2D classificationジョブのSTARファイル
提供: Eospedia
2D classificationジョブでは、各イテレーションごとに4種類のSTARファイルが生成されます。run_it<イテレーション番号> をルート名として、_data.star、_model.star、_optimiser.star、_sampling.star と名前が付いています。
目次
_data.star
data_ loop_ _rlnCoordinateX #1 _rlnCoordinateY #2 _rlnAutopickFigureOfMerit #3 _rlnClassNumber #4 _rlnAnglePsi #5 _rlnImageName #6 _rlnMicrographName #7 _rlnMagnification #8 _rlnDetectorPixelSize #9 _rlnCtfMaxResolution #10 _rlnCtfFigureOfMerit #11 _rlnVoltage #12 _rlnDefocusU #13 _rlnDefocusV #14 _rlnDefocusAngle #15 _rlnSphericalAberration #16 _rlnCtfBfactor #17 _rlnCtfScalefactor #18 _rlnPhaseShift #19 _rlnAmplitudeContrast #20 _rlnOriginX #21 _rlnOriginY #22 _rlnGroupNumber #23 _rlnAngleRot #24 _rlnAngleTilt #25 _rlnNormCorrection #26 _rlnLogLikeliContribution #27 _rlnMaxValueProbDistribution #28 _rlnNrOfSignificantSamples #29 3555.794139 406.376473 0.662536 35 125.449124 000001@Extract/job012/Movies/20170629_00021_frameImage.mrcs MotionCorr/job002/Movies/20170629_00021_frameImage.mrc 10000.000000 3.540000 4.632000 0.103875 200.000000 10407.339844 10826.280273 2.460000 1.400000 0.000000 1.000000 0.000000 0.100000 1.302067 -0.69793 1 0.000000 0.000000 2.004590 5253.829275 0.516257 3 3600.947080 485.394120 0.193001 35 -93.92588 000002@Extract/job012/Movies/20170629_00021_frameImage.mrcs MotionCorr/job002/Movies/20170629_00021_frameImage.mrc 10000.000000 3.540000 4.632000 0.103875 200.000000 10407.339844 10826.280273 2.460000 1.400000 0.000000 1.000000 0.000000 0.100000 1.302067 3.302067 1 0.000000 0.000000 1.507015 5225.000115 0.919596 3 (以下略)
新しく現れたパラメータや特記事項があるパラメータについて以下にまとめます。
ラベル名 | 説明 |
---|---|
_rlnCoordinateX, _rlnCoordinateY | 単粒子切り出し元画像内での座標[pixel]。2D classificationではアラインメントを行うが、この値は変化しない。この座標からの単粒子の中心位置ずれは_rlnOriginX, _rlnOriginYで表現される。 |
_rlnClassNumber | 所属確率がもっとも高いクラスの番号。2D classificationの結果割り当てられる。 |
_rlnAnglePsi | 3番目のオイラー角Ψ(面内回転) [度]の値。2D classificationにより推定される。 |
_rlnOriginX, _rlnOriginY | 単粒子画像の回転中心の座標[pixel]。単粒子切り出し時には(0, 0) (+ 何らかの誤差)だが、2D classificationのアラインメントにより(0, 0)以外の値になっている。 |
_rlnGroupNumber | 切り出し元の画像でグループ分けされている。n枚目の画像から切り出されたならばnが割り当てられている。 |
_rlnAngleRot, _rlnAngleTilt | それぞれ1番目(rot)と2番目(tilt)のオイラー角[度]。3Dでの推定をまだ実行していない場合は、0, 0になっている。 |
_rlnNormCorrection | 正規化補正値 |
_rlnLogLikeliContribution | その単粒子の対数尤度関数に対する貢献量 |
_rlnMaxValueProbDistribution | その単粒子の確率質量関数の最大値 |
_rlnNrOfSignificantSamples | Number of orientational/class assignments (for a particle) with sign.probabilities in the 1st pass of adaptive oversampling (所属クラスの割り当てが変更された回数に関係する量?) |
_model.star
データブロックが大きく分けて5種類ある。
data_model_general
