Crystallography - Revision history

Kay: /* Software Packages */ fix XDS links

2026-01-15T11:02:11Z

Software Packages: fix XDS links

← Older revision		Revision as of 13:02, 15 January 2026
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	* [[SHELX C/D/E]] and [[SHELXL]] (homepage at [http://shelx.uni-ac.gwdg.de/SHELX], [http://dx.doi.org/10.1107/S0108767307043930 overview paper])		* [[SHELX C/D/E]] and [[SHELXL]] (homepage at [http://shelx.uni-ac.gwdg.de/SHELX], [http://dx.doi.org/10.1107/S0108767307043930 overview paper])
	* moleman, lsqman, ... from [http://xray.bmc.uu.se/usf/ Uppsala Software Factory]		* moleman, lsqman, ... from [http://xray.bmc.uu.se/usf/ Uppsala Software Factory]
	* XDS [http://~~www~~.~~mpimf-heidelberg~~.mpg.de~~/~kabsch/xds~~ homepage] and [~~http~~://~~strucbio.biologie~~.uni-konstanz.de/~~xdswiki~~/index.php/~~XDS~~ XDSwiki]		* XDS [http://https://xds.mr.mpg.de homepage] and [https://wiki.uni-konstanz.de/xds/index.php/Main_Page XDSwiki]
	* HKL [http://www.hkl-xray.com homepage]		* HKL [http://www.hkl-xray.com homepage]
	* [[COOT]]		* [[COOT]]

ClemensVonrhein: /* Software Packages */

2021-04-23T13:57:03Z

Software Packages

← Older revision		Revision as of 15:57, 23 April 2021
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	* [http://www.solve.lanl.gov/index.html Solve/Resolve]		* [http://www.solve.lanl.gov/index.html Solve/Resolve]
	* [http://rna.ucsc.edu/pdbrestraints/ PDB coordinates to Restraints] - This Web-server generates custom RNA/DNA base stacking and base pairing restraints for crystallographic refinement. Input is in PDB format. Output is Pymol , CNS and PHENIX formatted.		* [http://rna.ucsc.edu/pdbrestraints/ PDB coordinates to Restraints] - This Web-server generates custom RNA/DNA base stacking and base pairing restraints for crystallographic refinement. Input is in PDB format. Output is Pymol , CNS and PHENIX formatted.
			* [https://www.globalphasing.com/ Global Phasing Ltd] (data processing, structure solution, refinement - BUSTER, SHARP/autoSHARP, autoPROC, Grade, Rhofit, Pipedream, STARANISO)

	=== Libraries for crystallography and related areas ===		=== Libraries for crystallography and related areas ===

ClemensVonrhein: /* Web services */

2021-04-23T13:55:06Z

Web services

← Older revision		Revision as of 15:55, 23 April 2021
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	* [https://portal.nebiogrid.org/secure/apps/wsmr/ brute force MR] - with up to the full set of SCOP domains (100k) to attempt a Phaser MR placement of each domain. The server then ranks the results, allowing you to identify a single well placed domain. PNAS paper at [http://dx.doi.org/10.1073/pnas.1012095107].		* [https://portal.nebiogrid.org/secure/apps/wsmr/ brute force MR] - with up to the full set of SCOP domains (100k) to attempt a Phaser MR placement of each domain. The server then ranks the results, allowing you to identify a single well placed domain. PNAS paper at [http://dx.doi.org/10.1073/pnas.1012095107].
	* [http://witold.med.virginia.edu/fitmunk/server/ Fitmunk] takes a PDB and MTZ file, and helps to identify your protein by electron density based sequencing, and by fitting different conformations. See https://www.ncbi.nlm.nih.gov/pubmed/26894674 and https://www.ncbi.nlm.nih.gov/pubmed/26660914		* [http://witold.med.virginia.edu/fitmunk/server/ Fitmunk] takes a PDB and MTZ file, and helps to identify your protein by electron density based sequencing, and by fitting different conformations. See https://www.ncbi.nlm.nih.gov/pubmed/26894674 and https://www.ncbi.nlm.nih.gov/pubmed/26660914
			* [https://staraniso.globalphasing.org/ STARANISO] analyses, corrects and visualises diffraction data for data anisotropy; see also [https://staraniso.globalphasing.org/cgi-bin/PDBpeep.cgi PDBpeep] for deposited PDB entries.
			* [http://grade.globalphasing.org/ Grade] to create restraint dictionaries for refinement

