autoPROC Documentation : Advanced features

Contents

• Setting parameters
  • On the command-line
  • In a macro file

• Sorted list of parameters

Setting parameters

Remember that command-line arguments (including reading of macro files) are processed in the order given - so a later argument can potentially overwrite an earlier setting.

On the command-line

process <parameter>="<value-1> [...<value-N>]"

If only a single value is given the quotes can be omitted.

In a macro file(s)

The syntax of this file is similar to the command-line setting:

• any line starting with hash (#) is a comment (and ignored)

• each line has the format:

  variable="value"

  or

  variable="value-1 value-2 ... value-N"

Sorted list of parameters

• Procedural:
  • automatic masking of regions using DEFPIX:

    XdsOptimizeDefpix XdsOptimizeDefpixCut XdsOptimizeDefpixEnd XdsOptimizeDefpixStart XdsOptimizeDefpixStep

  • visualisation of predictions:

    autoPROC_CreateGpxPictures autoPROC_CreateGpxPicturesAtStages autoPROC_CreateGpxScript autoPROC_CreateMosflmScript

  • misc:

    RunWithSubSubDir StopIfSubdirExists UseMrfadd UseMrfedit XdsOptimizeIdxref XdsScaleKeepXdsAsciiMtz XdsUpdateCorrectionTables XdsUpdateMosaicityScale XdsUpdateParKeepFixed autoPROC_ImginfoReportWarnings autoPROC_LinkImagesIntoSubdir autoPROC_MacroDirs autoPROC_ReRunIdxrefAtEnd autoPROC_ScaleEachDatasetSeparately autoPROC_SupportedFreeRflagColumnNames autoPROC_TestSetFraction

• Setup related:
  • automatic finding of image sets:

    FindImagesRecursive FindImages_AllowCompressedImages FindImages_CombineSubsequentRanges FindImages_CombineSubsequentRangesMaxGap FindImages_DisallowedExtns FindImages_ExcludeLastImage FindImages_ImageExtns FindImages_MaxImageNumWidth FindImages_MinNumImages FindImages_NonIdCharacters FindImages_SortByCollectionDate FindImages_TestFollowLinks FindImages_TruncateLeft FindImages_max_size FindImages_min_size

  • misc:

    IgnoreImageZero autoPROC_IgnoreTwoThetaBelow autoPROC_XdsMinimumImagesForDelphi pname xname

• Beamline/Instrument specific:
  • image header related:

    BeamCentreFrom autoPROC_SupportTwoTheta autoPROC_TwoThetaAxis autoPROC_TwoThetaAxisRotationAxisFactor autoPROC_XdsDistanceFac

  • Pilatus detectors:

    autoPROC_Img2Xds_Pilatus2MGaps autoPROC_Img2Xds_Pilatus2MIncludeUntrustedRectangle autoPROC_Img2Xds_Pilatus6MGaps autoPROC_Img2Xds_Pilatus6MIncludeUntrustedRectangle

• Handling multi-axis goniostat:

  KapparotAngles_Eulerian KapparotAngles_Kappa KapparotSitesFile XdsGetRotationAxisViaKapparot XdsGetRotationAxisViaKapparotStopOnError

• Related to spot-searching:
  • background determination

    DistributeBackgroundImages XdsBackgroundRangeCoverAngle XdsBackgroundRangeNumSegments XdsBackgroundRangeNumSubsequentImages XdsNumImagesBackgroundRange XdsStartImageBackgroundRange

  • spot-search:

    XdsIndexingStopIfSpotsLessPercent XdsSpotSearchAngularRange XdsSpotSearchMinNumSpotsPerImage XdsSpotSearchMinNumSpotsPerImageUseSlidingWindow XdsSpotSearchNumAllowedEmptyImages XdsSpotSearchNumImages XdsSpotSearchNumRanges XdsSpotSearchWindowImageNum

• Influencing indexing:
  • iterative indexing:

    RunIdxrefCollectAllFailedSpots RunIdxrefExcludeHighRes RunIdxrefExcludeIceRingShells RunIdxrefMaxNumLattices RunIdxrefNumSpotMin RunIdxrefOutputPrefix RunIdxrefStartWithTop RunIdxref_SpotVersusImage_MinFrac

  • known cell/SG:

    cell symm

  • picking solution:

    XdsOptimizeIdxrefPickSolution

• Spacegroup determination:

  PointlessIsiglimitResultingCutWarning PointlessKeywordSetting SpacegroupEnantiomorphGroups SpacegroupIndistinguishableGroups SpacegroupScrewAxesGroups UpdateparsFromPointless

• Integration:

  autoPROC_XdsAcceptOverloads autoPROC_XdsAnalyseOverloads autoPROC_XdsDelphiDefault autoPROC_XdsIntegrateScaleOutlierSigma autoPROC_XdsIntegPostrefNumCycle autoPROC_XdsMaxDistanceJitter