data_model_general _rlnReferenceDimensionality 2 _rlnDataDimensionality 2 _rlnOriginalImageSize 64 _rlnCurrentResolution 18.880000 _rlnCurrentImageSize 44 _rlnPaddingFactor 2.000000 _rlnIsHelix 0 _rlnFourierSpaceInterpolator 1 _rlnMinRadiusNnInterpolation 10 _rlnPixelSize 3.540000 _rlnNrClasses 50 _rlnNrBodies 1 _rlnNrGroups 5 _rlnTau2FudgeFactor 2.000000 _rlnNormCorrectionAverage 0.767096 _rlnSigmaOffsets 7.610923e+07 _rlnOrientationalPriorMode 0 _rlnSigmaPriorRotAngle 0.000000 _rlnSigmaPriorTiltAngle 0.000000 _rlnSigmaPriorPsiAngle 0.000000 _rlnLogLikelihood 7.989805e+06 _rlnAveragePmax 0.801794
_rlnLogLikelihoodは適当なスケール感がよくわからないが、_rlnSigmaOffsetsは明らかにおかしな値を取っている?
data_model_classes
data_model_classes loop_ _rlnReferenceImage #1 _rlnClassDistribution #2 _rlnAccuracyRotations #3 _rlnAccuracyTranslations #4 _rlnEstimatedResolution #5 _rlnOverallFourierCompleteness #6 _rlnClassPriorOffsetX #7 _rlnClassPriorOffsetY #8 000001@Class2D/job016/run_it025_classes.mrcs 0.001263 999.000000 999.000000 45.312000 0.837927 -0.00277 0.001014 000002@Class2D/job016/run_it025_classes.mrcs 0.001893 999.000000 999.000000 25.173333 0.903520 -0.00132 -0.00132 000003@Class2D/job016/run_it025_classes.mrcs 0.001262 999.000000 999.000000 inf 0.000000 -1.55170e-04 0.002272 000004@Class2D/job016/run_it025_classes.mrcs 0.176713 4.200000 0.990000 18.880000 1.000000 -0.18862 0.030962 000005@Class2D/job016/run_it025_classes.mrcs 0.006312 999.000000 999.000000 20.596364 0.997405 -0.00172 -0.00187 000006@Class2D/job016/run_it025_classes.mrcs 0.005679 999.000000 999.000000 25.173333 0.999509 0.001226 0.009499 000007@Class2D/job016/run_it025_classes.mrcs 0.008204 999.000000 999.000000 20.596364 0.999941 -0.01909 -0.00824 000008@Class2D/job016/run_it025_classes.mrcs 0.009268 999.000000 999.000000 20.596364 1.000000 0.016227 0.013045 000009@Class2D/job016/run_it025_classes.mrcs 0.001893 999.000000 999.000000 25.173333 0.946921 -5.88182e-05 -0.00597 000010@Class2D/job016/run_it025_classes.mrcs 0.008204 999.000000 999.000000 18.880000 0.999687 -0.00510 0.014447 000011@Class2D/job016/run_it025_classes.mrcs 0.001894 999.000000 999.000000 22.656000 0.964738 -0.00700 -6.90429e-04 000012@Class2D/job016/run_it025_classes.mrcs 6.312204e-04 999.000000 999.000000 37.760000 0.715045 -0.00107 0.001453 000013@Class2D/job016/run_it025_classes.mrcs 0.001894 999.000000 999.000000 25.173333 0.972685 -0.00448 0.010672 000014@Class2D/job016/run_it025_classes.mrcs 0.044337 3.600000 0.920000 18.880000 0.999995 -0.04375 4.117778e-04 000015@Class2D/job016/run_it025_classes.mrcs 0.001262 999.000000 999.000000 25.173333 0.682552 -8.81100e-04 -8.81100e-04 000016@Class2D/job016/run_it025_classes.mrcs 0.066754 4.600000 1.120000 20.596364 1.000000 -0.08779 -0.04739 000017@Class2D/job016/run_it025_classes.mrcs 0.001262 999.000000 999.000000 32.365714 0.873057 -0.00467 -0.00277 000018@Class2D/job016/run_it025_classes.mrcs 0.008718 999.000000 999.000000 20.596364 1.000000 -0.00344 -0.00599 000019@Class2D/job016/run_it025_classes.mrcs 0.005049 999.000000 999.000000 22.656000 0.979285 0.004031 -0.00936 000020@Class2D/job016/run_it025_classes.mrcs 0.003787 999.000000 999.000000 25.173333 0.954192 5.072791e-04 -1.35846e-04 000021@Class2D/job016/run_it025_classes.mrcs 0.001894 999.000000 999.000000 inf 0.000000 -0.00574 0.001203 000022@Class2D/job016/run_it025_classes.mrcs 0.002525 999.000000 999.000000 22.656000 0.841171 -0.00113 1.315801e-04 000023@Class2D/job016/run_it025_classes.mrcs 0.002525 999.000000 999.000000 20.596364 0.950705 -0.00555 -0.00366 000024@Class2D/job016/run_it025_classes.mrcs 0.008205 999.000000 999.000000 20.596364 1.000000 -0.00698 0.006907 000025@Class2D/job016/run_it025_classes.mrcs 0.005886 999.000000 999.000000 22.656000 0.987004 -0.00176 0.014236 000026@Class2D/job016/run_it025_classes.mrcs 0.001894 999.000000 999.000000 28.320000 0.812544 -6.90438e-04 0.002468 000027@Class2D/job016/run_it025_classes.mrcs 0.002563 999.000000 999.000000 inf 0.000000 -0.26518 -5.42214e+06 000028@Class2D/job016/run_it025_classes.mrcs 0.003787 999.000000 999.000000 22.656000 0.992796 -0.00580 -0.00761 000029@Class2D/job016/run_it025_classes.mrcs 0.008204 999.000000 999.000000 22.656000 0.996776 -0.00380 0.006930 000030@Class2D/job016/run_it025_classes.mrcs 0.004418 999.000000 999.000000 18.880000 0.992158 -0.00750 -0.01445 000031@Class2D/job016/run_it025_classes.mrcs 0.141641 3.600000 0.910000 18.880000 1.000000 -0.15440 -0.02175 000032@Class2D/job016/run_it025_classes.mrcs 0.001262 999.000000 999.000000 32.365714 0.824708 -0.00404 -0.00341 000033@Class2D/job016/run_it025_classes.mrcs 0.005677 999.000000 999.000000 22.656000 0.999650 -0.00521 0.007474 000034@Class2D/job016/run_it025_classes.mrcs 0.003787 999.000000 999.000000 22.656000 0.990255 -0.00345 0.003036 000035@Class2D/job016/run_it025_classes.mrcs 0.017606 3.300000 0.780000 20.596364 0.999941 0.013362 0.019218 000036@Class2D/job016/run_it025_classes.mrcs 0.001894 999.000000 999.000000 25.173333 0.946325 -0.00511 0.004359 000037@Class2D/job016/run_it025_classes.mrcs 0.068714 3.700000 0.800000 18.880000 1.000000 -0.05880 -0.03796 000038@Class2D/job016/run_it025_classes.mrcs 0.010116 3.200000 0.940000 22.656000 1.000000 -0.03026 -0.00118 000039@Class2D/job016/run_it025_classes.mrcs 6.312204e-04 999.000000 999.000000 20.596364 0.793902 -0.01054 -0.00107 000040@Class2D/job016/run_it025_classes.mrcs 0.002525 999.000000 999.000000 20.596364 0.978380 0.002025 0.002656 000041@Class2D/job016/run_it025_classes.mrcs 0.063898 3.600000 0.780000 18.880000 1.000000 -0.04911 -0.04688 000042@Class2D/job016/run_it025_classes.mrcs 0.004418 999.000000 999.000000 22.656000 0.999921 -0.00372 -0.01886 000043@Class2D/job016/run_it025_classes.mrcs 