Crystallography Links & Resources
“Small Angle X-ray Scattering Links”
Links Related to the Course “Biochem 6321-004 Molecular Structure Analysis and Graphics in Biomedical Sciences” are found at the bottom of this page
Crystallographic Computing in Oklahoma
OU Supercomputing Center for Education and Research (OSCER) – has massive supercomputing resources open to all academics in Oklahoma. It has a number of computationally intensive crystallographic programs installed in /home/software/, including some listed below.
Data Reduction:Structure Determination:Refinement:Visualization:
XDS
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CCP4
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SGXPro
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PyMol
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MOSFLM
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Phenix
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Phenix
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VMD
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CCP4
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SGXPro
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Shelxl
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Shelx
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SuperFlip
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SIR
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wARP
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Recommended Textbooks on Crystallography:
The leading textbook:
A highly readable textbook of intermediate level:
A concise but clear introduction to the basic principles:
A non-expert explains crystallography:
A collection of contributions from highly regarded contributors:
2001 version is available on-line in Bissel Library on main campus
A comprehensive treatment of all of crystallography:
The following volumes in the series Methods in Enzymology have excellent coverage of specific crystallography methods:
- 114 Diffraction Methods for Biological Macromolecules Part A
- 115 Diffraction Methods for Biological Macromolecules Part B
- 276 Macromolecular Crystallography Part A
- 277 Macromolecular Crystallography Part B
- 368 Macromolecular Crystallography, Part C (its about crystallization)
Additional crystallography chapters are embedded in other volumes (e.g., volume 493 has several chapters on drug fragment screening by crystallography)
Sites & Software
General Packages:
- Phenix - a rapidly evolving integrated system of crystallographic software
- Uppsala software factory - a nexus of useful software
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CCP4 - a large and integrated collection of programs
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CNS - the descendent of xplor
Visualizing and Producing Publication Quality Figures of Structures:
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Molscript - requires it’s own language, making it more painful than other programs, but highly effective and worth the effort
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Bobscript -take-off of molscript, but allows inclusion of electron density maps
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Conscript -it’s essentially like bobscript but allows Gouraud shaded isosurfaces versus chickenwire representations of electron density.
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Raster3D-required for molscript/bobscript, a rendering program
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PyMOL - available for many platforms, does many representation styles, make movies, and outputs quality rendered images
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Grasp - all time favorite for generating molecular surfaces and electrostatics
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Visualizing and Building Structures:
- Coot - Crystallographic Object-Oriented Toolkit for serious model building into electron density maps
- O-excellent capabilities for building, be sure to check out extras available
- OOPS2 - plug in to work with O in rebuilding
- 3DNA - graphics program for rebuilding nucleic acid structures
- Chimera - program for interactive visualization and analysis of molecular structures
- Swiss- Pdb Viewer DeepView
- Assemble - semiautomated 3-D modeling of RNA
- Rosetta RNA structure prediction
Model Building, Loop Modelling:
Structural Analysis, General:
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EDPDB - manipulate and extract information form pdb files by Dr. Cai Zhang at OMRF
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Surfnet - user friendly program to identify cavities and crevices in molecules, and to produce figures
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CCP4 - has many individual structural analysis modules
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HBPLUS - Hydrogen bond calculation program
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LIGPLOT- Plots schematic diagrams of protein-ligand interactions
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PROCHECK - Protein structure validation program
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Chimera - comprehensive program for the analysis of molecular structures
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APBS - Adaptive Poisson-Boltzmann Solver- Software for evaluating the electrostatic properties of biomolecular systems (integrates nicely with PyMOL), comparable to grasp
