README.md

Serial_xds: Data Processing in Serial Oscillation Crystallography

Introduction

serial_xds is a simple Python3.6 routine 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 Detector Software (XDS): download from XDS website
• h5py, an HDF5 plugin for python: [download instructions here] (https://www.h5py.org/)
• xdsstat (available from XDSwiki)
• Neggia plugin: download from Dectris website this is not strictly necessary if you also have the H5toXds program in your PATH, but Neggia improves performance.
• For scaling and filtering of data, XSCALE_ISOCLUSTER is also a useful tool to have.

Installation

Simply ensure that the XDS binaries are in your path.

Assumptions

• Data is in EIGER HDF5 format. This may work with other HDF5 files but they are not yet tested.
• Data is collected serially, with oscillation. This routine will not work with still images. Use nXDS for still processing.

Acknowledgements

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