0.007906 999.000000 999.000000 22.656000 0.996626 0.001697 0.001370 000044@Class2D/job016/run_it025_classes.mrcs 0.010727 3.100000 0.850000 20.596364 1.000000 -0.01353 0.003779 000045@Class2D/job016/run_it025_classes.mrcs 0.015034 3.100000 0.900000 20.596364 1.000000 -0.03451 -0.03108 000046@Class2D/job016/run_it025_classes.mrcs 0.002525 999.000000 999.000000 28.320000 0.951131 -0.00366 -0.00870 000047@Class2D/job016/run_it025_classes.mrcs 0.003787 999.000000 999.000000 inf 0.000000 0.023268 -0.00391 000048@Class2D/job016/run_it025_classes.mrcs 0.127775 4.600000 0.920000 18.880000 1.000000 -0.11470 -0.02822 000049@Class2D/job016/run_it025_classes.mrcs 0.110004 4.100000 0.840000 18.880000 1.000000 -0.12282 -0.02916 000050@Class2D/job016/run_it025_classes.mrcs 0.001893 999.000000 999.000000 32.365714 0.923481 0.003096 0.007515
data_model_class_n
data_model_class_1 loop_ _rlnSpectralIndex #1 _rlnResolution #2 _rlnAngstromResolution #3 _rlnSsnrMap #4 _rlnGoldStandardFsc #5 _rlnFourierCompleteness #6 _rlnReferenceSigma2 #7 _rlnReferenceTau2 #8 _rlnSpectralOrientabilityContribution #9 0 0.000000 999.000000 3.665691 0.000000 1.000000 0.007461 0.013675 0.000000 1 0.004414 226.560000 3.026267 0.000000 0.785714 0.020578 0.031138 0.000000 2 0.008828 113.280000 6.453868 0.000000 0.833333 0.005567 0.017965 0.000000 3 0.013242 75.520000 5.166827 0.000000 0.850000 0.002592 0.006697 0.000000 4 0.017655 56.640000 4.207441 0.000000 0.851852 8.892138e-04 0.001871 0.000000 5 0.022069 45.312000 1.970419 0.000000 0.640625 4.820656e-04 4.749356e-04 0.000000 6 0.026483 37.760000 0.821692 0.000000 0.324324 3.159420e-04 1.298035e-04 0.000000 7 0.030897 32.365714 0.832150 0.000000 0.282609 1.859071e-04 7.735125e-05 0.000000 8 0.035311 28.320000 0.666574 0.000000 0.224490 1.295436e-04 4.317520e-05 0.000000 9 0.039725 25.173333 0.784156 0.000000 0.275000 9.953982e-05 3.902737e-05 0.000000 10 0.044138 22.656000 0.584009 0.000000 0.169355 8.523505e-05 2.488904e-05 0.000000 11 0.048552 20.596364 0.291531 0.000000 0.007042 8.202475e-05 1.195639e-05 0.000000 12 0.052966 18.880000 0.049583 0.000000 0.000000 1.162804e-04 2.882795e-06 0.000000 13 0.057380 17.427692 0.009578 0.000000 0.000000 3.011485e-04 1.442150e-06 0.000000 14 0.061794 16.182857 0.001354 0.000000 0.000000 0.001081 7.319991e-07 0.000000 15 0.066208 15.104000 0.006224 0.000000 0.000000 1.345070e-04 4.185799e-07 0.000000 16 0.070621 14.160000 0.007359 0.000000 0.000000 6.040973e-05 2.222673e-07 0.000000 17 0.075035 13.327059 0.004576 0.000000 0.000000 5.058901e-05 1.157448e-07 0.000000 18 0.079449 12.586667 0.002190 0.000000 0.000000 6.317357e-05 6.916016e-08 0.000000 19 0.083863 11.924211 4.442074e-04 0.000000 0.000000 1.901498e-04 4.223298e-08 0.000000 20 0.088277 11.328000 1.641651e-04 