Crystallography: Difference between revisions
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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)] | ||
*[ | *[https://www.globalphasing.com/sharp/ autoSHARP] | ||
*[[BALBES]] | *[[BALBES]] | ||
*[[BNP]] | *[[BNP]] | ||
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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 === | ||
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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 === | ||
Latest revision as of 15:57, 23 April 2021
Crystallographic TheoryEdit
ProceduresEdit
Crystallography SoftwareEdit
For Specific TasksEdit
- 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
- Loop modelling
Automated Pipelines for Structure SolutionEdit
- Ants
- 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 servicesEdit
- ARP/wARP web services (model building)
- Auto-Rickshaw (Structure determination) - see example at xds:1RQW
- Bias removal server
- York suite (Balbes, Modsearch, Zanuda)
- Diffraction Anisotropy Server
- Bravais Lattice Determination by Projections
- 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 [1].
- 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
- STARANISO analyses, corrects and visualises diffraction data for data anisotropy; see also PDBpeep for deposited PDB entries.
- Grade to create restraint dictionaries for refinement
Software PackagesEdit
(large packages first)
- CCP4
- CNS
- PHENIX
- SHELX C/D/E and SHELXL (homepage at [2], overview paper)
- moleman, lsqman, ... from Uppsala Software Factory
- XDS homepage and XDSwiki
- HKL homepage
- COOT
- PyMol wiki
- CCP4mg
- O
- ARP/wARP
- SHARP homepage
- Solve/Resolve
- 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.
- Global Phasing Ltd (data processing, structure solution, refinement - BUSTER, SHARP/autoSHARP, autoPROC, Grade, Rhofit, Pipedream, STARANISO)
Edit
- Clipper
- Crystallographic Toolbox
- CCP4 library; documentation at [3]
- mmdb
Tips and TricksEdit
Teaching crystallographyEdit
Crystallography courses on the webEdit
Crystallography booksEdit
Test data setsEdit
The effect of resolution on electron densityEdit
- James Holton's movie [[4]]
Understanding and extending the properties and limitations of crystallographic computationsEdit
Ensemble refinement, and molecular dynamicsEdit
- 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]
- Heterogeneity and Inaccuracy in Protein Structures Solved by X-Ray Crystallography. DePristo MA,de Bakker PIW, Blundell TL (2004) Structure 12, 831-838 [6]
- Ensemble Refinement of Protein Crystal Structures: Validation and Application. Levin EJ, Kondrashov DA, Wesenberg GE, Phillips GN, Structure 15, 1040 - 1052 [7]
- 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-rayEdit
- 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-rayEdit
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 [10]
- 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.
- 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]