -0.25987056 0.93756744 1.42083351]\n [ 0.68211487 0.73044093 0.03428335 -11.13573004]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "21", "_classId": "1", "_rlnOpticsGroup": "1", "item_id": 23, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/1602.outputParticles_23_output_images.jpg" }, { "_index": "26", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=25831.73, defV=25543.44, ast=288.28, psh=None, res=4.20, fit=0.04", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[-0.49377169 -0.2195848 0.84141074 -0.5792198 ]\n [-0.52352223 -0.69753145 -0.48925898 0.36759447]\n [ 0.69434429 -0.68207946 0.22946376 2.90769517]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "21", "_classId": "1", "_rlnOpticsGroup": "1", "item_id": 26, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/1602.outputParticles_26_output_images.jpg" }, { "_index": "27", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=25831.73, defV=25543.44, ast=288.28, psh=None, res=4.20, fit=0.04", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[-0.13446623 0.68736937 -0.71375219 2.5230404 ]\n [-0.7137522 0.4324601 0.55094107 -2.80882573]\n [ 0.68736936 0.58352516 0.43246012 7.74250138]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "21", "_classId": "1", "_rlnOpticsGroup": "1", "item_id": 27, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/1602.outputParticles_27_output_images.jpg" } ] } ], "summary": "From input SetOfClasses3D of size 6 we selected 2 items to create output SetOfParticles of size 218011Input: SetOfClasses3D (6 items) \nOutput: SetOfParticles (218011 items, 300 x 300, 1.40 \u212b/px)", "log": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/1602_ProtUserSubSet.log", "label": [ "C3" ], "labelColor": [ "#21d173" ], "plugin": "pwem", "pluginVersion": "3.0.10" }, { "object.className": "ProtCryoSparcNewNonUniformRefine3D", "object.id": "1656", "object.label": "cryosparc2 - 3D non-uniform refinement_classes01_02_03_inimodelclass03_symC1", "object.comment": "", "_useQueue": false, "_prerequisites": "", "_queueParams": null, "runName": null, "runMode": 0, "symmetryGroup": 0, "symmetryOrder": 1, "refine_symmetry_do_align": true, "refine_do_init_scale_est": true, "refine_num_final_iterations": 0, "refine_res_init": 30, "refine_res_gsfsc_split": 20, "refine_highpass_res": null, "refine_clip": false, "refine_window": true, "refine_skip_premult": true, "refine_ignore_dc": true, "refine_batchsize_init": 0, "refine_batchsize_epsilon": 0.001, "refine_batchsize_snrfactor": 40.0, "refine_scale_min": false, "refine_scale_start_iter": 0, "refine_noise_model": 0, "refine_noise_priorw": 50, "refine_noise_initw": 200, "refine_noise_init_sigmascale": 3, "refine_mask": 0, "refine_dynamic_mask_thresh_factor": 0.2, "refine_dynamic_mask_near_ang": 6.0, "refine_dynamic_mask_far_ang": 14.0, "refine_dynamic_mask_start_res": 12, "refine_dynamic_mask_use_abs": false, "refine_defocus_refine": false, "crl_num_plots": 3, "crl_min_res_A": 20.0, "crl_df_range": 2000.0, "refine_ctf_global_refine": false, "crg_num_plots": 3, "crg_min_res_A": 10.0, "crg_do_tilt": true, "crg_do_trefoil": true, "crg_do_spherical": true, "crg_do_tetrafoil": true, "compute_use_ssd": false, "gpuList": "2", "compute_lane": "default", "refine_do_marg": true, "refine_nu_enable": true, "refine_nu_filtertype": 0, "refine_nu_order": 8, "refine_nu_awf": 3.0, "referenceVolume": "972.outputVolumes.4", "inputParticles": "1548.outputParticles", "output": [ { "outputName": "1656.outputVolume", "outputType": "Volume", "outputItems": [ { "_index": "0", "_filename": "Runs/001656_ProtCryoSparcNewNonUniformRefine3D/extra/cryosparc_P13_J23_006_volume_map.mrc", "_samplingRate": "1.4", "_classId": "None", "_halfMapFilenames": "['Runs/001656_ProtCryoSparcNewNonUniformRefine3D/extra/cryosparc_P13_J23_006_volume_map_half_A.mrc', 'Runs/001656_ProtCryoSparcNewNonUniformRefine3D/extra/cryosparc_P13_J23_006_volume_map_half_B.mrc']", "item_id": 1896, "item_representation": "['Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/1656.outputVolume_cryosparc_P13_J23_006_volume_map/slicesX_0000.jpg', 'Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/1656.outputVolume_cryosparc_P13_J23_006_volume_map/slicesX_0001.jpg', 'Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/1656.outputVolume_cryosparc_P13_J23_006_volume_map/slicesX_0002.jpg', 'Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/1656.outputVolume_cryosparc_P13_J23_006_volume_map/slicesX_0003.jpg', 'Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/1656.outputVolume_cryosparc_P13_J23_006_volume_map/slicesX_0004.jpg', 'Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/1656.outputVolume_cryosparc_P13_J23_006_volume_map/slicesX_0005.jpg', 'Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/1656.outputVolume_cryosparc_P13_J23_006_volume_map/slicesX_0006.jpg', 'Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/1656.outputVolume_cryosparc_P13_J23_006_volume_map/slicesX_0007.jpg', 'Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/1656.outputVolume_cryosparc_P13_J23_006_volume_map/slicesX_0008.jpg', 'Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/1656.outputVolume_cryosparc_P13_J23_006_volume_map/slicesX_0009.jpg', 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[[sci-open:1927][1739.outputVolume.1927]]\nMap Resolution: 3.178\u00c5\nEstimated Bfactor: -161.6Input: SetOfParticles (218011 items, 300 x 300, 1.40 \u212b/px) \nInput: Volume (300 x 300 x 300, 1.40 \u212b/px) \nOutput: Volume (300 x 300 x 300, 1.40 \u212b/px) - w/halvesSetOfParticles (218011 items, 300 x 300, 1.40 \u212b/px)FSC", "log": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/1739_ProtCryoSparcNewNonUniformRefine3D.log", "label": [ "C3" ], "labelColor": [ "#21d173" ], "plugin": "cryosparc2", "pluginVersion": "3.2.10" }, { "object.className": "ProtRelionExpandSymmetry", "object.id": "1956", "object.label": "relion - expand symmetry_C3", "object.comment": "", "_useQueue": false, "_prerequisites": "", "_queueParams": null, "runName": null, "runMode": 0, "symmetryGroup": "C3", "hostName": "localhost", "inputParticles": "1455.outputParticles", "output": [ { "outputName": "1956.outputParticles", "outputType": "SetOfParticles", "outputSize": 930486, "outputItems": [ { "_index": "2", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=25831.73, defV=25543.44, ast=288.29, psh=0.00, res=0.00, fit=0.00", "_acquisition": "\n mag=10000.0\n volt= None\n Cs=None\n Q0=None\n\n", "_transform": "[[ 0.61189721 -0.02696181 0.79047762 1.64003194]\n [ 0.1366562 0.98799233 -0.07208489 -10.39703734]\n [ -0.77904229 0.15213221 0.60823425 -3.36363463]\n [ 0. 0. 0. 1. ]]", "_micId": "None", "_classId": "None", "_rlnPhaseShift": "0.0", "_rlnRandomSubset": "1", "item_id": 1, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/1956.outputParticles_2_output_images.jpg" }, { "_index": "2", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=25831.73, defV=25543.44, ast=288.29, psh=0.00, res=0.00, fit=0.00", "_acquisition": "\n mag=10000.0\n volt= None\n Cs=None\n Q0=None\n\n", "_transform": "[[-0.42429633 -0.84214558 -0.33281144 8.18408272]\n [ 0.46159044 -0.51734575 0.72061615 6.61882771]\n [-0.77904229 0.15213221 0.60823425 -3.36363463]\n [ 0. 0. 0. 1. ]]", "_micId": "None", "_classId": "None", "_rlnPhaseShift": "0.0", "_rlnRandomSubset": "1", "item_id": 2, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/1956.outputParticles_2_output_images.jpg" }, { "_index": "2", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=25831.73, defV=25543.44, ast=288.29, psh=0.00, res=0.00, fit=0.00", "_acquisition": "\n mag=10000.0\n volt= None\n Cs=None\n Q0=None\n\n", "_transform": "[[-0.18760087 0.86910736 -0.45766615 -9.82411443]\n [-0.59824663 -0.47064656 -0.64853126 3.77820934]\n [-0.77904229 0.15213221 0.60823425 -3.36363463]\n [ 0. 0. 0. 1. ]]", "_micId": "None", "_classId": "None", "_rlnPhaseShift": "0.0", "_rlnRandomSubset": "1", "item_id": 3, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/1956.outputParticles_2_output_images.jpg" }, { "_index": "4", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=25831.73, defV=25543.44, ast=288.29, psh=0.00, res=0.00, fit=0.00", "_acquisition": "\n mag=10000.0\n volt= None\n Cs=None\n Q0=None\n\n", "_transform": "[[ -0.88809127 -0.45417379 -0.0708524 -13.51072254]\n [ -0.21536941 0.5473007 -0.80875086 7.66377765]\n [ 0.40609101 -0.70298514 -0.58386812 -8.9760333 ]\n [ 0. 0. 0. 1. ]]", "_micId": "None", "_classId": "None", "_rlnPhaseShift": "0.0", "_rlnRandomSubset": "2", "item_id": 4, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/1956.outputParticles_4_output_images.jpg" }, { "_index": "4", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=25831.73, defV=25543.44, ast=288.29, psh=0.00, res=0.00, fit=0.00", "_acquisition": "\n mag=10000.0\n volt= None\n Cs=None\n Q0=None\n\n", "_transform": "[[ 0.63056097 -0.24688946 0.73582502 0.11833405]\n [ -0.66142494 -0.66697637 0.3430154 -15.53251778]\n [ 0.40609101 -0.70298514 -0.58386812 -8.9760333 ]\n [ 0. 0. 0. 1. ]]", "_micId": "None", "_classId": "None", "_rlnPhaseShift": "0.0", "_rlnRandomSubset": "2", "item_id": 5, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/1956.outputParticles_4_output_images.jpg" }, { "_index": "4", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=25831.73, defV=25543.44, ast=288.29, psh=0.00, res=0.00, fit=0.00", "_acquisition": "\n mag=10000.0\n volt= None\n Cs=None\n Q0=None\n\n", "_transform": "[[ 0.25753031 0.70106322 -0.66497256 13.39238795]\n [ 0.87679429 0.11967564 0.46573545 7.86873918]\n [ 0.40609101 -0.70298514 -0.58386812 -8.9760333 ]\n [ 0. 0. 0. 1. ]]", "_micId": "None", "_classId": "None", "_rlnPhaseShift": "0.0", "_rlnRandomSubset": "2", "item_id": 6, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/1956.outputParticles_4_output_images.jpg" }, { "_index": "5", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=25831.73, defV=25543.44, ast=288.29, psh=0.00, res=0.00, fit=0.00", "_acquisition": "\n mag=10000.0\n volt= None\n Cs=None\n Q0=None\n\n", "_transform": "[[ -0.8110557 0.47875962 0.33612182 -12.1487896 ]\n [ 0.18838044 -0.33022175 0.92491427 4.98801562]\n [ 0.55380634 0.81347576 0.17763929 -2.98365052]\n [ 0. 0. 0. 1. ]]", "_micId": "None", "_classId": "None", "_rlnPhaseShift": "0.0", "_rlnRandomSubset": "1", "item_id": 7, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/1956.outputParticles_5_output_images.jpg" }, { "_index": "5", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=25831.73, defV=25543.44, ast=288.29, psh=0.00, res=0.00, fit=0.00", "_acquisition": "\n mag=10000.0\n volt= None\n Cs=None\n Q0=None\n\n", "_transform": "[[ 0.24238562 0.0466006 -0.96906016 1.75464678]\n [ -0.79658505 0.57972887 -0.17136712 -13.0151682 ]\n [ 0.55380634 0.81347576 0.17763929 -2.98365052]\n [ 0. 0. 0. 1. ]]", "_micId": "None", "_classId": "None", "_rlnPhaseShift": "0.0", "_rlnRandomSubset": "1", "item_id": 8, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/1956.outputParticles_5_output_images.jpg" }, { "_index": "5", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=25831.73, defV=25543.44, ast=288.29, psh=0.00, res=0.00, fit=0.00", "_acquisition": "\n mag=10000.0\n volt= None\n Cs=None\n Q0=None\n\n", "_transform": "[[ 0.56867008 -0.52536023 0.63293836 10.3941429 ]\n [ 0.60820463 -0.24950713 -0.75354716 8.02715279]\n [ 0.55380634 0.81347576 0.17763929 -2.98365052]\n [ 0. 0. 0. 1. ]]", "_micId": "None", "_classId": "None", "_rlnPhaseShift": "0.0", "_rlnRandomSubset": "1", "item_id": 9, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/1956.outputParticles_5_output_images.jpg" }, { "_index": "6", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=25831.73, defV=25543.44, ast=288.29, psh=0.00, res=0.00, fit=0.00", "_acquisition": "\n mag=10000.0\n volt= None\n Cs=None\n Q0=None\n\n", "_transform": "[[-0.93342161 -0.11233105 -0.34074307 -4.91638825]\n [ 0.14934435 -0.98518263 -0.08432936 5.72400681]\n [-0.32622135 -0.1296029 0.93636676 -1.27356442]\n [ 0. 0. 0. 1. ]]", "_micId": "None", "_classId": "None", "_rlnPhaseShift": "0.0", "_rlnRandomSubset": "2", "item_id": 10, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/1956.outputParticles_6_output_images.jpg" }, { "_index": "6", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=25831.73, defV=25543.44, ast=288.29, psh=0.00, res=0.00, fit=0.00", "_acquisition": "\n mag=10000.0\n volt= None\n Cs=None\n Q0=None\n\n", "_transform": "[[ 0.3373748 0.90935871 0.24340291 -2.49894119]\n [-0.883039 0.39530978 -0.25292748 -7.11972052]\n [-0.32622135 -0.1296029 0.93636676 -1.27356442]\n [ 0. 0. 0. 1. ]]", "_micId": "None", "_classId": "None", "_rlnPhaseShift": "0.0", "_rlnRandomSubset": "2", "item_id": 11, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/1956.outputParticles_6_output_images.jpg" }, { "_index": "6", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=25831.73, defV=25543.44, ast=288.29, psh=0.00, res=0.00, fit=0.00", "_acquisition": "\n mag=10000.0\n volt= None\n Cs=None\n Q0=None\n\n", "_transform": "[[ 0.59604674 -0.79702772 0.09734014 7.41532931]\n [ 0.7336947 0.58987279 0.33725685 1.39571436]\n [-0.32622135 -0.1296029 0.93636676 -1.27356442]\n [ 0. 0. 0. 1. ]]", "_micId": "None", "_classId": "None", "_rlnPhaseShift": "0.0", "_rlnRandomSubset": "2", "item_id": 12, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/1956.outputParticles_6_output_images.jpg" }, { "_index": "7", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=25831.73, defV=25543.44, ast=288.29, psh=0.00, res=0.00, fit=0.00", "_acquisition": "\n mag=10000.0\n volt= None\n Cs=None\n Q0=None\n\n", "_transform": "[[-0.58325161 -0.74714091 -0.31874443 11.41995749]\n [ 0.79445313 -0.44290576 -0.41554628 5.3266841 ]\n [ 0.16929788 -0.49559555 0.85189394 6.87119756]\n [ 0. 0. 0. 1. ]]", "_micId": "None", "_classId": "None", "_rlnPhaseShift": "0.0", "_rlnRandomSubset": "1", "item_id": 13, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/1956.outputParticles_7_output_images.jpg" }, { "_index": "7", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=25831.73, defV=25543.44, ast=288.29, psh=0.00, res=0.00, fit=0.00", "_acquisition": "\n mag=10000.0\n volt= None\n Cs=None\n Q0=None\n\n", "_transform": "[[ -0.39639079 0.75713809 0.51924585 -10.32302249]\n [ -0.90233728 -0.42559013 -0.06826763 7.22663124]\n [ 0.16929788 -0.49559555 0.85189394 6.87119756]\n [ 0. 0. 0. 1. ]]", "_micId": "None", "_classId": "None", "_rlnPhaseShift": "0.0", "_rlnRandomSubset": "1", "item_id": 14, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/1956.outputParticles_7_output_images.jpg" }, { "_index": "7", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=25831.73, defV=25543.44, ast=288.29, psh=0.00, res=0.00, fit=0.00", "_acquisition": "\n mag=10000.0\n volt= None\n Cs=None\n Q0=None\n\n", "_transform": "[[ 9.79642409e-01 -9.99713592e-03 -2.00501392e-01 -1.09693566e+00]\n [ 1.07884096e-01 8.68495891e-01 4.83813920e-01 -1.25533153e+01]\n [ 1.69297882e-01 -4.95595546e-01 8.51893939e-01 6.87119756e+00]\n [ 0.00000000e+00 0.00000000e+00 0.00000000e+00 1.00000000e+00]]", "_micId": "None", "_classId": "None", "_rlnPhaseShift": "0.0", "_rlnRandomSubset": "1", "item_id": 15, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/1956.outputParticles_7_output_images.jpg" } ] } ], "summary": "Symmetry used: C3Input: SetOfParticles (310162 items, 300 x 300, 1.40 \u212b/px) \nOutput: SetOfParticles (930486 items, 300 x 300, 1.40 \u212b/px)", "log": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/1956_ProtRelionExpandSymmetry.log", "plugin": "relion", "pluginVersion": "3.0.0" }, { "object.className": "XmippProtAngBreakSymmetry", "object.id": "2029", "object.label": "xmipp3 - break symmetry_C3", "object.comment": "", "_useQueue": false, "_prerequisites": "", "_queueParams": null, "runName": null, "runMode": 0, "symmetryGroup": "C3", "hostName": "localhost", "inputParticles": "1455.outputParticles", "output": [ { "outputName": "2029.outputParticles", "outputType": "SetOfParticles", "outputSize": 310162, "outputItems": [ { "_index": "2", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=25831.73, defV=25543.44, ast=288.29, psh=0.00, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[-0.42429633 -0.84214558 -0.33281144 8.18407971]\n [ 0.46159044 -0.51734575 0.72061615 6.61882586]\n [-0.77904229 0.15213221 0.60823425 -3.36363409]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "21", "_classId": "14", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "1", "item_id": 2, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/2029.outputParticles_2_output_images.jpg" }, { "_index": "4", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=25831.73, defV=25543.44, ast=288.29, psh=0.00, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[ -0.8880913 -0.45417372 -0.07085246 -13.5107216 ]\n [ -0.21536933 0.54730074 -0.80875086 7.66377884]\n [ 0.40609099 -0.70298516 -0.58386812 -8.9760337 ]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "21", "_classId": "49", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "2", "item_id": 4, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/2029.outputParticles_4_output_images.jpg" }, { "_index": "5", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=25831.73, defV=25543.44, ast=288.29, psh=0.00, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[ 0.2423856 0.04660061 -0.96906016 1.75464672]\n [ -0.79658506 0.57972887 -0.1713671 -13.01516616]\n [ 0.55380634 0.81347576 0.17763929 -2.98364761]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "21", "_classId": "86", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "1", "item_id": 5, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/2029.outputParticles_5_output_images.jpg" }, { "_index": "6", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=25831.73, defV=25543.44, ast=288.29, psh=0.00, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[-0.93342161 -0.11233099 -0.34074307 -4.91638816]\n [ 0.1493443 -0.98518264 -0.08432939 5.72401008]\n [-0.32622135 -0.12960291 0.93636676 -1.27356388]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "21", "_classId": "44", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "2", "item_id": 6, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/2029.outputParticles_6_output_images.jpg" }, { "_index": "7", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=25831.73, defV=25543.44, ast=288.29, psh=0.00, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[ -0.39639084 0.75713807 0.51924584 -10.32302623]\n [ -0.90233726 -0.42559017 -0.06826766 7.22663008]\n [ 0.16929788 -0.49559555 0.85189394 6.87119993]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "21", "_classId": "5", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "1", "item_id": 7, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/2029.outputParticles_7_output_images.jpg" }, { "_index": "8", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=25831.73, defV=25543.44, ast=288.29, psh=0.00, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[ 0.74555887 0.49707866 -0.44390853 17.39292465]\n [-0.655042 0.66924346 -0.35076084 -3.09830204]\n [ 0.12272715 0.55229159 0.8245678 8.04555374]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "21", "_classId": "5", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "2", "item_id": 8, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/2029.outputParticles_8_output_images.jpg" }, { "_index": "9", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=25831.73, defV=25543.44, ast=288.29, psh=0.00, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[ 0.3375742 0.54273762 -0.76907707 4.73479007]\n [ 0.8321451 0.20982492 0.51333034 1.99493842]\n [ 0.43997522 -0.81327079 -0.38080497 -6.87321932]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "21", "_classId": "11", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "1", "item_id": 9, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/2029.outputParticles_9_output_images.jpg" }, { "_index": "10", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=25831.73, defV=25543.44, ast=288.29, psh=0.00, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[ 0.81140042 -0.38309327 -0.44143957 22.12704993]\n [ 0.36656028 -0.25474402 0.89484023 11.88367223]\n [-0.45526137 -0.88788796 -0.06627263 13.0707444 ]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "21", "_classId": "90", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "2", "item_id": 10, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/2029.outputParticles_10_output_images.jpg" }, { "_index": "14", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=25831.73, defV=25543.44, ast=288.29, psh=0.00, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[-0.3206808 -0.77707275 0.54159188 0.59731786]\n [ 0.70545688 0.18560914 0.68401742 2.18607403]\n [-0.6320557 0.60142098 0.48867003 -3.72197007]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "21", "_classId": "86", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "1", "item_id": 14, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/2029.outputParticles_14_output_images.jpg" }, { "_index": "15", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=25831.73, defV=25543.44, ast=288.29, psh=0.00, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[ 0.54202284 0.2090759 0.81394011 -1.23159857]\n [-0.42286604 -0.76914493 0.47916635 5.19359998]\n [ 0.72622004 -0.60390674 -0.32848302 4.52428523]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "21", "_classId": "11", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "2", "item_id": 15, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/2029.outputParticles_15_output_images.jpg" }, { "_index": "16", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=25831.73, defV=25543.44, ast=288.29, psh=0.00, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[-0.74646818 0.64610456 0.15916708 10.12849393]\n [ 0.6640766 0.7385324 0.11649958 -1.43843122]\n [-0.04227914 0.19266236 -0.98035386 1.47349466]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "21", "_classId": "22", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "1", "item_id": 16, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/2029.outputParticles_16_output_images.jpg" }, { "_index": "17", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=25831.73, defV=25543.44, ast=288.29, psh=0.00, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[ 0.6919314 0.59110179 -0.41452335 -2.26298581]\n [-0.55451237 0.8027963 0.21916692 23.89308263]\n [ 0.46232776 0.07820985 0.88325322 -6.99078533]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "21", "_classId": "42", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "2", "item_id": 17, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/2029.outputParticles_17_output_images.jpg" }, { "_index": "19", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=25831.73, defV=25543.44, ast=288.29, psh=0.00, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[-0.84670231 0.44838326 -0.28643962 -0.72368924]\n [ 0.41071365 0.20855023 -0.88759287 0.53078279]\n [-0.33824473 -0.86917159 -0.36073709 -0.73135187]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "21", "_classId": "96", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "1", "item_id": 19, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/2029.outputParticles_19_output_images.jpg" }, { "_index": "21", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=25831.73, defV=25543.44, ast=288.29, psh=0.00, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[ -0.80452842 -0.07637281 -0.5889832 5.89567068]\n [ -0.55519423 -0.25549992 0.79150437 7.00589721]\n [ -0.21093457 0.96378783 0.1631552 -12.70414452]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "21", "_classId": "11", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "2", "item_id": 21, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/2029.outputParticles_21_output_images.jpg" }, { "_index": "22", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=25831.73, defV=25543.44, ast=288.29, psh=0.00, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[ 0.44327006 0.04135911 0.89543346 1.04333912]\n [-0.81511168 -0.39703685 0.42184675 -2.11415398]\n [ 0.37296729 -0.91687031 -0.14228225 0.2979414 ]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "21", "_classId": "96", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "1", "item_id": 22, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/2029.outputParticles_22_output_images.jpg" } ] } ], "summary": "Symmetry: C3Input: SetOfParticles (310162 items, 300 x 300, 1.40 \u212b/px) \nOutput: SetOfParticles (310162 items, 300 x 300, 1.40 \u212b/px)", "log": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/2029_XmippProtAngBreakSymmetry.log", "plugin": "xmipp3" }, { "object.className": "ProtSubSet", "object.id": "2101", "object.label": "pwem - subset_10000particles", "object.comment": "", "_useQueue": false, "_prerequisites": "", "_queueParams": null, "runName": null, "runMode": 0, "chooseAtRandom": true, "nElements": 10000, "setOperation": 0, "inputFullSet": "2029.outputParticles", "output": [ { "outputName": "2101.outputParticles", "outputType": "SetOfParticles", "outputSize": 10000, "outputItems": [ { "_index": "31", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=25831.73, defV=25543.44, ast=288.29, psh=0.00, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[ 0.78683859 0.61104117 0.08668171 -12.91957536]\n [ -0.54903619 0.75719312 -0.35386134 1.63618377]\n [ -0.28185865 0.23084036 0.93127248 1.82424924]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "21", "_classId": "42", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "1", "item_id": 31, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/2101.outputParticles_31_output_images.jpg" }, { "_index": "74", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=25831.73, defV=25543.44, ast=288.29, psh=0.00, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[ 0.94402617 -0.29398632 0.14962166 -2.39829444]\n [ 0.03849551 -0.35229524 -0.93509687 0.04576936]\n [ 0.32761668 0.88851568 -0.32125877 -1.25019338]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "21", "_classId": "11", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "2", "item_id": 74, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/2101.outputParticles_74_output_images.jpg" }, { "_index": "101", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=25831.73, defV=25543.44, ast=288.29, psh=0.00, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[-0.64924998 0.42773792 -0.62889962 -3.09811652]\n [-0.24152603 0.66812446 0.70375769 -4.80302662]\n [ 0.72120707 0.6088103 -0.33046995 -4.33250477]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "21", "_classId": "96", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "2", "item_id": 101, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/2101.outputParticles_101_output_images.jpg" }, { "_index": "128", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=13915.24, defV=13592.83, ast=322.41, psh=0.00, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[-0.97003244 0.15873736 -0.18395522 -9.68758218]\n [-0.14763328 0.21625648 0.96511012 1.16394676]\n [ 0.19298054 0.96334604 -0.18634089 15.59195202]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "12", "_classId": "24", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "1", "item_id": 128, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/2101.outputParticles_128_output_images.jpg" }, { "_index": "147", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=13915.24, defV=13592.83, ast=322.41, psh=0.00, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[ 0.64595568 -0.23958652 0.72480312 -11.33527314]\n [ -0.31876938 0.77807123 0.54128666 11.3776865 ]\n [ -0.69363344 -0.58069223 0.42622668 4.82666024]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "12", "_classId": "21", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "1", "item_id": 147, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/2101.outputParticles_147_output_images.jpg" }, { "_index": "163", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=13915.24, defV=13592.83, ast=322.41, psh=0.00, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[ 7.67015493e-02 -9.46941476e-01 -3.12119709e-01 5.31534419e+00]\n [-2.71155240e-01 -3.21054284e-01 9.07413347e-01 -6.56943302e+00]\n [-9.59474704e-01 1.50328851e-02 -2.81393504e-01 -2.70802800e+01]\n [ 0.00000000e+00 0.00000000e+00 0.00000000e+00 1.00000000e+00]]", "_coordinate": "Coordinate", "_micId": "12", "_classId": "57", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "1", "item_id": 163, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/2101.outputParticles_163_output_images.jpg" }, { "_index": "186", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=13915.24, defV=13592.83, ast=322.41, psh=0.00, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[ 0.4516212 -0.26355628 -0.8523945 2.31042207]\n [ 0.35201135 -0.82523938 0.44166499 8.27981926]\n [-0.81983309 -0.49951782 -0.2799208 6.02854537]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "12", "_classId": "61", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "2", "item_id": 186, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/2101.outputParticles_186_output_images.jpg" }, { "_index": "241", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=24957.51, defV=24507.44, ast=450.07, psh=0.00, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[ 0.17168425 0.90634602 -0.38608471 2.8687597 ]\n [ 0.96851233 -0.08355719 0.23452519 1.81186784]\n [ 0.18030082 -0.41419208 -0.89215275 -0.76517793]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "44", "_classId": "73", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "2", "item_id": 241, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/2101.outputParticles_241_output_images.jpg" }, { "_index": "303", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=24957.51, defV=24507.44, ast=450.07, psh=0.00, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[-0.06999546 0.37584804 0.92403403 3.75004083]\n [ 0.9765669 -0.16316157 0.14034029 -0.16432857]\n [ 0.20351346 0.91220423 -0.35562019 9.67915641]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "44", "_classId": "96", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "2", "item_id": 303, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/2101.outputParticles_303_output_images.jpg" }, { "_index": "345", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=24957.51, defV=24507.44, ast=450.07, psh=0.00, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[ 0.30944194 0.18280497 -0.93318167 -0.02517285]\n [ 0.9506961 -0.03825793 0.3077552 6.81200318]\n [ 0.02055758 -0.98240454 -0.18563058 11.42010214]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "44", "_classId": "81", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "1", "item_id": 345, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/2101.outputParticles_345_output_images.jpg" }, { "_index": "380", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=19666.03, defV=19225.26, ast=440.78, psh=0.00, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[-0.66415395 0.42462351 0.61530025 -4.07066512]\n [ 0.01281594 0.82938449 -0.55853121 -0.2748032 ]\n [-0.74748597 -0.36306507 -0.55628094 -4.22663253]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "36", "_classId": "86", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "2", "item_id": 380, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/2101.outputParticles_380_output_images.jpg" }, { "_index": "389", "_filename": 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"[[ 0.7240472 0.62793571 -0.28539867 -3.13717336]\n [ 0.42344078 -0.73128313 -0.53471758 1.1003993 ]\n [-0.5444755 0.26631133 -0.79537709 0.38590784]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "36", "_classId": "71", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "2", "item_id": 499, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/2101.outputParticles_499_output_images.jpg" }, { "_index": "587", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=22615.70, defV=22160.71, ast=454.99, psh=0.00, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[-0.78176204 0.61106399 -0.12429362 2.94310022]\n [-0.59754253 -0.67709839 0.42951216 -2.09469125]\n [ 0.17830041 0.41004703 0.89446654 1.41481418]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "48", "_classId": "30", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "2", "item_id": 587, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/2101.outputParticles_587_output_images.jpg" }, { "_index": "811", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=6993.03, defV=6627.23, ast=365.80, psh=0.00, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[-0.38211217 -0.89199274 -0.24153517 -6.28553581]\n [-0.89665217 0.4211146 -0.13666519 14.12499406]\n [ 0.22361835 0.1643516 -0.96072024 -0.42907089]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "14", "_classId": "30", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "2", "item_id": 811, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/2101.outputParticles_811_output_images.jpg" } ] } ], "summary": "The elements of 2101.inputFullSet that also are referenced in 2101.inputSubSetare now in 2101.outputParticlesInput: SetOfParticles (310162 items, 300 x 300, 1.40 \u212b/px) \nOutput: SetOfParticles (10000 items, 300 x 300, 1.40 \u212b/px)", "log": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/2101_ProtSubSet.log", "plugin": "pwem", "pluginVersion": "3.0.10" }, { "object.className": "ProtRelionReconstruct", "object.id": "2157", "object.label": "relion - reconstruct_10000particles", "object.comment": "", "_useQueue": false, "_prerequisites": "", "_queueParams": null, "runName": null, "runMode": 0, "symmetryGroup": "c1", "maxRes": 30.0, "pad": 2.0, "subset": 0, "classNum": -1, "extraParams": "", "doCTF": true, "ctfIntactFirstPeak": false, "hostName": "localhost", "numberOfMpi": 20, "inputParticles": "2101.outputParticles", "output": [ { "outputName": "2157.outputVolume", "outputType": "Volume", "outputItems": [ { "_index": "0", "_filename": "Runs/002157_ProtRelionReconstruct/extra/output_volume.mrc", "_samplingRate": 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'Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/2226.outputVolumes_relion_it025_class010/slicesZ_0296.jpg', 'Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/2226.outputVolumes_relion_it025_class010/slicesZ_0297.jpg', 'Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/2226.outputVolumes_relion_it025_class010/slicesZ_0298.jpg', 'Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/2226.outputVolumes_relion_it025_class010/slicesZ_0299.jpg']" } ] } ], "summary": "Iteration 25/25Current resolution: *8.08 A*Input Particles: *310162*\nClassified into *10* 3D classes\nInput: SetOfParticles (310162 items, 300 x 300, 1.40 \u212b/px) \nInput: Volume (300 x 300 x 300, 1.40 \u212b/px) \nOutput: SetOfClasses3D (10 items)SetOfVolumes (10 items, 300 x 300 x 300, 1.40 \u212b/px)", "log": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/2226_ProtRelionClassify3D.log", "label": [ "symrelax" ], "labelColor": [ "#e4ee89" ], "plugin": "relion", "pluginVersion": "3.0.0" }, { "object.className": "ProtRelionClassify3D", "object.id": "2421", "object.label": "relion - 3D classification_symexp_10classes_T25", "object.comment": "", "_useQueue": false, "_prerequisites": "", "_queueParams": null, "runName": null, "runMode": 0, "isClassify": true, "is2D": false, "doContinue": false, "copyAlignment": true, "alignmentAsPriors": false, "fillRandomSubset": true, "maskDiameterA": 336, "maskZero": 0, "continueIter": "last", "solventFscMask": false, "isMapAbsoluteGreyScale": true, "symmetryGroup": "C1", "initialLowPassFilterA": 3.2, "continueMsg": "True", "doCTF": true, "hasReferenceCTFCorrected": true, "haveDataBeenPhaseFlipped": null, "ignoreCTFUntilFirstPeak": false, "doCtfManualGroups": true, "defocusRange": 1000.0, "numParticles": 100.0, "numberOfClasses": 10, "regularisationParamT": 25.0, "numberOfIterations": 25, "useFastSubsets": false, "limitResolEStep": -1.0, "doImageAlignment": 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'Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/2421.outputVolumes_relion_it025_class010/slicesZ_0273.jpg', 'Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/2421.outputVolumes_relion_it025_class010/slicesZ_0274.jpg', 'Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/2421.outputVolumes_relion_it025_class010/slicesZ_0275.jpg', 'Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/2421.outputVolumes_relion_it025_class010/slicesZ_0276.jpg', 'Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/2421.outputVolumes_relion_it025_class010/slicesZ_0277.jpg', 'Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/2421.outputVolumes_relion_it025_class010/slicesZ_0278.jpg', 'Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/2421.outputVolumes_relion_it025_class010/slicesZ_0279.jpg', 'Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/2421.outputVolumes_relion_it025_class010/slicesZ_0280.jpg', 'Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/2421.outputVolumes_relion_it025_class010/slicesZ_0281.jpg', 'Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/2421.outputVolumes_relion_it025_class010/slicesZ_0282.jpg', 'Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/2421.outputVolumes_relion_it025_class010/slicesZ_0283.jpg', 'Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/2421.outputVolumes_relion_it025_class010/slicesZ_0284.jpg', 'Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/2421.outputVolumes_relion_it025_class010/slicesZ_0285.jpg', 'Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/2421.outputVolumes_relion_it025_class010/slicesZ_0286.jpg', 'Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/2421.outputVolumes_relion_it025_class010/slicesZ_0287.jpg', 'Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/2421.outputVolumes_relion_it025_class010/slicesZ_0288.jpg', 'Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/2421.outputVolumes_relion_it025_class010/slicesZ_0289.jpg', 'Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/2421.outputVolumes_relion_it025_class010/slicesZ_0290.jpg', 'Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/2421.outputVolumes_relion_it025_class010/slicesZ_0291.jpg', 'Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/2421.outputVolumes_relion_it025_class010/slicesZ_0292.jpg', 'Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/2421.outputVolumes_relion_it025_class010/slicesZ_0293.jpg', 'Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/2421.outputVolumes_relion_it025_class010/slicesZ_0294.jpg', 'Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/2421.outputVolumes_relion_it025_class010/slicesZ_0295.jpg', 'Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/2421.outputVolumes_relion_it025_class010/slicesZ_0296.jpg', 'Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/2421.outputVolumes_relion_it025_class010/slicesZ_0297.jpg', 'Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/2421.outputVolumes_relion_it025_class010/slicesZ_0298.jpg', 'Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/2421.outputVolumes_relion_it025_class010/slicesZ_0299.jpg']" } ] } ], "summary": "Iteration 25/25Current resolution: *2.82 A*Input Particles: *930486*\nClassified into *10* 3D classes\nInput: SetOfParticles (930486 items, 300 x 300, 1.40 \u212b/px) \nInput: Volume (300 x 300 x 300, 1.40 \u212b/px) - w/halves \nOutput: SetOfClasses3D (10 items)SetOfVolumes (10 items, 300 x 300 x 300, 1.40 \u212b/px)", "log": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/2421_ProtRelionClassify3D.log", "plugin": "relion", "pluginVersion": "3.0.0" }, { "object.className": "ProtUserSubSet", "object.id": "2531", "object.label": "172309_vol1_1UP", "object.comment": "", "_useQueue": false, "_prerequisites": "", "_queueParams": null, "runName": null, "runMode": 0, "other": "1840", "sqliteFile": "Runs/002226_ProtRelionClassify3D/classes3D_state.sqlite,", "outputClassName": "SetOfParticles", "inputObject": "2226.", "output": [ { "outputName": "2531.outputParticles", "outputType": "SetOfParticles", "outputSize": 172309, "outputItems": [ { "_index": "2", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=25831.73, defV=25543.44, ast=288.29, psh=0.00, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[-0.42262131 -0.83805888 -0.34503413 8.24392558]\n [ 0.42712176 -0.51994858 0.73974352 6.51832095]\n [-0.79934863 0.16525979 0.57769453 -3.42300281]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "21", "_classId": "1", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "1", "_rlnPhaseShift": "0.0", "_rlnGroupName": "ctf_group_023", "_rlnGroupNumber": "6", "item_id": 2, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/2531.outputParticles_2_output_images.jpg" }, { "_index": "4", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=25831.73, defV=25543.44, ast=288.29, psh=0.00, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[ -0.87947973 -0.47274186 -0.05505039 -14.28923578]\n [ -0.23680263 0.53498302 -0.81099795 7.50139458]\n [ 0.4128437 -0.70022018 -0.58245324 -9.09427105]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "21", "_classId": "1", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "2", "_rlnPhaseShift": "0.0", "_rlnGroupName": "ctf_group_023", "_rlnGroupNumber": "6", "item_id": 4, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/2531.outputParticles_4_output_images.jpg" }, { "_index": "5", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=25831.73, defV=25543.44, ast=288.29, psh=0.00, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[ 0.25421954 0.04192821 -0.96623726 1.90903812]\n [ -0.79476066 0.57835715 -0.18400678 -12.9658995 ]\n [ 0.55111516 0.81470549 0.18035258 -3.00095352]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "21", "_classId": "1", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "1", "_rlnPhaseShift": "0.0", "_rlnGroupName": "ctf_group_023", "_rlnGroupNumber": "6", "item_id": 5, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/2531.outputParticles_5_output_images.jpg" }, { "_index": "6", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=25831.73, defV=25543.44, ast=288.29, psh=0.00, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[-0.93106512 -0.12757412 -0.34182246 -4.98687505]\n [ 0.16352307 -0.98342108 -0.07837853 5.86854041]\n [-0.32615634 -0.12887137 0.93649037 -1.32906687]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "21", "_classId": "1", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "2", "_rlnPhaseShift": "0.0", "_rlnGroupName": "ctf_group_023", "_rlnGroupNumber": "6", "item_id": 6, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/2531.outputParticles_6_output_images.jpg" }, { "_index": "7", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=25831.73, defV=25543.44, ast=288.29, psh=0.00, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[-0.59154138 -0.73928122 -0.32177954 10.89326471]\n [ 0.78840325 -0.44680601 -0.42282941 5.47925641]\n [ 0.16881682 -0.50381313 0.84715596 6.87243051]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "21", "_classId": "1", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "1", "_rlnPhaseShift": "0.0", "_rlnGroupName": "ctf_group_023", "_rlnGroupNumber": "6", "item_id": 7, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/2531.outputParticles_7_output_images.jpg" }, { "_index": "8", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=25831.73, defV=25543.44, ast=288.29, psh=0.00, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[ 0.77095435 0.47684087 -0.4221992 17.75050729]\n [-0.62925754 0.67262025 -0.3893802 -2.66339057]\n [ 0.09830734 0.56586639 0.81861523 7.88792862]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "21", "_classId": "1", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "2", "_rlnPhaseShift": "0.0", "_rlnGroupName": "ctf_group_023", "_rlnGroupNumber": "6", "item_id": 8, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/2531.outputParticles_8_output_images.jpg" }, { "_index": "9", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=25831.73, defV=25543.44, ast=288.29, psh=0.00, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[ 0.35192756 0.52995717 -0.77155193 4.83675862]\n [ 0.8269163 0.21019928 0.52156082 2.01206063]\n [ 0.43858456 -0.8215605 -0.3642553 -7.36406154]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "21", "_classId": "1", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "1", "_rlnPhaseShift": "0.0", "_rlnGroupName": "ctf_group_023", "_rlnGroupNumber": "6", "item_id": 9, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/2531.outputParticles_9_output_images.jpg" }, { "_index": "14", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=25831.73, defV=25543.44, ast=288.29, psh=0.00, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[-0.32351244 -0.77304629 0.54565477 0.21231536]\n [ 0.71231306 0.18062642 0.67822136 2.52035084]\n [-0.62285617 0.60809007 0.49221607 -3.7081411 ]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "21", "_classId": "1", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "1", "_rlnPhaseShift": "0.0", "_rlnGroupName": "ctf_group_023", "_rlnGroupNumber": "6", "item_id": 14, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/2531.outputParticles_14_output_images.jpg" }, { "_index": "15", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=25831.73, defV=25543.44, ast=288.29, psh=0.00, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[ 0.07688681 0.54551483 -0.83456695 -3.78836626]\n [ 0.68985233 0.57523389 0.4395563 -3.91181823]\n [ 0.71985567 -0.60952403 -0.33209678 4.34265248]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "21", "_classId": "1", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "2", "_rlnPhaseShift": "0.0", "_rlnGroupName": "ctf_group_023", "_rlnGroupNumber": "6", "item_id": 15, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/2531.outputParticles_15_output_images.jpg" }, { "_index": "17", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=25831.73, defV=25543.44, ast=288.29, psh=0.00, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[ 0.11762001 -0.99243442 0.035206 -19.11948411]\n [ 0.88454585 0.08858743 -0.45796386 -14.37172483]\n [ 0.45138029 0.08500703 0.8882734 -6.65179223]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "21", "_classId": "1", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "2", "_rlnPhaseShift": "0.0", "_rlnGroupName": "ctf_group_023", "_rlnGroupNumber": "6", "item_id": 17, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/2531.outputParticles_17_output_images.jpg" }, { "_index": "19", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=25831.73, defV=25543.44, ast=288.29, psh=0.00, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[ 0.08238151 -0.40512822 0.91054073 0.0384135 ]\n [-0.93718231 0.27926536 0.20904587 -1.02681081]\n [-0.33897287 -0.87056417 -0.3566727 -0.50374896]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "21", "_classId": "1", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "1", "_rlnPhaseShift": "0.0", "_rlnGroupName": "ctf_group_023", "_rlnGroupNumber": "6", "item_id": 19, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/2531.outputParticles_19_output_images.jpg" }, { "_index": "22", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=25831.73, defV=25543.44, ast=288.29, psh=0.00, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[-0.92305463 -0.37265294 -0.09539353 -2.26570662]\n [ 0.02919396 0.17940767 -0.98334155 0.24535338]\n [ 0.38355945 -0.91046289 -0.15472387 -0.16243407]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "21", "_classId": "1", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "1", "_rlnPhaseShift": "0.0", "_rlnGroupName": "ctf_group_023", "_rlnGroupNumber": "6", "item_id": 22, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/2531.outputParticles_22_output_images.jpg" }, { "_index": "23", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=25831.73, defV=25543.44, ast=288.29, psh=0.00, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[ 3.43487781e-02 1.71690461e-02 -9.99262421e-01 -8.37828168e-01]\n [-7.77742065e-01 6.28381472e-01 -1.59375344e-02 -6.31920500e+00]\n [ 6.27644359e-01 7.77715854e-01 3.49372252e-02 -2.68459429e+01]\n [ 0.00000000e+00 0.00000000e+00 0.00000000e+00 1.00000000e+00]]", "_coordinate": "Coordinate", "_micId": "21", "_classId": "1", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "2", "_rlnPhaseShift": "0.0", "_rlnGroupName": "ctf_group_023", "_rlnGroupNumber": "6", "item_id": 23, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/2531.outputParticles_23_output_images.jpg" }, { "_index": "26", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=25831.73, defV=25543.44, ast=288.29, psh=0.00, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[-0.19208079 -0.37790348 -0.90570079 1.23562649]\n [ 0.71427656 0.5790424 -0.39308892 -0.57619383]\n [ 0.67298884 -0.72242567 0.15870468 5.6243616 ]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "21", "_classId": "1", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "1", "_rlnPhaseShift": "0.0", "_rlnGroupName": "ctf_group_023", "_rlnGroupNumber": "6", "item_id": 26, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/2531.outputParticles_26_output_images.jpg" }, { "_index": "27", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=25831.73, defV=25543.44, ast=288.29, psh=0.00, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[ 0.68336651 -0.67520708 -0.27767897 3.43936117]\n [ 0.12164777 0.48033335 -0.86860906 7.29987472]\n [ 0.71986946 0.55979931 0.41038116 17.77804697]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "21", "_classId": "1", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "2", "_rlnPhaseShift": "0.0", "_rlnGroupName": "ctf_group_023", "_rlnGroupNumber": "6", "item_id": 27, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/2531.outputParticles_27_output_images.jpg" } ] } ], "summary": "From input SetOfClasses3D of size 10 was selected 1 item to create output SetOfParticles of size 172309Input: relion - 3D classification_symrelax_10classes_T4 \nOutput: SetOfParticles (172309 items, 300 x 300, 1.40 \u212b/px)", "log": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/2531_ProtUserSubSet.log", "label": [ "symrelax" ], "labelColor": [ "#e4ee89" ], "plugin": "pwem", "pluginVersion": "3.0.10" }, { "object.className": "ProtUserSubSet", "object.id": "2605", "object.label": "21149_vol8_2UP", "object.comment": "", "_useQueue": false, "_prerequisites": "", "_queueParams": null, "runName": null, "runMode": 0, "other": "1840", "sqliteFile": "Runs/002226_ProtRelionClassify3D/classes3D_state.sqlite,", "outputClassName": "SetOfParticles", "inputObject": "2226.", "output": [ { "outputName": "2605.outputParticles", "outputType": "SetOfParticles", "outputSize": 21149, "outputItems": [ { "_index": "30", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=25831.73, defV=25543.44, ast=288.29, psh=0.00, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[ -0.5833733 -0.76014556 -0.28610192 -23.7016995 ]\n [ -0.10892249 0.42229186 -0.89989193 4.05835921]\n [ 0.80486737 -0.49380999 -0.32915074 9.50633463]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "21", "_classId": "8", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "2", "_rlnPhaseShift": "0.0", "_rlnGroupName": "ctf_group_023", "_rlnGroupNumber": "6", "item_id": 30, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/2605.outputParticles_30_output_images.jpg" }, { "_index": "69", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=25831.73, defV=25543.44, ast=288.29, psh=0.00, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[ 0.41811982 -0.83575214 0.35594125 9.17911924]\n [ 0.58887455 0.54772769 0.59432411 -2.53287226]\n [-0.69166653 -0.03889395 0.72116897 -2.44308918]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "21", "_classId": "8", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "2", "_rlnPhaseShift": "0.0", "_rlnGroupName": "ctf_group_023", "_rlnGroupNumber": "6", "item_id": 69, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/2605.outputParticles_69_output_images.jpg" }, { "_index": "128", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=13915.24, defV=13592.83, ast=322.41, psh=0.00, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[-0.97314631 0.13509409 -0.18637557 -9.8032923 ]\n [-0.1590201 0.19085434 0.96865227 0.78395832]\n [ 0.16642978 0.97227785 -0.16424652 15.74753118]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "12", "_classId": "8", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "1", "_rlnPhaseShift": "0.0", "_rlnGroupName": "ctf_group_011", "_rlnGroupNumber": "1", "item_id": 128, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/2605.outputParticles_128_output_images.jpg" }, { "_index": "145", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=13915.24, defV=13592.83, ast=322.41, psh=0.00, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[-0.11632787 0.08451473 -0.98960855 0.41990882]\n [ 0.46712702 0.88395066 0.02058083 -3.96619377]\n [ 0.87650452 -0.45987877 -0.14230722 -3.49365916]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "12", "_classId": "8", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "2", "_rlnPhaseShift": "0.0", "_rlnGroupName": "ctf_group_011", "_rlnGroupNumber": "1", "item_id": 145, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/2605.outputParticles_145_output_images.jpg" }, { "_index": "192", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=13915.24, defV=13592.83, ast=322.41, psh=0.00, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[ 0.44013435 -0.30534349 0.84442117 4.33993099]\n [ -0.63867658 -0.76748031 0.0553733 -10.09425395]\n [ 0.63116874 -0.56368371 -0.53281018 5.82905045]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "12", "_classId": "8", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "2", "_rlnPhaseShift": "0.0", "_rlnGroupName": "ctf_group_011", "_rlnGroupNumber": "1", "item_id": 192, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/2605.outputParticles_192_output_images.jpg" }, { "_index": "202", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=13915.24, defV=13592.83, ast=322.41, psh=0.00, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[-0.97353066 -0.15835781 -0.16480554 1.89021849]\n [ 0.03143824 -0.80699863 0.58971591 -0.17167552]\n [-0.22638396 0.56892532 0.7906164 0.52207146]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "12", "_classId": "8", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "1", "_rlnPhaseShift": "0.0", "_rlnGroupName": "ctf_group_011", "_rlnGroupNumber": "1", "item_id": 202, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/2605.outputParticles_202_output_images.jpg" }, { "_index": "205", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=13915.24, defV=13592.83, ast=322.41, psh=0.00, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[ 0.85799231 -0.1716038 -0.48415011 8.93086573]\n [-0.02003432 -0.95300761 0.30228318 6.36019167]\n [-0.51327168 -0.24965703 -0.82111117 -2.92445258]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "12", "_classId": "8", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "1", "_rlnPhaseShift": "0.0", "_rlnGroupName": "ctf_group_011", "_rlnGroupNumber": "1", "item_id": 205, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/2605.outputParticles_205_output_images.jpg" }, { "_index": "217", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=24957.51, defV=24507.44, ast=450.07, psh=0.00, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[-0.70122292 -0.70729153 -0.08958297 -2.20115341]\n [-0.7093124 0.70478662 -0.01231814 -7.71402012]\n [ 0.0718494 0.05490455 -0.99590319 0.29341031]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "44", "_classId": "8", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "1", "_rlnPhaseShift": "0.0", "_rlnGroupName": "ctf_group_022", "_rlnGroupNumber": "14", "item_id": 217, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/2605.outputParticles_217_output_images.jpg" }, { "_index": "229", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=24957.51, defV=24507.44, ast=450.07, psh=0.00, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[-0.47257812 0.32237169 -0.8202112 -3.94795465]\n [-0.31467272 0.80762132 0.49872727 -5.5128499 ]\n [ 0.8231956 0.49378568 -0.28022259 1.74414229]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "44", "_classId": "8", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "2", "_rlnPhaseShift": "0.0", "_rlnGroupName": "ctf_group_022", "_rlnGroupNumber": "14", "item_id": 229, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/2605.outputParticles_229_output_images.jpg" }, { "_index": "233", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=24957.51, defV=24507.44, ast=450.07, psh=0.00, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[ 0.56169364 0.82287057 0.08593183 1.09487025]\n [ 0.77597555 -0.48794049 -0.39971993 -5.04523011]\n [-0.28698815 0.29120114 -0.91260051 2.31291041]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "44", "_classId": "8", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "1", "_rlnPhaseShift": "0.0", "_rlnGroupName": "ctf_group_022", "_rlnGroupNumber": "14", "item_id": 233, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/2605.outputParticles_233_output_images.jpg" }, { "_index": "240", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=24957.51, defV=24507.44, ast=450.07, psh=0.00, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[-4.65172130e-01 -8.84149977e-01 4.35167448e-02 5.54006049e+00]\n [-8.85210606e-01 4.64375201e-01 -2.75291551e-02 -4.19316872e+00]\n [ 4.13180469e-03 -5.13272797e-02 -9.98673339e-01 3.56993399e-01]\n [ 0.00000000e+00 0.00000000e+00 0.00000000e+00 1.00000000e+00]]", "_coordinate": "Coordinate", "_micId": "44", "_classId": "8", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "1", "_rlnPhaseShift": "0.0", "_rlnGroupName": "ctf_group_022", "_rlnGroupNumber": "14", "item_id": 240, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/2605.outputParticles_240_output_images.jpg" }, { "_index": "284", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=24957.51, defV=24507.44, ast=450.07, psh=0.00, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[-0.65223445 0.67873239 -0.33750936 -0.7281185 ]\n [ 0.41352204 -0.05456443 -0.90885766 -0.61445052]\n [-0.63528714 -0.73235583 -0.245082 3.28132972]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "44", "_classId": "8", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "1", "_rlnPhaseShift": "0.0", "_rlnGroupName": "ctf_group_022", "_rlnGroupNumber": "14", "item_id": 284, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/2605.outputParticles_284_output_images.jpg" }, { "_index": "364", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=19666.03, defV=19225.26, ast=440.78, psh=0.00, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[-0.67956118 0.66486764 0.31007681 -3.3689526 ]\n [ 0.56424191 0.74381132 -0.35829566 0.2524932 ]\n [-0.46885783 -0.06852549 -0.88061149 -1.28899214]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "36", "_classId": "8", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "2", "_rlnPhaseShift": "0.0", "_rlnGroupName": "ctf_group_017", "_rlnGroupNumber": "18", "item_id": 364, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/2605.outputParticles_364_output_images.jpg" }, { "_index": "386", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=19666.03, defV=19225.26, ast=440.78, psh=0.00, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[ 0.04614441 0.9983652 -0.03372861 2.08071814]\n [ 0.94356101 -0.05464716 -0.32665931 0.86647267]\n [-0.32796846 -0.0167515 -0.94454014 -0.3739609 ]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "36", "_classId": "8", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "2", "_rlnPhaseShift": "0.0", "_rlnGroupName": "ctf_group_017", "_rlnGroupNumber": "18", "item_id": 386, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/2605.outputParticles_386_output_images.jpg" }, { "_index": "395", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=19666.03, defV=19225.26, ast=440.78, psh=0.00, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[-0.00738006 -0.99256438 0.12149682 1.99318255]\n [-0.95362395 0.04354746 0.29783382 5.601678 ]\n [-0.30091012 -0.11366425 -0.94685455 2.01776975]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "36", "_classId": "8", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "2", "_rlnPhaseShift": "0.0", "_rlnGroupName": "ctf_group_017", "_rlnGroupNumber": "18", "item_id": 395, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/2605.outputParticles_395_output_images.jpg" } ] } ], "summary": "From input SetOfClasses3D of size 10 was selected 1 item to create output SetOfParticles of size 21149Input: relion - 3D classification_symrelax_10classes_T4 \nOutput: SetOfParticles (21149 items, 300 x 300, 1.40 \u212b/px)", "log": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/2605_ProtUserSubSet.log", "label": [ "symrelax" ], "labelColor": [ "#e4ee89" ], "plugin": "pwem", "pluginVersion": "3.0.10" }, { "object.className": "ProtUserSubSet", "object.id": "2659", "object.label": "17093_vol7_3down", "object.comment": "", "_useQueue": false, "_prerequisites": "", "_queueParams": null, "runName": null, "runMode": 0, "other": "1840", "sqliteFile": "Runs/002226_ProtRelionClassify3D/classes3D_state.sqlite,", "outputClassName": "SetOfParticles", "inputObject": "2226.", "output": [ { "outputName": "2659.outputParticles", "outputType": "SetOfParticles", "outputSize": 17093, "outputItems": [ { "_index": "10", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=25831.73, defV=25543.44, ast=288.29, psh=0.00, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[ 0.78732583 -0.39447613 -0.47382131 21.72368313]\n [ 0.37715778 -0.29978486 0.87628822 12.94011748]\n [-0.48771924 -0.86862974 -0.08724862 11.99020169]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "21", "_classId": "7", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "2", "_rlnPhaseShift": "0.0", "_rlnGroupName": "ctf_group_023", "_rlnGroupNumber": "6", "item_id": 10, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/2659.outputParticles_10_output_images.jpg" }, { "_index": "16", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=25831.73, defV=25543.44, ast=288.29, psh=0.00, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[-0.05634418 -0.98330565 -0.17301832 -5.53436839]\n [-0.9977899 0.04934353 0.04450326 9.14696487]\n [-0.03522297 0.17514343 -0.98391266 1.38692882]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "21", "_classId": "7", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "1", "_rlnPhaseShift": "0.0", "_rlnGroupName": "ctf_group_023", "_rlnGroupNumber": "6", "item_id": 16, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/2659.outputParticles_16_output_images.jpg" }, { "_index": "98", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=25831.73, defV=25543.44, ast=288.29, psh=0.00, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[ 0.4324469 -0.54580518 -0.71769519 4.70368261]\n [ 0.30952773 0.83746467 -0.45038374 -0.27319254]\n [ 0.84686614 -0.02737951 0.53110083 6.12457881]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "21", "_classId": "7", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "2", "_rlnPhaseShift": "0.0", "_rlnGroupName": "ctf_group_023", "_rlnGroupNumber": "6", "item_id": 98, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/2659.outputParticles_98_output_images.jpg" }, { "_index": "151", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=13915.24, defV=13592.83, ast=322.41, psh=0.00, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[-0.40913806 0.84615166 -0.34151634 1.87637847]\n [ 0.61735794 0.53230005 0.57924592 6.46053081]\n [ 0.67191906 0.02615372 -0.74016265 4.19019005]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "12", "_classId": "7", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "2", "_rlnPhaseShift": "0.0", "_rlnGroupName": "ctf_group_011", "_rlnGroupNumber": "1", "item_id": 151, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/2659.outputParticles_151_output_images.jpg" }, { "_index": "178", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=13915.24, defV=13592.83, ast=322.41, psh=0.00, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[-0.98850995 -0.10368597 -0.10998775 4.01262344]\n [ 0.13456378 -0.27219466 -0.95278678 -0.01261508]\n [ 0.06885254 -0.95663958 0.2830195 1.51692702]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "12", "_classId": "7", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "2", "_rlnPhaseShift": "0.0", "_rlnGroupName": "ctf_group_011", "_rlnGroupNumber": "1", "item_id": 178, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/2659.outputParticles_178_output_images.jpg" }, { "_index": "247", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=24957.51, defV=24507.44, ast=450.07, psh=0.00, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[ 0.18561003 -0.9796283 0.07666358 8.74150387]\n [-0.81015835 -0.10841638 0.57609837 5.09083527]\n [-0.55605068 -0.16903928 -0.81377722 4.4274733 ]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "44", "_classId": "7", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "1", "_rlnPhaseShift": "0.0", "_rlnGroupName": "ctf_group_022", "_rlnGroupNumber": "14", "item_id": 247, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/2659.outputParticles_247_output_images.jpg" }, { "_index": "356", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=19666.03, defV=19225.26, ast=440.78, psh=0.00, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[-0.3622294 -0.90599571 0.21900145 -7.11237747]\n [ 0.84707312 -0.41801196 -0.32822727 -1.21639227]\n [ 0.38891772 0.06661667 0.91886083 1.26065649]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "36", "_classId": "7", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "2", "_rlnPhaseShift": "0.0", "_rlnGroupName": "ctf_group_017", "_rlnGroupNumber": "18", "item_id": 356, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/2659.outputParticles_356_output_images.jpg" }, { "_index": "381", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=19666.03, defV=19225.26, ast=440.78, psh=0.00, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[ 0.52206581 -0.66790398 0.53042583 1.61312019]\n [ 0.24272287 0.71253498 0.65831567 0.78705058]\n [-0.81763861 -0.21493762 0.53410572 -2.57209067]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "36", "_classId": "7", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "1", "_rlnPhaseShift": "0.0", "_rlnGroupName": "ctf_group_017", "_rlnGroupNumber": "18", "item_id": 381, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/2659.outputParticles_381_output_images.jpg" }, { "_index": "455", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=19666.03, defV=19225.26, ast=440.78, psh=0.00, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[ 0.15227732 0.36189404 0.91969795 -0.71108231]\n [ 0.6887252 -0.70625994 0.1638734 3.49384297]\n [ 0.70885063 0.60846495 -0.35679291 -0.22823606]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "36", "_classId": "7", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "2", "_rlnPhaseShift": "0.0", "_rlnGroupName": "ctf_group_017", "_rlnGroupNumber": "18", "item_id": 455, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/2659.outputParticles_455_output_images.jpg" }, { "_index": "473", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=19666.03, defV=19225.26, ast=440.78, psh=0.00, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[-0.5045974 -0.83728382 0.21056416 -6.25342602]\n [-0.34767404 0.42030665 0.8381319 0.71346861]\n [-0.7902558 0.34971148 -0.5031875 -1.42842704]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "36", "_classId": "7", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "2", "_rlnPhaseShift": "0.0", "_rlnGroupName": "ctf_group_017", "_rlnGroupNumber": "18", "item_id": 473, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/2659.outputParticles_473_output_images.jpg" }, { "_index": "476", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=19666.03, defV=19225.26, ast=440.78, psh=0.00, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[ 0.06372552 -0.61496097 -0.78597841 -9.43556297]\n [ -0.34460178 -0.75269557 0.56098039 -10.29638332]\n [ -0.93658351 0.23510079 -0.25988256 6.31084916]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "36", "_classId": "7", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "2", "_rlnPhaseShift": "0.0", "_rlnGroupName": "ctf_group_017", "_rlnGroupNumber": "18", "item_id": 476, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/2659.outputParticles_476_output_images.jpg" }, { "_index": "505", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=19666.03, defV=19225.26, ast=440.78, psh=0.00, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[ 0.10112988 -0.94852997 -0.30010606 -7.55617278]\n [ 0.45458608 0.31237759 -0.83412933 7.38504677]\n [ 0.88494307 -0.05206864 0.46277923 8.41098862]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "36", "_classId": "7", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "1", "_rlnPhaseShift": "0.0", "_rlnGroupName": "ctf_group_017", "_rlnGroupNumber": "18", "item_id": 505, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/2659.outputParticles_505_output_images.jpg" }, { "_index": "539", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=22615.70, defV=22160.71, ast=454.99, psh=0.00, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[-0.61557102 0.73916076 0.27333804 1.80627246]\n [ 0.73651515 0.41618005 0.53323504 9.72112257]\n [ 0.28038858 0.52956165 -0.80059147 7.0914647 ]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "48", "_classId": "7", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "1", "_rlnPhaseShift": "0.0", "_rlnGroupName": "ctf_group_020", "_rlnGroupNumber": "12", "item_id": 539, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/2659.outputParticles_539_output_images.jpg" }, { "_index": "556", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=22615.70, defV=22160.71, ast=454.99, psh=0.00, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[ 0.5297487 -0.74590504 0.40372265 5.64581696]\n [ 0.81039137 0.30468836 -0.50043065 -4.32258024]\n [ 0.25026415 0.59227584 0.76588327 -5.80048682]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "48", "_classId": "7", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "2", "_rlnPhaseShift": "0.0", "_rlnGroupName": "ctf_group_020", "_rlnGroupNumber": "12", "item_id": 556, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/2659.outputParticles_556_output_images.jpg" }, { "_index": "609", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=22615.70, defV=22160.71, ast=454.99, psh=0.00, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[-0.60677256 -0.76418624 -0.21873832 5.09645619]\n [ 0.48581148 -0.57433614 0.65888178 -6.49580696]\n [-0.62913771 0.2935258 0.71974186 7.49540831]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "48", "_classId": "7", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "2", "_rlnPhaseShift": "0.0", "_rlnGroupName": "ctf_group_020", "_rlnGroupNumber": "12", "item_id": 609, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/2659.outputParticles_609_output_images.jpg" } ] } ], "summary": "From input SetOfClasses3D of size 10 was selected 1 item to create output SetOfParticles of size 17093Input: relion - 3D classification_symrelax_10classes_T4 \nOutput: SetOfParticles (17093 items, 300 x 300, 1.40 \u212b/px)", "log": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/2659_ProtUserSubSet.log", "label": [ "symrelax" ], "labelColor": [ "#e4ee89" ], "plugin": "pwem", "pluginVersion": "3.0.10" }, { "object.className": "ProtCryoSparcInitialModel", "object.id": "2713", "object.label": "cryosparc2 - initial model", "object.comment": "", "_useQueue": false, "_prerequisites": "", "_queueParams": null, "runName": null, "runMode": 0, "abinit_K": 1, "abinit_max_res": 12.0, "abinit_init_res": 35.0, "abinit_num_init_iters": 200, "abinit_num_final_iters": 300, "abinit_radwn_step": 0.04, "abinit_window": true, "abinit_center": true, "abinit_scale_mg_correct": false, "abinit_scale_compute": false, "abinit_mom": 0.0, "abinit_sparsity": 0.0, "abinit_minisize_init": 90, "abinit_minisize": 300, "abinit_minisize_epsilon": 0.05, "abinit_minisize_minp": 0.01, "abinit_minisize_num_init_iters": 300, "abinit_noise_model": 0, "abinit_noise_priorw": 50, "abinit_noise_initw": 5000, "abinit_class_anneal_beta": 0.1, "abinit_class_anneal_start": 300, "abinit_class_anneal_end": 350, "abinit_target_initial_ess_fraction": 0.011, "symmetryGroup": 0, "symmetryOrder": 1, "abinit_r_grid": 25.0, "abinit_high_lr_duration": 100.0, "abinit_high_lr": 0.4, "abinit_nonneg": true, "abinit_ignore_dc": true, "abinit_init_radwn_cutoff": 7, "abinit_search_start_iter": 200, "abinit_use_engine": true, "intermediate_plots": true, "compute_use_ssd": false, "gpuList": "0", "compute_lane": "default", "inputParticles": "2531.outputParticles", "output": [ { "outputName": "2713.outputClasses", "outputType": "SetOfClasses3D", "outputSize": 1, "outputItems": [ { "_size": "172309", "_streamState": "2", "_mapperPath": "['Runs/002713_ProtCryoSparcInitialModel/classes3D.sqlite', 'Class001']", "_representative": "Volume (300 x 300 x 300, 1.40 \u212b/px)", "_samplingRate": "1.4", "_hasCtf": "True", "_alignment": "Projection", "_isPhaseFlipped": "False", "_isAmplitudeCorrected": "False", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_firstDim": "300 x 300", "item_id": 1, "item_representation": "['Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/2713.outputClasses_cryosparc_P13_J32_class_00_final_volume_scaled/slicesX_0000.jpg', 'Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/2713.outputClasses_cryosparc_P13_J32_class_00_final_volume_scaled/slicesX_0001.jpg', 'Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/2713.outputClasses_cryosparc_P13_J32_class_00_final_volume_scaled/slicesX_0002.jpg', 'Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/2713.outputClasses_cryosparc_P13_J32_class_00_final_volume_scaled/slicesX_0003.jpg', 'Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/2713.outputClasses_cryosparc_P13_J32_class_00_final_volume_scaled/slicesX_0004.jpg', 'Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/2713.outputClasses_cryosparc_P13_J32_class_00_final_volume_scaled/slicesX_0005.jpg', 'Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/2713.outputClasses_cryosparc_P13_J32_class_00_final_volume_scaled/slicesX_0006.jpg', 'Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/2713.outputClasses_cryosparc_P13_J32_class_00_final_volume_scaled/slicesX_0007.jpg', 'Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/2713.outputClasses_cryosparc_P13_J32_class_00_final_volume_scaled/slicesX_0008.jpg', 'Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/2713.outputClasses_cryosparc_P13_J32_class_00_final_volume_scaled/slicesX_0009.jpg', 'Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/2713.outputClasses_cryosparc_P13_J32_class_00_final_volume_scaled/slicesX_0010.jpg', 'Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/2713.outputClasses_cryosparc_P13_J32_class_00_final_volume_scaled/slicesX_0011.jpg', 'Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/2713.outputClasses_cryosparc_P13_J32_class_00_final_volume_scaled/slicesX_0012.jpg', 'Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/2713.outputClasses_cryosparc_P13_J32_class_00_final_volume_scaled/slicesX_0013.jpg', 'Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/2713.outputClasses_cryosparc_P13_J32_class_00_final_volume_scaled/slicesX_0014.jpg', 'Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/2713.outputClasses_cryosparc_P13_J32_class_00_final_volume_scaled/slicesX_0015.jpg', 'Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/2713.outputClasses_cryosparc_P13_J32_class_00_final_volume_scaled/slicesX_0016.jpg', 'Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/2713.outputClasses_cryosparc_P13_J32_class_00_final_volume_scaled/slicesX_0017.jpg', 'Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/2713.outputClasses_cryosparc_P13_J32_class_00_final_volume_scaled/slicesX_0018.jpg', 'Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/2713.outputClasses_cryosparc_P13_J32_class_00_final_volume_scaled/slicesX_0019.jpg', 'Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/2713.outputClasses_cryosparc_P13_J32_class_00_final_volume_scaled/slicesX_0020.jpg', 'Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/2713.outputClasses_cryosparc_P13_J32_class_00_final_volume_scaled/slicesX_0021.jpg', 'Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/2713.outputClasses_cryosparc_P13_J32_class_00_final_volume_scaled/slicesX_0022.jpg', 'Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/2713.outputClasses_cryosparc_P13_J32_class_00_final_volume_scaled/slicesX_0023.jpg', 'Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/2713.outputClasses_cryosparc_P13_J32_class_00_final_volume_scaled/slicesX_0024.jpg', 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"abinit_class_anneal_beta": 0.1, "abinit_class_anneal_start": 300, "abinit_class_anneal_end": 350, "abinit_target_initial_ess_fraction": 0.011, "symmetryGroup": 0, "symmetryOrder": 1, "abinit_r_grid": 25.0, "abinit_high_lr_duration": 100.0, "abinit_high_lr": 0.4, "abinit_nonneg": true, "abinit_ignore_dc": true, "abinit_init_radwn_cutoff": 7, "abinit_search_start_iter": 200, "abinit_use_engine": true, "intermediate_plots": true, "compute_use_ssd": false, "gpuList": "2", "compute_lane": "default", "inputParticles": "2659.outputParticles", "output": [ { "outputName": "2855.outputClasses", "outputType": "SetOfClasses3D", "outputSize": 1, "outputItems": [ { "_size": "17093", "_streamState": "2", "_mapperPath": "['Runs/002855_ProtCryoSparcInitialModel/classes3D.sqlite', 'Class001']", "_representative": "Volume (300 x 300 x 300, 1.40 \u212b/px)", "_samplingRate": "1.4", "_hasCtf": "True", "_alignment": "Projection", "_isPhaseFlipped": "False", "_isAmplitudeCorrected": "False", "_acquisition": 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"Coordinate", "_micId": "12", "_classId": "8", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "2", "_rlnPhaseShift": "0.0", "_rlnGroupName": "ctf_group_011", "_rlnGroupNumber": "1", "item_id": 145, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/3276.outputParticles_145_output_images.jpg" }, { "_index": "192", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=13915.24, defV=13592.83, ast=322.41, psh=0.00, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[ 0.44013435 -0.30534349 0.84442117 4.33993099]\n [ -0.63867658 -0.76748031 0.0553733 -10.09425395]\n [ 0.63116874 -0.56368371 -0.53281018 5.82905045]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "12", "_classId": "8", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "2", "_rlnPhaseShift": "0.0", "_rlnGroupName": "ctf_group_011", "_rlnGroupNumber": "1", "item_id": 192, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/3276.outputParticles_192_output_images.jpg" }, { "_index": "202", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=13915.24, defV=13592.83, ast=322.41, psh=0.00, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[-0.97353066 -0.15835781 -0.16480554 1.89021849]\n [ 0.03143824 -0.80699863 0.58971591 -0.17167552]\n [-0.22638396 0.56892532 0.7906164 0.52207146]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "12", "_classId": "8", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "1", "_rlnPhaseShift": "0.0", "_rlnGroupName": "ctf_group_011", "_rlnGroupNumber": "1", "item_id": 202, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/3276.outputParticles_202_output_images.jpg" }, { "_index": "205", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=13915.24, defV=13592.83, ast=322.41, psh=0.00, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[ 0.85799231 -0.1716038 -0.48415011 8.93086573]\n [-0.02003432 -0.95300761 0.30228318 6.36019167]\n [-0.51327168 -0.24965703 -0.82111117 -2.92445258]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "12", "_classId": "8", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "1", "_rlnPhaseShift": "0.0", "_rlnGroupName": "ctf_group_011", "_rlnGroupNumber": "1", "item_id": 205, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/3276.outputParticles_205_output_images.jpg" }, { "_index": "217", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=24957.51, defV=24507.44, ast=450.07, psh=0.00, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[-0.70122292 -0.70729153 -0.08958297 -2.20115341]\n [-0.7093124 0.70478662 -0.01231814 -7.71402012]\n [ 0.0718494 0.05490455 -0.99590319 0.29341031]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "44", "_classId": "8", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "1", "_rlnPhaseShift": "0.0", "_rlnGroupName": "ctf_group_022", "_rlnGroupNumber": "14", "item_id": 217, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/3276.outputParticles_217_output_images.jpg" }, { "_index": "229", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=24957.51, defV=24507.44, ast=450.07, psh=0.00, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[-0.47257812 0.32237169 -0.8202112 -3.94795465]\n [-0.31467272 0.80762132 0.49872727 -5.5128499 ]\n [ 0.8231956 0.49378568 -0.28022259 1.74414229]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "44", "_classId": "8", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "2", "_rlnPhaseShift": "0.0", "_rlnGroupName": "ctf_group_022", "_rlnGroupNumber": "14", "item_id": 229, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/3276.outputParticles_229_output_images.jpg" }, { "_index": "233", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=24957.51, defV=24507.44, ast=450.07, psh=0.00, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[ 0.56169364 0.82287057 0.08593183 1.09487025]\n [ 0.77597555 -0.48794049 -0.39971993 -5.04523011]\n [-0.28698815 0.29120114 -0.91260051 2.31291041]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "44", "_classId": "8", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "1", "_rlnPhaseShift": "0.0", "_rlnGroupName": "ctf_group_022", "_rlnGroupNumber": "14", "item_id": 233, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/3276.outputParticles_233_output_images.jpg" }, { "_index": "240", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=24957.51, defV=24507.44, ast=450.07, psh=0.00, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[-4.65172130e-01 -8.84149977e-01 4.35167448e-02 5.54006049e+00]\n [-8.85210606e-01 4.64375201e-01 -2.75291551e-02 -4.19316872e+00]\n [ 4.13180469e-03 -5.13272797e-02 -9.98673339e-01 3.56993399e-01]\n [ 0.00000000e+00 0.00000000e+00 0.00000000e+00 1.00000000e+00]]", "_coordinate": "Coordinate", "_micId": "44", "_classId": "8", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "1", "_rlnPhaseShift": "0.0", "_rlnGroupName": "ctf_group_022", "_rlnGroupNumber": "14", "item_id": 240, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/3276.outputParticles_240_output_images.jpg" }, { "_index": "284", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=24957.51, defV=24507.44, ast=450.07, psh=0.00, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[-0.65223445 0.67873239 -0.33750936 -0.7281185 ]\n [ 0.41352204 -0.05456443 -0.90885766 -0.61445052]\n [-0.63528714 -0.73235583 -0.245082 3.28132972]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "44", "_classId": "8", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "1", "_rlnPhaseShift": "0.0", "_rlnGroupName": "ctf_group_022", "_rlnGroupNumber": "14", "item_id": 284, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/3276.outputParticles_284_output_images.jpg" }, { "_index": "364", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=19666.03, defV=19225.26, ast=440.78, psh=0.00, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[-0.67956118 0.66486764 0.31007681 -3.3689526 ]\n [ 0.56424191 0.74381132 -0.35829566 0.2524932 ]\n [-0.46885783 -0.06852549 -0.88061149 -1.28899214]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "36", "_classId": "8", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "2", "_rlnPhaseShift": "0.0", "_rlnGroupName": "ctf_group_017", "_rlnGroupNumber": "18", "item_id": 364, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/3276.outputParticles_364_output_images.jpg" }, { "_index": "386", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=19666.03, defV=19225.26, ast=440.78, psh=0.00, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[ 0.04614441 0.9983652 -0.03372861 2.08071814]\n [ 0.94356101 -0.05464716 -0.32665931 0.86647267]\n [-0.32796846 -0.0167515 -0.94454014 -0.3739609 ]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "36", "_classId": "8", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "2", "_rlnPhaseShift": "0.0", "_rlnGroupName": "ctf_group_017", "_rlnGroupNumber": "18", "item_id": 386, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/3276.outputParticles_386_output_images.jpg" }, { "_index": "395", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=19666.03, defV=19225.26, ast=440.78, psh=0.00, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[-0.00738006 -0.99256438 0.12149682 1.99318255]\n [-0.95362395 0.04354746 0.29783382 5.601678 ]\n [-0.30091012 -0.11366425 -0.94685455 2.01776975]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "36", "_classId": "8", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "2", "_rlnPhaseShift": "0.0", "_rlnGroupName": "ctf_group_017", "_rlnGroupNumber": "18", "item_id": 395, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/3276.outputParticles_395_output_images.jpg" } ] } ], "summary": "The elements of 3276.inputFullSet that also are referenced in 3276.inputSubSetare now in 3276.outputParticlesInput: SetOfParticles (21149 items, 300 x 300, 1.40 \u212b/px) \nInput: SetOfParticles (509466 items, 300 x 300, 1.40 \u212b/px) \nOutput: SetOfParticles (21149 items, 300 x 300, 1.40 \u212b/px)", "log": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/3276_ProtSubSet.log", "label": [ "symrelax" ], "labelColor": [ "#e4ee89" ], "plugin": "pwem", "pluginVersion": "3.0.10" }, { "object.className": "ProtCryoSparcInitialModel", "object.id": "3332", "object.label": "cryosparc2 - initial model (copy 3)", "object.comment": "", "_useQueue": false, "_prerequisites": "", "_queueParams": null, "runName": null, "runMode": 0, "abinit_K": 1, "abinit_max_res": 12.0, "abinit_init_res": 35.0, "abinit_num_init_iters": 200, "abinit_num_final_iters": 300, "abinit_radwn_step": 0.04, "abinit_window": true, "abinit_center": true, "abinit_scale_mg_correct": false, "abinit_scale_compute": false, "abinit_mom": 0.0, "abinit_sparsity": 0.0, "abinit_minisize_init": 90, "abinit_minisize": 300, "abinit_minisize_epsilon": 0.05, "abinit_minisize_minp": 0.01, "abinit_minisize_num_init_iters": 300, "abinit_noise_model": 0, "abinit_noise_priorw": 50, "abinit_noise_initw": 5000, "abinit_class_anneal_beta": 0.1, "abinit_class_anneal_start": 300, "abinit_class_anneal_end": 350, "abinit_target_initial_ess_fraction": 0.011, "symmetryGroup": 0, "symmetryOrder": 1, "abinit_r_grid": 25.0, "abinit_high_lr_duration": 100.0, "abinit_high_lr": 0.4, "abinit_nonneg": true, "abinit_ignore_dc": true, "abinit_init_radwn_cutoff": 7, "abinit_search_start_iter": 200, "abinit_use_engine": true, "intermediate_plots": true, "compute_use_ssd": false, "gpuList": "1", "compute_lane": "default", "inputParticles": "3276.outputParticles", "output": [ { "outputName": "3332.outputClasses", "outputType": "SetOfClasses3D", "outputSize": 1, "outputItems": [ { "_size": "21149", "_streamState": "2", "_mapperPath": "['Runs/003332_ProtCryoSparcInitialModel/classes3D.sqlite', 'Class001']", "_representative": "Volume (300 x 300 x 300, 1.40 \u212b/px)", "_samplingRate": "1.4", "_hasCtf": "True", "_alignment": "Projection", "_isPhaseFlipped": "False", "_isAmplitudeCorrected": "False", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_firstDim": "300 x 300", "item_id": 1, "item_representation": "['Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/3332.outputClasses_cryosparc_P13_J40_class_00_final_volume_scaled/slicesX_0000.jpg', 'Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/3332.outputClasses_cryosparc_P13_J40_class_00_final_volume_scaled/slicesX_0001.jpg', 'Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/3332.outputClasses_cryosparc_P13_J40_class_00_final_volume_scaled/slicesX_0002.jpg', 'Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/3332.outputClasses_cryosparc_P13_J40_class_00_final_volume_scaled/slicesX_0003.jpg', 'Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/3332.outputClasses_cryosparc_P13_J40_class_00_final_volume_scaled/slicesX_0004.jpg', 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"Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=25831.73, defV=25543.44, ast=288.29, psh=0.00, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[ 6.48801703e-03 -8.99930212e-01 4.35985687e-01 2.01828891e-02]\n [-8.81296873e-01 -2.11165872e-01 -4.22758555e-01 -7.17808538e+00]\n [ 4.72518494e-01 -3.81489957e-01 -7.94475730e-01 3.83069783e+00]\n [ 0.00000000e+00 0.00000000e+00 0.00000000e+00 1.00000000e+00]]", "_coordinate": "Coordinate", "_micId": "21", "_classId": "9", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "1", "_rlnPhaseShift": "0.0", "_rlnGroupName": "ctf_group_023", "_rlnGroupNumber": "6", "item_id": 77, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/3515.outputParticles_77_output_images.jpg" }, { "_index": "86", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=25831.73, defV=25543.44, ast=288.29, psh=0.00, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[ 0.73294917 0.66441328 0.14608394 2.27041913]\n [ -0.51918827 0.4075745 0.75121673 -11.23681167]\n [ 0.43957828 -0.62644874 0.64368697 12.59868468]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "21", "_classId": "2", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "2", "_rlnPhaseShift": "0.0", "_rlnGroupName": "ctf_group_023", "_rlnGroupNumber": "6", "item_id": 86, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/3515.outputParticles_86_output_images.jpg" }, { "_index": "91", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=25831.73, defV=25543.44, ast=288.29, psh=0.00, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[ -0.81499485 0.52911507 -0.2362639 3.86166119]\n [ -0.54276175 -0.55422845 0.631063 -13.8706119 ]\n [ 0.20296077 0.6425481 0.73887675 13.08147949]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "21", "_classId": "2", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "1", "_rlnPhaseShift": "0.0", "_rlnGroupName": "ctf_group_023", "_rlnGroupNumber": "6", "item_id": 91, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/3515.outputParticles_91_output_images.jpg" }, { "_index": "98", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=25831.73, defV=25543.44, ast=288.29, psh=0.00, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[ 