Tuesday 5 February 2013

Full list of command-line options

Just gathered these to add to the manual, thought I should copy them here:


-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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