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Joint Research Group Macromolecular Crystallography



Which operating systems are supported by XDSAPP3?

We tested the installation of XDSAPP3 successfully on various Linux systems, including:

  • Scientific Linux  6.3
  • RHEL 6 + 7
  • centOS 6
  • openSUSE 15
  • Kubuntu 20
  • Ubuntu 20

as well as on:

  • macOS 12 (Monterey, incl. M1), 11 (Big Sur, incl M1), 10.15 (Catalina), 10.14 (Mojave), 10.13 (High Sierra)
  • Windows10 WSL2 with Ubuntu 20

Which detectors are supported by XDSAPP3?

XDSAPP3 uses the script generate_XDS.INP by Kay Diederichs (revision 1.11) to create the XDS.INP input file for XDS. In principle, all detectors supported by this script can be used with XDSAPP3, including Dectris Eiger and Eiger2. It is possible to load .pck files, but those are not currently supported by generate_XDS.INP. Unless you modify the script yourself, processing .pck files with XDSAPP3 will fail.

Can I process Eiger data sets with XDSAPP3?

You can process generic Eiger data, provided that the suffix of the data files is  ".h5". If the data has been converted to the cbf format, xdsapp3 will treat it internally as Pilatus data.

To process Eiger data with XDS, you need to install one of the plugins dectris-neggia from Dectris or durin-plugin from Diamond Light Source.

The recommended way is to use the script generate_XDS.INP from Kay Diederichs to generate the initial XDS.INP, but it is also possible (but not recommended) to use Dectris Albula-API (only Linux) and a modified XDS_from_H5.py.

Both, generate_XDS.INP and XDS_from_H5.py are included in the XDSAPP3 package.

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.

What are the criteria for the detection of anomalous signal?

Per default, the value UNKNOWN is used in the Settings tab for Friedel's law. After the first integration run in P1, CORRECT is run with FRIEDEL=FALSE and XDSAPP investigates the CORRECT.LP file to check the anomalous signal.

The anomalous resolution is estimated from the resolution shell for which the anomalous signal is at least 1.2 and the anomalous correlation is significantly greater than 30%.

  • if there are more than three resolution shells with anomalous signal, FRIEDEL=FALSE,
  • for three anomalous shells, the sum of the anomalous signal must be at least 3.7 and the sum of anomalous correlations 100% for FRIEDEL=FALSE,
  • for two anomalous shells, the sum of the anomalous signal must be at least 2.7 and the sum of anomalous correlations 80%,
  • for one anomalous shell, the anomalous signal must be at least 1.5 and the anomalous correlation 50%.

If FRIEDEL=FALSE, the strict absorption correction in CORRECT is set to TRUE if at least one of the three χ2 values at the beginning of CORRECT.LP is higher than 1.5.

By using TRUE or FALSE in the Settings tab, no check for anomalous signal will be made.


"ERROR: Python module 'PyQt5' not found, please install this mandatory module."

If this error occurs when starting XDSAPP3, you're missing the Qt5 bindings for Python. Install PyQt5 with you systems (Python) package manager.

Customizing XDSAPP3

Can I change the location of the output folder for XDSAPP3?

Per default, the GUI version of XDSAPP3 writes the results in the subfolder xdsapp created within the folder you started XDSAPP3.

In the Settings tab, you can choose another output folder, either before or after loading a data set, or even between processing steps. If you change the output folder between processing steps, all files in the current output folder will be copied to the new one before further processing. No output file will be deleted.

For the command line version, you can define an output directory with the option --dir.

For a full list of options:

xdsapp3 -h

Preferences Menu

Currently, there are three options in the Preferences Menu.

CORRECT plots x-axis as Resolution: In the CORRECT plots tab, plots for I/SigI, CC1/2, R_meas, SigAno, AnoCor, and Completeness can be displayed with x-axis as "Resolution" or "1/R2"

Use new Find Files dialog: There is a choice of a generic file selection dialog and a streamlined new Find Files dialog which displays a dataset with its frame number instead of single files.