autoPROC Documentation previous
Appendix 1

autoPROC Documentation : Appendix 1

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Alphabetical list of parameters

Most parameters are given in the table below. However, for some tools/steps there could be additional parameters available: if you want to change a specific behaviour please contact us.

Parameter
[module/step affected]
default explanation
AnaIdxrefSolutionScoreCutNum
[XDS]
"2" When printing the table of possible indexing solutions: how many solutions above the cut-ff level should be shown?
AnaIdxrefSolutionScoreCutOff
[XDS]
"100" When printing the table of possible indexing solutions: what is the cut-off level for the score value?
AutomaticChunking
[Scaling/Merging aP_scale]
"no" Should we split the set of images automatically into smaler chunks to apply different resolution cut-offs to each of them?
AutomaticChunking_DegreeMin
[Scaling/Merging aP_scale]
"10.0" When determining appropriate chunking parameters (number of images), try to give a result with at least this degree of rotation.
AutoProcScaleMaxAllowedGapSize
[aP_scale]
"0" If the user has not defined a specific layout of images/batches (via -b switch) and it needs to be determined automaticaly: what is the maximum alllowed size for a gap in batch number?
AutoProcScaleStatsUseMrfanaSetNshellOutside
[aP_scale]
"no" Should we override the automatic binning determined within MRFANA?
AutomaticChunking_MaxRuns
[Scaling/Merging aP_scale]
"40" When doing AutomaticChunking: into how many different runs (maximum) can we split the dataset (this number is mainly determined by some settings in SCALA).
AutomaticChunking_NumBatchesMin
[Scaling/Merging aP_scale]
"10" When doing AutomaticChunking: how many batches/images should one run at least contain?
AutoProcScaleAgainstReference
[aP_scale]
Scaling/Merging
"no" should we scale against a reference dataset (e.g. scaling derivatives against a native) in SCALA/AIMLESS? Requires setting of ref_mtz.
AutoProcScaleAgainstReferencePutRunFirst
[aP_scale]
Scaling/Merging
"yes" if scaling against a reference dataset: should that reference RUN be placed first in list of runs?
AutoProcScaleCombineCrystalDatasetInCrystal
[aP_scale]
"yes" when combining several dataset before scaling: should we create a combined crystal/dataset identifier at th crystal level (within the Project/Crystal/Dataset hierarchy used in MTZ files)? This will ensure that the Crystal part is unique (important for keeping cell parameters correctly associated, since those are a feature of the crystal).
AutoProcScaleDefaultDnameIsWavelength
[Scaling/Merging aP_scale]
"yes" should the default dataset identifier (DNAME) be based on wavelength? Since merging in SCALA/AIMLESS is based on the dataset identifier, this will ensure that all sweeps with identical wavelength are merged together.
AutoProcScaleMaximumCycles
[aP_scale]
Scaling/Merging
"10" maximum number of scaling cycles (with adjustment of error model, resolution cut-offs and image exclusion in between).
AutoProcScaleMinimumCycles
[aP_scale]
Scaling/Merging
"4" minimum number of scaling cycles (with adjustment of error model, resolution cut-offs and image exclusion in between).
AutoProcScaleNumBins
[aP_scale]
Scaling/Merging
"10" Number of bins to use in SCALA/AIMLESS.
AutoProcScaleResolutionCompareDigits
[aP_scale]
Scaling/Merging
"3" Up to how many significant digits should we compare high-resolution cutoffs during iterative scaling? A change in those values signals another cycle of scaling to be done.
AutoProcScaleRestrictLowRes
[aP_scale]
Scaling/Merging
"no" Should we try and restrict the low resolution limit automatically during scaling?
AutoProcScaleRestrictLowResFromCycle
[aP_scale]
"3" If an automatic low-resolution cut-off is determined (see AutoProcScaleRestrictLowRes), from which big cycle onwards should the be done?
AutoProcScaleRestrictLowResMinIsig_12345
[aP_scale]
"0.0 0.0 1.0 2.0" value used in successive cycles of scaling to determine low-resolution limit based on I/sig(I) values
AutoProcScaleRestrictLowResMinRes
[aP_scale]
"20.0" Limit below which an automatic low-resolution cut-off will not be applied.
AutoProcScaleSameCrystal
[Scaling/Merging aP_scale]
"yes" During scaling: can we assume that different dataset come from the same crystal? This setting has an effect on the way the absorption correction is parametrised.
AutoProcScaleTestIndexing
[Scaling/Merging aP_scale]
"yes" should we test for consistent indexing when using a reference dataset or an MTZ file with a FreeR_flag column?
AutoProcScaleSameIndexing
[Scaling/Merging aP_scale]
"yes|no" Can we assume that different datasets are consistently indexed? Default depends on setting of EnsureConsistentIndexing.
AutoProcScaleStatsUseMrfana
[aP_scale]
"yes" Use the stand-alone MRFANA program to calculate various statistics (versus resolution for single runs and complete datasets) and to apply high-resolution cut-off criteria?
