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
