Difference between revisions of "Crystallography"

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* [[Twinning]]
 
* [[Twinning]]
 
* [[R-factors]]
 
* [[R-factors]]
 +
* [[Bulk solvent correction]]
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* [http://www.mpimf-heidelberg.mpg.de/~holmes/ Fiber diffraction]
 +
* [[Disorder]]
 
* [[References and links]]
 
* [[References and links]]
 +
 +
== Procedures ==
 +
* [[Solve-TAT|Solving a structure]]
 +
* [[Solve a small-molecule structure]]
 +
* [[Buildn-TAT|Model building and refinement]]
 +
* [[Evaluation-TAT|Model Evaluation and Interpretation]]
  
 
== Crystallography Software ==
 
== Crystallography Software ==
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* [[Model validation]]
 
* [[Model validation]]
 
* [[Model Evaluation]]
 
* [[Model Evaluation]]
 +
* [[Loop modelling]]
  
 
=== Automated Pipelines for Structure Solution ===
 
=== Automated Pipelines for Structure Solution ===
 
*[[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]]
 
*[[CRANK]]
 
*[[CRANK]]
 
*[[Elves]]
 
*[[Elves]]
*[[MrBUMP]]
+
*[[MrBUMP]] - molecular replacement
*[[Phenix]]
+
*[[Phenix]] - comprehensive package
*[[HKL2MAP]]
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*[[HKL2MAP]] - SAD/MAD/SIRAS/SIR phasing based on [[SHELXC/D/E]]
  
 
=== Web services ===
 
=== Web services ===
*[http://cluster.embl-hamburg.de/ARPwARP/remote-http.html ARP/wARP web services (model building)]
+
* [http://cluster.embl-hamburg.de/ARPwARP/remote-http.html ARP/wARP web services (model building)]
*[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)]
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* 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]
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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].
 +
* [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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* [[COOT]]
 
* [[COOT]]
 
* [http://www.pymolwiki.org/index.php/Main_Page PyMol] wiki
 
* [http://www.pymolwiki.org/index.php/Main_Page PyMol] wiki
 +
* [[CCP4mg]]
 
* [[O]]
 
* [[O]]
 
* [[ARP/wARP]]
 
* [[ARP/wARP]]
 
* [[SHARP]] [http://www.globalphasing.com homepage]
 
* [[SHARP]] [http://www.globalphasing.com homepage]
 
* [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.
 +
* [https://www.globalphasing.com/ Global Phasing Ltd] (data processing, structure solution, refinement - BUSTER, SHARP/autoSHARP, autoPROC, Grade, Rhofit, Pipedream, STARANISO)
  
===Tricks and Tips===
+
=== Libraries for crystallography and related areas ===
* [[Solve-TAT|Solving a structure]]
+
* [[Clipper]]
* [[Buildn-TAT|Model building and refinement]]
+
* [[cctbx|Crystallographic Toolbox]]
* [[Evaluation-TAT|Model Evaluation and Interpretation]]
+
* [[CCP4]] library; documentation at [http://www.ccp4.ac.uk/html/INDEX.html]
 +
* [[mmdb]]
 +
 
 +
=== Tips and Tricks ===
 +
* [[Finding symmetry elements in P1]]
 +
* [[Programs to convert X-ray diffraction image file formats to graphics file formats]]
 +
 
 +
== Teaching crystallography ==
 +
=== [[Crystallography courses on the web]] ===
 +
=== [[Crystallography books]] ===
 +
=== [[Test data sets]] ===
 +
=== 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 ==
 +
 
 +
=== Ensemble refinement, and molecular dynamics ===
 +
# Direct Observation of Protein Solvation and Discrete Disorder with Experimental Crystallographic Phases. Burling FT, Weis WI, Flaherty KM, Brünger AT. Science (1996) 271, 72-77 [http://dx.DOI.org/10.1126/science.271.5245.72]
 +
# Heterogeneity and Inaccuracy in Protein Structures Solved by X-Ray Crystallography. DePristo MA,de Bakker PIW, Blundell TL (2004) Structure 12, 831-838 [http://dx.doi.org/10.1016/j.str.2004.02.031]
 +
# Ensemble Refinement of Protein Crystal Structures: Validation and Application. Levin EJ, Kondrashov DA, Wesenberg GE, Phillips GN, Structure 15, 1040 - 1052 [http://dx.doi.org/10.1016/j.str.2007.06.019]  
 +
# A comparison between molecular dynamics and X-ray results for dissociated CO in myoglobin. Vitkup D, Petsko GA, Karplus M. Nature Structural Biology  4, 202 - 208 (1997) [http://dx.doi.org/10.1038/nsb0397-202] (Vitkup et al showed that fitting a single model to MD-simulation derived "data" gave ~20% R, which means multiple conformers are sufficient to explain the "R-Factor Gap" between the 20% usually obtained for macromolecules, and the 5% routinely obtained for small molecules)
 +
 
