Crystallography: Difference between revisions
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* [[Test data sets]] | * [[Test data sets]] | ||
== Crystallography versus NMR == | == Understanding and extending the properties and limitations of crystallographic computations == | ||
=== Why is the final R-factor about 20% for macromolecules, but as low as 5% for small molecules? === | |||
# Burling et al. 1996 | |||
# DePriso et al. (2004) Structure 12, 831-838 | |||
=== Molecular dynamics and X-ray === | |||
# 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] | |||
=== Crystallography versus NMR === | |||
A couple of papers analysing and comparing NMR and X-ray methods/structures: | A couple of papers analysing and comparing NMR and X-ray methods/structures: | ||
# Science (1992), vol. 257, p. 961 | # Science (1992), vol. 257, p. 961 | ||
# 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. | # 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. | # 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 | ||
Revision as of 17:26, 15 November 2008
Crystallographic Theory
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
Web services
- 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
Software Packages
(large packages first)
- CCP4
- CNS
- PHENIX
- SHELX C/D/E and SHELXL (homepage at [1], overview paper)
- moleman, lsqman, ... from Uppsala Software Factory
- XDS homepage and XDSwiki
- HKL homepage
- COOT
- PyMol wiki
- O
- ARP/wARP
- SHARP homepage
- Solve/Resolve
- ...
Tricks and Tips
- Solving a structure
- Model building and refinement
- Model Evaluation and Interpretation
- Finding symmetry elements in P1
Teaching crystallography
Understanding and extending the properties and limitations of crystallographic computations
Why is the final R-factor about 20% for macromolecules, but as low as 5% for small molecules?
- Burling et al. 1996
- DePriso et al. (2004) Structure 12, 831-838
Molecular dynamics and X-ray
- 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) [2]
Crystallography versus NMR
A couple of papers analysing and comparing NMR and X-ray methods/structures:
- Science (1992), vol. 257, p. 961
- 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. http://dx.doi.org/10.1371/journal.pcbi.0020009