0.4324469 -0.54580518 -0.71769519 4.70368261]\n [ 0.30952773 0.83746467 -0.45038374 -0.27319254]\n [ 0.84686614 -0.02737951 0.53110083 6.12457881]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "21", "_classId": "7", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "2", "_rlnPhaseShift": "0.0", "_rlnGroupName": "ctf_group_023", "_rlnGroupNumber": "6", "item_id": 98, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/3515.outputParticles_98_output_images.jpg" }, { "_index": "127", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=13915.24, defV=13592.83, ast=322.41, psh=0.00, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[-0.37833157 -0.79410546 -0.47566979 -2.04646223]\n [ 0.88262953 -0.46433875 0.07317539 -2.2604927 ]\n [-0.27898089 -0.39215564 0.87657493 -0.92180119]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "12", "_classId": "2", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "2", "_rlnPhaseShift": "0.0", "_rlnGroupName": "ctf_group_011", "_rlnGroupNumber": "1", "item_id": 127, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/3515.outputParticles_127_output_images.jpg" }, { "_index": "131", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=13915.24, defV=13592.83, ast=322.41, psh=0.00, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[ 0.07178381 -0.99533735 0.06442553 20.38295311]\n [-0.58008156 -0.09420592 -0.80909247 -2.25889032]\n [ 0.81138922 0.02070767 -0.5841393 5.37685742]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "12", "_classId": "9", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "1", "_rlnPhaseShift": "0.0", "_rlnGroupName": "ctf_group_011", "_rlnGroupNumber": "1", "item_id": 131, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/3515.outputParticles_131_output_images.jpg" }, { "_index": "134", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=13915.24, defV=13592.83, ast=322.41, psh=0.00, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[-0.47003181 -0.52919898 -0.70641244 7.13261081]\n [ 0.17752114 -0.8406565 0.51164724 -0.65048633]\n [-0.8646134 0.11508733 0.48907931 10.98264533]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "12", "_classId": "2", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "1", "_rlnPhaseShift": "0.0", "_rlnGroupName": "ctf_group_011", "_rlnGroupNumber": "1", "item_id": 134, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/3515.outputParticles_134_output_images.jpg" }, { "_index": "139", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=13915.24, defV=13592.83, ast=322.41, psh=0.00, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[-0.86126432 0.46987228 0.19350405 1.44141536]\n [ 0.28760077 0.13678512 0.94793229 -2.79083216]\n [ 0.41893863 0.87207217 -0.25294377 -9.35623046]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "12", "_classId": "9", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "1", "_rlnPhaseShift": "0.0", "_rlnGroupName": "ctf_group_011", "_rlnGroupNumber": "1", "item_id": 139, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/3515.outputParticles_139_output_images.jpg" }, { "_index": "141", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=13915.24, defV=13592.83, ast=322.41, psh=0.00, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[-0.83143587 0.5542917 0.03840717 1.5696888 ]\n [-0.44385268 -0.62101495 -0.64601488 0.80474013]\n [-0.33422926 -0.55416707 0.76235796 0.60284907]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "12", "_classId": "10", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "2", "_rlnPhaseShift": "0.0", "_rlnGroupName": "ctf_group_011", "_rlnGroupNumber": "1", "item_id": 141, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/3515.outputParticles_141_output_images.jpg" } ] } ], "summary": "From input SetOfClasses3D of size 10 we selected 5 items to create output SetOfParticles of size 74335Input: SetOfClasses3D (10 items) \nOutput: SetOfParticles (74335 items, 300 x 300, 1.40 \u212b/px)", "log": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/3515_ProtUserSubSet.log", "label": [ "symrelax" ], "labelColor": [ "#e4ee89" ], "plugin": "pwem", "pluginVersion": "3.0.10" }, { "object.className": "ProtCryoSparcNewNonUniformRefine3D", "object.id": "3574", "object.label": "cryosparc2 - 3D non-uniform refinement_class02_06_07_09_10_3down_inimodelclass07", "object.comment": "", "_useQueue": false, "_prerequisites": "", "_queueParams": null, "runName": null, "runMode": 0, "symmetryGroup": 0, "symmetryOrder": 1, "refine_symmetry_do_align": true, "refine_do_init_scale_est": true, "refine_num_final_iterations": 0, "refine_res_init": 30, "refine_res_gsfsc_split": 20, "refine_highpass_res": null, "refine_clip": false, "refine_window": true, "refine_skip_premult": true, "refine_ignore_dc": true, "refine_batchsize_init": 0, "refine_batchsize_epsilon": 0.001, "refine_batchsize_snrfactor": 40.0, "refine_scale_min": false, "refine_scale_start_iter": 0, "refine_noise_model": 0, "refine_noise_priorw": 50, "refine_noise_initw": 200, "refine_noise_init_sigmascale": 3, "refine_mask": 0, "refine_dynamic_mask_thresh_factor": 0.2, "refine_dynamic_mask_near_ang": 6.0, "refine_dynamic_mask_far_ang": 14.0, "refine_dynamic_mask_start_res": 12, "refine_dynamic_mask_use_abs": false, "refine_defocus_refine": false, "crl_num_plots": 3, "crl_min_res_A": 20.0, "crl_df_range": 2000.0, "refine_ctf_global_refine": false, "crg_num_plots": 3, "crg_min_res_A": 10.0, "crg_do_tilt": true, "crg_do_trefoil": true, "crg_do_spherical": true, "crg_do_tetrafoil": true, "compute_use_ssd": false, "gpuList": "2", "compute_lane": "default", "refine_do_marg": true, "refine_nu_enable": true, "refine_nu_filtertype": 0, "refine_nu_order": 8, "refine_nu_awf": 3.0, "referenceVolume": "2226.outputVolumes.7", "inputParticles": "3515.outputParticles", "output": [ { "outputName": "3574.outputVolume", "outputType": "Volume", "outputItems": [ { "_index": "0", "_filename": "Runs/003574_ProtCryoSparcNewNonUniformRefine3D/extra/cryosparc_P13_J46_002_volume_map.mrc", "_samplingRate": "1.4", "_classId": "None", "_halfMapFilenames": "['Runs/003574_ProtCryoSparcNewNonUniformRefine3D/extra/cryosparc_P13_J46_002_volume_map_half_A.mrc', 'Runs/003574_ProtCryoSparcNewNonUniformRefine3D/extra/cryosparc_P13_J46_002_volume_map_half_B.mrc']", "item_id": 3780, "item_representation": "['Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/3574.outputVolume_cryosparc_P13_J46_002_volume_map/slicesX_0000.jpg', 'Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/3574.outputVolume_cryosparc_P13_J46_002_volume_map/slicesX_0001.jpg', 'Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/3574.outputVolume_cryosparc_P13_J46_002_volume_map/slicesX_0002.jpg', 'Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/3574.outputVolume_cryosparc_P13_J46_002_volume_map/slicesX_0003.jpg', 'Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/3574.outputVolume_cryosparc_P13_J46_002_volume_map/slicesX_0004.jpg', 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'Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/3845.outputVolumes_relion_it025_class010/slicesZ_0275.jpg', 'Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/3845.outputVolumes_relion_it025_class010/slicesZ_0276.jpg', 'Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/3845.outputVolumes_relion_it025_class010/slicesZ_0277.jpg', 'Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/3845.outputVolumes_relion_it025_class010/slicesZ_0278.jpg', 'Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/3845.outputVolumes_relion_it025_class010/slicesZ_0279.jpg', 'Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/3845.outputVolumes_relion_it025_class010/slicesZ_0280.jpg', 'Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/3845.outputVolumes_relion_it025_class010/slicesZ_0281.jpg', 'Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/3845.outputVolumes_relion_it025_class010/slicesZ_0282.jpg', 'Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/3845.outputVolumes_relion_it025_class010/slicesZ_0283.jpg', 'Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/3845.outputVolumes_relion_it025_class010/slicesZ_0284.jpg', 'Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/3845.outputVolumes_relion_it025_class010/slicesZ_0285.jpg', 'Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/3845.outputVolumes_relion_it025_class010/slicesZ_0286.jpg', 'Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/3845.outputVolumes_relion_it025_class010/slicesZ_0287.jpg', 'Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/3845.outputVolumes_relion_it025_class010/slicesZ_0288.jpg', 'Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/3845.outputVolumes_relion_it025_class010/slicesZ_0289.jpg', 'Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/3845.outputVolumes_relion_it025_class010/slicesZ_0290.jpg', 'Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/3845.outputVolumes_relion_it025_class010/slicesZ_0291.jpg', 'Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/3845.outputVolumes_relion_it025_class010/slicesZ_0292.jpg', 'Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/3845.outputVolumes_relion_it025_class010/slicesZ_0293.jpg', 'Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/3845.outputVolumes_relion_it025_class010/slicesZ_0294.jpg', 'Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/3845.outputVolumes_relion_it025_class010/slicesZ_0295.jpg', 'Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/3845.outputVolumes_relion_it025_class010/slicesZ_0296.jpg', 'Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/3845.outputVolumes_relion_it025_class010/slicesZ_0297.jpg', 'Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/3845.outputVolumes_relion_it025_class010/slicesZ_0298.jpg', 'Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/3845.outputVolumes_relion_it025_class010/slicesZ_0299.jpg']" } ] } ], "summary": "Iteration 25/25Current resolution: *3.07 A*Input Particles: *930486*\nClassified into *10* 3D classes\nInput: SetOfParticles (930486 items, 300 x 300, 1.40 \u212b/px) \nInput: Volume (300 x 300 x 300, 1.40 \u212b/px) - w/halves \nOutput: SetOfClasses3D (10 items)SetOfVolumes (10 items, 300 x 300 x 300, 1.40 \u212b/px)", "log": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/3845_ProtRelionClassify3D.log", "plugin": "relion", "pluginVersion": "3.0.0" }, { "object.className": "ProtSubSet", "object.id": "3955", "object.label": "pwem - subset (copy)", "object.comment": "", "_useQueue": false, "_prerequisites": "", "_queueParams": null, "runName": null, "runMode": 0, "chooseAtRandom": false, "nElements": 2, "setOperation": 0, "inputSubSet": "787.outputParticles", "inputFullSet": "2659.outputParticles", "output": [ { "outputName": "3955.outputParticles", "outputType": "SetOfParticles", "outputSize": 17093, "outputItems": [ { "_index": "10", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=25831.73, defV=25543.44, ast=288.29, psh=0.00, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[ 0.78732583 -0.39447613 -0.47382131 21.72368313]\n [ 0.37715778 -0.29978486 0.87628822 12.94011748]\n [-0.48771924 -0.86862974 -0.08724862 11.99020169]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "21", "_classId": "7", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "2", "_rlnPhaseShift": "0.0", "_rlnGroupName": "ctf_group_023", "_rlnGroupNumber": "6", "item_id": 10, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/3955.outputParticles_10_output_images.jpg" }, { "_index": "16", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=25831.73, defV=25543.44, ast=288.29, psh=0.00, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[-0.05634418 -0.98330565 -0.17301832 -5.53436839]\n [-0.9977899 0.04934353 0.04450326 9.14696487]\n [-0.03522297 0.17514343 -0.98391266 1.38692882]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "21", "_classId": "7", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "1", "_rlnPhaseShift": "0.0", "_rlnGroupName": "ctf_group_023", "_rlnGroupNumber": "6", "item_id": 16, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/3955.outputParticles_16_output_images.jpg" }, { "_index": "98", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=25831.73, defV=25543.44, ast=288.29, psh=0.00, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[ 0.4324469 -0.54580518 -0.71769519 4.70368261]\n [ 0.30952773 0.83746467 -0.45038374 -0.27319254]\n [ 0.84686614 -0.02737951 0.53110083 6.12457881]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "21", "_classId": "7", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "2", "_rlnPhaseShift": "0.0", "_rlnGroupName": "ctf_group_023", "_rlnGroupNumber": "6", "item_id": 98, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/3955.outputParticles_98_output_images.jpg" }, { "_index": "151", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=13915.24, defV=13592.83, ast=322.41, psh=0.00, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[-0.40913806 0.84615166 -0.34151634 1.87637847]\n [ 0.61735794 0.53230005 0.57924592 6.46053081]\n [ 0.67191906 0.02615372 -0.74016265 4.19019005]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "12", "_classId": "7", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "2", "_rlnPhaseShift": "0.0", "_rlnGroupName": "ctf_group_011", "_rlnGroupNumber": "1", "item_id": 151, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/3955.outputParticles_151_output_images.jpg" }, { "_index": "178", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=13915.24, defV=13592.83, ast=322.41, psh=0.00, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[-0.98850995 -0.10368597 -0.10998775 4.01262344]\n [ 0.13456378 -0.27219466 -0.95278678 -0.01261508]\n [ 0.06885254 -0.95663958 0.2830195 1.51692702]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "12", "_classId": "7", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "2", "_rlnPhaseShift": "0.0", "_rlnGroupName": "ctf_group_011", "_rlnGroupNumber": "1", "item_id": 178, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/3955.outputParticles_178_output_images.jpg" }, { "_index": "247", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=24957.51, defV=24507.44, ast=450.07, psh=0.00, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[ 0.18561003 -0.9796283 0.07666358 8.74150387]\n [-0.81015835 -0.10841638 0.57609837 5.09083527]\n [-0.55605068 -0.16903928 -0.81377722 4.4274733 ]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "44", "_classId": "7", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "1", "_rlnPhaseShift": "0.0", "_rlnGroupName": "ctf_group_022", "_rlnGroupNumber": "14", "item_id": 247, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/3955.outputParticles_247_output_images.jpg" }, { "_index": "356", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=19666.03, defV=19225.26, ast=440.78, psh=0.00, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[-0.3622294 -0.90599571 0.21900145 -7.11237747]\n [ 0.84707312 -0.41801196 -0.32822727 -1.21639227]\n [ 0.38891772 0.06661667 0.91886083 1.26065649]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "36", "_classId": "7", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "2", "_rlnPhaseShift": "0.0", "_rlnGroupName": "ctf_group_017", "_rlnGroupNumber": "18", "item_id": 356, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/3955.outputParticles_356_output_images.jpg" }, { "_index": "381", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=19666.03, defV=19225.26, ast=440.78, psh=0.00, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[ 0.52206581 -0.66790398 0.53042583 1.61312019]\n [ 0.24272287 0.71253498 0.65831567 0.78705058]\n [-0.81763861 -0.21493762 0.53410572 -2.57209067]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "36", "_classId": "7", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "1", "_rlnPhaseShift": "0.0", "_rlnGroupName": "ctf_group_017", "_rlnGroupNumber": "18", "item_id": 381, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/3955.outputParticles_381_output_images.jpg" }, { "_index": "455", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=19666.03, defV=19225.26, ast=440.78, psh=0.00, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[ 0.15227732 0.36189404 0.91969795 -0.71108231]\n [ 0.6887252 -0.70625994 0.1638734 3.49384297]\n [ 0.70885063 0.60846495 -0.35679291 -0.22823606]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "36", "_classId": "7", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "2", "_rlnPhaseShift": "0.0", "_rlnGroupName": "ctf_group_017", "_rlnGroupNumber": "18", "item_id": 455, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/3955.outputParticles_455_output_images.jpg" }, { "_index": "473", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=19666.03, defV=19225.26, ast=440.78, psh=0.00, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[-0.5045974 -0.83728382 0.21056416 -6.25342602]\n [-0.34767404 0.42030665 0.8381319 0.71346861]\n [-0.7902558 0.34971148 -0.5031875 -1.42842704]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "36", "_classId": "7", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "2", "_rlnPhaseShift": "0.0", "_rlnGroupName": "ctf_group_017", "_rlnGroupNumber": "18", "item_id": 473, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/3955.outputParticles_473_output_images.jpg" }, { "_index": "476", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=19666.03, defV=19225.26, ast=440.78, psh=0.00, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[ 0.06372552 -0.61496097 -0.78597841 -9.43556297]\n [ -0.34460178 -0.75269557 0.56098039 -10.29638332]\n [ -0.93658351 0.23510079 -0.25988256 6.31084916]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "36", "_classId": "7", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "2", "_rlnPhaseShift": "0.0", "_rlnGroupName": "ctf_group_017", "_rlnGroupNumber": "18", "item_id": 476, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/3955.outputParticles_476_output_images.jpg" }, { "_index": "505", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=19666.03, defV=19225.26, ast=440.78, psh=0.00, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[ 0.10112988 -0.94852997 -0.30010606 -7.55617278]\n [ 0.45458608 0.31237759 -0.83412933 7.38504677]\n [ 0.88494307 -0.05206864 0.46277923 8.41098862]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "36", "_classId": "7", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "1", "_rlnPhaseShift": "0.0", "_rlnGroupName": "ctf_group_017", "_rlnGroupNumber": "18", "item_id": 505, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/3955.outputParticles_505_output_images.jpg" }, { "_index": "539", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=22615.70, defV=22160.71, ast=454.99, psh=0.00, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[-0.61557102 0.73916076 0.27333804 1.80627246]\n [ 0.73651515 0.41618005 0.53323504 9.72112257]\n [ 0.28038858 0.52956165 -0.80059147 7.0914647 ]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "48", "_classId": "7", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "1", "_rlnPhaseShift": "0.0", "_rlnGroupName": "ctf_group_020", "_rlnGroupNumber": "12", "item_id": 539, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/3955.outputParticles_539_output_images.jpg" }, { "_index": "556", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=22615.70, defV=22160.71, ast=454.99, psh=0.00, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[ 0.5297487 -0.74590504 0.40372265 5.64581696]\n [ 0.81039137 0.30468836 -0.50043065 -4.32258024]\n [ 0.25026415 0.59227584 0.76588327 -5.80048682]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "48", "_classId": "7", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "2", "_rlnPhaseShift": "0.0", "_rlnGroupName": "ctf_group_020", "_rlnGroupNumber": "12", "item_id": 556, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/3955.outputParticles_556_output_images.jpg" }, { "_index": "609", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=22615.70, defV=22160.71, ast=454.99, psh=0.00, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[-0.60677256 -0.76418624 -0.21873832 5.09645619]\n [ 0.48581148 -0.57433614 0.65888178 -6.49580696]\n [-0.62913771 0.2935258 0.71974186 7.49540831]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "48", "_classId": "7", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "2", "_rlnPhaseShift": "0.0", "_rlnGroupName": "ctf_group_020", "_rlnGroupNumber": "12", "item_id": 609, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/3955.outputParticles_609_output_images.jpg" } ] } ], "summary": "The elements of 3955.inputFullSet that also are referenced in 3955.inputSubSetare now in 3955.outputParticlesInput: SetOfParticles (17093 items, 300 x 300, 1.40 \u212b/px) \nInput: SetOfParticles (509466 items, 300 x 300, 1.40 \u212b/px) \nOutput: SetOfParticles (17093 items, 300 x 300, 1.40 \u212b/px)", "log": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/3955_ProtSubSet.log", "label": [ "symrelax" ], "labelColor": [ "#e4ee89" ], "plugin": "pwem", "pluginVersion": "3.0.10" }, { "object.className": "ProtCryoSparcInitialModel", "object.id": "4011", "object.label": "cryosparc2 - initial model (copy 4)", "object.comment": "", "_useQueue": false, "_prerequisites": "", "_queueParams": null, "runName": null, "runMode": 0, "abinit_K": 1, "abinit_max_res": 12.0, "abinit_init_res": 35.0, "abinit_num_init_iters": 200, "abinit_num_final_iters": 300, "abinit_radwn_step": 0.04, "abinit_window": true, "abinit_center": true, "abinit_scale_mg_correct": false, "abinit_scale_compute": false, "abinit_mom": 0.0, 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'Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/4230.outputVolumes_cryosparc_P13_J56_class_03_final_volume_scaled/slicesZ_0297.jpg', 'Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/4230.outputVolumes_cryosparc_P13_J56_class_03_final_volume_scaled/slicesZ_0298.jpg', 'Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/4230.outputVolumes_cryosparc_P13_J56_class_03_final_volume_scaled/slicesZ_0299.jpg']" } ] } ], "summary": "Input Particles: [[sci-open:3991][3955.outputParticles.3991]]Number of Ab-Initio classes: 4Symmetry: C1------------------------------------------Output volume [[sci-open:4312][4230.outputVolumes.4312]]Output classes [[sci-open:4305][4230.outputClasses.4305]]Input: SetOfParticles (17093 items, 300 x 300, 1.40 \u212b/px) \nOutput: SetOfClasses3D (4 items)SetOfVolumes (4 items, 300 x 300 x 300, 1.40 \u212b/px)", "log": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/4230_ProtCryoSparcInitialModel.log", "label": [ "symrelax" ], "labelColor": [ "#e4ee89" ], "plugin": "cryosparc2", "pluginVersion": "3.2.10" }, { "object.className": "ProtUserSubSet", "object.id": "4330", "object.label": "8798_vol1", "object.comment": "", "_useQueue": false, "_prerequisites": "", "_queueParams": null, "runName": null, "runMode": 0, "other": null, "sqliteFile": "Runs/004230_ProtCryoSparcInitialModel/classes3D_state.sqlite,", "outputClassName": "SetOfParticles", "inputObject": "4230.outputClasses", "output": [ { "outputName": "4330.outputParticles", "outputType": "SetOfParticles", "outputSize": 8798, "outputItems": [ { "_index": "98", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=25831.73, defV=25543.44, ast=288.29, psh=0.00, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[-0.50069482 0.16442377 -0.84986441 -1.94909085]\n [ 0.12812384 0.98505697 0.11509581 -1.00342321]\n [ 0.85608935 -0.05126001 -0.51427953 2.99637268]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "21", "_classId": "1", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "2", "_rlnPhaseShift": "0.0", "_rlnGroupName": "ctf_group_023", "_rlnGroupNumber": "6", "item_id": 98, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/4330.outputParticles_98_output_images.jpg" }, { "_index": "151", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=13915.24, defV=13592.83, ast=322.41, psh=0.00, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[-0.70586945 0.29689637 0.64311808 -0.57448166]\n [-0.12340106 -0.94557885 0.30108606 -3.18015944]\n [ 0.69751021 0.133166 0.70409255 1.88464035]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "12", "_classId": "1", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "2", "_rlnPhaseShift": "0.0", "_rlnGroupName": "ctf_group_011", "_rlnGroupNumber": "1", "item_id": 151, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/4330.outputParticles_151_output_images.jpg" }, { "_index": "247", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=24957.51, defV=24507.44, ast=450.07, psh=0.00, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[ 0.72092127 -0.6504456 0.23915069 0.90809424]\n [ 0.47743793 0.71628174 0.50891404 -3.68569062]\n [-0.50232017 -0.25270734 0.82693013 2.00564504]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "44", "_classId": "1", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "1", "_rlnPhaseShift": "0.0", "_rlnGroupName": "ctf_group_022", "_rlnGroupNumber": "14", "item_id": 247, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/4330.outputParticles_247_output_images.jpg" }, { "_index": "356", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=19666.03, defV=19225.26, ast=440.78, psh=0.00, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[ 0.79895783 -0.53841011 0.26791964 -1.27284927]\n [-0.4591501 -0.8338314 -0.30644147 -2.79829013]\n [ 0.38839099 0.12181848 -0.91340719 0.56545518]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "36", "_classId": "1", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "2", "_rlnPhaseShift": "0.0", "_rlnGroupName": "ctf_group_017", "_rlnGroupNumber": "18", "item_id": 356, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/4330.outputParticles_356_output_images.jpg" }, { "_index": "455", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=19666.03, defV=19225.26, ast=440.78, psh=0.00, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[-0.34015084 -0.17247008 0.92441953 -0.13624062]\n [ 0.64929641 -0.75416771 0.09821012 1.1403146 ]\n [ 0.68022906 0.63362854 0.36851499 0.03786292]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "36", "_classId": "1", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "2", "_rlnPhaseShift": "0.0", "_rlnGroupName": "ctf_group_017", "_rlnGroupNumber": "18", "item_id": 455, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/4330.outputParticles_455_output_images.jpg" }, { "_index": "473", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=19666.03, defV=19225.26, ast=440.78, psh=0.00, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[-0.21957449 -0.87985928 0.4214673 -2.39391556]\n [ 0.54638943 0.24699388 0.80028283 1.85359882]\n [-0.80823612 0.40600698 0.42651226 -1.11238581]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "36", "_classId": "1", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "2", "_rlnPhaseShift": "0.0", "_rlnGroupName": "ctf_group_017", "_rlnGroupNumber": "18", "item_id": 473, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/4330.outputParticles_473_output_images.jpg" }, { "_index": "476", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=19666.03, defV=19225.26, ast=440.78, psh=0.00, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[ 0.19490483 0.03727087 0.98011376 0.21664514]\n [ 0.06853944 0.9963174 -0.05151676 6.62682704]\n [-0.97842448 0.07721731 0.19163254 0.6734543 ]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "36", "_classId": "1", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "2", "_rlnPhaseShift": "0.0", "_rlnGroupName": "ctf_group_017", "_rlnGroupNumber": "18", "item_id": 476, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/4330.outputParticles_476_output_images.jpg" }, { "_index": "505", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=19666.03, defV=19225.26, ast=440.78, psh=0.00, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[-0.17075919 -0.97095508 -0.16759335 -4.84278114]\n [-0.31687384 0.21517114 -0.92373825 -0.13726862]\n [ 0.9329696 -0.10463084 -0.34441272 2.72469093]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "36", "_classId": "1", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "1", "_rlnPhaseShift": "0.0", "_rlnGroupName": "ctf_group_017", "_rlnGroupNumber": "18", "item_id": 505, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/4330.outputParticles_505_output_images.jpg" }, { "_index": "539", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=22615.70, defV=22160.71, ast=454.99, psh=0.00, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[ 0.32548681 -0.7962177 0.5099958 -1.24181521]\n [ 0.93488753 0.19023473 -0.29965991 4.08149187]\n [ 0.14157561 0.57432406 0.80629289 2.30236436]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "48", "_classId": "1", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "1", "_rlnPhaseShift": "0.0", "_rlnGroupName": "ctf_group_020", "_rlnGroupNumber": "12", "item_id": 539, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/4330.outputParticles_539_output_images.jpg" }, { "_index": "556", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=22615.70, defV=22160.71, ast=454.99, psh=0.00, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[-0.01297476 -0.79782276 -0.60275243 3.26013056]\n [-0.95350665 0.19138676 -0.23280071 0.61699477]\n [ 0.30109254 0.57170792 -0.76321251 -2.76291127]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "48", "_classId": "1", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "2", "_rlnPhaseShift": "0.0", "_rlnGroupName": "ctf_group_020", "_rlnGroupNumber": "12", "item_id": 556, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/4330.outputParticles_556_output_images.jpg" }, { "_index": "624", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=22615.70, defV=22160.71, ast=454.99, psh=0.00, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[ 0.62236428 0.7338683 -0.2722132 -0.31393977]\n [-0.6934744 0.3557005 -0.6265544 1.30321296]\n [-0.36298204 0.57871796 0.73029416 1.00106958]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "48", "_classId": "1", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "2", "_rlnPhaseShift": "0.0", "_rlnGroupName": "ctf_group_020", "_rlnGroupNumber": "12", "item_id": 624, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/4330.outputParticles_624_output_images.jpg" }, { "_index": "808", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=6993.03, defV=6627.23, ast=365.80, psh=0.00, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[-0.53040597 -0.33406985 -0.77914495 -1.23190628]\n [ 0.04295001 0.90731078 -0.41826122 -2.33196163]\n [ 0.84665507 -0.25531253 -0.46689475 4.14483708]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "14", "_classId": "1", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "1", "_rlnPhaseShift": "0.0", "_rlnGroupName": "ctf_group_004", "_rlnGroupNumber": "11", "item_id": 808, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/4330.outputParticles_808_output_images.jpg" }, { "_index": "849", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=22536.14, defV=22030.56, ast=505.58, psh=0.00, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[-0.132863 -0.79078199 -0.5975042 1.86276038]\n [ 0.6366864 0.39391836 -0.66291685 -0.64979138]\n [ 0.75959058 -0.46849992 0.45114296 1.51226897]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "43", "_classId": "1", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "2", "_rlnPhaseShift": "0.0", "_rlnGroupName": "ctf_group_020", "_rlnGroupNumber": "12", "item_id": 849, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/4330.outputParticles_849_output_images.jpg" }, { "_index": "992", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=16337.28, defV=16008.29, ast=328.99, psh=0.00, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[ 0.97805399 -0.08534869 0.19006841 -2.86942725]\n [ 0.15331095 0.91255369 -0.37913258 4.81645366]\n [-0.14108916 0.3999517 0.90561166 2.61863016]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "51", "_classId": "1", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "1", "_rlnPhaseShift": "0.0", "_rlnGroupName": "ctf_group_013", "_rlnGroupNumber": "4", "item_id": 992, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/4330.outputParticles_992_output_images.jpg" }, { "_index": "1046", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=16337.28, defV=16008.29, ast=328.99, psh=0.00, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[-0.6567056 0.69912285 0.28278081 -3.67654807]\n [ 0.69690261 0.70587976 -0.12673005 2.25472198]\n [-0.28820912 0.11384636 -0.95077574 -1.39401776]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "51", "_classId": "1", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "1", "_rlnPhaseShift": "0.0", "_rlnGroupName": "ctf_group_013", "_rlnGroupNumber": "4", "item_id": 1046, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/4330.outputParticles_1046_output_images.jpg" } ] } ], "summary": "From input SetOfClasses3D of size 4 was selected 1 item to create output SetOfParticles of size 8798Input: SetOfClasses3D (4 items) \nOutput: SetOfParticles (8798 items, 300 x 300, 1.40 \u212b/px)", "log": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/4330_ProtUserSubSet.log", "label": [ "symrelax" ], "labelColor": [ "#e4ee89" ], "plugin": "pwem", "pluginVersion": "3.0.10" }, { "object.className": "ProtUserSubSet", "object.id": "4384", "object.label": "vol1", "object.comment": "", "_useQueue": false, "_prerequisites": "", "_queueParams": null, "runName": null, "runMode": 0, "other": null, "sqliteFile": "Runs/004230_ProtCryoSparcInitialModel/classes3D_state.sqlite,", "outputClassName": "SetOfVolumes,Representatives", "inputObject": "4230.outputClasses", "output": [ { "outputName": "4384.outputRepresentatives", "outputType": "SetOfVolumes", "outputSize": 1, "outputItems": [ { "_index": "1", "_filename": "Runs/004230_ProtCryoSparcInitialModel/extra/J56/cryosparc_P13_J56_class_00_final_volume_scaled.mrc", "_samplingRate": "1.4", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_classId": "None", "_halfMapFilenames": "[]", "item_id": 1, "item_representation": "['Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/4384.outputRepresentatives_cryosparc_P13_J56_class_00_final_volume_scaled/slicesX_0000.jpg', 'Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/4384.outputRepresentatives_cryosparc_P13_J56_class_00_final_volume_scaled/slicesX_0001.jpg', 'Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/4384.outputRepresentatives_cryosparc_P13_J56_class_00_final_volume_scaled/slicesX_0002.jpg', 'Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/4384.outputRepresentatives_cryosparc_P13_J56_class_00_final_volume_scaled/slicesX_0003.jpg', 'Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/4384.outputRepresentatives_cryosparc_P13_J56_class_00_final_volume_scaled/slicesX_0004.jpg', 'Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/4384.outputRepresentatives_cryosparc_P13_J56_class_00_final_volume_scaled/slicesX_0005.jpg', 'Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/4384.outputRepresentatives_cryosparc_P13_J56_class_00_final_volume_scaled/slicesX_0006.jpg', 'Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/4384.outputRepresentatives_cryosparc_P13_J56_class_00_final_volume_scaled/slicesX_0007.jpg', 'Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/4384.outputRepresentatives_cryosparc_P13_J56_class_00_final_volume_scaled/slicesX_0008.jpg', 'Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/4384.outputRepresentatives_cryosparc_P13_J56_class_00_final_volume_scaled/slicesX_0009.jpg', 'Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/4384.outputRepresentatives_cryosparc_P13_J56_class_00_final_volume_scaled/slicesX_0010.jpg', 'Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/4384.outputRepresentatives_cryosparc_P13_J56_class_00_final_volume_scaled/slicesX_0011.jpg', 'Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/4384.outputRepresentatives_cryosparc_P13_J56_class_00_final_volume_scaled/slicesX_0012.jpg', 'Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/4384.outputRepresentatives_cryosparc_P13_J56_class_00_final_volume_scaled/slicesX_0013.jpg', 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'Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/4556.outputVolumes_relion_it025_class010/slicesZ_0299.jpg']" } ] } ], "summary": "Iteration 25/25Current resolution: *7.00 A*Input Particles: *930486*\nClassified into *10* 3D classes\nInput: SetOfParticles (930486 items, 300 x 300, 1.40 \u212b/px) \nInput: Volume (300 x 300 x 300, 1.40 \u212b/px) - w/halves \nInput: VolumeMask (300 x 300 x 300, 1.40 \u212b/px) \nOutput: SetOfClasses3D (10 items)SetOfVolumes (10 items, 300 x 300 x 300, 1.40 \u212b/px)", "log": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/4556_ProtRelionClassify3D.log", "plugin": "relion", "pluginVersion": "3.0.0" }, { "object.className": "XmippProtDeepVolPostProc", "object.id": "4641", "object.label": "xmipp3 - deepEMhancer", "object.comment": "", "_useQueue": false, "_prerequisites": "", "_queueParams": null, "runName": null, "runMode": 0, "gpuList": "3", "useHalfMapsInsteadVol": false, "halfMapsAttached": true, 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\u212b/px)", "log": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/4701_XmippProtDeepVolPostProc.log", "label": [ "symrelax" ], "labelColor": [ "#e4ee89" ], "plugin": "xmipp3" }, { "object.className": "ProtCryo2D", "object.id": "4812", "object.label": "cryosparc2 - 2d classification_consensus_1.40Apx (copy)", "object.comment": "", "_useQueue": false, "_prerequisites": "", "_queueParams": null, "runName": null, "runMode": 0, "numberOfClasses": 20, "maximunResolution": 6, "initialClassification": 2.0, "useCircular2D": true, "class2D_window_inner_A": null, "class2D_window_outer_A": null, "reCenter2D": true, "reCenterMask": 0.2, "reCenterMaskBinary": false, "forceMaxover": true, "ctfFlipPhases": false, "numberFinalIterator": 1, "numberOnlineEMIterator": 20, "batchSizeClass": 100, "initialScale2D": 1, "zeropadFactor": 2, "useFRCRegularized": true, "useFullFRC": true, "iterationToStartAnneling": 2, "iterationToStartAnneal": 15, "useWhiteNoiseModel": false, "compute_use_ssd": false, "gpuList": "2", "compute_lane": "default", "inputParticles": "3276.outputParticles", "output": [ { "outputName": "4812.outputClasses", "outputType": "SetOfClasses2D", "outputSize": 20, "outputItems": [ { "_size": "838", "_streamState": "2", "_mapperPath": "['Runs/004812_ProtCryo2D/classes2D.sqlite', 'Class001']", "_representative": "Particle (300 x 300, 1.40 \u212b/px)", "_samplingRate": "1.4", "_hasCtf": "True", "_alignment": "2D", "_isPhaseFlipped": "False", "_isAmplitudeCorrected": "False", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_firstDim": "300 x 300", "item_id": 1, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/4812.outputClasses_1_cryosparc_P13_J63_020_class_averages_scaled.jpg" }, { "_size": "1351", "_streamState": "2", "_mapperPath": "['Runs/004812_ProtCryo2D/classes2D.sqlite', 'Class002']", "_representative": "Particle (300 x 300, 1.40 \u212b/px)", "_samplingRate": "1.4", "_hasCtf": "True", "_alignment": "2D", "_isPhaseFlipped": "False", "_isAmplitudeCorrected": "False", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_firstDim": "300 x 300", "item_id": 2, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/4812.outputClasses_2_cryosparc_P13_J63_020_class_averages_scaled.jpg" }, { "_size": "625", "_streamState": "2", "_mapperPath": "['Runs/004812_ProtCryo2D/classes2D.sqlite', 'Class003']", "_representative": "Particle (300 x 300, 1.40 \u212b/px)", "_samplingRate": "1.4", "_hasCtf": "True", "_alignment": "2D", "_isPhaseFlipped": "False", "_isAmplitudeCorrected": "False", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_firstDim": "300 x 300", "item_id": 3, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/4812.outputClasses_3_cryosparc_P13_J63_020_class_averages_scaled.jpg" }, { "_size": "722", "_streamState": "2", "_mapperPath": "['Runs/004812_ProtCryo2D/classes2D.sqlite', 'Class004']", "_representative": "Particle (300 x 300, 1.40 \u212b/px)", "_samplingRate": "1.4", "_hasCtf": "True", "_alignment": "2D", "_isPhaseFlipped": "False", "_isAmplitudeCorrected": "False", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_firstDim": "300 x 300", "item_id": 4, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/4812.outputClasses_4_cryosparc_P13_J63_020_class_averages_scaled.jpg" }, { "_size": "1401", "_streamState": "2", "_mapperPath": "['Runs/004812_ProtCryo2D/classes2D.sqlite', 'Class005']", "_representative": "Particle (300 x 300, 1.40 \u212b/px)", "_samplingRate": "1.4", "_hasCtf": "True", "_alignment": "2D", "_isPhaseFlipped": "False", "_isAmplitudeCorrected": "False", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_firstDim": "300 x 300", "item_id": 5, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/4812.outputClasses_5_cryosparc_P13_J63_020_class_averages_scaled.jpg" }, { "_size": "629", "_streamState": "2", "_mapperPath": "['Runs/004812_ProtCryo2D/classes2D.sqlite', 'Class006']", "_representative": "Particle (300 x 300, 1.40 \u212b/px)", "_samplingRate": "1.4", "_hasCtf": "True", "_alignment": "2D", "_isPhaseFlipped": "False", "_isAmplitudeCorrected": "False", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_firstDim": "300 x 300", "item_id": 6, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/4812.outputClasses_6_cryosparc_P13_J63_020_class_averages_scaled.jpg" }, { "_size": "1598", "_streamState": "2", "_mapperPath": "['Runs/004812_ProtCryo2D/classes2D.sqlite', 'Class007']", "_representative": "Particle (300 x 300, 1.40 \u212b/px)", "_samplingRate": "1.4", "_hasCtf": "True", "_alignment": "2D", "_isPhaseFlipped": "False", "_isAmplitudeCorrected": "False", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_firstDim": "300 x 300", "item_id": 7, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/4812.outputClasses_7_cryosparc_P13_J63_020_class_averages_scaled.jpg" }, { "_size": "2406", "_streamState": "2", "_mapperPath": "['Runs/004812_ProtCryo2D/classes2D.sqlite', 'Class008']", "_representative": "Particle (300 x 300, 1.40 \u212b/px)", "_samplingRate": "1.4", "_hasCtf": "True", "_alignment": "2D", "_isPhaseFlipped": "False", "_isAmplitudeCorrected": "False", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_firstDim": "300 x 300", "item_id": 8, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/4812.outputClasses_8_cryosparc_P13_J63_020_class_averages_scaled.jpg" }, { "_size": "390", "_streamState": "2", "_mapperPath": "['Runs/004812_ProtCryo2D/classes2D.sqlite', 'Class009']", "_representative": "Particle (300 x 300, 1.40 \u212b/px)", "_samplingRate": "1.4", "_hasCtf": "True", "_alignment": "2D", "_isPhaseFlipped": "False", "_isAmplitudeCorrected": "False", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_firstDim": "300 x 300", "item_id": 9, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/4812.outputClasses_9_cryosparc_P13_J63_020_class_averages_scaled.jpg" }, { "_size": "1691", "_streamState": "2", "_mapperPath": "['Runs/004812_ProtCryo2D/classes2D.sqlite', 'Class010']", "_representative": "Particle (300 x 300, 1.40 \u212b/px)", "_samplingRate": "1.4", "_hasCtf": "True", "_alignment": "2D", "_isPhaseFlipped": "False", "_isAmplitudeCorrected": "False", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_firstDim": "300 x 300", "item_id": 10, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/4812.outputClasses_10_cryosparc_P13_J63_020_class_averages_scaled.jpg" }, { "_size": "1337", "_streamState": "2", "_mapperPath": "['Runs/004812_ProtCryo2D/classes2D.sqlite', 'Class011']", "_representative": "Particle (300 x 300, 1.40 \u212b/px)", "_samplingRate": "1.4", "_hasCtf": "True", "_alignment": "2D", "_isPhaseFlipped": "False", "_isAmplitudeCorrected": "False", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_firstDim": "300 x 300", "item_id": 11, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/4812.outputClasses_11_cryosparc_P13_J63_020_class_averages_scaled.jpg" }, { "_size": "1045", "_streamState": "2", "_mapperPath": "['Runs/004812_ProtCryo2D/classes2D.sqlite', 'Class012']", "_representative": "Particle (300 x 300, 1.40 \u212b/px)", "_samplingRate": "1.4", "_hasCtf": "True", "_alignment": "2D", "_isPhaseFlipped": "False", "_isAmplitudeCorrected": "False", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_firstDim": "300 x 300", "item_id": 12, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/4812.outputClasses_12_cryosparc_P13_J63_020_class_averages_scaled.jpg" }, { "_size": "589", "_streamState": "2", "_mapperPath": "['Runs/004812_ProtCryo2D/classes2D.sqlite', 'Class013']", "_representative": "Particle (300 x 300, 1.40 \u212b/px)", "_samplingRate": "1.4", "_hasCtf": "True", "_alignment": "2D", "_isPhaseFlipped": "False", "_isAmplitudeCorrected": "False", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_firstDim": "300 x 300", "item_id": 13, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/4812.outputClasses_13_cryosparc_P13_J63_020_class_averages_scaled.jpg" }, { "_size": "1189", "_streamState": "2", "_mapperPath": "['Runs/004812_ProtCryo2D/classes2D.sqlite', 'Class014']", "_representative": "Particle (300 x 300, 1.40 \u212b/px)", "_samplingRate": "1.4", "_hasCtf": "True", "_alignment": "2D", "_isPhaseFlipped": "False", "_isAmplitudeCorrected": "False", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_firstDim": "300 x 300", "item_id": 14, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/4812.outputClasses_14_cryosparc_P13_J63_020_class_averages_scaled.jpg" }, { "_size": "678", "_streamState": "2", "_mapperPath": "['Runs/004812_ProtCryo2D/classes2D.sqlite', 'Class015']", "_representative": "Particle (300 x 300, 1.40 \u212b/px)", "_samplingRate": "1.4", "_hasCtf": "True", "_alignment": "2D", "_isPhaseFlipped": "False", "_isAmplitudeCorrected": "False", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_firstDim": "300 x 300", "item_id": 15, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/4812.outputClasses_15_cryosparc_P13_J63_020_class_averages_scaled.jpg" }, { "_size": "732", "_streamState": "2", "_mapperPath": "['Runs/004812_ProtCryo2D/classes2D.sqlite', 'Class016']", "_representative": "Particle (300 x 300, 1.40 \u212b/px)", "_samplingRate": "1.4", "_hasCtf": "True", "_alignment": "2D", "_isPhaseFlipped": "False", "_isAmplitudeCorrected": "False", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_firstDim": "300 x 300", "item_id": 16, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/4812.outputClasses_16_cryosparc_P13_J63_020_class_averages_scaled.jpg" }, { "_size": "1403", "_streamState": "2", "_mapperPath": "['Runs/004812_ProtCryo2D/classes2D.sqlite', 'Class017']", "_representative": "Particle (300 x 300, 1.40 \u212b/px)", "_samplingRate": "1.4", "_hasCtf": "True", "_alignment": "2D", "_isPhaseFlipped": "False", "_isAmplitudeCorrected": "False", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_firstDim": "300 x 300", "item_id": 17, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/4812.outputClasses_17_cryosparc_P13_J63_020_class_averages_scaled.jpg" }, { "_size": "809", "_streamState": "2", "_mapperPath": "['Runs/004812_ProtCryo2D/classes2D.sqlite', 'Class018']", "_representative": "Particle (300 x 300, 1.40 \u212b/px)", "_samplingRate": "1.4", "_hasCtf": "True", "_alignment": "2D", "_isPhaseFlipped": "False", "_isAmplitudeCorrected": "False", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_firstDim": "300 x 300", "item_id": 18, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/4812.outputClasses_18_cryosparc_P13_J63_020_class_averages_scaled.jpg" }, { "_size": "653", "_streamState": "2", "_mapperPath": "['Runs/004812_ProtCryo2D/classes2D.sqlite', 'Class019']", "_representative": "Particle (300 x 300, 1.40 \u212b/px)", "_samplingRate": "1.4", "_hasCtf": "True", "_alignment": "2D", "_isPhaseFlipped": "False", "_isAmplitudeCorrected": "False", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_firstDim": "300 x 300", "item_id": 19, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/4812.outputClasses_19_cryosparc_P13_J63_020_class_averages_scaled.jpg" }, { "_size": "1063", "_streamState": "2", "_mapperPath": "['Runs/004812_ProtCryo2D/classes2D.sqlite', 'Class020']", "_representative": "Particle (300 x 300, 1.40 \u212b/px)", "_samplingRate": "1.4", "_hasCtf": "True", "_alignment": "2D", "_isPhaseFlipped": "False", "_isAmplitudeCorrected": "False", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_firstDim": "300 x 300", "item_id": 20, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/4812.outputClasses_20_cryosparc_P13_J63_020_class_averages_scaled.jpg" } ] } ], "summary": "Input Particles: [[sci-open:3312][3276.outputParticles.3312]]Classified into *20* classes.Output set: [[sci-open:4941][4812.outputClasses.4941]]Input: SetOfParticles (21149 items, 300 x 300, 1.40 \u212b/px) \nOutput: SetOfClasses2D (20 items)", "log": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/4812_ProtCryo2D.log", "label": [ "symrelax" ], "labelColor": [ "#e4ee89" ], "plugin": "cryosparc2", "pluginVersion": "3.2.10" }, { "object.className": "ProtCryo2D", "object.id": "4869", "object.label": "cryosparc2 - 2d classification_consensus_1.40Apx (copy 2)", "object.comment": "", "_useQueue": false, "_prerequisites": "", "_queueParams": null, "runName": null, "runMode": 0, "numberOfClasses": 20, "maximunResolution": 6, "initialClassification": 2.0, "useCircular2D": true, "class2D_window_inner_A": null, "class2D_window_outer_A": null, "reCenter2D": true, "reCenterMask": 0.2, "reCenterMaskBinary": false, "forceMaxover": true, "ctfFlipPhases": false, "numberFinalIterator": 1, "numberOnlineEMIterator": 20, "batchSizeClass": 100, "initialScale2D": 1, "zeropadFactor": 2, "useFRCRegularized": true, "useFullFRC": true, "iterationToStartAnneling": 2, "iterationToStartAnneal": 15, "useWhiteNoiseModel": false, "compute_use_ssd": false, "gpuList": "1", "compute_lane": "default", "inputParticles": "3955.outputParticles", "output": [ { "outputName": "4869.outputClasses", "outputType": "SetOfClasses2D", "outputSize": 20, "outputItems": [ { "_size": "621", "_streamState": "2", "_mapperPath": "['Runs/004869_ProtCryo2D/classes2D.sqlite', 'Class001']", "_representative": "Particle (300 x 300, 1.40 \u212b/px)", "_samplingRate": "1.4", "_hasCtf": "True", "_alignment": "2D", "_isPhaseFlipped": "False", "_isAmplitudeCorrected": "False", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_firstDim": "300 x 300", "item_id": 1, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/4869.outputClasses_1_cryosparc_P13_J62_020_class_averages_scaled.jpg" }, { "_size": "501", "_streamState": "2", "_mapperPath": "['Runs/004869_ProtCryo2D/classes2D.sqlite', 'Class002']", "_representative": "Particle (300 x 300, 1.40 \u212b/px)", "_samplingRate": "1.4", "_hasCtf": "True", "_alignment": "2D", "_isPhaseFlipped": "False", "_isAmplitudeCorrected": "False", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_firstDim": "300 x 300", "item_id": 2, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/4869.outputClasses_2_cryosparc_P13_J62_020_class_averages_scaled.jpg" }, { "_size": "439", "_streamState": "2", "_mapperPath": "['Runs/004869_ProtCryo2D/classes2D.sqlite', 'Class003']", "_representative": "Particle (300 x 300, 1.40 \u212b/px)", "_samplingRate": "1.4", "_hasCtf": "True", "_alignment": "2D", "_isPhaseFlipped": "False", "_isAmplitudeCorrected": "False", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_firstDim": "300 x 300", "item_id": 3, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/4869.outputClasses_3_cryosparc_P13_J62_020_class_averages_scaled.jpg" }, { "_size": "1033", "_streamState": "2", "_mapperPath": "['Runs/004869_ProtCryo2D/classes2D.sqlite', 'Class004']", "_representative": "Particle (300 x 300, 1.40 \u212b/px)", "_samplingRate": "1.4", "_hasCtf": "True", "_alignment": "2D", "_isPhaseFlipped": "False", "_isAmplitudeCorrected": "False", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_firstDim": "300 x 300", "item_id": 4, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/4869.outputClasses_4_cryosparc_P13_J62_020_class_averages_scaled.jpg" }, { "_size": "956", "_streamState": "2", "_mapperPath": "['Runs/004869_ProtCryo2D/classes2D.sqlite', 'Class005']", "_representative": "Particle (300 x 300, 1.40 \u212b/px)", "_samplingRate": "1.4", "_hasCtf": "True", "_alignment": "2D", "_isPhaseFlipped": "False", "_isAmplitudeCorrected": "False", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_firstDim": "300 x 300", "item_id": 5, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/4869.outputClasses_5_cryosparc_P13_J62_020_class_averages_scaled.jpg" }, { "_size": "1029", "_streamState": "2", "_mapperPath": "['Runs/004869_ProtCryo2D/classes2D.sqlite', 'Class006']", "_representative": "Particle (300 x 300, 1.40 \u212b/px)", "_samplingRate": "1.4", "_hasCtf": "True", "_alignment": "2D", "_isPhaseFlipped": "False", "_isAmplitudeCorrected": "False", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_firstDim": "300 x 300", "item_id": 6, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/4869.outputClasses_6_cryosparc_P13_J62_020_class_averages_scaled.jpg" }, { "_size": "1245", "_streamState": "2", "_mapperPath": "['Runs/004869_ProtCryo2D/classes2D.sqlite', 'Class007']", "_representative": "Particle (300 x 300, 1.40 \u212b/px)", "_samplingRate": "1.4", "_hasCtf": "True", "_alignment": "2D", "_isPhaseFlipped": "False", "_isAmplitudeCorrected": "False", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_firstDim": "300 x 300", "item_id": 7, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/4869.outputClasses_7_cryosparc_P13_J62_020_class_averages_scaled.jpg" }, { "_size": "1718", "_streamState": "2", "_mapperPath": "['Runs/004869_ProtCryo2D/classes2D.sqlite', 'Class008']", "_representative": "Particle (300 x 300, 1.40 \u212b/px)", "_samplingRate": "1.4", "_hasCtf": "True", "_alignment": "2D", "_isPhaseFlipped": "False", "_isAmplitudeCorrected": "False", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_firstDim": "300 x 300", "item_id": 8, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/4869.outputClasses_8_cryosparc_P13_J62_020_class_averages_scaled.jpg" }, { "_size": "456", "_streamState": "2", "_mapperPath": "['Runs/004869_ProtCryo2D/classes2D.sqlite', 'Class009']", "_representative": "Particle (300 x 300, 1.40 \u212b/px)", "_samplingRate": "1.4", "_hasCtf": "True", "_alignment": "2D", "_isPhaseFlipped": "False", "_isAmplitudeCorrected": "False", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_firstDim": "300 x 300", "item_id": 9, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/4869.outputClasses_9_cryosparc_P13_J62_020_class_averages_scaled.jpg" }, { "_size": "87", "_streamState": "2", "_mapperPath": "['Runs/004869_ProtCryo2D/classes2D.sqlite', 'Class010']", "_representative": "Particle (300 x 300, 1.40 \u212b/px)", "_samplingRate": "1.4", "_hasCtf": "True", "_alignment": "2D", "_isPhaseFlipped": "False", "_isAmplitudeCorrected": "False", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_firstDim": "300 x 300", "item_id": 10, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/4869.outputClasses_10_cryosparc_P13_J62_020_class_averages_scaled.jpg" }, { "_size": "323", "_streamState": "2", "_mapperPath": "['Runs/004869_ProtCryo2D/classes2D.sqlite', 'Class011']", "_representative": "Particle (300 x 300, 1.40 \u212b/px)", "_samplingRate": "1.4", "_hasCtf": "True", "_alignment": "2D", "_isPhaseFlipped": "False", "_isAmplitudeCorrected": "False", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_firstDim": "300 x 300", "item_id": 11, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/4869.outputClasses_11_cryosparc_P13_J62_020_class_averages_scaled.jpg" }, { "_size": "560", "_streamState": "2", "_mapperPath": "['Runs/004869_ProtCryo2D/classes2D.sqlite', 'Class012']", "_representative": "Particle (300 x 300, 1.40 \u212b/px)", "_samplingRate": "1.4", "_hasCtf": "True", "_alignment": "2D", "_isPhaseFlipped": "False", "_isAmplitudeCorrected": "False", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_firstDim": "300 x 300", "item_id": 12, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/4869.outputClasses_12_cryosparc_P13_J62_020_class_averages_scaled.jpg" }, { "_size": "1831", "_streamState": "2", "_mapperPath": "['Runs/004869_ProtCryo2D/classes2D.sqlite', 'Class013']", "_representative": "Particle (300 x 300, 1.40 \u212b/px)", "_samplingRate": "1.4", "_hasCtf": "True", "_alignment": "2D", "_isPhaseFlipped": "False", "_isAmplitudeCorrected": "False", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_firstDim": "300 x 300", "item_id": 13, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/4869.outputClasses_13_cryosparc_P13_J62_020_class_averages_scaled.jpg" }, { "_size": "796", "_streamState": "2", "_mapperPath": "['Runs/004869_ProtCryo2D/classes2D.sqlite', 'Class014']", "_representative": "Particle (300 x 300, 1.40 \u212b/px)", "_samplingRate": "1.4", "_hasCtf": "True", "_alignment": "2D", "_isPhaseFlipped": "False", "_isAmplitudeCorrected": "False", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_firstDim": "300 x 300", "item_id": 14, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/4869.outputClasses_14_cryosparc_P13_J62_020_class_averages_scaled.jpg" }, { "_size": "577", "_streamState": "2", "_mapperPath": "['Runs/004869_ProtCryo2D/classes2D.sqlite', 'Class015']", "_representative": "Particle (300 x 300, 1.40 \u212b/px)", "_samplingRate": "1.4", "_hasCtf": "True", "_alignment": "2D", "_isPhaseFlipped": "False", "_isAmplitudeCorrected": "False", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_firstDim": "300 x 300", "item_id": 15, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/4869.outputClasses_15_cryosparc_P13_J62_020_class_averages_scaled.jpg" }, { "_size": "880", "_streamState": "2", "_mapperPath": "['Runs/004869_ProtCryo2D/classes2D.sqlite', 'Class016']", "_representative": "Particle (300 x 300, 1.40 \u212b/px)", "_samplingRate": "1.4", "_hasCtf": "True", "_alignment": "2D", "_isPhaseFlipped": "False", "_isAmplitudeCorrected": "False", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_firstDim": "300 x 300", "item_id": 16, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/4869.outputClasses_16_cryosparc_P13_J62_020_class_averages_scaled.jpg" }, { "_size": "462", "_streamState": "2", "_mapperPath": "['Runs/004869_ProtCryo2D/classes2D.sqlite', 'Class017']", "_representative": "Particle (300 x 300, 1.40 \u212b/px)", "_samplingRate": "1.4", "_hasCtf": "True", "_alignment": "2D", "_isPhaseFlipped": "False", "_isAmplitudeCorrected": "False", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_firstDim": "300 x 300", "item_id": 17, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/4869.outputClasses_17_cryosparc_P13_J62_020_class_averages_scaled.jpg" }, { "_size": "645", "_streamState": "2", "_mapperPath": "['Runs/004869_ProtCryo2D/classes2D.sqlite', 'Class018']", "_representative": "Particle (300 x 300, 1.40 \u212b/px)", "_samplingRate": "1.4", "_hasCtf": "True", "_alignment": "2D", "_isPhaseFlipped": "False", "_isAmplitudeCorrected": "False", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_firstDim": "300 x 300", "item_id": 18, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/4869.outputClasses_18_cryosparc_P13_J62_020_class_averages_scaled.jpg" }, { "_size": "2368", "_streamState": "2", "_mapperPath": "['Runs/004869_ProtCryo2D/classes2D.sqlite', 'Class019']", "_representative": "Particle (300 x 300, 1.40 \u212b/px)", "_samplingRate": "1.4", "_hasCtf": "True", "_alignment": "2D", "_isPhaseFlipped": "False", "_isAmplitudeCorrected": "False", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_firstDim": "300 x 300", "item_id": 19, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/4869.outputClasses_19_cryosparc_P13_J62_020_class_averages_scaled.jpg" }, { "_size": "566", "_streamState": "2", "_mapperPath": "['Runs/004869_ProtCryo2D/classes2D.sqlite', 'Class020']", "_representative": "Particle (300 x 300, 1.40 \u212b/px)", "_samplingRate": "1.4", "_hasCtf": "True", "_alignment": "2D", "_isPhaseFlipped": "False", "_isAmplitudeCorrected": "False", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_firstDim": "300 x 300", "item_id": 20, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/4869.outputClasses_20_cryosparc_P13_J62_020_class_averages_scaled.jpg" } ] } ], "summary": "Input Particles: [[sci-open:3991][3955.outputParticles.3991]]Classified into *20* classes.Output set: [[sci-open:4934][4869.outputClasses.4934]]Input: SetOfParticles (17093 items, 300 x 300, 1.40 \u212b/px) \nOutput: SetOfClasses2D (20 