0.000000 0.000000 3.900355e-04 3.201511e-08 0.000000 21 0.092691 10.788571 8.273337e-04 0.000000 0.000000 6.366484e-05 2.633604e-08 0.000000 22 0.097105 10.298182 8.021799e-04 0.000000 0.000000 6.291855e-05 2.523600e-08 0.000000 23 0.101518 9.850435 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 24 0.105932 9.440000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 25 0.110346 9.062400 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 26 0.114760 8.713846 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 27 0.119174 8.391111 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 28 0.123588 8.091429 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 29 0.128001 7.812414 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 30 0.132415 7.552000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 31 0.136829 7.308387 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 32 0.141243 7.080000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
data_model_groups
data_model_groups loop_ _rlnGroupNumber #1 _rlnGroupName #2 _rlnGroupNrParticles #3 _rlnGroupScaleCorrection #4 1 Movies/20170629_00021_frameImage.mrc 348 0.989576 2 Movies/20170629_00022_frameImage.mrc 322 1.006113 3 Movies/20170629_00023_frameImage.mrc 315 0.996019 4 Movies/20170629_00024_frameImage.mrc 279 0.999816 5 Movies/20170629_00025_frameImage.mrc 321 1.009236
data_model_group_n
data_model_group_1 loop_ _rlnSpectralIndex #1 _rlnResolution #2 _rlnSigma2Noise #3 0 0.000000 6.699176e-04 1 0.004414 5.044234e-04 2 0.008828 3.852414e-04 3 0.013242 2.962146e-04 4 0.017655 2.536162e-04 5 0.022069 2.571982e-04 6 0.026483 2.749977e-04 7 0.030897 2.489669e-04 8 0.035311 2.283906e-04 9 0.039725 2.044940e-04 10 0.044138 1.694933e-04 11 0.048552 1.281033e-04 12 0.052966 9.658166e-05 13 0.057380 7.243675e-05 14 0.061794 6.748875e-05 15 0.066208 7.883464e-05 16 0.070621 9.554841e-05 17 0.075035 9.866697e-05 18 0.079449 7.982541e-05 19 0.083863 6.505653e-05 20 0.088277 6.598636e-05 21 0.092691 7.684159e-05 22 0.097105 7.732326e-05 23 0.101518 6.778179e-05 24 0.105932 6.208213e-05 25 0.110346 6.746794e-05 26 0.114760 6.921340e-05 27 0.119174 6.147887e-05 28 0.123588 6.069812e-05 29 0.128001 6.416122e-05 30 0.132415 6.190670e-05 31 0.136829 5.747373e-05 32 0.141243 5.758882e-05
_optimiser.star
最適化計算のパラメータが記述されたファイルになります。
# RELION optimiser; version 3.0.5 # --o Class2D/job016/run --i Extract/job012/particles.star --dont_combine_weights_via_disc --preread_images --pool 30 --pad 2 --ctf --iter 25 --tau2_fudge 2 --particle_diameter 200 --K 50 --flatten_solvent --zero_mask --oversampling 1 --psi_step 12 --offset_range 5 --offset_step 2 --norm --scale --j 3 --gpu 0:1:2:3 data_optimiser_general _rlnOutputRootName Class2D/job016/run _rlnModelStarFile