Structural Analysis, Glycoproteins:
- pdb-care - PDB CArbohydrate REsidue check
- getCarbo - checj biological reasonableness of glycan primary structure in a pdb file by matching N-glycan primary structure with those stored in the KEGG glycan database
- carp - CArbohydrate Ramachandran Plot
- GlyProt - adds N-glycans in silico to proteins
- pdb2linucs - automatically extracts carbohydrate information from pdb-files and displays it using the LINUCS-Code
- GlycomeDB.org - searchable database for specific glycan structure
- Glycosciences.de - searchable database for specific glycan structure
- GDB:Structures database - searchable database for specific glycan structure
Structural Analysis, RNA:
Refinement Programs:
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CNS (Crystallography and NMR Systems, this is X-Plore for the new century)
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ARP/wARP - for automatic interpretation of electron density and model building (now interfaced to CCP4)
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CNS - the descendent of Xplor from the 1990s
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BUSTER - for difficult refinements (uses TNT in part)
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TNT - for fast and robust refinements
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Shelxl - for high resolution structures and twinned structures
Phasing with Heavy Atoms:
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SnB -dual space direct methods for isomorphous or anomalous techniques
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FindNCS - detects non-crystallographic symmetry directly from heavy atom sites
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RAVE - for electron density averaging (follow software links)
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SHARP -for isomorphous or anomalous techniques, including locating sites, refinement and phasing (now interfaces with ARP/warp)
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- SIR2011
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CNS- the descendent of xplor
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Phasing by Molecular Replacement:
X-ray Data Collection and Reduction:
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adxv -gui to view images and to check for split spots in 3D
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iMosflm -gui interface to the data integration program mosflm
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XDS - X-ray Detector Software- an efficient suite of programs for data reduction
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Pointless -Laue group determination and a check on reality
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Phenix.xtriage - analyze data for quality, symmetry, pseudosymmetry and twinning
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Denzo/scalpack - data reduction programs, requires an expensive license
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D*trek - data reduction programs, generous trial demo versions available from developer
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Scala -scaling program available through ccp4 with lots of valuable statistical analysis of data quality
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Synchrotron Radiation Labs in North America with macromolecular Beamlines:
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SSRL - Stanford Synchrotron Radiation Lab, Menlo Park, CA
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ALS - Advanced Light Source, Berkeley, CA
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APS - Advanced Photon Source, Chicago, IL
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NSLS- National Light Source, Brookhaven, NY
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CHESS- Cornell Hight energy synchrotron Source, Ithaca, NY
- CAMD- Center for Advanced Microstructures & Devices, Baton Rouge, LA
- Canadian Light Source - Saskatoon, CA
Structural Genomics:
Sources of Commercical Crystallization Screens:
Tools for Computing Grid Sceens:
Other Links:
Links for the course “Molecular Structure Analysis and Graphics in Biomedical Sciences”
Bicohem that is offer in the first third of Spring Semester every year since 2010.
Advice on text editors for writing PyMOL script files
Computer scripts are written in plain text. Text editors are easier to use than word processors to make these files. The following are links to free text editors:
For Windows:
For Mac (note: textedit is NOT a text editor)
Lecture 1: Introduction and PyMOL installation
Lecture 2: PDB files and PyMOL Basics
Chapter 10: PDB, mmCIF and other data formats
- PDB file format guide
- mmCIF
Chapter 11: The Worldwide Protein Data Bank
PBDEditor
- PDBJ–PDB Japan
- Web-based server for PDB2PQR
- NDB-Nucleic Acid Database
Molecular Visualization
Physical Molecular Models
Molecular Models as Art:
Lecture 3: Heteroatoms and Molecular Surfaces
Lecture 4: Structure Evaluation
Lecture 5: Protein Evolution and Prediction of Protein-Protein Interations
InterPro Database
Protein-Protein Interaction Databases:
Lecture 6: Structure Superposition and Identifying Molecular Motion from Static Models
Lecture 7: Modeling and Dynamics
TBA
Lecture 8: Using Rosetta with PyMOL
Lecture 9: Ligand Docking and Designing Mutants
Lecture 10: Molecular Movies and Journal Cover Art