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Joint Research Group Macromolecular Crystallography

Installation instructions

Installation of XDSAPP3

After downloading the file xdsapp3v1-yyyy-mm-dd.tar.gz in the directory of your choice, run the command
   tar -zxf xdsapp3v1-yyyy-mm-dd.tar.gz
or
   tar -xf xdsapp3v1-yyyy-mm-dd.tar

depending of the archive you received.

A new directory will be created, containing 19 files:

  • beamlines.py
  • eiger2cbf.py
  • generate_XDS.INP
  • logo_hzb.gif
  • messages.py
  • mp_xdsconv_job.py
  • myutils.py
  • plotting3.py
  • README
  • ReleaseNotes.txt
  • signals.py
  • XDS_from_H5.py
  • xdsapp3_gui.py
  • xdsapp3_help.html
  • xdsapp3_help.txt
  • xdsapp3.1.py
  • xdsenv.py
  • xdsit.py

Create an alias "xdsapp3" or "xdsapp" pointing to the file xdsapp3.1.py for easy use of the program.

Installation of the GUI components

Read carefully the README file for installation instructions.

The instructions are provided for x86_64 architecture and have been tested by us with the specified operating systems. They may not work with different or older systems. Please note that we can not provide solutions for all operating systems.
Before starting the installation, ensure that your OS and package management software are up to date.
You can check the installation of packages by using the search command of your package manager (e.g. yum search pyqt5). The packages for your architecture will be listed.

Setting up the environment

The environment for XDSAPP3 is defined in the file xdsenv.py.  There are 3 sections:

- Section 1: path settings
- Section 2: performance parameter (optional)
- Section 3: miscellaneous (optional)

Section 1 Here the path to various programs are defined if these are not found via the PATH environment variable.  For the image viewer, select only one: xds-viewer or albula, not both. 

Please take special care if you will evaluate data from Dectris Eiger detectors. It is strongly recommended to define only the path to the dectris-neggia or durin plugin (only one!) in the file xdsenv.py. This setting will use the script generate_XDS.INP to generate the necessary file XDS.INP. If you define the path to the albula-api in addition to one of the plugins, XDS.INP will be generated with XDS_from_H5.py. This is not recommended, as the script XDS_from_H5.py is not well tested. A third method to read Eiger data files is to use eiger2cbf. This should only be necessary, if you cannot use one of the plugins, and may have the drawback, that not all header informations are supplied to XDS.INP. This is the least recommended possibility.

Section 2 With the performance parameters you may define the number of CPUs to use, the number of jobs XDS is running and the nice level. You can define these parameters on a per computer basis, if necessary.

Section 3 Miscellaneous , see comments in xdsenv.py