 +
=== Electron microscopy and X-ray ===
 +
# Elucidating the medium-resolution structure of ribosomal particles: an interplay between electron cryo-microscopy and X-ray crystallography. Harms J, Tocilj A, Levin I, Agmon I, Stark H, Kölln I, van Heel M, Cuff M, Schlünzen F, Bashan A, Franceschi F, Yonath A. Structure 7, 931-941 (1999) [http://dx.doi.org/10.1016/S0969-2126(99)80120-8]
 +
 
 +
=== NMR versus X-ray ===
 +
A couple of papers analysing and comparing NMR and X-ray methods/structures:
 +
# Combining experimental information from crystal and solution studies: joint X-ray and NMR refinement. Shaanan B, Gronenborn AM, Cohen GH, Gilliland GL, Veerapandian B, Davies DR, Clore GM. Science (1992), 257, 961 [http://dx.doi.org/10.1126/science.1502561]
 +
# X-ray Crystallography and NMR: Complementary Views of Structure and Dynamics, Nature Structural Biology 4, 862-865 (1997). Preprint [http://atbweb.stanford.edu/scripts/papers.php?sendfile=162 available] from Axel Brunger's "publications" website.
 +
# Traditional Biomolecular Structure Determination by NMR Spectroscopy Allows for Major Errors. S.B. Nabuurs, C.A.E.M. Spronk, G.W. Vuister, G. Vriend. PLoS Comput Biol 2(2): e9. [http://dx.doi.org/10.1371/journal.pcbi.0020009]

Latest revision as of 13:57, 23 April 2021

Crystallographic Theory[edit | edit source]

Procedures[edit | edit source]

Crystallography Software[edit | edit source]

For Specific Tasks[edit | edit source]

Automated Pipelines for Structure Solution[edit | edit source]

Web services[edit | edit source]

Software Packages[edit | edit source]

(large packages first)

Libraries for crystallography and related areas[edit | edit source]

Tips and Tricks[edit | edit source]

Teaching crystallography[edit | edit source]

Crystallography courses on the web[edit | edit source]

Crystallography books[edit | edit source]

Test data sets[edit | edit source]

The effect of resolution on electron density[edit | edit source]

  • James Holton's movie [[4]]

Understanding and extending the properties and limitations of crystallographic computations[edit | edit source]

Ensemble refinement, and molecular dynamics[edit | edit source]

  1. Direct Observation of Protein Solvation and Discrete Disorder with Experimental Crystallographic Phases. Burling FT, Weis WI, Flaherty KM, Brünger AT. Science (1996) 271, 72-77 [5]
  2. Heterogeneity and Inaccuracy in Protein Structures Solved by X-Ray Crystallography. DePristo MA,de Bakker PIW, Blundell TL (2004) Structure 12, 831-838 [6]
  3. Ensemble Refinement of Protein Crystal Structures: Validation and Application. Levin EJ, Kondrashov DA, Wesenberg GE, Phillips GN, Structure 15, 1040 - 1052 [7]
  4. A comparison between molecular dynamics and X-ray results for dissociated CO in myoglobin. Vitkup D, Petsko GA, Karplus M. Nature Structural Biology 4, 202 - 208 (1997) [8] (Vitkup et al showed that fitting a single model to MD-simulation derived "data" gave ~20% R, which means multiple conformers are sufficient to explain the "R-Factor Gap" between the 20% usually obtained for macromolecules, and the 5% routinely obtained for small molecules)

Electron microscopy and X-ray[edit | edit source]

  1. Elucidating the medium-resolution structure of ribosomal particles: an interplay between electron cryo-microscopy and X-ray crystallography. Harms J, Tocilj A, Levin I, Agmon I, Stark H, Kölln I, van Heel M, Cuff M, Schlünzen F, Bashan A, Franceschi F, Yonath A. Structure 7, 931-941 (1999) [9]

NMR versus X-ray[edit | edit source]

A couple of papers analysing and comparing NMR and X-ray methods/structures:

  1. Combining experimental information from crystal and solution studies: joint X-ray and NMR refinement. Shaanan B, Gronenborn AM, Cohen GH, Gilliland GL, Veerapandian B, Davies DR, Clore GM. Science (1992), 257, 961 [10]
  2. X-ray Crystallography and NMR: Complementary Views of Structure and Dynamics, Nature Structural Biology 4, 862-865 (1997). Preprint available from Axel Brunger's "publications" website.
  3. Traditional Biomolecular Structure Determination by NMR Spectroscopy Allows for Major Errors. S.B. Nabuurs, C.A.E.M. Spronk, G.W. Vuister, G. Vriend. PLoS Comput Biol 2(2): e9. [11]