AutoProcScaleStatsUseMrfanaFinalNumBin
[aP_scale]
"20" A final table of merging statistics will be created with a (usually) reduced number of bins: this will make it easier to include it into a publication or a database (while the finer binning required for accurate determination of an adequate high-resolution limit would result in a very narrow outer shell).
AutoProcScaleStatsUseMrfanaIgnoreIceRingReso
[aP_scale]
"" Colon-separated list of resolution ranges that should not be taken into account when applying high-resolution cutoff criteria. This list usually comes automatically from the ice-ring detection step in autoPROC (if it was employed).
AutoProcScaleStatsUseMrfanaIgnoreIceRingShells
[aP_scale]
"no" Flag to decide if resolution ranges of possible ice-rings should be excluded in high-resolution cut-off criteria analysis.
AutoProcScaleStatsUseMrfanaNrefPerBinRun
[aP_scale]
"200" How many reflection should each resolution shell have when calculating various statistics in MRFANA?
AutoProcScaleStatsUseMrfanaNumShellMax
[aP_scale]
"100" Maximum number of shells/bins to use within MRFANA when determining an adequate high-resolution limit.
AutoProcScaleStatsUseMrfanaNumShellMin
[aP_scale]
"5" Minimum number of shells/bins to use within MRFANA when determining an adequate high-resolution limit.
AutoProcScaleSetInitialHighRes
[aP_scale]
"no" Should we set an initial high-res limit in the scaling/merging module - to avoid getting locked into a poor local minimum when nearly all data is actually pure noise?
AutoProcScaleSetInitialHighResIsigI
[aP_scale]
"-0.2" Together with AutoProcScaleSetInitialHighRes flag: value to use as an initial high-resolution limit on I/sigI
BatchNumberIncrement
"1000" When processing several sets of diffraction images: increment the batch number for the final MTZ file(s) by this amount
BeamCentreFrom
[Setup]
"" How to get the initial beam centre. Default is to take the header value as-is. Other possibilities are:
  • using header value, but with change of reference:
    • header:x,y
    • header:x,-y
    • header:-x,y
    • header:-x,-y
    • header:y,x
    • header:y,-x
    • header:-y,x
    • header:-y,-x
  • analysing images using GETBEAM
    • getbeam:init
    • getbeam:refined
BeamCentreFromRunOnlyOnce
[General]
"no" Should the automatic determination of the direct beam position (via BeamCentreFrom) be run only once?
CheckIndexing_CheckAxisPermutationOrthorhombic
[check_indexing]
"yes" When comparing different MTZ files, should we take possible axis permutations in orthorhombic spacegroups into account?
CheckIndexing_CheckAxisPermutationOrthorhombicMethod
[check_indexing]
"hkl" How to do additional checks for orthorhombic spacegroups: if set to "cell" will try and analyse cell axes for matching lengths. If set to "hkl" will run axis-permutation tests.
CheckIndexing_RstatsBinningMaxNum
[check_indexing]
"10" During the detailed analysis when comparing MTZ files: how many shells should we look at as a maximum?
CheckIndexing_RstatsBinningMinWidth
[check_indexing]
"0.01" During the detailed analysis when comparing MTZ files: what is the minimum shell width?
CheckIndexing_RstatsBinningNumBin
[check_indexing]
"10" Guiding number of bins to use in calculating R-factor and CC values (as printed with the -v argument).
CombineFilesBatchStep
[File manipulation]
"1000" When combining reflection files (with integrated data): offset in batch numbering between successive files.
CombineFilesPickSpacegroup
[File manipulation]
"longest" When combining reflection files (with integrated data) that might have different spacegroups: how should we decide on common spacegroup? We will always use the spacegroup with the largest number of symmetry operators, but the screw axes might need some deciding. "longest" will take the spacegroup name that is the longest string; "extinctions" will take the spacegroup with the most extinctions and "resolution" takes the spacegroup from the dataset with the highest resolution limit.
CombineFilesRebatch
[File manipulation]
"yes" When combining reflection files (with integrated data): check for the correct multiple of CombineFilesBatchStep
CombineFilesRunReindexOnAll
[File manipulation]
"yes" During combination of reflection files (with integrated data) using "combine_files": when running REINDEX on at least one MTZ files (to set correct SG), we also need to run it on all to ensure the SG operators are given in the same (CCP4/REINDEX) order. Otherwise SORTMTZ will stop with an error (because ISYM values would be wrong for some of the data after combination).
DistributeBackgroundImages
[x_index]
"no" Should we take a series of images (distributed equally within the set of available images) for background determination?
EnforceUserSuppliedSpacegroup
[XDS path]
"yes" Even if the analysis of integrated intensities suggests a different spacegroup, should a user-supplied spacegroup be enforced?
EnsureConsistentIndexing
"yes" When processing several sets of diffraction images: should the orientation matrices after indexing be similar to the reference matrix (which defaults to the first set)?
ExpectLargeHeavyAtomSignal
[process/aP_scale]
"no" Do we expect a very large heavy atom signal in the data? This will trigger special handling at the stage of absorption correction as well as outlier rejection.
