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= Open-source tools for free-electron laser data processing =
News! See our [[https://doi.org/10.1107/S2059798318009191 new paper]]!  This paper shows current best practices using ''cctbx.xfel'' with ''DIALS'' for serial crystallographic data.  Also see the [https://github.com/phyy-nx/dials_refinement_brewster2018/wiki companion set of tutorials].


''cctbx.xfel'' is a suite of software tools designed to process diffraction data from serial femtosecond crystallography (SFX) measurements at an X-ray free-electron laser (XFEL).  Built on the Computational Crystallographic Toolbox ([http://cctbx.sourceforge.net ''cctbx'']), the same toolbox on which [http://www.phenix-online.org ''PHENIX''], [http://adder.lbl.gov/labelit ''LABELIT''], and post-refinement and merging program, [http://viper.lbl.gov/cctbx.xfel/index.php/Cctbx.prime ''PRIME''] are built, it enables the user to solve difficult problems relating to processing XFEL data.  The programs and modules provided by ''cctbx.xfel'' can reduce a large set of still diffraction images recorded at Stanford’s Linac Coherent Light Source ([http://lcls.slac.stanford.edu LCLS]) to a single MTZ file containing merged reflection intensities suitable for structure solution.
News! See our [[http://cci.lbl.gov/publications/download/CCN_2019_p22_Brewster.pdf newsletter article]] that describes the XFEL GUI, an interactive program for handling large XFEL datasets.
 
= Open-source tools for serial crystallographic data processing =
 
''cctbx.xfel'' is a suite of software tools designed to process diffraction data from serial femtosecond crystallography (SFX) measurements at an X-ray free-electron laser (XFEL) or a synchrotron.  Built on the Computational Crystallographic Toolbox ([http://cctbx.sourceforge.net ''cctbx'']), the same toolbox on which [http://www.phenix-online.org ''PHENIX''], [http://dials.github.io DIALS], [http://adder.lbl.gov/labelit ''LABELIT''], and post-refinement and merging program, [http://viper.lbl.gov/cctbx.xfel/index.php/Cctbx.prime ''PRIME''] are built, it enables the user to solve difficult problems relating to processing serial crystallographic data.  The programs and modules provided by ''cctbx.xfel'' can reduce a large set of still diffraction images recorded at Stanford’s Linac Coherent Light Source ([http://lcls.slac.stanford.edu LCLS]), [http://sacla.xfel.jp SACLA], the [https://www.xfel.eu/ European XFEL], or a synchrotron, to a single MTZ file containing merged reflection intensities suitable for structure solution.


== ''cctbx.xfel'' resources ==
== ''cctbx.xfel'' resources ==


The tutorials on this wiki provide detailed instructions for indexing and integrating still diffraction images extracted from the raw data streams recorded at the LCLS, including pre-processing steps such as dark pedestal generation and refinement of the detector geometry of the Cornell–SLAC pixel array detectors (CSPAD) in use at the CXI and XPP end stations.  The tutorials also cover tools to efficiently leverage the LCLS computing cluster to process the thousands to millions of diffraction images that can be recorded in a short time.
The tutorials on this wiki provide detailed instructions for indexing and integrating still diffraction images extracted from the raw data streams recorded at the LCLS, including pre-processing steps such as dark pedestal generation and refinement of the detector geometry of the Cornell–SLAC pixel array detectors (CSPAD) in use at the CXI and XPP end stations.  The tutorials also cover tools to efficiently leverage the LCLS computing cluster to process the thousands to millions of diffraction images that can be recorded in a short time.  Finally, processing approaches for data collection at non-LCLS sources are also provided.


* [[Overview]] to the system architecture at LCLS and real-time progress monitoring of data processing
* [[Overview]] to the system architecture at LCLS and real-time progress monitoring of data processing
* Installation: there are two ways to get ''cctbx.xfel'':
* Installation: there are two ways to get ''cctbx.xfel'':
** ''cctbx.xfel'' is installed for general use at SLAC.  To start using an existing installation, first [[Set up PSDM software | set up the PSDM software distribution]] and then [[Setup | set up ''cctbx.xfel'']].  
** ''cctbx.xfel'' is installed for general use at SLAC.  To start using an existing installation, [[Using the pre-built cctbx at LCLS|simply source the current build]].
** Configure ''cctbx.xfel'' from an [[Configure cctbx.xfel from existing Phenix install | existing Phenix installation]].
** [https://dials.github.io/installation.html Download] a binary bundle of DIALS. Use this option if you will not be processing LCLS data because, for example, if you have serial crystallographic data from a synchrotron.
** Build a psana/cctbx.xfel build [https://exafel.github.io/docs/psana-cctbx-install from scratch]. Use this option if you want to process LCLS data outside of LCLS or want your own build.
* [[Tutorials]] on pre-processing, data reduction, and merging.  
* [[Tutorials]] on pre-processing, data reduction, and merging.  
* ''[[cctbx.prime]]'': tutorials on post-refinement using PRIME.  
* ''[[cctbx.prime]]'': tutorials on post-refinement using PRIME.  
* "[[IOTA]]": tutorial on spotfinding optimization using IOTA.
* ''[[IOTA]]'': tutorial on spotfinding optimization using ''IOTA''.


