MX : macromolecular crystallography

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Welcome to my list of macromolecular crystallography links and resources - a mix of links to programs, tutorials and methods aggregated from around the web plus several I have developed myself over the years.

What's New?

• Literature for crystallograpic theory and practice
• Simple Unix C Shell Scripting
• Unix Quick Reference
• OSX Screen Capture

Crystallography/Lab Methods, Tuturials and Guides

Look further down the page for software and servers.

• Introductory:
  • X-ray Crystallography 101 v1.0 , Jan 2007.
  • Bernhard Rupp's Crystallography 101
  • MRC/Cambridge Crystallography Course, especially basic diffraction.
  • Kevin Cowtan's Interactive Structure Factor tutorial
  • Kevin Cowtan's Book of Fourier
  • Bragg's Law applet
  • MAXINF - teaching macromolecular crystallography.
  • CCP4 wiki crystallography theory.
  • Literature for crystallograpic theory and practice
• Crystals and crystal handling:
  • General advice for handling crystals for cryo work and heavy atom derivitization
  • Phil's Streak Seeding protocol.
  • Simple protocol for running a crystal on a gel to determine its composition.
  • Cambridge: crystallization theory and practice.
  • pictorial library of crystallization drop phenomena.
  • xtal protocols by Johan Zeelen.
  • Hampton Research crystallization tips
  • Cambridge crystallization course
  • Xtalbase crystallization Database.
  • Biological Macromolecule Crystallization Database (BMCD) v4.
  • High-throughput crystallization at HWI (free or for a fee) - now includes membrane protein screens.
  • Brandeis Flash-cooling: A practical guide
  • CCP4wiki: crystal cryo
• Data collection and processing:
  • X-ray Data Collection Guide, v0.3, Jan 2007.
  • Bart Hazes's Data Collection tutorial
  • X-ray Data Processing Guide, v1.0, Oct 2006. (very Denzo/Scalepack-oriented)
  • Data Wrangling v0.1, Jan 2007
  • Cambridge: structure factor statistics
  • Todd Yeates' Crystal Twinning tutorial (and server)
  • Software tutorials
    • XDS wiki
    • Mosflm and Scala via SSRL
    • autoPROC tutorial from the New Orleans ACA meeting
• Solving a structure by molecular replacement:
  • Molecular Replacement Guide v1.0, Sept 2005.
  • Cambridge: Molecular Replacement.
  • Molecular Replacement course from Birkbeck.
  • Molecular Replacement course from Southampton.
  • Gerard Kleywegt's making the most of your molecular replacement model
  • Theory of Molecular Replacement (advanced)
• Solving a structure by MIR, MAD, SAD:
  • Phil's notes for MAD data collection
  • MAD structure determination example v0.2, Oct 2006.
  • Cambridge: Experimental phasing by maximum likelihood
  • Ethan Merritt's Anomalous Scattering pages
  • Table of Anomalous Scatterers at CuKalpha
  • Sasaki tables: table of K edges and table of L edges (anomalous scattering edges).
  • Sasaki tables: F' and F'' for K edges and F' and F'' for L edges (anomalous scattering coefficients).
  • Notes on picking heavy atoms.
  • A little local Heavy Atom database.
  • Heavy atom notes from IMCA-CAT - useful info as well as beamline procedural stuff.
  • Imperial College Heavy Atom Database
  • HATODAS Heavy Atom Database
  • External-PDF: Hampton Research's documentation for their heavy atom screen contains some useful general info.
• Density modification and averaging:
  • Phil's notes on Averaging.
  • Averaging - local density correlation.
  • Cambridge: density modification
• Refinement:
  • Notes from a refinement workshop archived at St. Andrews.
  • Randy Read's notes on Maximum Likelihood for refinement, maps, and practical considerations
  • Cambridge: Fitting, refinement and validation
  • Where to find topology/parameter files for ligands and hetero groups.
• Validation:
  • Gerard Kleywegt's Braille for Pugilists (making the most out of your model).
  • Gerard Kleywegt's model validation tutorial.
  • Ethan Merritt's PARVATI - Anisotropic Validation and Analysis.
• Graphics:
  • Alwyn Jones' O essentials command summary.
  • Alwyn Jones' A-Z of O manual for O.
  • Alwyn Jones' How to O method reference.
  • HTML version of "O for Morons".
  • HTML version of "O for the Structurally Challenged" (text only).
  • O migration: v9 release notes
  • Phil's Notes on O (very much under construction and I have mostly decamped to Coot).
  • Presentation Graphics Guide v1.0, June 2005
  • PyMol for Dummies v0.000000000001, Feb 2006.
  • Phil's primer on how to show sequence conservation in GRASP .
  • Bill (Barton) and Phil's primer on GRASP .
  • Primer on working with GL_RENDER and POVRAY .
• Miscellany:
  • Introduction to Direct Methods
  • UCLA Lab Tutorials
  • Phil's Peek2 manual.
• High Resolution X-ray Diffraction
• Interactive Diffraction Tutorial
• Difference Patterson Tutorial