ExpectLargeHeavyAtomSignalScaleAndMerge
[aP_scale]
"no" Do we expect a very large heavy atom signal in the data? This will trigger special handling at the stage of outlier rejection.
FindImagesRecursive
[Setup]
"no" when looking for image files: shuold we search recursively or not (i.e. analysing only current directory)?
FindImages_AllowCompressedImages
[find_images]
"no" Do we allow processing of compressed images too? Can be set to "yes", "gz", "bz2" or "gz,bz".
FindImages_CombineSubsequentRanges
[Setup]
"yes" when encountering different ranges of images (e.g. one image missing in the middle): should these be combined into a single sweep?
FindImages_CombineSubsequentRangesMaxGap
[find_images]
"9" What is the maximum allowed gap for FindImages_CombineSubsequentRangesMaxGap?
FindImages_DisallowedExtns
[Setup]
"Z,gz,bz2,jpg,pgm" file name extensions that are not supported (and will be ignored) when finding sets of images
FindImages_ExcludeLastImage
[find_images]
"no" Should we exclude the last image from reporting - in case there is a synchronisation problem at the beamline and the last image of a scan is known to be damaged or out-of-sync.
FindImages_ImageExtns
[Setup]
"mar2300,mar1600" File name extensions for diffraction images containing numbers - which would otherwise confuse the method of tempate definition
FindImages_MaxImageNumWidth
[find_images]
"6" When automatically finding sets of images, this defines the maximum width for the image number field (only really relevant if image filenames don't use delimiters).
FindImages_MinNumImages
[Setup]
"1" Minimum number of files when searching for sets of diffraction images
FindImages_NonIdCharacters
[Setup]
"_-.+" When finding sets of images: characters that are not considered part of the identifier when encountered at the end of a string
FindImages_SortByCollectionDate
[find_images]
"yes" Should we use the timestamp recorded in the image header to sort several scans when generating the list of scans/identifiers?
FindImages_TestFollowLinks
[Setup]
"yes" Check if we can follow links
FindImages_TruncateLeft
[Setup]
"no" When dealing with image files that have no real delimiter between the identifier and the actual image number (resulting in a single long number like "34599001" e.g. for image 001): should we truncate the image number pattern from the left (resulting in template "34599###" instead of "########" in the example above)?
FindImages_max_size
[Setup]
"65536k" Maximum size for a file to be considered a diffraction image
FindImages_min_size
[Setup]
"512k" Minimum size for a file to be considered a diffraction image
GetbeamRemovePictures
"no" When running getbeam: should the graphic image be removed at the end?
IgnoreImageZero
"yes" Should a diffraction image file with number 0 be ignored? Often, these files are not part of the set of diffraction images and might contain e.g. a direct beam shot.
KapparotAngles_Eulerian
[x_index]
"Omega Chi Phi" Names of goniostat angles for an Eulerian setup.
KapparotAngles_Kappa
[x_index]
"Omega Alpha Kappa Phi" Names of goniostat angles for a Kappa setup.
KapparotSitesFile
[indexing, Kapparot]
"$BDG_home/autoPROC/lib/kapparot.sites" File containing descriptions of known beamline/instrument setups - to describe goniostat geometry, direction of goniostat axes etc.
MosaicityXdsMosflmFactor
"2.0" Multiplier to convert XDS values for mosaicity into MOSFLM values.
MosflmDetectorId
"" Detector identifier for MOSFLM: needed when creating the input file for visualisation of XDS results in MOSFLM. The default is to determine this automatically (resulting in one of ADSC, MAR, MARCCD, RAXIS4, RAXIS or PILATUS).
PointlessBlank
[combine_files]
"BLANK RESOFRACTION 0.50 NEGATIVE 0.50" Setting of BLANK keyword in POINTLESS within the "combine_files" tool.
PointlessIsiglimitResultingCutWarning
[x_postref]
"4.0" Give a warning if POINTLESS used only data below this high-resolution limit in determining most likely symmetry elements, point- and space-group.
PointlessKeywordSetting
[spacegroup determination]
"SYMMETRY-BASED" When using POINTLESS to determine correct spacegroup, which convention to use (CELL_BASED or SYMMETRY-BASED). See pointless manual for details.
ReportHostname
[process]
"yes" Write little header reporting OS, user name, date, hostname etc to have a record of the exact run conditions.
RunIdxrefCollectAllFailedSpots
[XDS]
"no" when doing iterative indexing in XDS (in cases a significant fraction of spots where not indexed): should we collect all failed spots for subsequent indexing? If set to "no" then only failed spots from the first indexing for a particular lattice are used.
RunIdxrefCreateMtv
[run_idxref]
"yes" Should we create MTV-formatted files to show different indexing solutions (color-coded crosses of indexed spots for a few typical images)?
RunIdxrefExcludeHighRes
[run_idxref]
"" Spots with resolution better than the given value will be ignored in indexing (when using the iterative indexing tool).
RunIdxrefExcludeIceRingShells
[run_idxref]
"no" Spots in resolution shells that often contain ice-rings will be ignored.