items)", "log": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/4869_ProtCryo2D.log", "label": [ "symrelax" ], "labelColor": [ "#e4ee89" ], "plugin": "cryosparc2", "pluginVersion": "3.2.10" }, { "object.className": "ProtRelionClassify3D", 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"Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/4948_ProtRelionClassify3D.log", "plugin": "relion", "pluginVersion": "3.0.0" }, { "object.className": "ProtCryoSparcNonUniformRefine3D", "object.id": "5033", "object.label": "cryosparc2 - 3D non-uniform refinement(Legacy)", "object.comment": "", "_useQueue": false, "_prerequisites": "", "_queueParams": null, "runName": null, "runMode": 0, "refine_N": 0, "symmetryGroup": 0, "symmetryOrder": 1, "refine_symmetry_do_align": true, "refine_do_init_scale_est": true, "refine_num_final_iterations": 0, "refine_res_init": 30, "refine_res_gsfsc_split": 20, "refine_SPW": false, "refine_clip": false, "refine_window": true, "refine_skip_premult": true, "refine_ignore_dc": true, "refine_batchsize_init": 0, "refine_batchsize_epsilon": 0.001, "refine_batchsize_snrfactor": 40.0, "refine_scale_min": false, "refine_scale_align_use_prev": false, "refine_scale_ctf_use_current": false, "refine_scale_start_iter": 0, "refine_noise_model": 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VolumeMask (300 x 300 x 300, 1.40 \u212b/px)", "log": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/5183_XmippProtCreateMask3D.log", "label": [ "symrelax" ], "labelColor": [ "#e4ee89" ], "plugin": "xmipp3" }, { "object.className": "ProtCryoSparcGlobalCtfRefinement", "object.id": "5259", "object.label": "cryosparc2 - global ctf refinement", "object.comment": "", "_useQueue": false, "_prerequisites": "", "_queueParams": null, "runName": null, "runMode": 0, "crg_num_iters": 1, "crg_num_plots": 50, "crg_plot_binfactor": 1, "crg_min_res_A": 10.0, "crg_do_tilt": true, "crg_do_trefoil": true, "crg_do_spherical": true, "crg_do_tetrafoil": true, "compute_use_ssd": false, "gpuList": "0", "compute_lane": "default", "inputParticles": "5033.outputParticles", "inputRefinement": "5033.", "refMask": "5183.outputMask", "output": [ { "outputName": "5259.outputParticles", "outputType": "SetOfParticles", "outputSize": 172309, "outputItems": [ { "_index": "2", "_filename": 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"_rlnRandomSubset": "2", "_rlnPhaseShift": "0.0", "_rlnGroupName": "ctf_group_023", "_rlnGroupNumber": "6", "item_id": 17, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/5259.outputParticles_17_output_images.jpg" }, { "_index": "19", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=25801.15, defV=25500.04, ast=301.11, psh=0.64, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[-0.90266451 0.25826031 0.34423597 -1.33554566]\n [-0.19530507 0.46693973 -0.86245187 0.07713597]\n [-0.38347454 -0.84573572 -0.37105037 -1.41832202]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "21", "_classId": "1", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "2", "_rlnPhaseShift": "0.0", "_rlnGroupName": "ctf_group_023", "_rlnGroupNumber": "6", "item_id": 19, "item_representation": 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"Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=25801.15, defV=25500.04, ast=301.11, psh=0.64, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[ 0.2601553 -0.29327409 0.91995083 4.0836833 ]\n [ 0.71026538 -0.58729422 -0.38808322 5.73764961]\n [ 0.65409656 0.75437113 0.05551473 -27.56209391]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "21", "_classId": "1", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "2", "_rlnPhaseShift": "0.0", "_rlnGroupName": "ctf_group_023", "_rlnGroupNumber": "6", "item_id": 23, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/5259.outputParticles_23_output_images.jpg" }, { "_index": "26", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=25801.15, defV=25500.04, ast=301.11, psh=0.64, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[-0.11154303 0.13639063 0.9843555 -0.96000883]\n [-0.74590531 -0.66600682 0.00775792 0.75556955]\n [ 0.65664559 -0.73337065 0.17602292 5.33526168]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "21", "_classId": "1", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "1", "_rlnPhaseShift": "0.0", "_rlnGroupName": "ctf_group_023", "_rlnGroupNumber": "6", "item_id": 26, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/5259.outputParticles_26_output_images.jpg" }, { "_index": "27", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=25801.15, defV=25500.04, ast=301.11, psh=0.64, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[-0.69858448 0.42679442 0.57430501 -6.02111461]\n [ 0.14861227 -0.69858437 0.69992448 -5.30034381]\n [ 0.69992437 0.57430515 0.42459331 16.88155819]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "21", "_classId": "1", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "2", "_rlnPhaseShift": "0.0", "_rlnGroupName": "ctf_group_023", "_rlnGroupNumber": "6", "item_id": 27, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/5259.outputParticles_27_output_images.jpg" } ] } ], "summary": "Input Particles: [[sci-open:5135][5033.outputParticles.5135]]Reference Mask: [[sci-open:5253][5183.outputMask.5253]]Number of Iterations: 1--------------------------------------------------Output particles [[sci-open:5407][5259.outputParticles.5407]]Input: SetOfParticles (172309 items, 300 x 300, 1.40 \u212b/px) \nInput: cryosparc2 - 3D non-uniform refinement(Legacy) \nInput: VolumeMask (300 x 300 x 300, 1.40 \u212b/px) \nOutput: SetOfParticles (172309 items, 300 x 300, 1.40 \u212b/px)", "log": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/5259_ProtCryoSparcGlobalCtfRefinement.log", "label": [ "symrelax" ], "labelColor": [ "#e4ee89" ], "plugin": "cryosparc2", "pluginVersion": "3.2.10" }, { "object.className": "ProtCryoSparcNonUniformRefine3D", "object.id": "5307", "object.label": "cryosparc2 - 3D non-uniform refinement(Legacy) (copy)", "object.comment": "", "_useQueue": false, "_prerequisites": "", "_queueParams": null, "runName": null, "runMode": 0, "refine_N": 0, "symmetryGroup": 0, "symmetryOrder": 1, "refine_symmetry_do_align": true, "refine_do_init_scale_est": true, "refine_num_final_iterations": 0, "refine_res_init": 30, "refine_res_gsfsc_split": 20, "refine_SPW": false, "refine_clip": false, "refine_window": true, "refine_skip_premult": true, "refine_ignore_dc": true, "refine_batchsize_init": 0, "refine_batchsize_epsilon": 0.001, "refine_batchsize_snrfactor": 40.0, "refine_scale_min": false, "refine_scale_align_use_prev": false, "refine_scale_ctf_use_current": false, "refine_scale_start_iter": 0, "refine_noise_model": 0, "refine_noise_priorw": 50, "refine_noise_initw": 200, "refine_noise_init_sigmascale": 3, "refine_minisize": 2000, "refine_mask": 0, "refine_dynamic_mask_thresh_factor": 0.2, "refine_dynamic_mask_near_ang": 6.0, "refine_dynamic_mask_far_ang": 14.0, "refine_dynamic_mask_start_res": 12, "refine_dynamic_mask_use_abs": false, "compute_use_ssd": false, "gpuList": "2", "compute_lane": "default", "refine_locproc_start_res": 8.0, "refine_early_stopping": 1, "locres_use_mask": true, "locres_step_size": 2, "locres_stop_subsampling": 5, "locres_fsc_thresh": 0.5, "locres_awf": 6, "locres_zeropad_factor": 2.0, "locres_cap": false, "locres_compute_facility": 0, "locres_anneal_factor": 0.0, "locres_fsc_weighting": false, "localfilter_kernel_type": "lanczos", "cross_validation": true, "temporal_locres": false, "use_phenix_sharpen": false, "use_monores": false, "extra_sharpen": false, "inputParticles": 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[[sci-open:5435][5307.outputParticles.5435]]Output volume [[sci-open:5429][5307.outputVolume.5429]]\nMap Resolution: 7.474\u00c5\nEstimated Bfactor: -348.7Input: SetOfParticles (21149 items, 300 x 300, 1.40 \u212b/px) \nInput: Volume (300 x 300 x 300, 1.40 \u212b/px) \nOutput: Volume (300 x 300 x 300, 1.40 \u212b/px) - w/halvesSetOfParticles (21149 items, 300 x 300, 1.40 \u212b/px)FSC", "log": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/5307_ProtCryoSparcNonUniformRefine3D.log", "label": [ "symrelax" ], "labelColor": [ "#e4ee89" ], "plugin": "cryosparc2", "pluginVersion": "3.2.10" }, { "object.className": "ProtCryoSparcLocalCtfRefinement", "object.id": "5458", "object.label": "cryosparc2 - local ctf refinement", "object.comment": "", "_useQueue": false, "_prerequisites": "", "_queueParams": null, "runName": null, "runMode": 0, "crl_N": null, "crl_num_plots": 50, "crl_min_res_A": 20, "crl_max_res_A": null, "crl_df_range": 2000, "compute_use_ssd": false, "gpuList": "1", "compute_lane": "default", "inputRefinement": "5033.", "refMask": "5183.outputMask", "inputParticles": "5259.outputParticles", "output": [ { "outputName": "5458.outputParticles", "outputType": "SetOfParticles", "outputSize": 172309, "outputItems": [ { "_index": "2", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=25816.35, defV=25515.23, ast=301.11, psh=0.64, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[ 0.2508534 0.96783268 0.01929968 -10.26323585]\n [ -0.56215482 0.16187835 -0.81103475 -3.33072691]\n [ -0.78807013 0.19260142 0.58467954 -4.28141904]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "21", "_classId": "1", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "1", "_rlnPhaseShift": "0.0", "_rlnGroupName": "ctf_group_023", "_rlnGroupNumber": "6", "item_id": 2, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/5458.outputParticles_2_output_images.jpg" }, { "_index": "4", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=25771.55, defV=25470.44, ast=301.11, psh=0.64, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[ 0.890931 0.25832086 0.37351343 9.96323444]\n [ -0.12579502 -0.64990807 0.74952993 -12.07476756]\n [ 0.43636861 -0.71476558 -0.54652777 -9.75064414]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "21", "_classId": "1", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "1", "_rlnPhaseShift": "0.0", "_rlnGroupName": "ctf_group_023", "_rlnGroupNumber": "6", "item_id": 4, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/5458.outputParticles_4_output_images.jpg" }, { "_index": "5", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=26001.15, defV=25700.04, ast=301.11, psh=0.64, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[ 0.06685117 -0.30598614 0.94968595 3.68591043]\n [ 0.81309746 -0.53493919 -0.2295922 12.41618623]\n [ 0.57827626 0.78753574 0.21303525 -3.05018908]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "21", "_classId": "1", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "2", "_rlnPhaseShift": "0.0", "_rlnGroupName": "ctf_group_023", "_rlnGroupNumber": "6", "item_id": 5, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/5458.outputParticles_5_output_images.jpg" }, { "_index": "6", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=25926.75, defV=25625.63, ast=301.11, psh=0.64, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[ 0.84144918 0.44640972 0.3044366 2.2132114 ]\n [-0.44967573 0.89092977 -0.06352862 -7.05965218]\n [-0.29959142 -0.08344165 0.95041174 -1.18082768]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "21", "_classId": "1", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "1", "_rlnPhaseShift": "0.0", "_rlnGroupName": "ctf_group_023", "_rlnGroupNumber": "6", "item_id": 6, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/5458.outputParticles_6_output_images.jpg" }, { "_index": "7", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=25837.95, defV=25536.84, ast=301.11, psh=0.64, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[ 0.22936001 0.87515477 0.42602595 -12.78472393]\n [ -0.96128635 0.13499474 0.24021859 -0.43035734]\n [ 0.15271719 -0.46462947 0.87223673 6.36295598]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "21", "_classId": "1", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "2", "_rlnPhaseShift": "0.0", "_rlnGroupName": "ctf_group_023", "_rlnGroupNumber": "6", "item_id": 7, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/5458.outputParticles_7_output_images.jpg" }, { "_index": "8", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=25790.75, defV=25489.63, ast=301.11, psh=0.64, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[ -0.44600145 -0.72698832 0.52208303 -15.00097483]\n [ 0.88540171 -0.44370543 0.13852543 9.34809515]\n [ 0.1309447 0.52403575 0.84156997 7.7673938 ]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "21", "_classId": "1", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "1", "_rlnPhaseShift": "0.0", "_rlnGroupName": "ctf_group_023", "_rlnGroupNumber": "6", "item_id": 8, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/5458.outputParticles_8_output_images.jpg" }, { "_index": "9", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=25773.95, defV=25472.84, ast=301.11, psh=0.64, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[-0.64455335 -0.5454831 0.53572303 -5.23940174]\n [-0.65016476 0.02237215 -0.7594638 0.05630789]\n [ 0.40228939 -0.83782318 -0.36907394 -7.72103274]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "21", "_classId": "1", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "2", "_rlnPhaseShift": "0.0", "_rlnGroupName": "ctf_group_023", "_rlnGroupNumber": "6", "item_id": 9, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/5458.outputParticles_9_output_images.jpg" }, { "_index": "14", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=25988.35, defV=25687.23, ast=301.11, psh=0.64, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[ 0.05325067 0.63995013 -0.76656911 -1.5427147 ]\n [-0.75731781 -0.47447595 -0.44871183 -1.91821122]\n [-0.6508718 0.60443064 0.45937947 -4.44800353]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "21", "_classId": "1", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "1", "_rlnPhaseShift": "0.0", "_rlnGroupName": "ctf_group_023", "_rlnGroupNumber": "6", "item_id": 14, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/5458.outputParticles_14_output_images.jpg" }, { "_index": "15", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=25772.35, defV=25471.23, ast=301.11, psh=0.64, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[-0.37477936 -0.71284377 0.59278512 4.63049692]\n [-0.60063986 -0.30037096 -0.74095144 2.01340972]\n [ 0.70623805 -0.63374368 -0.31558955 3.97050796]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "21", "_classId": "1", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "2", "_rlnPhaseShift": "0.0", "_rlnGroupName": "ctf_group_023", "_rlnGroupNumber": "6", "item_id": 15, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/5458.outputParticles_15_output_images.jpg" }, { "_index": "17", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=25821.95, defV=25520.84, ast=301.11, psh=0.64, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[-0.47648849 0.86907589 0.13291285 23.35805821]\n [-0.76342492 -0.48397758 0.42772432 5.84771207]\n [ 0.43605174 0.10233673 0.89408393 -6.26987538]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "21", "_classId": "1", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "2", "_rlnPhaseShift": "0.0", "_rlnGroupName": "ctf_group_023", "_rlnGroupNumber": "6", "item_id": 17, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/5458.outputParticles_17_output_images.jpg" }, { "_index": "19", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=25889.95, defV=25588.84, ast=301.11, psh=0.64, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[-0.90266451 0.25826031 0.34423597 -1.33554566]\n [-0.19530507 0.46693973 -0.86245187 0.07713597]\n [-0.38347454 -0.84573572 -0.37105037 -1.41832202]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "21", "_classId": "1", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "2", "_rlnPhaseShift": "0.0", "_rlnGroupName": "ctf_group_023", "_rlnGroupNumber": "6", "item_id": 19, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/5458.outputParticles_19_output_images.jpg" }, { "_index": "22", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=25651.55, defV=25350.44, ast=301.11, psh=0.64, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[-0.11218349 0.14268712 -0.98338967 -0.06942558]\n [ 0.91425018 0.40254301 -0.04588829 2.40022656]\n [ 0.38930897 -0.90421209 -0.17561041 -0.23842494]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "21", "_classId": "1", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "1", "_rlnPhaseShift": "0.0", "_rlnGroupName": "ctf_group_023", "_rlnGroupNumber": "6", "item_id": 22, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/5458.outputParticles_22_output_images.jpg" }, { "_index": "23", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=25681.95, defV=25380.84, ast=301.11, psh=0.64, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[ 0.26015522 -0.29327403 0.91995087 4.0836827 ]\n [ 0.71026541 -0.58729425 -0.38808312 5.73765004]\n [ 0.65409656 0.75437113 0.05551473 -27.56209391]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "21", "_classId": "1", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "2", "_rlnPhaseShift": "0.0", "_rlnGroupName": "ctf_group_023", "_rlnGroupNumber": "6", "item_id": 23, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/5458.outputParticles_23_output_images.jpg" }, { "_index": "26", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=25937.15, defV=25636.04, ast=301.11, psh=0.64, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[-0.11154303 0.13639063 0.9843555 -0.96000883]\n [-0.74590531 -0.66600682 0.00775792 0.75556955]\n [ 0.65664559 -0.73337065 0.17602292 5.33526168]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "21", "_classId": "1", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "1", "_rlnPhaseShift": "0.0", "_rlnGroupName": "ctf_group_023", "_rlnGroupNumber": "6", "item_id": 26, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/5458.outputParticles_26_output_images.jpg" }, { "_index": "27", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=25735.55, defV=25434.44, ast=301.11, psh=0.64, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[-0.69858447 0.42679437 0.57430506 -6.02111498]\n [ 0.14861232 -0.6985844 0.69992444 -5.30034339]\n [ 0.69992437 0.57430515 0.42459331 16.88155819]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "21", "_classId": "1", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "2", "_rlnPhaseShift": "0.0", "_rlnGroupName": "ctf_group_023", "_rlnGroupNumber": "6", "item_id": 27, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/5458.outputParticles_27_output_images.jpg" } ] } ], "summary": "Input Particles: [[sci-open:5407][5259.outputParticles.5407]]Reference Mask: [[sci-open:5253][5183.outputMask.5253]]--------------------------------------------------Output particles [[sci-open:5627][5458.outputParticles.5627]]Input: SetOfParticles (172309 items, 300 x 300, 1.40 \u212b/px) \nInput: cryosparc2 - 3D non-uniform refinement(Legacy) \nInput: VolumeMask (300 x 300 x 300, 1.40 \u212b/px) \nOutput: SetOfParticles (172309 items, 300 x 300, 1.40 \u212b/px)", "log": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/5458_ProtCryoSparcLocalCtfRefinement.log", "label": [ "symrelax" ], "labelColor": [ "#e4ee89" ], "plugin": "cryosparc2", "pluginVersion": "3.2.10" }, { "object.className": "XmippProtCreateMask3D", "object.id": "5509", "object.label": "xmipp3 - create 3d mask_2UP", "object.comment": "", "_useQueue": false, "_prerequisites": "", "_queueParams": null, "runName": null, "runMode": 0, "source": 0, "volumeOperation": 0, "threshold": 0.08, "segmentationType": 2, "nvoxels": null, "naminoacids": null, "dalton": null, "samplingRate": 1.0, "size": null, "geo": 0, "radius": -1, "shiftCenter": false, "centerX": 0, "centerY": 0, "centerZ": 0, "boxSize": -1, "innerRadius": 0, "outerRadius": -1, "height": -1, "sigma": -1.0, "borderDecay": 0, "featureFilePath": null, "doSmall": false, "smallSize": 50, "doBig": false, "doSymmetrize": false, "symmetry": "c1", "doMorphological": true, "morphologicalOperation": 0, "elementSize": 1, "doInvert": false, "doSmooth": true, "sigmaConvolution": 2.0, "inputVolume": "5307.outputVolume", "output": [ { "outputName": "5509.outputMask", "outputType": "VolumeMask", "outputItems": [ { "_index": "0", "_filename": "Runs/005509_XmippProtCreateMask3D/mask.vol", "_samplingRate": "1.4", "_classId": "None", "_halfMapFilenames": "[]", "item_id": 5573, "item_representation": "['Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/5509.outputMask_mask/slicesX_0000.jpg', 'Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/5509.outputMask_mask/slicesX_0001.jpg', 'Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/5509.outputMask_mask/slicesX_0002.jpg', 'Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/5509.outputMask_mask/slicesX_0003.jpg', 'Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/5509.outputMask_mask/slicesX_0004.jpg', 'Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/5509.outputMask_mask/slicesX_0005.jpg', 'Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/5509.outputMask_mask/slicesX_0006.jpg', 'Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/5509.outputMask_mask/slicesX_0007.jpg', 'Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/5509.outputMask_mask/slicesX_0008.jpg', 'Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/5509.outputMask_mask/slicesX_0009.jpg', 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'Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/5509.outputMask_mask/slicesZ_0298.jpg', 'Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/5509.outputMask_mask/slicesZ_0299.jpg']" } ] } ], "summary": "*Mask creation* Thresholding 0.080000*Mask processing* Morphological operation: dilation Smoothed (sigma=2.000000)Input: Volume (300 x 300 x 300, 1.40 \u212b/px) - w/halves \nOutput: VolumeMask (300 x 300 x 300, 1.40 \u212b/px)", "log": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/5509_XmippProtCreateMask3D.log", "label": [ "symrelax" ], "labelColor": [ "#e4ee89" ], "plugin": "xmipp3" }, { "object.className": "ProtCryoSparcGlobalCtfRefinement", "object.id": "5579", "object.label": "cryosparc2 - global ctf refinement (copy)", "object.comment": "", "_useQueue": false, "_prerequisites": "", "_queueParams": null, "runName": null, "runMode": 0, "crg_num_iters": 1, "crg_num_plots": 50, "crg_plot_binfactor": 1, 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-9.14473289]\n [ 0.45122375 0.12929595 -0.88299473 0.20580268]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "36", "_classId": "8", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "1", "_rlnPhaseShift": "0.0", "_rlnGroupName": "ctf_group_017", "_rlnGroupNumber": "18", "item_id": 364, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/5579.outputParticles_364_output_images.jpg" }, { "_index": "386", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=19257.57, defV=18571.23, ast=686.34, psh=6.18, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[-0.51072282 -0.82526805 -0.24102874 -1.54722265]\n [-0.8045468 0.55760104 -0.20441509 -0.08626194]\n [ 0.30309512 0.08951945 -0.94874634 0.41165731]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "36", "_classId": "8", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "1", "_rlnPhaseShift": "0.0", "_rlnGroupName": "ctf_group_017", "_rlnGroupNumber": "18", "item_id": 386, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/5579.outputParticles_386_output_images.jpg" }, { "_index": "395", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=19257.57, defV=18571.23, ast=686.34, psh=6.18, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[ 0.44995716 0.85250193 0.26604326 -4.45693858]\n [ 0.83840686 -0.50585212 0.2029472 -4.86863299]\n [ 0.30759143 0.13173494 -0.94235525 -2.30678813]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "36", "_classId": "8", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "2", "_rlnPhaseShift": "0.0", "_rlnGroupName": "ctf_group_017", "_rlnGroupNumber": "18", "item_id": 395, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/5579.outputParticles_395_output_images.jpg" } ] } ], "summary": "Input Particles: [[sci-open:5435][5307.outputParticles.5435]]Reference Mask: [[sci-open:5573][5509.outputMask.5573]]Number of Iterations: 1--------------------------------------------------Output particles [[sci-open:5653][5579.outputParticles.5653]]Input: SetOfParticles (21149 items, 300 x 300, 1.40 \u212b/px) \nInput: cryosparc2 - 3D non-uniform refinement(Legacy) (copy) \nInput: VolumeMask (300 x 300 x 300, 1.40 \u212b/px) \nOutput: SetOfParticles (21149 items, 300 x 300, 1.40 \u212b/px)", "log": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/5579_ProtCryoSparcGlobalCtfRefinement.log", "label": [ "symrelax" ], "labelColor": [ "#e4ee89" ], "plugin": "cryosparc2", "pluginVersion": "3.2.10" }, { "object.className": "ProtCryoSparcLocalCtfRefinement", "object.id": "5673", "object.label": "cryosparc2 - local ctf refinement (copy)", "object.comment": "", "_useQueue": false, "_prerequisites": "", "_queueParams": null, "runName": null, "runMode": 0, "crl_N": null, "crl_num_plots": 50, "crl_min_res_A": 20, "crl_max_res_A": null, "crl_df_range": 2000, "compute_use_ssd": false, "gpuList": "2", "compute_lane": "default", "inputRefinement": "5307.", "refMask": "5509.outputMask", "inputParticles": "5579.outputParticles", "output": [ { "outputName": "5673.outputParticles", "outputType": "SetOfParticles", "outputSize": 21149, "outputItems": [ { "_index": "30", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=25643.42, defV=25358.86, ast=284.56, psh=6.18, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[-4.44749116e-01 -8.81139651e-01 -1.60596200e-01 -2.23688059e+01]\n [-3.55161760e-01 8.89594337e-03 9.34762530e-01 -7.14141052e+00]\n [-8.22227674e-01 4.72772438e-01 -3.16903572e-01 -9.72907224e+00]\n [ 0.00000000e+00 0.00000000e+00 0.00000000e+00 1.00000000e+00]]", "_coordinate": "Coordinate", "_micId": "21", "_classId": "8", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "1", "_rlnPhaseShift": "0.0", "_rlnGroupName": "ctf_group_023", "_rlnGroupNumber": "6", "item_id": 30, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/5673.outputParticles_30_output_images.jpg" }, { "_index": "69", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=24279.42, defV=23994.86, ast=284.56, psh=6.18, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[-0.71584743 -0.23661452 -0.65694446 -5.95601663]\n [-0.50701929 0.82302576 0.25604693 -6.95818688]\n [ 0.48009779 0.51637405 -0.70912901 3.00530607]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "21", "_classId": "8", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "2", "_rlnPhaseShift": "0.0", "_rlnGroupName": "ctf_group_023", "_rlnGroupNumber": "6", "item_id": 69, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/5673.outputParticles_69_output_images.jpg" }, { "_index": "128", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=15767.59, defV=15111.58, ast=656.01, psh=6.18, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[ 0.69752914 -0.68872644 0.19775991 2.9548656 ]\n [-0.1169572 -0.38171512 -0.91685036 2.51103124]\n [ 0.70694703 0.6164004 -0.34680893 -4.95340745]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "12", "_classId": "8", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "1", "_rlnPhaseShift": "0.0", "_rlnGroupName": "ctf_group_011", "_rlnGroupNumber": "1", "item_id": 128, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/5673.outputParticles_128_output_images.jpg" }, { "_index": "145", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=15001.99, defV=14345.98, ast=656.01, psh=6.18, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[-0.21064796 0.02524651 0.97723592 -0.64928865]\n [ 0.61773309 0.7782194 0.11305038 0.98522524]\n [-0.75764983 0.6274848 -0.17952593 -2.9139417 ]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "12", "_classId": "8", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "2", "_rlnPhaseShift": "0.0", "_rlnGroupName": "ctf_group_011", "_rlnGroupNumber": "1", "item_id": 145, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/5673.outputParticles_145_output_images.jpg" }, { "_index": "192", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=13637.99, defV=12981.98, ast=656.01, psh=6.18, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[-0.43271758 -0.07042868 0.89877433 2.12642521]\n [-0.9012076 0.06043279 -0.42915352 3.60342674]\n [-0.02409073 -0.99568453 -0.08962119 4.06994255]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "12", "_classId": "8", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "1", "_rlnPhaseShift": "0.0", "_rlnGroupName": "ctf_group_011", "_rlnGroupNumber": "1", "item_id": 192, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/5673.outputParticles_192_output_images.jpg" }, { "_index": "202", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=15211.59, defV=14555.58, ast=656.01, psh=6.18, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[-0.09770836 -0.82959079 -0.54975649 -2.03759092]\n [ 0.96512431 0.05582391 -0.25577091 -4.67061316]\n [ 0.24287474 -0.55557431 0.79520378 -2.9109341 ]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "12", "_classId": "8", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "1", "_rlnPhaseShift": "0.0", "_rlnGroupName": "ctf_group_011", "_rlnGroupNumber": "1", "item_id": 202, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/5673.outputParticles_202_output_images.jpg" }, { "_index": "205", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=12639.59, defV=11983.58, ast=656.01, psh=6.18, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[ 0.76768577 0.31139331 0.56008282 4.32891104]\n [ 0.4100263 -0.91036099 -0.05586857 8.62076348]\n [ 0.49248046 0.27253819 -0.82655062 2.3506352 ]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "12", "_classId": "8", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "2", "_rlnPhaseShift": "0.0", "_rlnGroupName": "ctf_group_011", "_rlnGroupNumber": "1", "item_id": 205, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/5673.outputParticles_205_output_images.jpg" }, { "_index": "217", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=25005.49, defV=24460.97, ast=544.52, psh=6.18, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[-7.66741777e-01 6.41837499e-01 1.23155388e-02 -7.14362709e+00]\n [ 6.41908768e-01 7.66776524e-01 2.62616185e-03 1.76257294e+00]\n [-7.75769688e-03 