This list last curated October 2012

Macromolecular Software Home Pages

• AMBER - force fields and simulation suite
• AMMP - molecular mechanics, dynamics, modeling.
• APBS - adaptive poisson-boltzmann solver
• ARP/wARP - automated structure building
• Autostruct - automated structure determination.
• openBabel - coordinate format conversion program (also see iBabel)
• Bobscript - Robert Esnouf's modifications to Molscript - retired ??
• Buster-TNT - structure refinement (also see the wiki).
• CCP4 - suite for many aspects of protein structure determination.
• CCP4mg - molecular graphics project
• CE - combanitorial extension 3D alignment program
• CHARMM - relatively ancient molecular dynamics package
• CHIMERA - UCSF modeling package
• CNS - X-ray and NMR refinement program.
• COOT - macromolecular model-building and validation program.
• DALI server at EBI and Dali server at Lisa Holm's lab in Helsinki.
• DINO - molecular graphics.
• DSSP - protein secondary structure determination.
• Dunbrack rotamer libraries - backbone-dependent libraries (v.2010)
• openEPMR - a new version of the Genetic Algorithm program for molecular replacement
• ELVES - automated crystallography tasks.
• FREEHELIX - DNA bending parameters (source code, minimal web page)
• GROMOS molecular dynamics package
• HBPLUS - hydrogen bond calculator
• HKL (Denzo and Scalepack).
• HKL2MAP (Thomas Schneider's GUI for SHELX)
• HOLE - holes through molecular structures of ion channels.
• IUCr Crystallography online
• LigPlot+ - ligand plotting software
• MAID (auto chain tracing, last version ~2001).
• MIFit from Rigaku/MSC - son of XtalView ?
• MMTK - molecular modeling toolkit
• Molscript (last updated 1999).
• MSMS - molecular surface computation
• NACCESS - Atomic Solvent Accessible Area
• NAMD molecular graphics
• Alwyn's O site
• ORTEP - flexible and arcane molecular graphics
• PDB validation suite - as used by ADIT and other forms of creative torture
• PDB format v3.2 as of Oct 2008
• PHASER for molecular replacement (my favorite one, usually part of CCP4 and Phenix)
• PHENIX - Python-based Hierarchical ENvironment for Integrated Xtallography
• POV-Ray - persistence of vision raytracer
• PovScript+ - Povray compatible modification of Molscript
• PyMol - molecular graphics using Python
• Raster3D - rendering software
• REFMAC - refinement program (included as part of CCP4)
• RIBBONS - Mike Carson's molecular graphics programs.
• Shake and Bake - direct methods software..
• SHARP - Global Phasings rather good heavy atom phasing program.
• SHELX - software for heavy atom site determination, phasing, refinement.
• SOLVE/RESOLVE - phasing and solvent-flattening - now also part of Phenix.
• SPOCK - olde molecular graphics program.
• Swiss-PDB/DeepView - molecular graphics.
• TLSMD - estimate TLS parameters from refined B-factors (good starting point pre-REFMAC)
• TNT - refinement program (Ten-Eyck 'n' Tronrud)
• Uppsala Software Factory - no longer under development.
• VMD (Visual Molecular Dynamics).
• XDS - X-ray data processing software from Wolfgang Kabsch now via the XDS wiki
• XPLOR-NIH - derivative of the X-PLOR package which does not appear to be present on the web now - see CNS.
• XtalView - crystal structure package, not maintained post-2003, unlikely to work cleanly.
• Kevin Cowtan's CLIPPER C++ libraries for crystallographic computing.
• CCTBX - the Computational Crystallography Toolbox.
• Those of us that are Apple fanboys might find use in Macs in Chemistry or MacResearch.org

