PRETTY XDS

Introduction

This job template is built with the XDS environment and runs xds_par followed by xds_conv. The user must define paths to folders in an experiment or project containing the input files XDS.INP and XDSCONV.INP, respectively. These files must be prepared before running the job.

The job uses a Python script to generate visual output, including plots of CC1/2 and completeness as functions of resolution.

Quick Start

To run this job, you need to specify the following input variables:

• DC_XDS_INP_PATH: Path to a folder within your experiment or project where relevant the XDS.INP file is located (the file must have this exact name). This file must already be configured, e.g. with the correct path in the cloud to the data you want to analyze. Example value: DCEU:2025:85161/auxiliary
• DC_XDSCONV_INP_PATH: Path to a folder within your experiment or project where the relevant XDSCONV.INP  file is located (The file must have this exact name). This file must also be preconfigured. Example value: DCEU:2025:85161/auxiliary

Optionally, the following input variables can also be configured:

• DC_XDS_MAX_JOBS: Overrides the MAXIMUM_NUMBER_OF_JOB parameter defined in the XDS input file. This parameter defines how many portions the images are split into for the COLSPOT and INTEGRATE steps of xds_par. Example value: 4
• DC_XDS_MAX_PROCESSORS: Overrides the MAXIMUM_NUMBER_OF_PROCESSORS parameter in the XDS input file. This parameter defines the maximum number of CPUs that can be used by xds_par. Example value: 4

These optional variables can have a significant impact on the runtime of the job. Increase them if you are using a machine type with many CPUs.

In the above example, XDS.INP and XDSCONV.INP files have been uploaded to the auxiliary directory of the experiment. The job copies these files to the temporary working directory, where the programs are executed. Afterward, a Python script generate visualizations, and all relevant output is copied to the job output directory. 

Output

A successfully completed job generates the following outputs:

• At the top level of the output folder, the following plots and files are defined: 
  • CC_HALF_vs_Resolution.png: A plot of CC1/2 as a function of the resolution limit.
  • COMPLETENESS_vs_Resolution.png: A plot of the completeness as a function of the resolution limit.
  • I_SIGMA_vs_Resolution.png: A plot of the Mean I/σ(I) as a function of the resolution limit.
  • R-MEAS_vs_Resolution.png: Redundancy-independent R-factor (%) as a function of the resolution limit.
  • correct_summary.txt: Crystallographic statistics extracted from the CORRECT.LP
  • refined_unit_cell.txt: The refined unit cell
• Within the subdirectory xds_output, the typical XDS and XDS_CONV output files can be found:
  • ABS.cbf
  • COLSPOT.LP
  • CORRECT.LP
  • DEFPIX.LP
  • GXPARM.XDS
  • IDXREF.LP
  • INIT.LP
  • INTEGRATE.HKL
  • INTEGRATE.LP
  • F2MTZ.INP
  • SHOW_BKG.cbf
  • SPOT.XDS
  • temp.hkl
  • XDS.INP
  • XDSCONV.INP
  • XDSCONV.LP
  • XDS_ASCII.HKL
  • XPARM.XDS
  • XYCORR.LP

Versions

Version 0

• Initial version created with version 1 of the XDS environment.
• In this version, the input variables XDS_INP_PATH and XDSCONV_INP_PATH were specified as strings instead of path variables, so they had to be typed manually instead of selected via the job file browser:

Version 1

• In this version XDS_INP_PATH and XDSCONV_INP_PATH were updated to become PATH variables: