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Crystallography: Difference between revisions
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* [[Twinning]] | * [[Twinning]] | ||
* [[R-factors]] | * [[R-factors]] | ||
* [[Bulk solvent correction]] | |||
* [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)] | ||
*[ | *[https://www.globalphasing.com/sharp/ autoSHARP] | ||
*[[BALBES]] | *[[BALBES]] | ||
*[[BNP]] | *[[BNP]] | ||
*[[CRANK]] | *[[CRANK]] | ||
*[[Elves]] | *[[Elves]] | ||
*[[Phenix]] | *[[MrBUMP]] - molecular replacement | ||
*[[HKL2MAP]] | *[[Phenix]] - comprehensive package | ||
*[[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://tuna.tamu.edu/ Bias removal server] | * [http://www.embl-hamburg.de/Auto-Rickshaw/ Auto-Rickshaw (Structure determination)] - see example at [[xds:1RQW]] | ||
*[http://www. | * [http://tuna.tamu.edu/ Bias removal server] | ||
* 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://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]. | |||
* [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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* [[CNS]] | * [[CNS]] | ||
* [[PHENIX]] | * [[PHENIX]] | ||
* [[SHELX C/D/E | * [[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://www.mpimf-heidelberg.mpg.de/~kabsch/xds homepage] and [http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/XDS XDSwiki] | ||
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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) | |||
=== Libraries for crystallography and related areas === | |||
* [[Clipper]] | |||
* [[cctbx|Crystallographic Toolbox]] | |||
* [[CCP4]] library; documentation at [http://www.ccp4.ac.uk/html/INDEX.html] | |||
* [[mmdb]] | |||
===Tricks | === 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] | |||