	=== Software Packages ===		=== Software Packages ===

ClemensVonrhein: /* Automated Pipelines for Structure Solution */

2021-04-23T13:32:02Z

Automated Pipelines for Structure Solution

← Older revision		Revision as of 15:32, 23 April 2021
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	*[[Ants]]		*[[Ants]]
	*[http://www.embl-hamburg.de/Auto-Rickshaw/ Auto-Rickshaw (Structure determination)]		*[http://www.embl-hamburg.de/Auto-Rickshaw/ Auto-Rickshaw (Structure determination)]
	*[~~[AutoSHARP]~~]		*[https://www.globalphasing.com/sharp/ autoSHARP]
	*[[BALBES]]		*[[BALBES]]
	*[[BNP]]		*[[BNP]]

Kay: /* Web services */

2020-03-20T18:35:52Z

Web services

← Older revision		Revision as of 20:35, 20 March 2020
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	* [http://www.embl-hamburg.de/Auto-Rickshaw/ Auto-Rickshaw (Structure determination)] - see example at [[xds:1RQW]]		* [http://www.embl-hamburg.de/Auto-Rickshaw/ Auto-Rickshaw (Structure determination)] - see example at [[xds:1RQW]]
	* [http://tuna.tamu.edu/ Bias removal server]		* [http://tuna.tamu.edu/ Bias removal server]
	* [~~http~~://www.~~ysbl.york~~.ac.uk/~~YSBLPrograms~~/~~index~~.~~jsp York suite (Balbes, Modsearch,~~ Zanuda)]		* York suite (Balbes, Modsearch, [https://www.ccp4.ac.uk/newsletters/newsletter48/articles/Zanuda/zanuda.html Zanuda])
	* [http://www.doe-mbi.ucla.edu/~sawaya/anisoscale Diffraction Anisotropy Server]		* [http://www.doe-mbi.ucla.edu/~sawaya/anisoscale Diffraction Anisotropy Server]
	* [http://iterate.sourceforge.net/ Bravais Lattice Determination by Projections]		* [http://iterate.sourceforge.net/ Bravais Lattice Determination by Projections]

Kay: /* Slides showing the effect of resolution on electron density [http://www.ysbl.york.ac.uk/~emsley/coot/slides/reso-slides/] */

2018-07-08T07:07:36Z

Slides showing the effect of resolution on electron density [http://www.ysbl.york.ac.uk/~emsley/coot/slides/reso-slides/]

← Older revision		Revision as of 09:07, 8 July 2018
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	=== [[Crystallography books]] ===		=== [[Crystallography books]] ===
	=== [[Test data sets]] ===		=== [[Test data sets]] ===
	=== ~~Slides showing the~~ effect of resolution on electron density [~~http~~://~~www~~.~~ysbl~~.~~york~~.~~ac.uk~~/~~~emsley~~/~~coot/slides/reso-slides~~/] ~~===~~		=== The effect of resolution on electron density ===
			* James Holton's movie [[https://bl831.als.lbl.gov/~jamesh/movies/resolution.mpeg]]

	== Understanding and extending the properties and limitations of crystallographic computations ==		== Understanding and extending the properties and limitations of crystallographic computations ==