This list curated as of October 2012.

Bioinformatics Software and Database Search Sites

There are three kinds of lies: lies, damned lies and statistics - Mark Twain (and/or Benjamin Disraeli)

What makes it on this list are methods that aid or inform structural biology. There are huge swaths of activity under the bioinformatics label (e.g. much of genomics and proteomics) that don't enter in this list.

• BARTON group home page - a lot of bioinformatics software
• Searches: BLAST at NCBI (select the PDB sequence database to search for homologs)
• Searches: sequence similarity and homology at EBI/Hinxton
• Searches: WU-BLAST at WUSTL - gone commercial
• Searches: BLAST the Mouse genome project at Jackson Labs
• Searches: BLAST the Drosophila genome project at Indiana
• Searches: BLAST the Plasmodium genome project
• Searches: BLAST the bacterial genomes via NCBI
• Searches: WU-BLAST the yeast genomes via yeastgenome.org
• Searches: SMART - detection of functional domains/motifs in protein sequence
• Searches: HMMER (Hidden Markov Models) for finding domains/motifs in sequence space
• Searches: ELM - functional sites in proteins
• Searches: OWL - composite protein sequence database
• Searches: SwissProt - protein sequence annotations
• Validation: Molprobity
• Validation: ValLigURL - ligand validation with probably the most contrived URL/name of all time
• Validation: Phenix incorporates aspects of Molprobity and Polygon
• Str Alignment: many local programs do this: PEEK2, LSQMAN, O, COOT etc
• Str Alignment: PDBeFold aka SSM
• Str Alignment: CE pairwise structure alignment via RCSB
• Str Alignment: SuperPose server from U. Alberta
• Str Alignment: Fatcat pairwise alignment via Burnham Institute
• Str Alignment: SSAP alignment of PDB files or CATH domains
• Str Alignment: CE-MC multiple structure alignment
• Str Alignment: Multi-Prot multiple structure alignment
• Str Alignment: STAMP multiple structure alignment
• ... see Wikipedia entry for Structure Alignment Software for more options
• Alignment: Readseq format converter
• Alignment: Muscle server at EBI (multiple sequence alignment)
• Alignment: ClustalW server at EBI (multiple sequence alignment)
• Alignment: ClustalX/ClustalW binaries for OSX - now rather dated
• Alignment: EMBOSS - open source software for molecular biology (also web server)
• Alignment: ESPript - "pretty" representations of sequence alignments
• Alignment: Indonesia - Java package for biological sequence analysis
• Alignment: jAligner - Smith-Waterman in Java.
• Alignment: PFAM database of domains and HMMs
• Alignment: PHYLIP for phylogenies
• Alignment: Rate4Site for phylogeny-conservation
• Alignment: STRAP - multiple sequence alignment editor
• Structure: PDB database
• Structure: PISA - interfaces, surfaces and assemblies
• Structure: PDBreport database
• Structure: Yale protein geometry software
• Structure: Database of Macromolecular Movements
• Structure: Atlas of protein side-chain interactions
• Structure: Gerard Kleywegt's STructure ANalysis server STAN
• Structure: Metal coordination sites in proteins
• Structure Search: SSM
• Structure Search: MATRAS
• Structure Search: DALI server at EBI and Dali server at Lisa Holm's lab in Helsinki.
• Structure Search: VAST at NCBI.
• Structure Search: PINTS - patterns in non-homologous tertiary structures.
• Structure Search: SUMO - 3D search for functional sites.
