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

Oklahoma Medical Research Foundation
Crystallographic Organizations:
Protein Crystallography in Oklahoma
The University of Oklahoma in Norman
Sam Noble Foundation
Oklahoma State University
Oklahoma Structural Biology Nexus - an organization of Oklahoma’s structural biologists
CoBRE in Structural Biology

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:

“Biomolecular Crystallography: Principles, Practice, and Application to Structural Biology” by Bernhard Rupp

A highly readable textbook of intermediate level:

“Crystals, X-rays and Proteins: Comprehensive Protein Crystallography” by Dennis Sherwood and Jon Cooper

A concise but clear introduction to the basic principles:

“Protein Crystallography: A Concise Guide” by Eaton E. Lattman and Patrick J. Loll

A non-expert explains crystallography:

“Crystallography Made Crystal Clear, Third Edition: A Guide for Users of Macromolecular Models” by Gale Rhodes

A collection of contributions from highly regarded contributors:

“Volume F: Crystallography of biological macromolecules” Edited by Michael G. Rossmann.

2001 version is available on-line in Bissel Library on main campus

A comprehensive treatment of all of crystallography:

“Fundamentals of Crystallography, 3rd Ed.” Edited by Giacovazzo, Carmelo

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:

Rapper Server, loop modelling
Modeller - can do loop modelling too
Phenix.fit_loops - need phenix
Xpleo web server
Loopy in arp/warp - requires some weak electron density
SLOOP - can generate both a best conformation and ensembles
LoopTK - C++ library for generating a large number of clash-free conformations

Structural Analysis, General:

Uppsala software factory - O graphics package related analysis tools
EDPDB - manipulate and extract information form pdb files by Dr. Cai Zhang at OMRF
Verify3D Structure Evaluation
Surfnet - user friendly program to identify cavities and crevices in molecules, and to produce figures
CCP4 - has many individual structural analysis modules
Caver- finds cavities
HBPLUS - Hydrogen bond calculation program
LIGPLOT- Plots schematic diagrams of protein-ligand interactions
Promotif analysing protein structural motifs
Whatcheck - protein verification tools
PROCHECK - Protein structure validation program
Molprobity (built into Coot and Phenix) - must run before deposition of structure in PDB
Chimera - comprehensive program for the analysis of molecular structures
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:

RNA Secondary Structure Prediction
Mfold, RNA secondary structure prediction, USA server
RNAfold, Vienna RNA Secondary Structure Prediction
NDB - Nucleic Acid Database, 3D crystal and NMR structures
PDB - Protein Data Bank, has NDB’s structures too
SwS- Solvation Web Service, solvation server for nucleic acids, on macs optimized for Safari
Nonconical Base Pair Database
Noncoding RNA database
RNABase
RNAJunction Database
SCOR - Structural Classification of RNA
5S - Ribosomal RNA Database
MERNA - A Database of Metal Ion Binding Sites in 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)
Phenix.refine
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:

SOLVE/RESOLVE - for isomorphous or anomalous techniques
SnB -dual space direct methods for isomorphous or anomalous techniques
FindNCS - detects non-crystallographic symmetry directly from heavy atom sites
RAVE - for electron density averaging (follow software links)
SHARP -for isomorphous or anomalous techniques, including locating sites, refinement and phasing (now interfaces with ARP/warp)
Phenix.autosolve
Shelxc/Shelxd/Shelxe
SIR2011
CNS- the descendent of xplor
Alternate origins in noncentrosymmetric space groups

Phasing by Molecular Replacement:

Phaser - phasing with maximum likelihood methods; accessible through ccp4i
MolRep- automated molecular replacement accessible through ccp4i
EPMR - Molecular Replacement by Evolutionary Search
Molecular Replacement with REPLACE (GLRF and TF)
Molecular Replacement with AmoRe (“stand alone” no longer available – now bundled with CCP4), old manual
Phenix.autoMR
MRX- Molecular Replacement Package Program by Dr. Cia Zhang at OMRF

X-ray Data Collection and Reduction:

adxv -gui to view images and to check for split spots in 3D
iMosflm -gui interface to the data integration program mosflm
XDS - X-ray Detector Software- an efficient suite of programs for data reduction
Pointless -Laue group determination and a check on reality
Phenix.xtriage - analyze data for quality, symmetry, pseudosymmetry and twinning
Denzo/scalpack - data reduction programs, requires an expensive license
D*trek - data reduction programs, generous trial demo versions available from developer
Scala -scaling program available through ccp4 with lots of valuable statistical analysis of data quality
Space Group Diagrams
Space Groups Listed by Reflection Conditions
Twinning Services

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:

Gridzilla
Xtal Wizard

Crystallography Links & Resources