RunIdxrefMaxNumLattices
[XDS]
"9" If the indexing using all spots was inadequate and the iterative approach is taken: maximum number of separate indexing runs to try.
RunIdxrefNumSpotMin
"50" If the indexing using all spots was inadequate and the iterative approach is taken: stop if less than this number of spots left.
RunIdxrefOutputPrefix
[run_idxref]
"IterativeIndexing/Lattice" Prefix for output files of iterative indexing step: each solution will have this prefix followed by a 2-digit serial number.
RunIdxrefStartWithTop
"0" If the indexing using all spots was inadequate and the iterative approach is taken: use this top number of spots to try indexing (if set to 0 all spots will be used).
RunIdxrefXdsStats
[run_idxref]
"yes" Should we run "xds_stats" on each iterative-indexing solution?
RunIdxref_SpotVersusImage_MinFrac
[run_idxref]
"0.05" Minimum fraction of spots used in indexing (relative to most populated indexing solution) to classify an indexing solution as being interesting. Any solution with less than the default 5% of spots will not be analysed in detail.
RunTruncate
[various]
"yes" Should we run TRUNCATE from CCP4 (to go from intensities to amplitudes)?
RunWithExt
[Setup]
depends on context if several sets of diffraction images are encountered: should results for different sets be distinguished by a unique extension as part of the file name?
RunWithSubSubDir
[Setup]
depends on context if several sets of diffraction images are encountered: should results for different sets be distinguished by a unique extension as part of the file name?
ScaleAnaCChalfCut_123
[aP_scale]
"-1.0:-1.0 0.0:0.0 0.1:0.1 0.3:0.3" list of values - for subsequent scaling cycles 1, 2 and 3 (or higher) - to use for deciding on a high-resolution cut based on CC1/2 values. The first value in the colon-separated pair is for a specific RUN (e.g. when using chunking or if we deal with a high- and low-resolution pass), the second value for a full dataset.
ScaleAnaCompletenessCut_123
[aP_scale]
"0.0:0.0" list of values - for subsequent scaling cycles 1, 2 and 3 (or higher) - to use for deciding on a high-resolution cut based on completeness. The first value in the colon-separated pair is for a specific RUN (e.g. when using chunking or if we deal with a high- and low-resolution pass), the second value for a full dataset.
ScaleAnaISigmaCut_123
[aP_scale]
"0.1:0.1 0.5:0.5 0.5:1.0 1.0:2.0" list of values - for subsequent scaling cycles 1, 2 and 3 (or higher) - to use for deciding on a high-resolution cut based on I/sig(I) values. The first value in the colon-separated pair is for a specific RUN (e.g. when using chunking or if we deal with a high- and low-resolution pass), the second value for a full dataset.
ScaleAnaRmeasallCut_123
[aP_scale]
"99.9999:99.9999" list of values - for subsequent scaling cycles 1, 2 and 3 (or higher) - to use for deciding on a high-resolution cut based on Rmeas values. The first value in the colon-separated pair is for a specific RUN (e.g. when using chunking or if we deal with a high- and low-resolution pass), the second value for a full dataset.
ScaleAnaRmergeCut_123
[aP_scale]
"99.9999:99.9999" list of values - for subsequent scaling cycles 1, 2 and 3 (or higher) - to use for deciding on a high-resolution cut based on Rmerge values. The first value in the colon-separated pair is for a specific RUN (e.g. when using chunking or if we deal with a high- and low-resolution pass), the second value for a full dataset.
ScaleAnaRpimallCut_123
[aP_scale]
"99.9999:99.9999 0.9:0.9 0.8:0.8 0.6:0.6" list of values - for subsequent scaling cycles 1, 2 and 3 (or higher) - to use for deciding on a high-resolution cut based on Rpim values. The first value in the colon-separated pair is for a specific RUN (e.g. when using chunking or if we deal with a high- and low-resolution pass), the second value for a full dataset.
ScalaAnaRmergeSdCut
[Scaling analysis]
"3.0" Minimum Rmerge [sigma] for automatic suggestion of batches/images to be excluded (when analysing a SCALA/AIMLESS log-file by hand)
ScaleAllDatasetsTogether
[scaling]
"yes" When processing several datasets/sweeps in one go: should the different datasets be scaled together by default (applying automatic detection of real differences like different wavelength etc)?
SpacegroupEnantiomorphGroups
[x_postref]
"P41,P43:
P4122,P4322:
P41212,P43212:
P31,P32:
P3112,P3212:
P3121,P3221:
P61,P65:
P62,P64:
P6122,P6522:
P6222,P6422:
P4132,P4332"
List (colon-separated) of enantiomorph spacegroups (comma-separated) - without line breaks as shown here.
SpacegroupIndistinguishableGroups
[combine_files]
"I222,I212121:I23,I213" List (colon-separated) of indistinguishable spacegroups (comma-separated).
