Crystallography: Difference between revisions

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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 ===
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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]]
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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]
* [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
* [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 ===
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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 ===
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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 ==