Cppxfel

This page is under development.

cppxfel is a software suite primarily designed to showcase some methods which would benefit from being incorporated into larger XFEL-specific software suites. This suite currently covers the part of the XFEL data processing pipeline which stems from refining indexing solutions to generating merged MTZ files for use in structure refinement. These wiki files cover installation, step-by-step tutorials and a reference manual for each of the commands. This is meant to be read in conjunction with a paper (Ginn et al J Appl Cryst 2016).

Installation

Download and installation instructions for cppxfel can be found here. cppxfel relies on a distribution of the cctbx library and Diffraction Integration for Advanced Light Sources (DIALS). In case you wish to update your current version, please follow the updating instructions. Any major changes added to the cppxfel distribution is documented in this change log.

Step-by-step tutorials

Step-by-step tutorials are provided for a 1000-image downloadable data set for CPV17 (structure solution described in Ginn et al Nat. Comms. 2015). The tutorials are divided into several stages:

• Indexing with DIALS - cppxfel uses scripts to call on DIALS indexing programs to index individual images.
• Indexing with cppxfel - cppxfel's own indexing algorithm, TakeTwo
• Cppxfel Initial Orientation Matrix Refinement - performing initial refinement to produce high quality orientation matrices before post-refinement.
• Cppxfel Post-refinement - post-refinement of crystals against a reference data set generated from the previous stage
• Cppxfel Final Merge - producing a final MTZ file for use in structure solution.
• Cppxfel Statistics - how to assess the quality of the XFEL data processing.

Detailed tutorials

These are some more detailed tutorials on how to make decisions in the cppxfel pipeline.

• Spot-finding parameters with DIALS - how to choose the spot-finding parameters which give you the best spots for indexing.

Reference manual

The associated commands with the tutorials, in addition to several commands not used in the tutorials, are all documented in a reference manual.