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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"
  • --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"
  • --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
  • --yaxis YAXIS

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