SpacegroupScrewAxesGroups
[combine_files]
"P2,P21:
P222,P2221,P21212,P212121:
C222,C2221:
I222,I212121:
P4,P41,P42,P43:
P422,P4212,P4122,P41212,P4222,P42212,P4322,P43212:
I4,I41:
I422,I4122:
P3,P31,P32:
P312,P3112,P3212:
P321,P3121,P3221:
P6,P61,P62,P63,P64,P65:
P622,P6122,P6222,P6322,P6422,P6522:
H3,H32:
P23,P213:
P432,P4132,P4232,P4332:
F432,F4132:
I23,I213:
I432,I4132"
List (colon-separated) of spacegroups (comma-separated) that only differ in screw-axes (without line breaks as shown here).
StopAfterScalingError
"yes" If a scaling error is encountered, should we stop the complete processing? If set to "no" then this error will be reported but processing continues. When processing multiple scans of only very few images, the scaling of each scan/wedge might be instable and only when the final, complete scaling is performed, a stable scale refinement can be achieved.
StopIfSubdirExists
"yes" When output should be written into a (sub)directory that already exists: should we stop with an error or not?
StopOnFindingExistingFiles
[scaling]
"yes" If one or more files (that would be created by a scaling run) already exist: should we stop with an error or not?
TruncateAnom
"yes" Should we take anomalous data into account when running the TRUNCATE procedure (after scaling/merging) to produce a final MTZ file with amplitudes?
TruncateTruncate
[scaling/merging, aP_scale]
"YES" Should the truncation procedure be used as implemented in TRUNCATE
UpdateDetectorOriginBetweenScans
[x_index]
"yes" When handling multi-scan experiments within a single invocation of autoPROC: should we update the detector origin for subsequent scans based on the refined values of the previous one?
UpdateIncidentBeamBetweenScans
[x_index]
"yes" When handling multi-scan experiments within a single invocation of autoPROC: should we update the incident beam vector for subsequent scans based on the refined values of the previous one?
UpdateparsFromPointless
[Setup]
"yes" Should we update parameters based on analysis by Pointless? This includes spacegroup and cell parameters.
UpdateResolutionLimit
[x_postref]
"no"
UpdateResolutionLimitCutoffIsigI
[x_postref]
"0.5"
UseKapparotForConsistentIndexing
[indexing]
"no" When trying to ensure consistent indexing between datasets/sweeps, should we use Kapparot to apply changes in goniostat settings to the reference orientation matrix?
UseKapparotForConsistentIndexingStopOnError
[indexing]
"yes" Should we stop when encountering an error during use of Kapparot?
UseMrfadd
[aP_scale]
"yes" Use our own MRFADD program instead of the CCP4 SORTMTZ one (for combining multi-record MTZ files). This works around size limitations especially for datasets with a very large number of images.
UseMrfedit
[aP_scale]
"yes" Use our own MRFEDIT program instead of the CCP4 REBATCH one (for combining multi-record MTZ files). This works around size limitations especially for datasets with a very large number of images.
WavelengthSignificantDigits
[process]
"5" When combining different datasets together, how many digits of the wavelength value should be compared before they are considered identical and therefore should be merged together?
XdsBackgroundRangeCoverAngle
[x_index]
"90.0" When using a distributed set of images to determine the initial background from images: what angular range should they cover?
XdsBackgroundRangeNumSegments
[x_index]
"3" When using a distributed set of images to determine the initial background from images: how many segments should we use for the angular range covered?
XdsBackgroundRangeNumSubsequentImages
[x_index]
"10" When using a distributed set of images to determine the initial background from images: how many subsequent images should we try and pack into a single segment?
XdsExcludeIceRingsAutomatically
[indexing]
"yes" After indexing within XDS, should we try and exclude ice-rings visible in the images automatically?
XdsExcludeIceRingsAutomaticallyIfKnownValue
[indexing]
"yes"
XdsGetbeamNumImages
"10" How many images should be used within GETBEAM when determining direct beam centre?
XdsGetRotationAxisViaKapparot
[indexing]
"yes"
XdsGetRotationAxisViaKapparotStopOnError
[indexing]
"yes" Should we stop when encountering an error during Kapparot usage at this stage?
XdsIndexingStopIfSpotsLessPercent
[x_index]
"2" We will stop if the indexing solution uses less than 2% of found spots.
XdsNumImagesBackgroundRange
[XDS]
"10" How many images to use for initial background estimation in XDS?
XdsOptimizeDefpix
"yes" Should we try and optimize the masking of bad detector areas in the XDS DEFPIX step?
XdsOptimizeDefpixCut
"0.1" Optimization criteria to define best value for VALUE_RANGE_FOR_TRUSTED_DETECTOR_PIXELS parameter in XDS
XdsOptimizeDefpixEnd
"9000" Maximum value for VALUE_RANGE_FOR_TRUSTED_DETECTOR_PIXELS parameter in XDS
XdsOptimizeDefpixStart
"5000" Starting value for VALUE_RANGE_FOR_TRUSTED_DETECTOR_PIXELS parameter in XDS. Be careful when processing very weak datasets: in that case this value might need lowering!