Kay: /* Web services */

2017-12-18T12:27:59Z

Web services

← Older revision		Revision as of 14:27, 18 December 2017
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	* [http://iterate.sourceforge.net/ Bravais Lattice Determination by Projections]		* [http://iterate.sourceforge.net/ Bravais Lattice Determination by Projections]
	* [https://portal.nebiogrid.org/secure/apps/wsmr/ brute force MR] - with up to the full set of SCOP domains (100k) to attempt a Phaser MR placement of each domain. The server then ranks the results, allowing you to identify a single well placed domain. PNAS paper at [http://dx.doi.org/10.1073/pnas.1012095107].		* [https://portal.nebiogrid.org/secure/apps/wsmr/ brute force MR] - with up to the full set of SCOP domains (100k) to attempt a Phaser MR placement of each domain. The server then ranks the results, allowing you to identify a single well placed domain. PNAS paper at [http://dx.doi.org/10.1073/pnas.1012095107].
			* [http://witold.med.virginia.edu/fitmunk/server/ Fitmunk] takes a PDB and MTZ file, and helps to identify your protein by electron density based sequencing, and by fitting different conformations. See https://www.ncbi.nlm.nih.gov/pubmed/26894674 and https://www.ncbi.nlm.nih.gov/pubmed/26660914

	=== Software Packages ===		=== Software Packages ===

Kay at 17:24, 28 February 2011

2011-02-28T17:24:16Z

← Older revision		Revision as of 19:24, 28 February 2011
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	* [[References and links]]		* [[References and links]]

			== Procedures ==
	~~== Crystallography Software ==~~
	=== Procedures ===
	* [[Solve-TAT\|Solving a structure]]		* [[Solve-TAT\|Solving a structure]]
	* [[Solve a small-molecule structure]]		* [[Solve a small-molecule structure]]
	* [[Buildn-TAT\|Model building and refinement]]		* [[Buildn-TAT\|Model building and refinement]]
	* [[Evaluation-TAT\|Model Evaluation and Interpretation]]		* [[Evaluation-TAT\|Model Evaluation and Interpretation]]

			== Crystallography Software ==

	=== For Specific Tasks ===		=== For Specific Tasks ===

Kay at 17:22, 28 February 2011

2011-02-28T17:22:26Z

← Older revision		Revision as of 19:22, 28 February 2011
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	* [[Disorder]]		* [[Disorder]]
	* [[References and links]]		* [[References and links]]


	== Crystallography Software ==		== Crystallography Software ==
			=== Procedures ===
			* [[Solve-TAT\|Solving a structure]]
			* [[Solve a small-molecule structure]]
			* [[Buildn-TAT\|Model building and refinement]]
			* [[Evaluation-TAT\|Model Evaluation and Interpretation]]

	=== For Specific Tasks ===		=== For Specific Tasks ===
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	* [[mmdb]]		* [[mmdb]]

	=== Tricks ~~and Tips~~ ===		=== Tips and Tricks ===
	* [[Solve-TAT\|Solving a structure]]
	* [[Buildn-TAT\|Model building and refinement]]
	* [[Evaluation-TAT\|Model Evaluation and Interpretation]]
	* [[Finding symmetry elements in P1]]		* [[Finding symmetry elements in P1]]
	* [[Programs to convert X-ray diffraction image file formats to graphics file formats]]		* [[Programs to convert X-ray diffraction image file formats to graphics file formats]]

Kay: /* Web services */

2010-12-11T09:47:47Z

Web services

← Older revision		Revision as of 11:47, 11 December 2010
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	* [http://www.doe-mbi.ucla.edu/~sawaya/anisoscale Diffraction Anisotropy Server]		* [http://www.doe-mbi.ucla.edu/~sawaya/anisoscale Diffraction Anisotropy Server]
	* [http://iterate.sourceforge.net/ Bravais Lattice Determination by Projections]		* [http://iterate.sourceforge.net/ Bravais Lattice Determination by Projections]
	* [https://portal.nebiogrid.org/secure/apps/wsmr/ brute force MR] - with up to the full set of SCOP domains (100k) to attempt a Phaser MR placement of each domain. The server then ranks the results, allowing you to identify a single well placed domain.		* [https://portal.nebiogrid.org/secure/apps/wsmr/ brute force MR] - with up to the full set of SCOP domains (100k) to attempt a Phaser MR placement of each domain. The server then ranks the results, allowing you to identify a single well placed domain. PNAS paper at [http://dx.doi.org/10.1073/pnas.1012095107].

	=== Software Packages ===		=== Software Packages ===