• Folds: CATH Protein Structure Classification from U.C.L.
• Folds: ProDom database of protein domains
• Folds: SCOP - structural classification of proteins
• Folds: Macromolecular Structure Database at EMBL-EBI.
• Folds: PROSITE: database of protein families and domains
• SecStr Prediction: Secondary Structure Prediction methods and links
• SecStr Prediction: PredictProtein secondary structure predictions (remains free for academia - formerly my favorite site)
• SecStr Prediction: NPS@ - Network protein sequence @nalysis from IBCP, France
• SecStr Prediction: PSIPred server
• SecStr Prediction: JPRED3 - consensus secondary structure prediction
• SecStr Prediction: BSM Search Launcher for various ss prediction servers
• Domain Type Prediction: COILS - coiled-coil prediction server
• Domain Prediction: Weizmann FoldIndex (structure propensity, fold likelyhood)
• Domain Prediction: DisEMBL - protein disorder prediction
• Domain Prediction: GlobPlot - predictor of protein disorder and globularity
• Domain Prediction: DomPred domain prediction server.
• Domain Prediction: DomPro domain prediction server
• Modeling: Guide to structure prediction
• Modeling: ROBETTA structure prediciton server
• Modeling: 3D-PSSM - fold prediction via threading.
• Modeling: SCWRL3 - predict protein side-chain conformation.
• Modeling: Andrei Sali's MODELLER - homology modeling package.
• Modeling: Swiss-Model homology modeling server
• Modeling: NIH CEnter for Molecular Modeling
• Modeling: MODBASE database of protein homology models
• Modeling: JACKAL homology modeling package.
• Modeling: BINGO graphical environment for structure modeling.
• Modeling: 3DJigsaw - homology modeling server
• Threading: Threader from UCL(?)
• Threading: Robetta from the Baker lab.
• Docking: Software and Servers
• Docking: DOCK from UCSF
• Docking: AutoDock from Scripps
• Docking: 3D-Dock suite from ICRF
• Docking: HEX from Aberdeen
• Morphing: Yale protein structure Morph Server
• Morphing: Uppsala tutorial on Biomolecular Morphing
• Morphing: U.Mass protein morphing software
• Links: Software for molecular biology from IUBio Archive
• Links: Software for molecular biology from EBI (via FTP)
• Links: EBI Biocatolog of software for molecular biology and genetics.
• Links: Proteomics Tools - wide range of links from Expasy

Structural Genomics

Greg Petsko's "An idea whose time has gone" is a rather interesting alternative viewpoint on this subject.

• New York Structural Genomics Research Consortium
• Tuberculosis structural genomics
• Joint Center for Structural Genomics
• Northeast Structural Genomics Consortium
• Berkeley Structural Genomics Center
• Midwest Center for Structural Genomics
• Center for Eukaryotic Structural Genomics
• SouthEast Collaboratory for Structural Genomics
• Adventures in capitalism #1: Syrrx - bought by Takeda.
• Adventures in capitalism #2: StructuralGenomix - bought by Eli Lilly
• Search Google for other "structural genomics" hits.

Crystallographic Computing

The state of hardware running Unix (Linux variants and OSX) and the improvement in software installation methods has meant that installing and operating crystallographic software on one's own machine is no longer a Herculean task. Consequently the number of meaningful links here has shrunk dramatically. You can probably get decent operational systems running in virtual machines, if you so desire.