XdsOptimizeDefpixStep
"300" Step to determine best VALUE_RANGE_FOR_TRUSTED_DETECTOR_PIXELS parameter in XDS
XdsOptimizeIdxref
[XDS]
"yes" If the initial indexing in XDS (IDXREF step) encounters an error: should we try and optimise the indexing step?
XdsOptimizeIdxrefAlways
[XDS]
"yes" Should we always try and optimise the indexing step - even if the initial indexing using all spots seem to have worked anyway (i.e. no error message from XDS)? Defaults to the setting of XdsExcludeIceRingsAutomatically.
XdsOptimizeIdxrefPickSolution
[XDS]
"MostSpots" When running iterative indexing, how should the best solution be picked? Based on the most number of spots indexed (MostSpots) or just the first solution (One)?
XdsRunScriptOnFirstImage
[x_index]
"" Full path to executable (script or binary) that will be called with the first image file as only argument. This is done before the XDS.INP file is generated.
XdsScaleChunking
[x_scale]
"no"
XdsScaleChunkingMaxRuns
[x_scale]
"40"
XdsScaleChunkingNumBatchesMin
[x_scale]
"10"
XdsSetHighResFromFirstIntegrate
[x_integ]
"no"
XdsSetHighResFromFirstIntegrate_IsigIcut
[x_integ]
"0.5"
XdsSetHighResFromIndexedSpots
[x_index]
"no" Should we set an initial high-resolution limit already from the found and indexed spots?
XdsSetHighResFromIndexedSpotsSafetyMargin
[x_index]
"0.2"
XdsSetLowResFromIndexedSpots
[x_index]
"yes" Should we set an initial low-resolution limit already from the found and indexed spots?
XdsSetLowResFromIndexedSpotsSafetyMargin
[x_index]
"2.0"
XdsSetStrictAbsorptionChiSquareCut
[x_postref]
"1.5" If the CHI^2 value reported by CORRECT is above this value, then a large anomalous signal seems to be present.
XdsScaleKeepXdsAsciiMtz
"yes" Should we keep the XDS_ASCII.mtz file after scaling a XDS scan/wedge?
XdsSpotSearchAngularRange
[x_index]
"360"
XdsSpotSearchMinNumSpotsPerImage
[x_index]
"2" What is the minimum number of spots we want to see found per image?
XdsSpotSearchMinNumSpotsPerImageUseSlidingWindow
[x_index]
"yes" Use a sliding window to avoid getting thrown off by the odd image without any spots (when testing for empty images).
XdsSpotSearchNumAllowedEmptyImages
[x_index]
"5" How many empty images doe we allof per scan before giving a warning/error?
XdsSpotSearchNumImages
[XDS]
"999999" How many images should we use for finding spots in XDS step COLSPOT?
XdsSpotSearchNumRanges
[XDS]
"10" How many segments/ranges of images should be used for spot searching in COLSPOT?
XdsSpotSearchWindowImageNum
[x_index]
" 10" size of sliding window when analysing for empty images
XdsStats_gnuplot
[xds_stats]
"" Full path to working gnuplot binary. Usually, the OS-installed version will be found automatically.
XdsStartImageBackgroundRange
[XDS]
"11" What should ideally be the first image for the range used in determining the initial backgroun?
XdsUpdateCorrectionTables
[xds_update_pars]
"no" When updating parameters (and then re-doing the integration step), should we also update the spatial correction tables?
XdsUpdateMosaicityScale
[xds_update_pars]
"1.0" Scale factor for mosaicity value when updating XDS.INP file (for subsequent integration run). The value is interpreted as a scale factor to apply to the suggested value (from XDS) in subsequent integration runs.
XdsUpdateParKeepFixed
[XDS]
"BEAM_DIVERGENCE:no REFLECTING_RANGE:no" List of parameters that should be kept fixed (as opposed to being refined). A value of "no" has the effect that any parameter starting with this string is commented (with "!") when a new XDS.INP is written.
Xds_DefaultBinary
[x_check]
"parallel" 'parallel' or something else
Xds_Spot2Res_IceRingMinScore
[xds_spots2res]
"0.1"
Xds_Spot2Res_IceRingWidth
[xds_spots2res]
"0.03"
Xds_Spot2Res_IceRingWidthMult
[xds_spots2res]
"1.0"
Xds_Spot2Res_IceRingWidthMultForXds
[xds_spots2res]
"1.2" Multiplier for output resolution shells (to exclude ice-rings in XDS). A value above 1 will make these shells wider.