• Handling ice-rings:

  XdsExcludeIceRingsAutomatically XdsExcludeIceRingsAutomaticallyIfKnownValue Xds_Spot2Res_IceRingMinScore Xds_Spot2Res_IceRingWidth Xds_Spot2Res_IceRingWidthMult Xds_Spot2Res_IceRingWidthMultForXds Xds_Spot2Res_IceRings Xds_Spot2Res_Prec

• Scaling:
  • automatic chunking:

    AutomaticChunking AutomaticChunking_DegreeMin AutomaticChunking_MaxRuns AutomaticChunking_NumBatchesMin XdsScaleChunking XdsScaleChunkingMaxRuns XdsScaleChunkingNumBatchesMin

  • AIMLESS:

    AutoProcScaleMaxAllowedGapSize autoPROC_ScaleWithAimless autoPROC_ScaleWithAimlessRefineSdcorr autoPROC_ScaleWithAimlessRefineSdcorrSame

  • XSCALE:

    autoPROC_ScaleWithXscale autoPROC_ScaleWithXscaleReportMrfanaStats autoPROC_ScaleWithXscaleReportXscaleStats

  • low- and high-resolution handling:

    AutoProcScaleRestrictLowRes AutoProcScaleRestrictLowResFromCycle AutoProcScaleRestrictLowResMinIsig_12345 AutoProcScaleRestrictLowResMinRes AutoProcScaleSetInitialHighRes AutoProcScaleSetInitialHighResIsigI

  • computation of statistics (MRFANA):

    AutoProcScaleStatsUseMrfana AutoProcScaleStatsUseMrfanaFinalNumBin AutoProcScaleStatsUseMrfanaIgnoreIceRingReso AutoProcScaleStatsUseMrfanaIgnoreIceRingShells AutoProcScaleStatsUseMrfanaNrefPerBinRun AutoProcScaleStatsUseMrfanaNumShellMax AutoProcScaleStatsUseMrfanaNumShellMin AutoProcScaleStatsUseMrfanaSetNshellOutside

  • TRUNCATE:

    TruncateTruncate

  • iterative scaling:

    AutoProcScaleMaximumCycles AutoProcScaleMinimumCycles autoPROC_ExcludeBadBatchesFromCycle AutoProcScaleResolutionCompareDigits

  • misc:

    AutoProcScaleAgainstReference AutoProcScaleAgainstReferencePutRunFirst AutoProcScaleCombineCrystalDatasetInCrystal AutoProcScaleDefaultDnameIsWavelength AutoProcScaleNumBins AutoProcScaleSameCrystal AutoProcScaleTestIndexing AutoProcScaleSameIndexing StopAfterScalingError StopOnFindingExistingFiles autoPROC_PointlessTolerance

• Influencing resolution limit decision:
  • early limit on resolution:

    UpdateResolutionLimit UpdateResolutionLimitCutoffIsigI XdsSetHighResFromFirstIntegrate XdsSetHighResFromFirstIntegrate_IsigIcut XdsSetHighResFromIndexedSpots XdsSetHighResFromIndexedSpotsSafetyMargin XdsSetLowResFromIndexedSpots XdsSetLowResFromIndexedSpotsSafetyMargin

  • final limit on resolution:

    ScaleAnaCChalfCut_123 ScaleAnaCompletenessCut_123 ScaleAnaISigmaCut_123 ScaleAnaRmeasallCut_123 ScaleAnaRmergeCut_123 ScaleAnaRpimallCut_123

• Related to multiple datasets:

  BatchNumberIncrement BeamCentreFromRunOnlyOnce CombineFilesBatchStep EnsureConsistentIndexing ScaleAllDatasetsTogether UpdateDetectorOriginBetweenScans UpdateIncidentBeamBetweenScans UseKapparotForConsistentIndexing UseKapparotForConsistentIndexingStopOnError WavelengthSignificantDigits

• Concerning heavy atom (experimental phasing):

  ExpectLargeHeavyAtomSignal TruncateAnom XdsSetStrictAbsorptionChiSquareCut

• Small molecule data:

  RunTruncate

• Speeding up calculations:

  The default set of parameters are chosen relatively conservatively with the intention of achieving robust data processing. However, if datasets from well characterized, stable and well diffracting crystals are processed, some of the parameters could be changed.

  To speed up the indexing for the XDS-path, one could use spots from only a subset of images (default is to use spots from all images). This is controlled by the parameter XdsSpotSearchNumImages. The number of images given for that parameter is used to generate several ranges of images for spot searching.

  If the detector contains only a circular active area on the rectangular 2D image, setting a high-resolution limit (e.g. via the -R command-line flag) will make sure that only this area is being used. This is also helpful if the distance was set so that the highest resolution reflections are within the circular region of the detector (i.e. avoiding the corners of a square detector).