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Serial_xds: Data Processing in Serial Oscillation Crystallography

Introduction

serial_xds is a python program that process data for serial oscillation crystallography

Usage

serial_xds.py -h
usage: serial_xds.py [-h] -i INPUT [INPUT ...] -b BEAMCENTER BEAMCENTER
                     [-r OSCILLATIONS] -d DISTANCE [-w WAVELENGTH]
                     [-f FRAMESPERDEGREE] [--output OUTPUT] [-sg SPACEGROUP]
                     [-u UNITCELL]

Arguments required to process the data: input, beamcenter, distance.

optional arguments:
  -h, --help            show this help message and exit
  -i INPUT [INPUT ...], --input INPUT [INPUT ...]
                        Path of Directory containing HDF5 master file(s)
  -b BEAMCENTER BEAMCENTER, --beamcenter BEAMCENTER BEAMCENTER
                        Beam center in X and Y
  -r OSCILLATIONS, --oscillations OSCILLATIONS
                        Oscillation angle per well
  -d DISTANCE, --distance DISTANCE
                        Detector distance in mm
  -w WAVELENGTH, --wavelength WAVELENGTH
                        Wavelength in Angstrom
  -f FRAMESPERDEGREE, --framesperdegree FRAMESPERDEGREE
                        Number of frames per degree
  --output OUTPUT       Use this option to change output directly
  -sg SPACEGROUP, --spacegroup SPACEGROUP
                        Space group
  -u UNITCELL, --unitcell UNITCELL
                        Unit cell

Computer system with two or more processing units is required to leverage parallel operation in master.py script.

Dependencies

serial_xds depends on:

  • X-Ray Detectore Software (XDS)
  • Neggia plugin (available from Dectris website)
  • xdsstat (available from XDSwiki)

Installation

If files are on your local machine, no work is needed.

Assumptions

  • EIGER HDF5 data
  • Data is collected serially

Acknowledgements

serial_xds was developed at Cornell High Energy Synchrotron Source (CHESS) for serial oscillation crystallography data processing. Tested at MacCHESS ID7B2 beamline.