View source for Cppxfel

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''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 ([http://scripts.iucr.org/cgi-bin/paper?s1600576716006981 Ginn et al J Appl Cryst 2016]).

== Installation ==

Download and installation instructions for cppxfel can be found [[Cppxfel Installation | 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 cppxfel | updating instructions]]. Any major changes added to the cppxfel distribution is documented in this [[Cppxfel change log | 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 [http://dx.doi.org/10.1038/ncomms7435 Ginn et al Nat. Comms. 2015]). The tutorials are divided into several stages:

* [[Cppxfel Indexing with DIALS | Indexing with DIALS]] - cppxfel uses scripts to call on DIALS indexing programs to index individual images.
* [[Cppxfel Indexing | 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.

* [[Cppxfel spot finding | 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 [[Cppxfel Reference Manual | reference manual]].