9.91904034e-03 -9.99920712e-01 -8.33554239e-02]\n [ 0.00000000e+00 0.00000000e+00 0.00000000e+00 1.00000000e+00]]", "_coordinate": "Coordinate", "_micId": "44", "_classId": "8", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "2", "_rlnPhaseShift": "0.0", "_rlnGroupName": "ctf_group_022", "_rlnGroupNumber": "14", "item_id": 217, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/5673.outputParticles_217_output_images.jpg" }, { "_index": "229", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=24354.29, defV=23809.77, ast=544.52, psh=6.18, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[-0.36326072 0.78916627 -0.49523555 -5.12484648]\n [ 0.44499386 -0.32003842 -0.83639457 3.8225318 ]\n [-0.81854878 -0.52420608 -0.23491676 -2.80583932]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "44", "_classId": "8", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "2", "_rlnPhaseShift": "0.0", "_rlnGroupName": "ctf_group_022", "_rlnGroupNumber": "14", "item_id": 229, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/5673.outputParticles_229_output_images.jpg" }, { "_index": "233", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=23905.49, defV=23360.97, ast=544.52, psh=6.18, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[ 0.77106566 -0.5251993 0.36003254 -4.3465943 ]\n [-0.5709404 -0.82058853 0.02571993 -1.7139299 ]\n [ 0.28193049 -0.22538888 -0.93258515 -1.72530902]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "44", "_classId": "8", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "2", "_rlnPhaseShift": "0.0", "_rlnGroupName": "ctf_group_022", "_rlnGroupNumber": "14", "item_id": 233, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/5673.outputParticles_233_output_images.jpg" }, { "_index": "240", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=24343.89, defV=23799.37, ast=544.52, psh=6.18, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[ 0.1104821 -0.99246404 -0.05299835 7.08192767]\n [-0.99358749 -0.11158212 0.01825726 -0.57132664]\n [-0.02403334 0.0506414 -0.99842769 -0.38636884]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "44", "_classId": "8", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "1", "_rlnPhaseShift": "0.0", "_rlnGroupName": "ctf_group_022", "_rlnGroupNumber": "14", "item_id": 240, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/5673.outputParticles_240_output_images.jpg" }, { "_index": "284", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=25647.89, defV=25103.37, ast=544.52, psh=6.18, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[ 0.04218314 -0.29923436 0.95324676 1.55398607]\n [ 0.72664398 -0.64563509 -0.23482727 -0.07351882]\n [ 0.68571795 0.70257677 0.19020193 -7.87897566]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "44", "_classId": "8", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "1", "_rlnPhaseShift": "0.0", "_rlnGroupName": "ctf_group_022", "_rlnGroupNumber": "14", "item_id": 284, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/5673.outputParticles_284_output_images.jpg" }, { "_index": "364", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=19109.57, defV=18423.23, ast=686.34, psh=6.18, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[ 0.88013052 0.09910423 0.46427213 -0.96923277]\n [ 0.14753704 -0.98664122 -0.06907916 -9.14473309]\n [ 0.45122398 0.12929601 -0.8829946 0.20580279]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "36", "_classId": "8", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "1", "_rlnPhaseShift": "0.0", "_rlnGroupName": "ctf_group_017", "_rlnGroupNumber": "18", "item_id": 364, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/5673.outputParticles_364_output_images.jpg" }, { "_index": "386", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=20236.77, defV=19550.43, ast=686.34, psh=6.18, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[-0.51072259 -0.82526819 -0.24102874 -1.5472226 ]\n [-0.80454696 0.55760081 -0.20441509 -0.08626238]\n [ 0.30309509 0.08951953 -0.94874634 0.41165739]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "36", "_classId": "8", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "1", "_rlnPhaseShift": "0.0", "_rlnGroupName": "ctf_group_017", "_rlnGroupNumber": "18", "item_id": 386, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/5673.outputParticles_386_output_images.jpg" }, { "_index": "395", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=19724.77, defV=19038.43, ast=686.34, psh=6.18, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[ 0.4499572 0.85250184 0.26604349 -4.45693866]\n [ 0.83840675 -0.50585225 0.20294733 -4.86863206]\n [ 0.30759167 0.13173505 -0.94235516 -2.30678994]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "36", "_classId": "8", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "2", "_rlnPhaseShift": "0.0", "_rlnGroupName": "ctf_group_017", "_rlnGroupNumber": "18", "item_id": 395, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/5673.outputParticles_395_output_images.jpg" } ] } ], "summary": "Input Particles: [[sci-open:5653][5579.outputParticles.5653]]Reference Mask: [[sci-open:5573][5509.outputMask.5573]]--------------------------------------------------Output particles [[sci-open:5724][5673.outputParticles.5724]]Input: SetOfParticles (21149 items, 300 x 300, 1.40 \u212b/px) \nInput: cryosparc2 - 3D non-uniform refinement(Legacy) (copy) \nInput: VolumeMask (300 x 300 x 300, 1.40 \u212b/px) \nOutput: SetOfParticles (21149 items, 300 x 300, 1.40 \u212b/px)", "log": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/5673_ProtCryoSparcLocalCtfRefinement.log", "label": [ "symrelax" ], "labelColor": [ "#e4ee89" ], "plugin": "cryosparc2", "pluginVersion": "3.2.10" }, { "object.className": "ProtCryoSparcNonUniformRefine3D", "object.id": "5744", "object.label": "cryosparc2 - 3D non-uniform refinement(Legacy) (copy 2)", "object.comment": "", "_useQueue": false, "_prerequisites": "", "_queueParams": null, "runName": null, "runMode": 0, "refine_N": 0, "symmetryGroup": 0, "symmetryOrder": 1, "refine_symmetry_do_align": true, "refine_do_init_scale_est": true, "refine_num_final_iterations": 0, "refine_res_init": 30, "refine_res_gsfsc_split": 20, "refine_SPW": false, "refine_clip": false, "refine_window": true, "refine_skip_premult": true, "refine_ignore_dc": true, "refine_batchsize_init": 0, "refine_batchsize_epsilon": 0.001, "refine_batchsize_snrfactor": 40.0, "refine_scale_min": false, "refine_scale_align_use_prev": false, "refine_scale_ctf_use_current": false, "refine_scale_start_iter": 0, "refine_noise_model": 0, "refine_noise_priorw": 50, "refine_noise_initw": 200, "refine_noise_init_sigmascale": 3, "refine_minisize": 2000, "refine_mask": 0, 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], "labelColor": [ "#e4ee89" ], "plugin": "relion", "pluginVersion": "3.0.0" }, { "object.className": "XmippProtConsensusClasses3D", "object.id": "6269", "object.label": "xmipp3 - consensus classes 3D_x2_symrelax_10classes_T4", "object.comment": "", "_useQueue": false, "_prerequisites": "", "_queueParams": null, "runName": null, "runMode": 0, "inputMultiClasses": [ "2226.outputClasses", "6159.outputClasses" ], "output": [ { "outputName": "6269.outputClasses", "outputType": "SetOfClasses3D", "outputSize": 100 } ], "summary": "No summary information.Input: SetOfClasses3D (10 items) \nInput: SetOfClasses3D (10 items) \nOutput: SetOfClasses3D (100 items)", "log": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/6269_XmippProtConsensusClasses3D.log", "label": [ "symrelax" ], "labelColor": [ "#e4ee89" ], "plugin": "xmipp3" }, { "object.className": "ProtRelionClassify3D", "object.id": "6310", "object.label": "relion - 3D classification_symrelax_10classes_T4 (copy 2)", "object.comment": "", "_useQueue": false, "_prerequisites": "", "_queueParams": null, "runName": null, "runMode": 0, "isClassify": true, "is2D": false, "doContinue": false, "copyAlignment": true, "alignmentAsPriors": true, "fillRandomSubset": true, "maskDiameterA": 336, "maskZero": 0, "continueIter": "last", "solventFscMask": false, "isMapAbsoluteGreyScale": true, "symmetryGroup": "C1", "initialLowPassFilterA": 30.0, "continueMsg": "True", "doCTF": true, "hasReferenceCTFCorrected": true, "haveDataBeenPhaseFlipped": null, "ignoreCTFUntilFirstPeak": false, "doCtfManualGroups": true, "defocusRange": 1000.0, "numParticles": 100.0, "numberOfClasses": 10, "regularisationParamT": 4.0, "numberOfIterations": 25, "useFastSubsets": false, "limitResolEStep": -1.0, "doImageAlignment": true, "angularSamplingDeg": 5, "offsetSearchRangePix": 0.001, "offsetSearchStepPix": 0.1, "localAngularSearch": true, "localAngularSearchRange": 2.7, "relaxSymm": "", "allowCoarserSampling": false, "useParallelDisk": 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"_isAmplitudeCorrected": "False", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_firstDim": "300 x 300", "item_id": 977, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/6420.outputClasses_relion_it025_class007" }, { "_size": "607", "_streamState": "2", "_mapperPath": "['Runs/006420_XmippProtConsensusClasses3D/classes3D.sqlite', 'Class978']", "_representative": "Volume (300 x 300 x 300, 99999.00 \u212b/px)", "_samplingRate": "None", "_hasCtf": "False", "_alignment": "None", "_isPhaseFlipped": "False", "_isAmplitudeCorrected": "False", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_firstDim": "300 x 300", "item_id": 978, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/6420.outputClasses_relion_it025_class010" }, { "_size": "124", "_streamState": "2", "_mapperPath": "['Runs/006420_XmippProtConsensusClasses3D/classes3D.sqlite', 'Class979']", "_representative": "Volume (300 x 300 x 300, 99999.00 \u212b/px)", "_samplingRate": "None", "_hasCtf": "False", "_alignment": "None", "_isPhaseFlipped": "False", "_isAmplitudeCorrected": "False", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_firstDim": "300 x 300", "item_id": 979, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/6420.outputClasses_relion_it025_class009" }, { "_size": "138", "_streamState": "2", "_mapperPath": "['Runs/006420_XmippProtConsensusClasses3D/classes3D.sqlite', 'Class980']", "_representative": "Volume (300 x 300 x 300, 99999.00 \u212b/px)", "_samplingRate": "None", "_hasCtf": "False", "_alignment": "None", "_isPhaseFlipped": "False", "_isAmplitudeCorrected": "False", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_firstDim": "300 x 300", "item_id": 980, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/6420.outputClasses_relion_it025_class010" }, { "_size": "119", "_streamState": "2", "_mapperPath": "['Runs/006420_XmippProtConsensusClasses3D/classes3D.sqlite', 'Class981']", "_representative": "Volume (300 x 300 x 300, 99999.00 \u212b/px)", "_samplingRate": "None", "_hasCtf": "False", "_alignment": "None", "_isPhaseFlipped": "False", "_isAmplitudeCorrected": "False", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_firstDim": "300 x 300", "item_id": 981, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/6420.outputClasses_relion_it025_class001" }, { "_size": "176", "_streamState": "2", "_mapperPath": "['Runs/006420_XmippProtConsensusClasses3D/classes3D.sqlite', 'Class982']", "_representative": "Volume (300 x 300 x 300, 99999.00 \u212b/px)", "_samplingRate": "None", "_hasCtf": "False", "_alignment": "None", "_isPhaseFlipped": "False", "_isAmplitudeCorrected": "False", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_firstDim": "300 x 300", "item_id": 982, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/6420.outputClasses_relion_it025_class002" }, { "_size": "140", "_streamState": "2", "_mapperPath": "['Runs/006420_XmippProtConsensusClasses3D/classes3D.sqlite', 'Class983']", "_representative": "Volume (300 x 300 x 300, 99999.00 \u212b/px)", "_samplingRate": "None", "_hasCtf": "False", "_alignment": "None", "_isPhaseFlipped": "False", "_isAmplitudeCorrected": "False", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_firstDim": "300 x 300", "item_id": 983, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/6420.outputClasses_relion_it025_class003" }, { "_size": "143", "_streamState": "2", "_mapperPath": "['Runs/006420_XmippProtConsensusClasses3D/classes3D.sqlite', 'Class984']", "_representative": "Volume (300 x 300 x 300, 99999.00 \u212b/px)", "_samplingRate": "None", "_hasCtf": "False", "_alignment": "None", "_isPhaseFlipped": "False", "_isAmplitudeCorrected": "False", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_firstDim": "300 x 300", "item_id": 984, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/6420.outputClasses_relion_it025_class009" }, { "_size": "91", "_streamState": "2", "_mapperPath": "['Runs/006420_XmippProtConsensusClasses3D/classes3D.sqlite', 'Class985']", "_representative": "Volume (300 x 300 x 300, 99999.00 \u212b/px)", "_samplingRate": "None", "_hasCtf": "False", "_alignment": "None", "_isPhaseFlipped": "False", "_isAmplitudeCorrected": "False", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_firstDim": "300 x 300", "item_id": 985, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/6420.outputClasses_relion_it025_class005" }, { "_size": "71", "_streamState": "2", "_mapperPath": "['Runs/006420_XmippProtConsensusClasses3D/classes3D.sqlite', 'Class986']", "_representative": "Volume (300 x 300 x 300, 99999.00 \u212b/px)", "_samplingRate": "None", "_hasCtf": "False", "_alignment": "None", "_isPhaseFlipped": "False", "_isAmplitudeCorrected": "False", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_firstDim": "300 x 300", "item_id": 986, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/6420.outputClasses_relion_it025_class009" }, { "_size": "81", "_streamState": "2", "_mapperPath": "['Runs/006420_XmippProtConsensusClasses3D/classes3D.sqlite', 'Class987']", "_representative": "Volume (300 x 300 x 300, 99999.00 \u212b/px)", "_samplingRate": "None", "_hasCtf": "False", "_alignment": "None", "_isPhaseFlipped": "False", "_isAmplitudeCorrected": "False", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_firstDim": "300 x 300", "item_id": 987, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/6420.outputClasses_relion_it025_class007" }, { "_size": "44", "_streamState": "2", "_mapperPath": "['Runs/006420_XmippProtConsensusClasses3D/classes3D.sqlite', 'Class988']", "_representative": "Volume (300 x 300 x 300, 99999.00 \u212b/px)", "_samplingRate": "None", "_hasCtf": "False", "_alignment": "None", "_isPhaseFlipped": "False", "_isAmplitudeCorrected": "False", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_firstDim": "300 x 300", "item_id": 988, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/6420.outputClasses_relion_it025_class009" }, { "_size": "94", "_streamState": "2", "_mapperPath": "['Runs/006420_XmippProtConsensusClasses3D/classes3D.sqlite', 'Class989']", "_representative": "Volume (300 x 300 x 300, 99999.00 \u212b/px)", "_samplingRate": "None", "_hasCtf": "False", "_alignment": "None", "_isPhaseFlipped": "False", "_isAmplitudeCorrected": "False", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_firstDim": "300 x 300", "item_id": 989, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/6420.outputClasses_relion_it025_class009" }, { "_size": "116", "_streamState": "2", "_mapperPath": "['Runs/006420_XmippProtConsensusClasses3D/classes3D.sqlite', 'Class990']", "_representative": "Volume (300 x 300 x 300, 99999.00 \u212b/px)", "_samplingRate": "None", "_hasCtf": "False", "_alignment": "None", "_isPhaseFlipped": "False", "_isAmplitudeCorrected": "False", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_firstDim": "300 x 300", "item_id": 990, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/6420.outputClasses_relion_it025_class010" }, { "_size": "120", "_streamState": "2", "_mapperPath": "['Runs/006420_XmippProtConsensusClasses3D/classes3D.sqlite', 'Class991']", "_representative": "Volume (300 x 300 x 300, 99999.00 \u212b/px)", "_samplingRate": "None", "_hasCtf": "False", "_alignment": "None", "_isPhaseFlipped": "False", "_isAmplitudeCorrected": "False", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_firstDim": "300 x 300", "item_id": 991, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/6420.outputClasses_relion_it025_class001" }, { "_size": "169", "_streamState": "2", "_mapperPath": "['Runs/006420_XmippProtConsensusClasses3D/classes3D.sqlite', 'Class992']", "_representative": "Volume (300 x 300 x 300, 99999.00 \u212b/px)", "_samplingRate": "None", "_hasCtf": "False", "_alignment": "None", "_isPhaseFlipped": "False", "_isAmplitudeCorrected": "False", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_firstDim": "300 x 300", "item_id": 992, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/6420.outputClasses_relion_it025_class002" }, { "_size": "135", "_streamState": "2", "_mapperPath": "['Runs/006420_XmippProtConsensusClasses3D/classes3D.sqlite', 'Class993']", "_representative": "Volume (300 x 300 x 300, 99999.00 \u212b/px)", "_samplingRate": "None", "_hasCtf": "False", "_alignment": "None", "_isPhaseFlipped": "False", "_isAmplitudeCorrected": "False", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_firstDim": "300 x 300", "item_id": 993, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/6420.outputClasses_relion_it025_class003" }, { "_size": "169", "_streamState": "2", "_mapperPath": "['Runs/006420_XmippProtConsensusClasses3D/classes3D.sqlite', 'Class994']", "_representative": "Volume (300 x 300 x 300, 99999.00 \u212b/px)", "_samplingRate": "None", "_hasCtf": "False", "_alignment": "None", "_isPhaseFlipped": "False", "_isAmplitudeCorrected": "False", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_firstDim": "300 x 300", "item_id": 994, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/6420.outputClasses_relion_it025_class010" }, { "_size": "92", "_streamState": "2", "_mapperPath": "['Runs/006420_XmippProtConsensusClasses3D/classes3D.sqlite', 'Class995']", "_representative": "Volume (300 x 300 x 300, 99999.00 \u212b/px)", "_samplingRate": "None", "_hasCtf": "False", "_alignment": "None", "_isPhaseFlipped": "False", "_isAmplitudeCorrected": "False", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_firstDim": "300 x 300", "item_id": 995, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/6420.outputClasses_relion_it025_class005" }, { "_size": "99", "_streamState": "2", "_mapperPath": "['Runs/006420_XmippProtConsensusClasses3D/classes3D.sqlite', 'Class996']", "_representative": "Volume (300 x 300 x 300, 99999.00 \u212b/px)", "_samplingRate": "None", "_hasCtf": "False", "_alignment": "None", "_isPhaseFlipped": "False", "_isAmplitudeCorrected": "False", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_firstDim": "300 x 300", "item_id": 996, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/6420.outputClasses_relion_it025_class010" }, { "_size": "74", "_streamState": "2", "_mapperPath": "['Runs/006420_XmippProtConsensusClasses3D/classes3D.sqlite', 'Class997']", "_representative": "Volume (300 x 300 x 300, 99999.00 \u212b/px)", "_samplingRate": "None", "_hasCtf": "False", "_alignment": "None", "_isPhaseFlipped": "False", "_isAmplitudeCorrected": "False", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_firstDim": "300 x 300", "item_id": 997, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/6420.outputClasses_relion_it025_class007" }, { "_size": "62", "_streamState": "2", "_mapperPath": "['Runs/006420_XmippProtConsensusClasses3D/classes3D.sqlite', 'Class998']", "_representative": "Volume (300 x 300 x 300, 99999.00 \u212b/px)", "_samplingRate": "None", "_hasCtf": "False", "_alignment": "None", "_isPhaseFlipped": "False", "_isAmplitudeCorrected": "False", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_firstDim": "300 x 300", "item_id": 998, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/6420.outputClasses_relion_it025_class010" }, { "_size": "106", "_streamState": "2", "_mapperPath": "['Runs/006420_XmippProtConsensusClasses3D/classes3D.sqlite', 'Class999']", "_representative": "Volume (300 x 300 x 300, 99999.00 \u212b/px)", "_samplingRate": "None", "_hasCtf": "False", "_alignment": "None", "_isPhaseFlipped": "False", "_isAmplitudeCorrected": "False", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_firstDim": "300 x 300", "item_id": 999, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/6420.outputClasses_relion_it025_class009" }, { "_size": "117", "_streamState": "2", "_mapperPath": "['Runs/006420_XmippProtConsensusClasses3D/classes3D.sqlite', 'Class1000']", "_representative": "Volume (300 x 300 x 300, 99999.00 \u212b/px)", "_samplingRate": "None", "_hasCtf": "False", "_alignment": "None", "_isPhaseFlipped": "False", "_isAmplitudeCorrected": "False", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_firstDim": "300 x 300", "item_id": 1000, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/6420.outputClasses_relion_it025_class010" } ] } ], "summary": "No summary information.Input: SetOfClasses3D (10 items) \nInput: SetOfClasses3D (10 items) \nInput: SetOfClasses3D (10 items) \nOutput: SetOfClasses3D (1000 items)", "log": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/6420_XmippProtConsensusClasses3D.log", "label": [ "symrelax+consensusx3" ], "labelColor": [ "#f8ae00" ], "plugin": "xmipp3" }, { "object.className": "ProtUserSubSet", "object.id": "6463", "object.label": "create subset_1UP_id808_145681particles", "object.comment": "", "_useQueue": false, "_prerequisites": "", "_queueParams": null, "runName": null, "runMode": 0, "other": null, "sqliteFile": "Runs/006420_XmippProtConsensusClasses3D/classes3D_state.sqlite,", "outputClassName": "SetOfParticles", "inputObject": "6420.outputClasses", "output": [ { "outputName": "6463.outputParticles", "outputType": "SetOfParticles", "outputSize": 145681, "outputItems": [ { "_index": "2", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=25831.73, defV=25543.44, ast=288.29, psh=0.00, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[ 0.61189721 -0.02696177 0.79047762 1.64003148]\n [ 0.13665618 0.98799234 -0.07208491 -10.39703387]\n [ -0.77904229 0.15213221 0.60823425 -3.36363409]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "21", "_classId": "14", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "1", "item_id": 2, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/6463.outputParticles_2_output_images.jpg" }, { "_index": "4", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=25831.73, defV=25543.44, ast=288.29, psh=0.00, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[ -0.8880913 -0.45417372 -0.07085246 -13.5107216 ]\n [ -0.21536933 0.54730074 -0.80875086 7.66377884]\n [ 0.40609099 -0.70298516 -0.58386812 -8.9760337 ]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "21", "_classId": "49", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "2", "item_id": 4, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/6463.outputParticles_4_output_images.jpg" }, { "_index": "5", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=25831.73, defV=25543.44, ast=288.29, psh=0.00, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[ -0.8110557 0.47875962 0.33612182 -12.14878789]\n [ 0.18838044 -0.33022175 0.92491427 4.98801444]\n [ 0.55380634 0.81347576 0.17763929 -2.98364761]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "21", "_classId": "86", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "1", "item_id": 5, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/6463.outputParticles_5_output_images.jpg" }, { "_index": "6", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=25831.73, defV=25543.44, ast=288.29, psh=0.00, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[-0.93342161 -0.11233099 -0.34074307 -4.91638816]\n [ 0.1493443 -0.98518264 -0.08432939 5.72401008]\n [-0.32622135 -0.12960291 0.93636676 -1.27356388]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "21", "_classId": "44", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "2", "item_id": 6, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/6463.outputParticles_6_output_images.jpg" }, { "_index": "7", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=25831.73, defV=25543.44, ast=288.29, psh=0.00, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[-0.58325157 -0.74714094 -0.31874445 11.41995835]\n [ 0.79445316 -0.44290572 -0.41554626 5.32668792]\n [ 0.16929788 -0.49559555 0.85189394 6.87119993]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "21", "_classId": "5", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "1", "item_id": 7, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/6463.outputParticles_7_output_images.jpg" }, { "_index": "8", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=25831.73, defV=25543.44, ast=288.29, psh=0.00, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[ -0.94006245 0.3310425 -0.08181354 -11.37967059]\n [ -0.31815192 -0.76510448 0.55981648 -13.51356357]\n [ 0.12272715 0.55229159 0.8245678 8.04555374]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "21", "_classId": "5", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "2", "item_id": 8, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/6463.outputParticles_8_output_images.jpg" }, { "_index": "9", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=25831.73, defV=25543.44, ast=288.29, psh=0.00, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[ 0.55187169 -0.0896551 0.82909565 -0.63972769]\n [-0.70842038 -0.57493702 0.40937511 -5.09791769]\n [ 0.43997522 -0.81327079 -0.38080497 -6.87321932]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "21", "_classId": "11", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "1", "item_id": 9, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/6463.outputParticles_9_output_images.jpg" }, { "_index": "14", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=25831.73, defV=25543.44, ast=288.29, psh=0.00, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[-0.45060318 0.22779415 -0.86317241 -2.19185458]\n [-0.63044616 -0.76576931 0.12702362 -0.57574457]\n [-0.6320557 0.60142098 0.48867003 -3.72197007]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "21", "_classId": "86", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "1", "item_id": 14, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/6463.outputParticles_14_output_images.jpg" }, { "_index": "15", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=25831.73, defV=25543.44, ast=288.29, psh=0.00, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[ 0.54202284 0.2090759 0.81394011 -1.23159857]\n [-0.42286604 -0.76914493 0.47916635 5.19359998]\n [ 0.72622004 -0.60390674 -0.32848302 4.52428523]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "21", "_classId": "11", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "2", "item_id": 15, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/6463.outputParticles_15_output_images.jpg" }, { "_index": "17", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=25831.73, defV=25543.44, ast=288.29, psh=0.00, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[-0.8261875 0.39969109 0.39706579 21.82350944]\n [-0.32197399 -0.91330731 0.24940429 -9.98673811]\n [ 0.46232776 0.07820985 0.88325322 -6.99078533]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "21", "_classId": "42", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "2", "item_id": 17, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/6463.outputParticles_17_output_images.jpg" }, { "_index": "22", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=25831.73, defV=25543.44, ast=288.29, psh=0.00, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[ 0.44327006 0.04135911 0.89543346 1.04333912]\n [-0.81511168 -0.39703685 0.42184675 -2.11415398]\n [ 0.37296729 -0.91687031 -0.14228225 0.2979414 ]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "21", "_classId": "96", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "1", "item_id": 22, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/6463.outputParticles_22_output_images.jpg" }, { "_index": "26", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=25831.73, defV=25543.44, ast=288.29, psh=0.00, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[-0.17667188 -0.35693385 -0.91727056 1.28608492]\n [ 0.7116881 0.5974364 -0.3695535 -0.72923824]\n [ 0.67991698 -0.71810025 0.14847536 6.13027817]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "21", "_classId": "86", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "1", "item_id": 26, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/6463.outputParticles_26_output_images.jpg" }, { "_index": "27", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=25831.73, defV=25543.44, ast=288.29, psh=0.00, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[-0.4216569 -0.07049727 0.90401084 -7.37159033]\n [ 0.55058732 -0.81204519 0.19348438 -0.50311983]\n [ 0.72045754 0.57932093 0.38121936 17.73609664]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "21", "_classId": "34", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "2", "item_id": 27, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/6463.outputParticles_27_output_images.jpg" }, { "_index": "29", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=25831.73, defV=25543.44, ast=288.29, psh=0.00, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[ 0.70584138 -0.70778554 -0.02876761 7.69507168]\n [-0.69587934 -0.70041607 0.15864828 6.11164378]\n [-0.13243825 -0.09196173 -0.98691598 0.75815262]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "21", "_classId": "22", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "1", "item_id": 29, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/6463.outputParticles_29_output_images.jpg" }, { "_index": "31", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=25831.73, defV=25543.44, ast=288.29, psh=0.00, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[-0.86889858 0.35022789 -0.34979377 7.87676439]\n [-0.40690412 -0.90777373 0.10186211 10.37058859]\n [-0.28185865 0.23084036 0.93127248 1.82424924]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "21", "_classId": "42", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "1", "item_id": 31, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/6463.outputParticles_31_output_images.jpg" } ] } ], "summary": "From input SetOfClasses3D of size 1000 was selected 1 item to create output SetOfParticles of size 145681Input: SetOfClasses3D (1000 items) \nOutput: SetOfParticles (145681 items, 300 