Other related information:
Other related information:


* [[Serial XFEL Crystallography References]]
* [[Serial XFEL Crystallography References]]
* [[Indexing individual stills]]: how to index stills not necessarily from an XFEL source.
* [[Data Processing at SACLA]]
* [[Processing Blog]] describing how we solved typical problems.
* [[Processing L498 thermolysin]] details instructions to reproduce the results published in the forthcoming ''cctbx.xfel'' paper.
* [[2017 Tutorials]]. Berkeley Lab Serial Crystallography Workshop, 16-17 Feb 2017.
* [[2017 Tutorials]]. Berkeley Lab Serial Crystallography Workshop, 16-17 Feb 2017.
* [[2014 Tutorials | 2014 Workshop Tutorial: ''cctbx.xfel'' ]]. Note, due to recent changes at LCLS, many of these tutorials are out of date for data collected late 2014 and onwards.  For more up to date information, see above [[tutorials]].  For data collected before late 2014, these workshop tutorials are useful.
* [[Experiment-day guidelines]]: a short, very hands-on set of notes for online monitoring and data-processing using cctbx.xfel.
* [[2014_workshop | Powerpoint presentations]]
* [[Experiment-day guidelines]]: a short, very hands-on set of notes for online monitoring and data-processing using cctbx.xfel. This page assumes that the setup and tutorial have been completed.
* [[File formats]]: for developers, information on file formats ''cctbx.xfel'' uses
* [[File formats]]: for developers, information on file formats ''cctbx.xfel'' uses
* [[Cppxfel]]: XFEL data processing with the CPPXFEL package from Diamond/Wellcome Trust.
* [[Cppxfel]]: XFEL data processing with the CPPXFEL package from Diamond/Wellcome Trust.
* For developers only:  [[Installation]] instructions for cctbx developmental build.
* [[Ha14 documentation]]: tutorials and support for processing using the [https://doi.org/10.1038/nmeth.2887 Hattne 2014] methods.


This project is under active development.  For any assistance, please contact the authors.
This project is under active development.  For any assistance, please contact the authors.

Latest revision as of 16:53, 17 July 2020

News! See our [new paper]! This paper shows current best practices using cctbx.xfel with DIALS for serial crystallographic data. Also see the companion set of tutorials.

News! See our [newsletter article] that describes the XFEL GUI, an interactive program for handling large XFEL datasets.

Open-source tools for serial crystallographic data processing

cctbx.xfel is a suite of software tools designed to process diffraction data from serial femtosecond crystallography (SFX) measurements at an X-ray free-electron laser (XFEL) or a synchrotron. Built on the Computational Crystallographic Toolbox (cctbx), the same toolbox on which PHENIX, DIALS, LABELIT, and post-refinement and merging program, PRIME are built, it enables the user to solve difficult problems relating to processing serial crystallographic data. The programs and modules provided by cctbx.xfel can reduce a large set of still diffraction images recorded at Stanford’s Linac Coherent Light Source (LCLS), SACLA, the European XFEL, or a synchrotron, to a single MTZ file containing merged reflection intensities suitable for structure solution.

cctbx.xfel resources

The tutorials on this wiki provide detailed instructions for indexing and integrating still diffraction images extracted from the raw data streams recorded at the LCLS, including pre-processing steps such as dark pedestal generation and refinement of the detector geometry of the Cornell–SLAC pixel array detectors (CSPAD) in use at the CXI and XPP end stations. The tutorials also cover tools to efficiently leverage the LCLS computing cluster to process the thousands to millions of diffraction images that can be recorded in a short time. Finally, processing approaches for data collection at non-LCLS sources are also provided.

  • Overview to the system architecture at LCLS and real-time progress monitoring of data processing
  • Installation: there are two ways to get cctbx.xfel:
    • cctbx.xfel is installed for general use at SLAC. To start using an existing installation, simply source the current build.
    • Download a binary bundle of DIALS. Use this option if you will not be processing LCLS data because, for example, if you have serial crystallographic data from a synchrotron.
    • Build a psana/cctbx.xfel build from scratch. Use this option if you want to process LCLS data outside of LCLS or want your own build.
  • Tutorials on pre-processing, data reduction, and merging.
  • cctbx.prime: tutorials on post-refinement using PRIME.
  • IOTA: tutorial on spotfinding optimization using IOTA.

Other related information:

This project is under active development. For any assistance, please contact the authors.

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