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= Open-source tools for free-electron laser data processing =
 
= Open-source tools for free-electron laser 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).  Built on the Computational Crystallographic Toolbox ([http://cctbx.sourceforge.net ''cctbx'']), the same toolbox on which [http://www.phenix-online.org ''PHENIX''] and [http://adder.lbl.gov/labelit ''LABELIT''] 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.
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''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.
 
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== [[2014 Tutorials | 2014 Workshop Tutorial: cctbx.xfel ]]==
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== ''cctbx.xfel'' resources ==
 
== ''cctbx.xfel'' resources ==
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* [[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: ''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'']].  
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* Installation: there are two ways to get ''cctbx.xfel'':
** To install ''cctbx.xfel'' elsewhere, or to set up an installation for development purposes, see the [[Installation]] instructions. For most regular users this should not be necessary; SLAC as well as several other sites already have a generally accessible installation.
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** ''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'']].  
** [[Maintaining an installation]] describes how to keep a setup up-to-date.
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** Configure ''cctbx.xfel'' from an [[Configure cctbx.xfel from existing Phenix install | existing Phenix installation]].
 
* [[Tutorials]] on pre-processing, data reduction, and merging.  
 
* [[Tutorials]] on pre-processing, data reduction, and merging.  
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* ''[[cctbx.prime]]'': tutorials on post-refinement using PRIME.
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* "[[IOTA]]": tutorial on spotfinding optimization using IOTA.
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Other related information:
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* [[Serial XFEL Crystallography References]]
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* [[Indexing individual stills]]: how to index stills not necessarily from an XFEL source.
 
* [[Processing Blog]] describing how we solved typical problems.  
 
* [[Processing Blog]] describing how we solved typical problems.  
 
* [[Processing L498 thermolysin]] details instructions to reproduce the results published in the forthcoming ''cctbx.xfel'' paper.
 
* [[Processing L498 thermolysin]] details instructions to reproduce the results published in the forthcoming ''cctbx.xfel'' paper.
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* [[2017 Tutorials]]. Berkeley Lab Serial Crystallography Workshop, 16-17 Feb 2017.
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* [[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.
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* [[2014_workshop | Powerpoint presentations]]
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* [[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.
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* [[File formats]]: for developers, information on file formats ''cctbx.xfel'' uses
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* [[Cppxfel]]: XFEL data processing with the CPPXFEL package from Diamond/Wellcome Trust.
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* For developers only:  [[Installation]] instructions for cctbx developmental build.
  
 
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.
 
[[Serial XFEL Crystallography References]]
 
 
[[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.
 
 
[[Indexing individual stills]]: how to index still not necessarily from an XFEL source.
 

Revision as of 15:06, 8 February 2017

Open-source tools for free-electron laser 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). Built on the Computational Crystallographic Toolbox (cctbx), the same toolbox on which PHENIX, LABELIT, and post-refinement and merging program, 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 (LCLS) 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.

Other related information:

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