Xds_Spot2Res_IceRings
[xds_spots2res]
"3.906 3.873|
 3.671 3.642|
 3.450 3.420|
 2.681 2.649|
 2.258 2.235|
 2.076 2.056|
 1.955 1.936|
 1.922 1.906|
 1.888 1.872|
 1.721 1.713"
List (bar-separated) of ice-ring resolution ranges (without line breaks as shown here)
Xds_Spot2Res_KeepListWithResolution
[xds_spots2res]
"no"
Xds_Spot2Res_Prec
[xds_spots2res]
"0.01"
Xds_Spot2Res_SpotsToUse
[xds_spots2res]
"both" one of "both", "indexed" or "unindexed"
anom
[Setup]
"yes" assume anomalous signal being present
autoPROC_CreateGpxPictures
[various]
"yes" Should we create pictures of diffraction and predictions?
autoPROC_CreateGpxPicturesAndKeepFilterFile
[various]
"no" Should we keep the so-called filter file (containing prediction positions and shapes) after creating plots as part of an autoPROC run? These can become rather large and fill up disk space.
autoPROC_CreateGpxPicturesAtStages
[various]
"index run_idxref process" At what stages should we create diffraction-prediction images?
autoPROC_CreateGpxScript
[various]
"yes" Should we create GPX2-driving script for visualising processing progress?
autoPROC_CreateMosflmScript
(various)
"yes" Should we create script for visualising current status using the (old) MOSFLM interface?
autoPROC_ExcludeBadBatchesFromCycle
[Scaling module]
"2" single batches/images that show a significantly higher (> 5 sigma) Rmerge than the mean value over all images are automatically excluded from scaling iteration 2 onwards.
autoPROC_ExtraFilesDir
[Setup]
"" Directory location for (optional) extra files, e.g. spatial correction files for the Pilatus detector
autoPROC_IgnoreTwoThetaBelow
"0.1" Values of two-theta below this cut-off are treated as being zero
autoPROC_Img2Xds_Pilatus2MGaps
[img2xds]
" 0 1476  195  213|
  0 1476  407  425|
  0 1476  619  637|
  0 1476  831  849|
  0 1476 1043 1061|
  0 1476 1255 1273|
  0 1476 1467 1485|
487  495    0 1680|
981  989    0 1680"
Gap definitions for Pilatus 2M detector (without line breaks as shown here)
autoPROC_Img2Xds_Pilatus2MIncludeUntrustedRectangle
[img2xds]
"no" Should we include the Pilatus 2M gap definitions when processing data from this detector?
autoPROC_Img2Xds_Pilatus6MGaps
[img2xds]
"487  495    0 2528|
 981  989    0 2528|
1475 1483    0 2528|
1969 1977    0 2528|
   0 2464  195  213|
   0 2464  407  425|
   0 2464  619  637|
   0 2464  831  849|
   0 2464 1043 1061|
   0 2464 1255 1273|
   0 2464 1467 1485|
   0 2464 1679 1697|
   0 2464 1891 1909|
   0 2464 2103 2121|
   0 2464 2315 2333"
Gap definitions for Pilatus 6M detector (without line breaks as shown here)
autoPROC_Img2Xds_Pilatus6MIncludeUntrustedRectangle
[img2xds]
"no" Should we include the Pilatus 6M gap definitions when processing data from this detector?
autoPROC_ImginfoReportWarnings
[img2xds]
"yes" Should we report warnings coming from "imginfo"?
autoPROC_LinkImagesIntoSubdir
[x_index]
"Images" Should we have the diffraction image as symbolic links in a subdirectory (as named here) instead of the processing directory.
autoPROC_MacroDirs
"" colon-separated list od directories with additional (on top of our own provided) macros.
autoPROC_PointlessTolerance
"2.0" Parameter TOLERANCE as defined in POINTLESS. Increase this if the reference dataset is expected to deviate significantly from the dataset being processed.
autoPROC_ReRunIdxrefAtEnd
[x_process]
"no" Should we re-run the iterative indexing at the end of processing again? Since refined parameters (and most likely spacegroup) are available, this could give even clearer indication of potentially split crystals or multiple lattices.
autoPROC_ScaleEachDatasetSeparately
[process]
"yes" Every dataset/sweep should also be scaled separately - even if in the end only a combined dataset from several sweeps is going to be used.
autoPROC_ScaleWithAimless
[aP_scale]
"yes" Should we scale with AIMLESS program instead of SCALA?
autoPROC_ScaleWithAimlessRefineSdcorr
[aP_scale]
"yes" Should we refine the error model when scaling with AIMLESS?
autoPROC_ScaleWithAimlessRefineSdcorrSame
[aP_scale]
"no" When refinining the error model parameters, should we use the same corrections for all datasets?
autoPROC_ScaleWithXscale
[aP_scale]
"no" Use XSCALE for scaling (instead of default AIMLESS).
autoPROC_ScaleWithXscaleReportMrfanaStats
[aP_scale]
"yes" not only use MRFANA statistics for high-resolution limit decision, but also print the statistics from MRFANA.
autoPROC_ScaleWithXscaleReportXscaleStats
[aP_scale]
"no" Report the statistics as given by XSCALE (in the XSCALE-scaling path).
autoPROC_Setup_StopOnDateError
[x_setup]
"yes" Should we stop in cases where we can't extract the image date from the image header? This should only happen with seriously scrambled image headers ...
autoPROC_SupportTwoTheta
[Setup]
"yes" Is a two-theta offset supported?
autoPROC_TwoThetaAxis
[img2xds]
rotation axis (modified by autoPROC_TwoThetaAxisRotationAxisFactor) Axis definition of 2-theta arm. If processing data from a multi-axis goniostat using a rotation axis other than Omega, this might need setting explicitly.
