Cppxfel - Revision history

Helenginn: published paper link

2016-06-08T12:23:02Z

published paper link

← Older revision		Revision as of 12:23, 8 June 2016
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	This page is under development.		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 This is meant to be read in conjunction with ~~an unpublished~~ paper.		''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 ==		== Installation ==

Helenginn: Adding another tutorial

2016-05-04T01:57:36Z

Adding another tutorial

← Older revision		Revision as of 01:57, 4 May 2016
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	* [[Cppxfel Final Merge]] - producing a final MTZ file for use in structure solution.		* [[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.		* [[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 ==		== 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]].		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]].

Helenginn: adding extra tutorial page on cppxfel indexing

2016-05-04T01:22:40Z

adding extra tutorial page on cppxfel indexing

← Older revision		Revision as of 01:22, 4 May 2016
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	* [[Cppxfel Indexing with DIALS \| Indexing with DIALS]] - cppxfel uses scripts to call on DIALS indexing programs to index individual images.		* [[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 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 Post-refinement]] - post-refinement of crystals against a reference data set generated from the previous stage

Helenginn: changing link

2016-05-04T00:59:19Z

changing link

← Older revision		Revision as of 00:59, 4 May 2016
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	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:		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 \| Indexing with DIALS]] - cppxfel uses scripts to call on DIALS indexing programs to index individual images.		* [[Cppxfel Indexing with DIALS \| Indexing with DIALS]] - cppxfel uses scripts to call on DIALS indexing programs to index individual images.
	* [[Cppxfel Initial Orientation Matrix Refinement]] - performing initial refinement to produce high quality orientation matrices before post-refinement.		* [[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 Post-refinement]] - post-refinement of crystals against a reference data set generated from the previous stage

Helenginn at 12:21, 1 March 2016

2016-03-01T12:21:14Z

← Older revision		Revision as of 12:21, 1 March 2016
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	== Installation ==		== 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 changes added to the cppxfel distribution is documented in this [[Cppxfel change log \| change log]].		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 ==

Helenginn: Adding change log link

2016-02-06T16:18:34Z

Adding change log link

← Older revision		Revision as of 16:18, 6 February 2016
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	== Installation ==		== Installation ==

	~~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]].		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 changes added to the cppxfel distribution is documented in this [[Cppxfel change log \| change log]].

	== Step-by-step tutorials ==		== Step-by-step tutorials ==

Helenginn at 13:35, 28 January 2016

2016-01-28T13:35:14Z

← Older revision		Revision as of 13:35, 28 January 2016
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	== Installation ==		== Installation ==

	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'').		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]].

	== Step-by-step tutorials ==		== Step-by-step tutorials ==

Nicksauter at 23:33, 1 December 2015

2015-12-01T23:33:31Z

← Older revision		Revision as of 23:33, 1 December 2015
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	== Step-by-step tutorials ==		== 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:		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 \| Indexing with DIALS]] - cppxfel uses scripts to call on DIALS indexing programs to index individual images.		* [[Cppxfel Indexing \| Indexing with DIALS]] - cppxfel uses scripts to call on DIALS indexing programs to index individual images.

Nicksauter at 23:29, 1 December 2015

2015-12-01T23:29:32Z

← Older revision		Revision as of 23:29, 1 December 2015
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	== Step-by-step tutorials ==		== Step-by-step tutorials ==

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

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

Helenginn at 20:34, 24 November 2015

2015-11-24T20:34:16Z

← Older revision		Revision as of 20:34, 24 November 2015
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	* [[Cppxfel Post-refinement]] - post-refinement of crystals against a reference data set generated from the previous stage		* [[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 Final Merge]] - producing a final MTZ file for use in structure solution.
	* [[Cppxfel ~~Merging statistics~~]] - how to assess the quality of the XFEL data processing.		* [[Cppxfel Statistics]] - how to assess the quality of the XFEL data processing.

	== Reference manual ==		== 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]].		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]].