x 300, 1.40 \u212b/px)", "log": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/6463_ProtUserSubSet.log", "label": [ "symrelax+consensusx3" ], "labelColor": [ "#f8ae00" ], "plugin": "pwem", "pluginVersion": "3.0.10" }, { "object.className": "ProtUserSubSet", "object.id": "6517", "object.label": "create subset_2UP_id878_4808particles", "object.comment": "", "_useQueue": false, "_prerequisites": "", "_queueParams": null, "runName": null, "runMode": 0, "other": null, "sqliteFile": "Runs/006420_XmippProtConsensusClasses3D/classes3D_state.sqlite,", "outputClassName": "SetOfParticles", "inputObject": "6420.outputClasses", "output": [ { "outputName": "6517.outputParticles", "outputType": "SetOfParticles", "outputSize": 4808, "outputItems": [ { "_index": "217", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=24957.51, defV=24507.44, ast=450.07, psh=0.00, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[ 0.97808339 -0.20008977 0.05759302 7.9598951 ]\n [-0.19651861 -0.97852611 -0.06218592 2.74619488]\n [ 0.06879904 0.04950492 -0.9964015 0.28869864]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "44", "_classId": "22", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "1", "item_id": 217, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/6517.outputParticles_217_output_images.jpg" }, { "_index": "240", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=24957.51, defV=24507.44, ast=450.07, psh=0.00, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[ 9.99586949e-01 2.86062182e-02 -2.75978809e-03 7.86853680e-01]\n [ 2.86917556e-02 -9.98836572e-01 3.87593295e-02 6.91085170e+00]\n [-1.64781944e-03 -3.88225030e-02 -9.99244764e-01 2.65889238e-01]\n [ 0.00000000e+00 0.00000000e+00 0.00000000e+00 1.00000000e+00]]", "_coordinate": "Coordinate", "_micId": "44", "_classId": "22", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "1", "item_id": 240, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/6517.outputParticles_240_output_images.jpg" }, { "_index": "284", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=24957.51, defV=24507.44, ast=450.07, psh=0.00, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[-0.66057855 0.6769647 -0.32458402 -0.6026811 ]\n [ 0.40255012 -0.04555542 -0.91426369 -0.64766182]\n [-0.6337108 -0.73460432 -0.24241929 3.24955302]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "44", "_classId": "90", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "1", "item_id": 284, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/6517.outputParticles_284_output_images.jpg" }, { "_index": "408", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=19666.03, defV=19225.26, ast=440.78, psh=0.00, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[ 0.91017393 0.22590002 0.34720686 -0.72540686]\n [-0.05731972 0.89882798 -0.43453734 -5.81783762]\n [-0.41024124 0.37560276 0.83103832 -2.73898497]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "36", "_classId": "8", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "2", "item_id": 408, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/6517.outputParticles_408_output_images.jpg" }, { "_index": "424", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=19666.03, defV=19225.26, ast=440.78, psh=0.00, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[-0.95562827 -0.29234287 0.03619734 -4.16697588]\n [-0.17022839 0.44776578 -0.8777973 -1.04686448]\n [ 0.24040985 -0.84500973 -0.4776627 1.60804134]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "36", "_classId": "96", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "1", "item_id": 424, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/6517.outputParticles_424_output_images.jpg" }, { "_index": "456", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=19666.03, defV=19225.26, ast=440.78, psh=0.00, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[-0.00716127 -0.99848771 -0.05450701 1.38115284]\n [-0.99529244 0.01238565 -0.09612262 3.29562091]\n [ 0.09665236 0.05356205 -0.99387596 -0.39448204]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "36", "_classId": "22", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "1", "item_id": 456, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/6517.outputParticles_456_output_images.jpg" }, { "_index": "470", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=19666.03, defV=19225.26, ast=440.78, psh=0.00, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[ 0.98601518 -0.1575371 -0.05437037 2.05442592]\n [-0.15684785 -0.98748079 0.01674619 -2.27277904]\n [-0.05632784 -0.00798412 -0.9983804 -0.15000322]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "36", "_classId": "22", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "1", "item_id": 470, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/6517.outputParticles_470_output_images.jpg" }, { "_index": "472", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=19666.03, defV=19225.26, ast=440.78, psh=0.00, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[-0.9905225 -0.1241077 -0.05884266 -7.42321084]\n [-0.1369957 0.92348348 0.35834403 -0.71802809]\n [ 0.00986697 0.36300902 -0.93173338 0.19265206]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "36", "_classId": "6", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "1", "item_id": 472, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/6517.outputParticles_472_output_images.jpg" }, { "_index": "489", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=19666.03, defV=19225.26, ast=440.78, psh=0.00, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[-0.23535937 0.79193652 0.56342037 -4.72051895]\n [ 0.86257102 0.43733253 -0.25438454 9.62938517]\n [-0.44785846 0.4261183 -0.7860318 -6.4999956 ]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "36", "_classId": "97", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "2", "item_id": 489, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/6517.outputParticles_489_output_images.jpg" }, { "_index": "499", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=19666.03, defV=19225.26, ast=440.78, psh=0.00, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[ 0.00468687 -0.94727763 -0.32037967 2.52156043]\n [-0.83876365 -0.17816671 0.51452129 2.16667217]\n [-0.5444755 0.26631133 -0.79537709 0.38590784]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "36", "_classId": "71", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "2", "item_id": 499, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/6517.outputParticles_499_output_images.jpg" }, { "_index": "559", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=22615.70, defV=22160.71, ast=454.99, psh=0.00, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[-0.89952282 -0.34821576 -0.26382663 -3.80713785]\n [ 0.11597269 0.39190121 -0.91266849 1.38546946]\n [ 0.42119952 -0.85156282 -0.31214056 -0.83311818]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "48", "_classId": "96", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "1", "item_id": 559, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/6517.outputParticles_559_output_images.jpg" }, { "_index": "600", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=22615.70, defV=22160.71, ast=454.99, psh=0.00, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[-0.88918353 0.42628826 -0.16622563 1.27775801]\n [ 0.04117832 -0.2872638 -0.95696596 -0.57331769]\n [-0.45569397 -0.85776327 0.23787641 -1.41354658]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "48", "_classId": "96", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "2", "item_id": 600, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/6517.outputParticles_600_output_images.jpg" }, { "_index": "855", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=22536.14, defV=22030.56, ast=505.58, psh=0.00, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[ 0.8015316 0.59417996 0.06706167 -2.62805887]\n [ 0.59727658 -0.8009053 -0.04256044 4.5126214 ]\n [ 0.02842148 0.0741679 -0.99684068 -0.36946843]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "43", "_classId": "22", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "2", "item_id": 855, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/6517.outputParticles_855_output_images.jpg" }, { "_index": "885", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=22536.14, defV=22030.56, ast=505.58, psh=0.00, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[-0.62924766 0.70617345 -0.32460199 9.38939265]\n [-0.69057365 -0.69963266 -0.1833635 -3.45105012]\n [-0.35658859 0.10878053 0.92790699 2.60265191]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "43", "_classId": "44", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "1", "item_id": 885, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/6517.outputParticles_885_output_images.jpg" }, { "_index": "1043", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=16337.28, defV=16008.29, ast=328.99, psh=0.00, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[ 0.83225268 -0.04585339 -0.55249701 -5.23607269]\n [ 0.15780007 0.9749444 0.15678822 5.04736442]\n [ 0.5314646 -0.21767149 0.81863576 -4.50051418]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "51", "_classId": "42", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "2", "item_id": 1043, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/6517.outputParticles_1043_output_images.jpg" } ] } ], "summary": "From input SetOfClasses3D of size 1000 was selected 1 item to create output SetOfParticles of size 4808Input: SetOfClasses3D (1000 items) \nOutput: SetOfParticles (4808 items, 300 x 300, 1.40 \u212b/px)", "log": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/6517_ProtUserSubSet.log", "label": [ "symrelax+consensusx3" ], "labelColor": [ "#f8ae00" ], "plugin": "pwem", "pluginVersion": "3.0.10" }, { "object.className": "ProtUserSubSet", "object.id": "6571", "object.label": "create subset_3down_id508_1733particles", "object.comment": "", "_useQueue": false, "_prerequisites": "", "_queueParams": null, "runName": null, "runMode": 0, "other": null, "sqliteFile": "Runs/006420_XmippProtConsensusClasses3D/classes3D_state.sqlite,", "outputClassName": "SetOfParticles", "inputObject": "6420.outputClasses", "output": [ { "outputName": "6571.outputParticles", "outputType": "SetOfParticles", "outputSize": 1733, "outputItems": [ { "_index": "126", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=25831.73, defV=25543.44, ast=288.29, psh=0.00, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[ 0.62422914 0.10793272 0.77374964 -4.67754657]\n [ 0.54793771 0.64547752 -0.53209308 -11.10193915]\n [ -0.55686825 0.75611461 0.34378547 -6.65535684]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "21", "_classId": "35", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "1", "item_id": 126, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/6571.outputParticles_126_output_images.jpg" }, { "_index": "1012", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=16337.28, defV=16008.29, ast=328.99, psh=0.00, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[-0.53580491 -0.80526503 0.25389238 5.65812374]\n [ 0.30099192 0.09877893 0.94849702 -3.13127719]\n [-0.78887069 0.58462891 0.18945203 8.09414709]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "51", "_classId": "86", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "1", "item_id": 1012, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/6571.outputParticles_1012_output_images.jpg" }, { "_index": "1507", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=17771.63, defV=17395.35, ast=376.28, psh=0.00, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[ 0.95909752 -0.19784038 0.20246266 -6.64627799]\n [ 0.10551142 0.91352978 0.39284944 3.6968699 ]\n [-0.26267715 -0.3554188 0.89703857 -0.11893599]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "58", "_classId": "44", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "1", "item_id": 1507, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/6571.outputParticles_1507_output_images.jpg" }, { "_index": "1875", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=16922.96, defV=16531.57, ast=391.38, psh=0.00, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[-0.54909206 -0.82003325 0.16137963 -9.89201822]\n [-0.0457015 -0.1633433 -0.98551019 -1.6211966 ]\n [ 0.8345114 -0.54851111 0.05221376 -0.02557756]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "52", "_classId": "81", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "2", "item_id": 1875, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/6571.outputParticles_1875_output_images.jpg" }, { "_index": "2279", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=11635.84, defV=11319.93, ast=315.91, psh=0.00, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[-0.46009393 0.6924446 0.5557284 2.31945383]\n [-0.2385148 -0.69929767 0.67386457 1.79240829]\n [ 0.85523346 0.17749155 0.48690089 -5.12799802]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "29", "_classId": "34", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "1", "item_id": 2279, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/6571.outputParticles_2279_output_images.jpg" }, { "_index": "2591", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=18141.01, defV=17626.76, ast=514.26, psh=0.00, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[-0.90183736 0.31611696 0.29454954 -3.81764616]\n [-0.18005187 0.34474833 -0.92126539 -1.26340539]\n [-0.39277308 -0.88386574 -0.25398947 0.15530457]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "38", "_classId": "81", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "1", "item_id": 2591, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/6571.outputParticles_2591_output_images.jpg" }, { "_index": "2989", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=25889.76, defV=25290.68, ast=599.09, psh=0.00, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[ 0.62109845 -0.71488885 0.32120189 5.17906682]\n [-0.35462573 0.10913068 0.92861783 -2.41037434]\n [-0.69891151 -0.69066955 -0.18573708 -3.0946462 ]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "46", "_classId": "21", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "2", "item_id": 2989, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/6571.outputParticles_2989_output_images.jpg" }, { "_index": "3452", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=21136.64, defV=20696.91, ast=439.74, psh=0.00, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[-0.81519431 -0.21609945 -0.53736326 -3.40278954]\n [ 0.53022391 -0.65178967 -0.54224794 0.24477845]\n [-0.23306834 -0.72696028 0.64591632 -2.62542285]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "5", "_classId": "14", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "2", "item_id": 3452, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/6571.outputParticles_3452_output_images.jpg" }, { "_index": "3979", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=3844.30, defV=3513.38, ast=330.92, psh=0.00, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[-0.28483924 -0.95661961 0.06120071 9.53637498]\n [ 0.22170084 -0.12785811 -0.96669594 2.18785394]\n [ 0.9325853 -0.26178469 0.24850237 6.16234213]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "32", "_classId": "81", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "1", "item_id": 3979, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/6571.outputParticles_3979_output_images.jpg" }, { "_index": "4092", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=11267.80, defV=10704.29, ast=563.51, psh=0.00, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[ 0.20010317 -0.97936722 0.02825883 0.22789214]\n [ 0.96216383 0.20186857 0.18300232 1.03482728]\n [-0.18493105 -0.00942972 0.98270626 -0.19926174]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "15", "_classId": "24", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "2", "item_id": 4092, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/6571.outputParticles_4092_output_images.jpg" }, { "_index": "4180", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=11267.80, defV=10704.29, ast=563.51, psh=0.00, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[-0.6668131 0.40887121 0.62304464 2.60009174]\n [-0.21697177 -0.90634644 0.36257329 8.30039099]\n [ 0.71294007 0.10658552 0.69307718 -6.67959267]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "15", "_classId": "59", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "2", "item_id": 4180, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/6571.outputParticles_4180_output_images.jpg" }, { "_index": "4520", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=14711.88, defV=14286.60, ast=425.27, psh=0.00, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[ 0.81433754 -0.53907514 -0.21506364 -0.44623535]\n [-0.5019976 -0.84018043 0.2051713 0.54988435]\n [-0.29129501 -0.05911726 -0.95480488 0.21867241]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "55", "_classId": "73", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "2", "item_id": 4520, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/6571.outputParticles_4520_output_images.jpg" }, { "_index": "5558", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=15529.75, defV=15261.12, ast=268.63, psh=0.00, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[-0.73980581 -0.51848441 -0.42879048 1.84196041]\n [ 0.66339932 -0.45584489 -0.59338586 9.4408055 ]\n [ 0.11219937 -0.72344962 0.68119891 9.38324399]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "9", "_classId": "14", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "1", "item_id": 5558, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/6571.outputParticles_5558_output_images.jpg" }, { "_index": "6410", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=22272.85, defV=21754.35, ast=518.50, psh=0.00, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[ 0.41524789 -0.20099784 -0.88722548 -1.20153318]\n [ 0.552743 -0.71886402 0.42155629 0.02957682]\n [-0.72252637 -0.66545804 -0.18740662 5.75486155]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "62", "_classId": "11", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "1", "item_id": 6410, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/6571.outputParticles_6410_output_images.jpg" }, { "_index": "6604", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=18945.88, defV=18467.29, ast=478.58, psh=0.00, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[ 0.24142041 -0.84294361 0.48079335 2.76995109]\n [-0.2745533 0.41587518 0.86698807 -0.93667949]\n [-0.93077208 -0.34131202 -0.1310322 3.96607963]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "19", "_classId": "21", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "2", "item_id": 6604, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/6571.outputParticles_6604_output_images.jpg" } ] } ], "summary": "From input SetOfClasses3D of size 1000 was selected 1 item to create output SetOfParticles of size 1733Input: SetOfClasses3D (1000 items) \nOutput: SetOfParticles (1733 items, 300 x 300, 1.40 \u212b/px)", "log": 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"Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=14558.66, defV=14171.56, ast=387.10, psh=0.00, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[-0.62358237 0.53201643 -0.57280323 8.24269961]\n [-0.37391765 -0.84644237 -0.3791054 14.6121863 ]\n [-0.68653523 -0.02222221 0.72675687 14.11889458]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "35", "_classId": "70", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "1", "item_id": 1546, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/7107.outputParticles_1546_output_images.jpg" }, { "_index": "1563", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=14558.66, defV=14171.56, ast=387.10, psh=0.00, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[-0.80801275 -0.58589429 -0.06199426 -1.05435492]\n [-0.17019893 0.1313865 0.97661144 1.17532307]\n [-0.56404586 0.79966585 -0.20588054 5.89272743]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "35", "_classId": "91", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "1", "item_id": 1563, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/7107.outputParticles_1563_output_images.jpg" }, { "_index": "1610", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=14558.66, defV=14171.56, ast=387.10, psh=0.00, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[-0.50326091 -0.49042525 0.71148544 0.4972266 ]\n [-0.30509407 -0.66948516 -0.67727928 3.66843407]\n [ 0.8084838 -0.55791818 0.18729988 11.37632829]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "35", "_classId": "96", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "1", "item_id": 1610, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/7107.outputParticles_1610_output_images.jpg" }, { "_index": "1711", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=23496.30, defV=23016.93, ast=479.37, psh=0.00, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[ 0.90611851 0.29647353 0.30174937 2.47643253]\n [-0.42285915 0.65470749 0.62653671 1.03763602]\n [-0.01180602 -0.69531399 0.71860912 -1.94456064]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "24", "_classId": "8", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "2", "item_id": 1711, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/7107.outputParticles_1711_output_images.jpg" }, { "_index": "1875", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=16922.96, defV=16531.57, ast=391.38, psh=0.00, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[-0.54909206 -0.82003325 0.16137963 -9.89201822]\n [-0.0457015 -0.1633433 -0.98551019 -1.6211966 ]\n [ 0.8345114 -0.54851111 0.05221376 -0.02557756]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "52", "_classId": "81", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "2", "item_id": 1875, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/7107.outputParticles_1875_output_images.jpg" }, { "_index": "1896", "_filename": "Runs/000787_XmippProtCropResizeParticles/extra/output_images.stk", "_samplingRate": "1.4", "_ctfModel": "defU=16922.96, defV=16531.57, ast=391.38, psh=0.00, res=None, fit=None", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_transform": "[[-0.35828714 0.60590915 -0.71028475 4.44489524]\n [-0.56520517 -0.74630393 -0.35153033 4.85764338]\n [-0.74308374 0.27550781 0.60985408 7.97690857]\n [ 0. 0. 0. 1. ]]", "_coordinate": "Coordinate", "_micId": "52", "_classId": "8", "_rlnOpticsGroup": "1", "_rlnRandomSubset": "2", "item_id": 1896, "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/7107.outputParticles_1896_output_images.jpg" } ] } ], "summary": "From input SetOfClasses3D of size 1000 we selected 3 items to create output SetOfParticles of size 5740Input: SetOfClasses3D (1000 items) \nOutput: SetOfParticles (5740 items, 300 x 300, 1.40 \u212b/px)", "log": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/7107_ProtUserSubSet.log", "label": [ "symrelax+consensusx3" ], "labelColor": [ "#f8ae00" ], "plugin": "pwem", "pluginVersion": "3.0.10" }, { "object.className": "ProtCryoSparcInitialModel", "object.id": "7161", "object.label": "cryosparc2 - initial model_3down_5740particles", "object.comment": "", "_useQueue": false, "_prerequisites": "", "_queueParams": null, "runName": null, "runMode": 0, "abinit_K": 1, "abinit_max_res": 12.0, "abinit_init_res": 35.0, "abinit_num_init_iters": 200, "abinit_num_final_iters": 300, "abinit_radwn_step": 0.04, "abinit_window": true, "abinit_center": true, "abinit_scale_mg_correct": false, "abinit_scale_compute": false, "abinit_mom": 0.0, "abinit_sparsity": 0.0, "abinit_minisize_init": 90, "abinit_minisize": 300, "abinit_minisize_epsilon": 0.05, "abinit_minisize_minp": 0.01, "abinit_minisize_num_init_iters": 300, "abinit_noise_model": 0, "abinit_noise_priorw": 50, "abinit_noise_initw": 5000, "abinit_class_anneal_beta": 0.1, "abinit_class_anneal_start": 300, "abinit_class_anneal_end": 350, "abinit_target_initial_ess_fraction": 0.011, "symmetryGroup": 0, "symmetryOrder": 1, "abinit_r_grid": 25.0, "abinit_high_lr_duration": 100.0, "abinit_high_lr": 0.4, "abinit_nonneg": true, "abinit_ignore_dc": true, "abinit_init_radwn_cutoff": 7, "abinit_search_start_iter": 200, "abinit_use_engine": true, "intermediate_plots": true, "compute_use_ssd": false, "gpuList": "1", "compute_lane": "default", "inputParticles": "7107.outputParticles", "output": [ { "outputName": "7161.outputClasses", "outputType": "SetOfClasses3D", "outputSize": 1, "outputItems": [ { "_size": "5740", "_streamState": "2", "_mapperPath": "['Runs/007161_ProtCryoSparcInitialModel/classes3D.sqlite', 'Class001']", "_representative": "Volume (300 x 300 x 300, 1.40 \u212b/px)", "_samplingRate": "1.4", "_hasCtf": "True", "_alignment": "Projection", "_isPhaseFlipped": "False", "_isAmplitudeCorrected": "False", "_acquisition": "\n mag=120000.0\n volt= 200.0\n Cs=2.7\n Q0=0.1\n\n", "_firstDim": "300 x 300", "item_id": 1, "item_representation": "['Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/7161.outputClasses_cryosparc_P13_J105_class_00_final_volume_scaled/slicesX_0000.jpg', 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Percentage of total: 0.00.Number of atoms with FSC-Q<-0.5: 0. 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'Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/8629.fscq_Volume_diferencia/slicesZ_0296.jpg', 'Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/8629.fscq_Volume_diferencia/slicesZ_0297.jpg', 'Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/8629.fscq_Volume_diferencia/slicesZ_0298.jpg', 'Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/8629.fscq_Volume_diferencia/slicesZ_0299.jpg']" } ] } ], "summary": "Deviation from the signal of the Half MapsMean FSC-Q: 0.00Absotute Mean FSC-Q: 0.00 Deviation from the signal of the Half Maps divided by local resolutionMean FSC-Qr: 0.00Absotute Mean FSC-Qr: 0.00------------------------------------------Total number of atoms analyzed: 25570Number of atoms with FSC-Q>0.5: 0. Percentage of total: 0.00.Number of atoms with FSC-Q<-0.5: 0. Percentage of total: 0.00.Input: Volume (300 x 300 x 300, 1.40 \u212b/px) - w/halves \nInput: Volume (300 x 300 x 300, 1.40 \u212b/px) \nInput: VolumeMask (300 x 300 x 300, 1.40 \u212b/px) \nOutput: Volume (300 x 300 x 300, 1.40 \u212b/px)", "log": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/8629_XmippProtValFit.log", "plugin": "xmipp3" }, { "object.className": "SphireProtCRYOLOPicking", "object.id": "8687", "object.label": "sphire - cryolo picking (copy)", "object.comment": "", "_useQueue": false, "_prerequisites": "", "_queueParams": null, "runName": null, "runMode": 0, "inputModelFrom": 0, "conservPickVar": 0.3, "lowPassFilter": true, "absCutOffFreq": 0.1, "numCpus": 4, "input_size": 1024, "boxSize": 0, "max_box_per_image": 600, "useGpu": true, "gpuList": "0 1 2 3", "hostName": "localhost", "numberOfThreads": 12, "numberOfMpi": 1, "streamingWarning": null, "streamingSleepOnWait": 0, "streamingBatchSize": 16, "inputMicrographs": "212.outputMicrographs", "output": [ { "outputName": "8687.outputCoordinates", "outputType": "SetOfCoordinates", "outputSize": 46747, "outputItems": [ { "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/8687.outputCoordinates_GRID_01_DATA_Images-Disc1_GridSquare_3271608_Data_FoilHole_3276324_Data_3274746_3274748_20210205_072410_Fractions_aligned_mic_DW.jpg" }, { "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/8687.outputCoordinates_GRID_01_DATA_Images-Disc1_GridSquare_3271608_Data_FoilHole_3276325_Data_3274746_3274748_20210205_072544_Fractions_aligned_mic_DW.jpg" }, { "item_representation": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/8687.outputCoordinates_GRID_01_DATA_Images-Disc1_GridSquare_3271608_Data_FoilHole_3276326_Data_3274746_3274748_20210205_072716_Fractions_aligned_mic_DW.jpg" } ] } ], "summary": "Picking using (GENERAL) model: \n/home/spa/scipion/software/em/cryolo_model-202005_N63_c17/gmodel_phosnet_202005_N63_c17.h5*ERROR:*\u001b[31mProtocol failed: Command ' eval \"$(/home/spa/anaconda3/bin/conda shell.bash hook)\"&& conda activate cryolo-1.7.6 && cryolo_predict.py -c Runs/008687_SphireProtCRYOLOPicking/extra/config.json -w /home/spa/scipion/software/em/cryolo_model-202005_N63_c17/gmodel_phosnet_202005_N63_c17.h5 -i Runs/008687_SphireProtCRYOLOPicking/tmp/micrographs_278-293/ -o Runs/008687_SphireProtCRYOLOPicking/tmp/micrographs_278-293/ -t 0.300 -g 0 -nc 4 --otf' returned non-zero exit status 139.\u001b[0mInput: SetOfMicrographs (4330 items, 4096 x 4096, 0.85 \u212b/px) \nOutput: SetOfCoordinates (46747 items, 209 x 209)", "log": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/8687_SphireProtCRYOLOPicking.log", "plugin": "sphire", "pluginVersion": "3.0.6" }, { "object.className": "EmpiarDepositor", "object.id": "9196", "object.label": "empiar - Empiar deposition_D614G_A222V (copy 2)", "object.comment": "", "_useQueue": false, "_prerequisites": "", "_queueParams": null, "runName": null, "runMode": 0, "deposit": true, "resume": false, "submit": false, "jsonTemplate": "", "entryTopLevel": "averaged_movies", "entryTitle": "SARS-CoV-2 spike protein S:D614G + S:A222V variant", "entryAuthor": "Ginex, T; Marco-Marin, C; Wieczor, M; Mata, CP; Krieger, JM; Lopez-Redondo, ML; Frances-Gomez, C; Ruiz-Rodriguez, P; Melero, R; Sorzano, COS; Martinez, M; Gougeard, N; Forcada-Nadl, A; Zamora-Caballero, S; Gozalbo-Rovira, R; Sanz-Frasquet, C; Bravo, J; Rubio, V; Marina, A; Geller, R; Comas, I; Gil, C; Coscolla, M; Orozco, M; Llacer, JL; Carazo, JM", "experimentType": 2, "releaseDate": 2, "citations": null, "workflowHubURLs": null, "inputSets": [ "2.outputMicrographs" ], "piFirstName": "Jose M", "piLastName": "Carazo", "piOrg": "National Centre for Biotechnology, CSIC", "piEmail": "carazo@cnb.csic.es", "piPost": "28049", "piTown": "Madrid", "piCountry": "ES", "caFirstName": "Jose M", "caLastName": "Carazo", "caOrg": "National Centre for Biotechnology, CSIC", "caEmail": "carazo@cnb.csic.es", "caPost": "28049", "caTown": "Madrid", "caCountry": "ES", "ownershipBasedOn": 0, "newOwnerId": "", "EMDBrefs": null, "output": [], "summary": "No deposition files generated yetInput: SetOfMicrographs (4841 items, 4096 x 4096, 0.85 \u212b/px) \n", "log": "Runs/009196_EmpiarDepositor/extra/averaged_movies/images_representation/9196_EmpiarDepositor.log", "plugin": "empiar", "pluginVersion": "3.0.6" } ]