Crystallography

2009-10-09T15:36:14Z

Yayahjb: /* Web services */

== Crystallographic Theory ==
* [[Basics of Crystallography]]
* [[Phase problem]], and [[Phasing]]
* [[Twinning]]
* [[R-factors]]
* [http://www.mpimf-heidelberg.mpg.de/~holmes/ Fiber diffraction]
* [[References and links]]

== Crystallography Software ==

=== For Specific Tasks ===
* [[Data reduction]]
* [[Molecular replacement]] (MR)
* [[Substructure determination]]
* [[Experimental phasing]] (SIR/MIR and SAD/MAD)
* [[Electron density modification]]
* [[Automated Model building]]
* [[Interactive Model building]]
* [[Refinement]]
* [[Model validation]]
* [[Model Evaluation]]

=== Automated Pipelines for Structure Solution ===
*[[Ants]]
*[http://www.embl-hamburg.de/Auto-Rickshaw/ Auto-Rickshaw (Structure determination)]
*[[AutoSHARP]]
*[[BALBES]]
*[[BNP]]
*[[CRANK]]
*[[Elves]]
*[[MrBUMP]] - molecular replacement
*[[Phenix]] - comprehensive package
*[[HKL2MAP]] - SAD/MAD/SIRAS/SIR phasing based on [[SHELXC/D/E]]

=== Web services ===
*[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://tuna.tamu.edu/ Bias removal server]
*[http://www.ysbl.york.ac.uk/YSBLPrograms/index.jsp York suite (Balbes, Modsearch, Zanuda)]
*[http://www.doe-mbi.ucla.edu/~sawaya/anisoscale Diffraction Anisotropy Server]
*[http://iterate.sourceforge.net/ Bravais Lattice Determination by Projections]

=== Software Packages ===
(large packages first)
* [[CCP4]]
* [[CNS]]
* [[PHENIX]]
* [[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]
* XDS [http://www.mpimf-heidelberg.mpg.de/~kabsch/xds homepage] and [http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/XDS XDSwiki]
* HKL [http://www.hkl-xray.com homepage]
* [[COOT]]
* [http://www.pymolwiki.org/index.php/Main_Page PyMol] wiki
* [[CCP4mg]]
* [[O]]
* [[ARP/wARP]]
* [[SHARP]] [http://www.globalphasing.com homepage]
* [http://www.solve.lanl.gov/index.html Solve/Resolve]
* ...

=== Libraries for crystallography and related areas ===
* [[Clipper]]
* [[cctbx|Crystallographic Toolbox]]
* [[CCP4]] library; documentation at [http://www.ccp4.ac.uk/html/INDEX.html]
* [[mmdb]]

=== Tricks and Tips ===
* [[Solve-TAT|Solving a structure]]
* [[Buildn-TAT|Model building and refinement]]
* [[Evaluation-TAT|Model Evaluation and Interpretation]]
* [[Finding symmetry elements in P1]]

== Teaching crystallography ==
* [[Crystallography courses on the web]]
* [[Test data sets]]

== 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]

CCP4 wiki - User contributions [en]

Crystallography