Joint Research Group Macromolecular Crystallography

Command line mode and Multiple datasets

Full automatic command line mode

Allows the processing from the command line, without GUI, optional of all data sets contained in a directory tree.

Usage:

xdsapp3 [-h][options]

• xdsapp3 --cmd -i abcd_01_00299.img
  processes all images of dataset abcd_01_
• xdsapp3 --cmd -r 4 -j 3 -i abcd_01_00299.img
  processes all images of dataset abcd_01_ , does 4 reintegration steps, uses 3 parallel jobs for INTEGRATE
• xdsapp3 --cmd -a [/my/beautiful/data]
  processes all datasets in a diretory (recursively), optionally with the starting directory given.
• xdsapp3 --cmd -i abcd_02_0001.img --live 300
  processes dataset abcd_02_ with 300 images live (in 4 steps) during data collection
• xdsapp3 --cmd --cont [/my/live/data]
  looks continuously for datasets (recursively) and processes them, optionally with the starting directory given. Most useful on beam line use.

Results are always stored in the files "results_<dataset>.txt" and "results_<dataset>.html" within the results directory.

Available options:

• -h, --help
  show this help message and exit
• -v
  print version information
• --cmd
  start the command line version of XDSAPP3
• -a, --all [directory]
  multi-mode: process all datasets in a (optional) directory (absolute or relative, recursively). If [directory] is not given, the current working directory is used. Mutually exclusive with --cont and --image/-i

• --cache CACHE

  number of images in cache
• --cont [directory]
  multi-mode: look continuously for datasets in a (optional)  directory and process them, recursively. If [directory] is not given, the current working directory is used. Mutually exclusive with --all/-a and --image/-i
• -c CPU_NO, --cpu=CPU_NO
  set number of cpus for xds, default: all cpus of the machine 

• -d DB, --database DB

  write results in database, only on HZB-MX beamlines, default for multi data set mode
• --delphi=DELPHI
  give delphi manually
• --dir=RESULT_DIR
  give resultdir (relative or absolute), e.g. --dir myresults, default: xdsit/surname

• --esrf ESRF
  ignore all data sets starting with "line-", "mesh-", "ref-"

• -f FRIEDEL, --fried=FRIEDEL
  set friedel law, give "true" or "false", default: false

• -i IMAGE, --image=IMAGE
  single mode: give one image of a dataset, this dataset will be processed, e.g. -i abcd_01_010.img, mutually exclusive with --all/-a and --cont
• --index
  index dataset, only in single mode
• -j JOBS_NO, --jobs=JOBS_NO
  set number of parallel jobs for xds, default: 1
• --live=LIVE_NO
  live processing, give last image no., e.g. --live 200
• --nice=NICE_LEVEL
  set nice level of xds, default: 19
• --org=ORGXY
  give orgx, orgy manually: --org "orgx orgy"
• -p, --predictions
  With generate_adx prepares .adx files for each image to visualize the spot predictions with adxv, not for Eiger data yet.
• --polar POLAR
  

  polarization plane normal, e.g. --polar "0.0 1.0 0.0" (default)

• --range=DATA_RANGE
  give datarange in format --range "start end"
• --raxis RAXIS
  

  rotation axis, e.g. --raxis "1.0 0.0 0.0" (default)

• --ref REFERENCE
  

  use reference data set

• -r REINT, --reint=REINT
  no of reintegration cycles, default: 2 for Pilatus and Eiger, 4 else
• --res=RESOLUTION
  use data up to resolution
• -s SG, --spacegroup=SG
  give spacegroup and unit cell constants in format -s "sg a b c α β γ"
• --spotrange=SPOT_RANGE
  give spotrange manually, can be 1-3 pairs, e.g. --spotrange "1 10 20 40 60 80"
• --sx
  use for serial crystallography with partial data sets that are to be merged with XSCALE after processing

• --xaxis XAXIS

  direction of detector X axis, e.g. --xaxis "1.0 0.0 0.0" (default)
• --xdsinp
  genereate XDS.INP for this dataset, only in single mode
• --xdsidx XDSIDX
  REFINE(IDXREF) parameter, any combination of ['AXIS', 'BEAM', 'CELL', 'ORIENTATION', 'POSITION']
• --xdsint XDSINT
  REFINE(INTEGRATE) parameter, any combination of
  ['AXIS', 'BEAM', 'CELL', 'ORIENTATION', 'POSITION']
• --xdscor XDSCOR
  REFINE(CORRECT) parameter, any combination of
  ['AXIS', 'BEAM', 'CELL', 'ORIENTATION', 'POSITION']
• --xycor XYCOR
  absolute paths for user defined correction files:
  --xycor "X-CORRECTIONS.cbf Y-CORRECTIONS.cbf"
  

• --yaxis YAXIS

  direction of detector X axis, e.g. --yaxis "0.0 1.0 0.0" (default)