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

• 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:

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:

• Structural Genomics
• South East Collaboratory for Structural Genomics
• Center for High-Throughput Structural Biology
• JCIMPT
• Center for Structures of Membrane Proteins

Sources of Commercical Crystallization Screens:

• Hampton Research Inc.
• Emerald Biosystems
• Molecular Dimensions
• Qiagen (Nextal)
• Jena Biosciences
• Database of Screens

Tools for Computing Grid Sceens:

• Gridzilla
• Xtal Wizard

Other Links:

• Tips for improving crystal quality
• Tips of cryoprotection of fragile crystals
• Protocol for making Se-Met Proteins
• Tips on mounting fragile needle-shaped crystals

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:

• EidtPad Lite
• Notepad2

For Mac (note: textedit is NOT a text editor)

• TextWrangler (Mooers’s favorite)
• Fraise
• Smultron

Lecture 1: Introduction and PyMOL installation

• Pymol Related:
• Pymol Dwnload Links
• Pymol wiki
• Pymol plugins
• PyMOL Commands
• Pymol scripts
• EZ-Viz

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 

• wwPDB–The Worldwide Protein Data Bank
• PDB–Research Collaboratory for Structural Bioinformatics
• PDBe–Protein Data Bank Europe
• PDBj–PDB Japan
• NDB–Nucleic Acid Database
• PDBEditor–platform independent, gui-driven pdb file editor that is easy to use.

PBDEditor

• PDBJ–PDB Japan
• Web-based server for PDB2PQR
• NDB-Nucleic Acid Database

Molecular Visualization

• Qutemol

Physical Molecular Models

• The Center for BioMolecular Modeling
• PDB file format documentation
• The Scripps Molecular Graphics Laboratory 

Molecular Models as Art: 

• PyMOL Cover Art
• Molecular Graphics Art Show
• Biografx

Lecture 3: Heteroatoms and Molecular Surfaces

• Metal Sites in Proteins – MESPEUS database
• Molesoft Browser Pro (alternative molecular graphic program)
• ValLigURL–Ligand Validator at Uppsala University
• PRODRG
• PymolWiki page on Surfaces
• PymolWiki page on Displaying Biochemical Properties
• Mole
• On-line alternative for Mole
• APBS
• APBS Plugin
• APBS electrostatics in PyMOL
• PDB2PQR Server (calculates pdb2pqr file parameters and an run APBS on-line to generate a *.dx file of electrostatic potentials that can be displayed in PyMOL)
• Download site for PDB2PQR

Lecture 4: Structure Evaluation

• TLS Motion Determination Home
• SF-TOOL
• MOLPROBITY

Lecture 5: Protein Evolution and Prediction of Protein-Protein Interations

InterPro Database

Protein-Protein Interaction Databases: 

• InterDom (domain interactions)
• DIP (DB of Interacting Proteins)
• BOND (PPI, Prot-DNA, Prot-SM)
• MINT – Molecular Interactions Database
• STRING (EMBL)
• Human Protein Reference Database

Lecture 6: Structure Superposition and Identifying Molecular Motion from Static Models

• Superposition of pairs of models in PyMOL
• Fitting multiple models in PyMOL 

• NIH Molecular Modelling Database
• ExPASy Proteomics tools
• Tertiary Structure Analysis Links at the Weizmann Institute
• Protein Crystallography Universe Links
• EMBL-EBI links

Lecture 7: Modeling and Dynamics

TBA

Lecture 8: Using Rosetta with PyMOL

• PyRosetta

Lecture 9: Ligand Docking and Designing Mutants

• dock
• autodock 4.2
• autodock vina

Lecture 10:   Molecular Movies and Journal Cover Art

• PNAS Cover Art
• PDBEditor
• unicode fonts

• PyMOL Cover Art
• PNNL Cover Art
• Vendor of Cover Art
• Lawrence-Berkeley National Lab
• Nature Chemistry Advice