Crystallography Links & Resources

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  CCP4  SGXPro    PyMol
 MOSFLM  Phenix  Phenix    VMD
 CCP4  SGXPro  Shelxl  
   Shelx    
   SuperFlip    
   SIR    
   wARP    
       

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
  • CCP4 - a large and integrated collection of programs
  • CNS - the descendent of xplor

Visualizing and Producing Publication Quality Figures of Structures:

  • Molscript - requires it’s own language, making it more painful than other programs, but highly effective and worth the effort
  • Bobscript -take-off of molscript, but allows inclusion of electron density maps
  • Conscript -it’s essentially like bobscript but allows Gouraud shaded isosurfaces versus chickenwire representations of electron density.
  • Ribbons - self explanatory
  • Raster3D-required for molscript/bobscript, a rendering program
  • PyMOL - available for many platforms, does many representation styles, make movies, and outputs quality rendered images
  • Mage(Kinemage homepage) -real time visualization of structures, but can also display results from molprobity
  • Grasp - all time favorite for generating molecular surfaces and electrostatics
  • Protein Explorer - this is RasMol for the new century
  • VMD (Visual Molecular Dynamics) - another viewer (works well with Macs)
  • MolMol - old standard

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:

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:

  • CNS (Crystallography and NMR Systems, this is X-Plore for the new century)
  • ARP/wARP - for automatic interpretation of electron density and model building (now interfaced to CCP4)
  • CNS - the descendent of Xplor from the 1990s
  • REFMAC - accessible via ccp4i
  • BUSTER - for difficult refinements (uses TNT in part)
  • TNT - for fast and robust refinements
  • Shelxl - for high resolution structures and twinned structures

Phasing with Heavy Atoms:

Phasing by Molecular Replacement:

X-ray Data Collection and Reduction:

Synchrotron Radiation Labs in North America with macromolecular Beamlines:

  • SSRL - Stanford Synchrotron Radiation Lab, Menlo Park, CA
  • ALS - Advanced Light Source, Berkeley, CA
  • APS - Advanced Photon Source, Chicago, IL
  • NSLS- National Light Source, Brookhaven, NY
  • 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