autoPROC_TwoThetaAxisRotationAxisFactor
[img2xds]
"1.0" Set to "1.0" if 2-theta arm identical to rotation axis (usually Omega) or to "-1.0" if rotating into the opposite direction.
autoPROC_SupportedFreeRflagColumnNames
[aP_scale]
"FreeR_flag|FREE|FreeRflag"
autoPROC_TestSetFraction
[aP_scale]
"0.05" Size of test-set fraction to use for final MTZ file(s) - unless a reference MTZ file with test set flags has been given.
autoPROC_XdsAcceptOverloads
[XDS]
"no" Should overloaded reflections be accepted (usually a very bad idea)?
autoPROC_XdsAnalyseOverloads
[x_process]
"no" Should we analyse for overloads?
autoPROC_XdsDelphiDefault
[XDS]
"5.0" Default value for DELPHI parameter (but might get adjusted)
autoPROC_XdsDistanceFac
[XDS]
"1" factor to apply to distance parameter (to allow distinction between positive/negative definition). Various defaults depending on detector type are defined:
Detectorparameterdefault
R-AXISautoPROC_XdsDistanceFacRaxis-1
R-AXIS IVautoPROC_XdsDistanceFacRaxis4-1
R-AXIS IV+autoPROC_XdsDistanceFacRaxis4p-1
R-AXIS VautoPROC_XdsDistanceFacRaxis5-1
SaturnautoPROC_XdsDistanceFacSaturn-1
Saturn944+autoPROC_XdsDistanceFacSaturnp-1
JupiterautoPROC_XdsDistanceFacJupiter-1
autoPROC_XdsKeyword_*
"" All currently defined XDS keywords can be set directly via a autoPROC_XdsKeyword_<keyword> parameter. The <keyword> is the same string as given in the official list pof parameters with two exceptions:
  1. the trailing "=" is omitted
  2. characters like "/", "-", "(" or ")" are omitted
autoPROC_XdsIntegrateScaleOutlierSigma
[x_integ]
"5" report images for which the image scale factor is more than N sigma different from the mean
autoPROC_XdsIntegPostrefNumCycle
[x_process]
"1" How many cycles of integration/post-refinement should be done?
autoPROC_XdsMaxDistanceJitter
[x_integ]
"1.0" Maximum expected/allowed variation of crystal-detector distance (in mm)?
autoPROC_XdsMinimumImagesForDelphi
[XDS]
"4" minimum number of images for a DELPHI block during XDS INTEGRATE step
cell
[indexing]
"" User-defined set of cell parameters (instead of leaving that decision to autoPROC).
convert
[GETBEAM]
"convert" name or full path for convert tool from the ImageMagick package
free_mtz
[Scaling/Merging]
"" MTZ file with FreeR_flag
imgdir
[Setup]
current directory directory with set of diffraction images
init_reso
[scaling module]
"1000.0 0.1" initial low and high resolution limit
init_sdcorr
[Scaling]
"SDCORRECTION ADJUST 1.0 0.000 0.0" Initial values for correction of measurement standard uncertainties (for SCALA 3.2.X and earlier)
init_sdcorr_scala33
[Scaling]
"SDCORRECTION NOREFINE ADJUST 1.0 0.000 0.0" Initial values for correction of measurement standard uncertainties (for SCALA 3.3.X and later)
matref
[Indexing]
"" file with reference orientation matrix (formatted as expected by processing package)
minnum
"10" minimum number of consecutive images within a dataset for processing
minproc
[MOSFLM]
"5" number of images to use in initial integration (to determine additional parameters like gain or high resolution limit)
mosaic
"0.4" default and starting value for mosaicity
mosflm
[MOSFLM path]
first found from mosflm_exes list The default is to test each value of mosflm_exes to find first accessible executable.
mosflm_exes
[MOSFLM path]
"mosflm ipmosflm $CBIN/ipmosflm" List of possible names/locations of MOSFLM binary.
mtzdump
""
nres
[Scaling]
"0" number of residues in asymmetric unit
pname
[Setup]
"test" Project name (in the CCP4 MTZ data hierarchy)
ref_mtz
[Scaling/Indexing]
"" MTZ file with reference dataset - usually set via "-ref" argument to process
reindex
""
rstats
""
scala
""
scala_extra
[Scaling/Merging]
"" file with extra SCALA keywords/commands
scales
[Scaling]
"ROTATION SPACING 5.0 ABSORPTION 6 BFACTOR ON" default scale layout
sharp_mrf
[Scaling module]
"no" do we want to ouput a scaled, multi-record file, e.g. for use in dose-dependent occupancy refinement in SHARP? Note :this will only be done for single-scan datasets
sortmtz
""
symm
[throughout]
"" Spacegroup name - leaving out spaces (i.e. using P212121 instead of "P 21 21 21")
xname
"A" Crystal name (in the CCP4 MTZ data hierarchy)


Last modification: 14.09.2015