Class2D/job016/run_it025_model.star _rlnExperimentalDataStarFile Class2D/job016/run_it025_data.star _rlnOrientSamplingStarFile Class2D/job016/run_it025_sampling.star _rlnCurrentIteration 25 _rlnNumberOfIterations 25 _rlnDoSplitRandomHalves 0 _rlnJoinHalvesUntilThisResolution -1.00000 _rlnAdaptiveOversampleOrder 1 _rlnAdaptiveOversampleFraction 0.999000 _rlnRandomSeed 1558432768 _rlnParticleDiameter 200.000000 _rlnWidthMaskEdge 5 _rlnDoZeroMask 1 _rlnDoSolventFlattening 1 _rlnDoSolventFscCorrection 0 _rlnSolventMaskName None _rlnSolventMask2Name None _rlnBodyStarFile None _rlnTauSpectrumName None _rlnCoarseImageSize 36 _rlnMaximumCoarseImageSize 64 _rlnHighresLimitExpectation -1.00000 _rlnIncrementImageSize 10 _rlnDoMapEstimation 1 _rlnDoFastSubsetOptimisation 0 _rlnDoStochasticGradientDescent 0 _rlnSgdInitialIterations 50 _rlnSgdFinalIterations 50 _rlnSgdInBetweenIterations 200 _rlnSgdInitialResolution 35.000000 _rlnSgdFinalResolution 15.000000 _rlnSgdInitialSubsetSize 100 _rlnSgdFinalSubsetSize 500 _rlnSgdMuFactor 0.000000 _rlnSgdSigma2FudgeInitial 8.000000 _rlnSgdSigma2FudgeHalflife -1 _rlnSgdSkipAnneal 0 _rlnSgdSubsetSize -1 _rlnSgdWriteEverySubset 1 _rlnSgdStepsize 0.500000 _rlnDoAutoRefine 0 _rlnAutoLocalSearchesHealpixOrder 4 _rlnNumberOfIterWithoutResolutionGain 14 _rlnBestResolutionThusFar 0.052966 _rlnNumberOfIterWithoutChangingAssignments 0 _rlnDoSkipAlign 0 _rlnDoSkipRotate 0 _rlnOverallAccuracyRotations 3.100000 _rlnOverallAccuracyTranslations 0.780000 _rlnChangesOptimalOrientations 3.564572 _rlnChangesOptimalOffsets 0.490543 _rlnChangesOptimalClasses 0.017666 _rlnSmallestChangesOrientations 3.564572 _rlnSmallestChangesOffsets 0.411772 _rlnSmallestChangesClasses 0 _rlnLocalSymmetryFile None _rlnDoHelicalRefine 0 _rlnIgnoreHelicalSymmetry 0 _rlnHelicalTwistInitial 0.000000 _rlnHelicalRiseInitial 0.000000 _rlnHelicalCentralProportion 0.300000 _rlnHelicalMaskTubeInnerDiameter -1.00000 _rlnHelicalMaskTubeOuterDiameter -1.00000 _rlnHelicalSymmetryLocalRefinement 0 _rlnHelicalSigmaDistance -1.00000 _rlnHelicalKeepTiltPriorFixed 0 _rlnHasConverged 0 _rlnHasHighFscAtResolLimit 0 _rlnHasLargeSizeIncreaseIterationsAgo 0 _rlnDoCorrectNorm 1 _rlnDoCorrectScale 1 _rlnDoCorrectCtf 1 _rlnDoRealignMovies 0 _rlnDoIgnoreCtfUntilFirstPeak 0 _rlnCtfDataArePhaseFlipped 0 _rlnCtfDataAreCtfPremultiplied 0 _rlnDoOnlyFlipCtfPhases 0 _rlnRefsAreCtfCorrected 1 _rlnFixSigmaNoiseEstimates 0 _rlnFixSigmaOffsetEstimates 0 _rlnMaxNumberOfPooledParticles 90
_sampling.star
データのサンプリング方法、範囲や刻み量に関わる設定値が記述されています。
data_sampling_general _rlnIs3DSampling 0 _rlnIs3DTranslationalSampling 0 _rlnPsiStep 11.250000 _rlnOffsetRange 5.000000 _rlnOffsetStep 2.000000 _rlnHelicalOffsetStep -1.00000 _rlnSamplingPerturbInstance -0.09897 _rlnSamplingPerturbFactor 0.500000