-2d Use Mosflm and Scala
-2da Use Mosflm and Aimless
-2dai Use Mosflm (inc. for indexing) and Aimless
-2di Use Mosflm (inc. for indexing) and Scala
-2dia Pun of -2dai
-3d Use XDS and XSCALE, Scala to merge
-3da Use XDS and XSCALE, Aimless to merge
-3dai Use XDS and XSCALE, Aimless to merge, XDS to index
-3daii Use XDS and XSCALE, Aimless to merge, XDS to index (allframes)
-3di Use XDS and XSCALE, Scala to merge, XDS to index
-3dii Use XDS and XSCALE, Scala to merge, XDS to index (allframes)
-3diia Pun for -3daii
-atom X Switch on separating anomalous pairs
-batch_scale Use batch rather than smooth scaling
-beam Beam coordinates, in Mosflm convention
-blend Save files for BLEND
-cell Set the input cell constants (needs symmetry)
-spacegroup Set the spacegroup
-crystal Assign the crystal ID
-project Assign the project ID
-debug Switch on debugging output (a bad idea)
-executable Override location of executable (deprecated)
-failover Continue to process if one sweep fails
-image image Process only sweep containing image
-start_end Assign start and end of sweep, needs -image
-free_fraction Fraction of reflections to use in free set
-free_total Total number of reflections in free set
-freer_file Copy FreeR_flags from this file
-hdr_in Input header information (developer tool)
-hdr_out Output header information (developer tool)
-ice Exclude ice ring regions
-indexer Assign indexer to use (developer tool)
-integrater Assign integrater to use (developer tool)
-scaler Assign scaler to use (development tool)
-interactive Manual selection of images for indexing (developertool)
-isigma Unmerged limit for resolution limit calculations
-misigma Merged limit for resolution limit calculations
-mask Additional mask for detector e.g. for backstop.
-microcrystal Options for microcrystal processing
-min_images Min no. of images to make a sweep
-no_lattice_test Switch off Bravais lattice tests
-parallel N Number of cores to use
-phil Pass in Phil override file (developer tool)
-quick Cut corners to go quicker
-reference_reflection_file ref.mtz Assign reference reflection file
-resolution Set the resolution limit
-reversephi Warn of backwards phi axis
-scale_model decay,absorption,... Manually set the scale model
-serial Non-parallel (-parallel 1)
-small_molecule Settings for processing small molecule data
-trust_timestamps If no timestamp in header, trust file timestamps
-xinfo Pass xinfo file in
-xparallel N (XDS) use forkintegrate with N machines
-xparm GXPARM.XDS Pass in refined coordinate description from calibration set
-xparm_ub GXPARM.XDS Also use UB matrix from ... (developer tool)
-zero_dose Switch on zero-dose extrapolation
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