• Crystallography on OSX - Bill Scott's site
• Simple Unix C Shell Scripting
• Unix Quick Reference
• CCP4 community wiki.
• Kevin Cowtan's Clipper Project
• CCTBX - Computational Crystallography Toolbox
• Eugene Krissinel's MMDB library
• However programming still remains at a premium in order to exploit all these useful new resources. Too many grad students emerge without having any sort of idea how to program in any sort of scripting or compiled language, which hobbles them the moment they hit a difficult problem. C and especially C++ are widely taught these days at the undergraduate level, so correspondingly there are a ton of tutorials out there. Python seems to be currently rather trendy, thankfully eclipsing Perl, and Fortran is very much on the wane despite the fact that some crystallographic software remains written in it. Even I have shifted from Fortran to C to C++ for writing new programs.
  • Programming in C .
  • University of Strathclyde's C Programming .
  • Eskimo.com C Programming .
  • Eskimo.com Intermediate C Programming
  • Brian Kernighan's old K&R style Programming in C: A Tutorial .
  • A whole host of links on C programming .
  • C++.com's C++ Tutorial
  • Iowa State Fortran Programming Tutorial .
  • Oxford Chemistry Dept Programming in FORTRAN .
  • A whole host of links on Fortran programming .
  • Since they are now a dime a dozen, use Google to search for HTML tutorials
  • Mathematical and Greek Symbols in HTML
  • A First Guide to PostScript.
  • IlliGAL: Illinois Genetic Algorithms Lab Fortran Genetic Algorithm software
  • Or search Google for more.
• Screen capture on OSX.

Manufacturers/Vendors

Inclusion or exclusion here doesn't infer support to one vendor or another. I'm more interested in keeping up with methods than I am with (e.g.) the proliferation of vendors offering crystallization screens.

• Crystallization:
  • Hampton Research - one of the earliest supplies of crystallization screens.
  • Jena bioscience
  • Emerald BioSystems - Wizard Screen(s), screen making hardware, etc.
  • Molecular Dimensions, another manufacturer of crystallization screens and some cryocrystallography mounting items.
  • Crystallization robot: Douglas Instruments (Oryx)
  • Crystallization robot: TTP Lab Tech (Mosquito and Mosquito LCP)
  • Crystallization robot: Art Robbins (Phoenix, Gryphon and Gryphon LCP)
  • Crystallization robot: Rigaku has a wide range of robots devoted to various phases of crystallization
  • ... and also have one of the few commercial crystal mounting robots
• Heavy atoms:
  • Sigma-Aldrich offers a decent range of heavy atoms
  • Hampton Research heavy atom kits
  • Jena bioscience - Ta clusters, the "magic triangle", and halogenated ATP/GTP.
• Cryo crystallography:
  • Hampton Research cryo products
  • MiteGen - polymer-based crystal mounts and tools.
  • Spearlab foam dewars
  • Oxford Cryosystems 700 series and Cryostream Plus
  • Oxford Instruments Cryojet - despite name similarities these are not affiliated with Oxford Cryosystems but have a wide range of other products
• X-ray generators, optics and detectors:
  • Rigaku - generators, detectors, optics.
  • Bruker - detectors and generators.
  • MAR research - detectors (including the venerable 345) and generator
  • Xenocs make multilayer X-ray optics comparable to the same sort of thing from Rigaku. We recently installed a Xenocs Fox 2D 25-25P optic on our Ru3HR generator and are happy with it.
  • ADSC detectors - by far the most numerous CCD detectors found at synchrotrons (Quantum 4, Quantum 210, Quantum 315 etc).
  • Pilatus pixel array detectors - look to be the coming wave of technology destined to replace CCDs
• Charles Supper Co. make an interesting set of extended arc goniometer heads and some other crystallographic equipment.
• The P212121 store offer some crystallography supplies
• The historically invaluable Polycrystal Book Service closed in 1999 after many, many years of great service to the community (see this IUCr link)

Broken links ? Search for it's new location via Google, then let me know the new URL....

Content © Phil Jeffrey. Contact me at: phil.jeffrey~at~gmail.com