Macromolecular Crystallography Facility Home Page

This is the home page of the Macromolecular Crystallography Facility in the Dept. of Molecular Biology at Princeton University. In contrast to the Molbio Crystallography Facility Home Page this page is not an official Molbio or Princeton product. It contains a lot of utilitarian data intended for use by crystallographers during structure determination. Use at your own risk. Nevertheless the content here is provided in the hope that some of it will be useful. Copyright is maintained by the original authors - there are many links to outside sources of information within these pages. Comments to the Facility Manager: Phil Jeffrey, 8-3978, Schultz 417 or preferably via EMAIL.

Caveat: there is still a lot of inconsistency about the look-and-feel of these pages. It's a choice between adding content or spending a month hacking HTML and CSS. The content tends to win because I'm not a graphic designer. I am, however, working on it. Slowly.

What's New?

An idea whose time has gone - Prof. Greg Petsko's commentary on the Protein Structure Initiative, deserves special mention.
Facility wiki for simple content presentation
Simple Unix scripting v0.1
Data Wrangling v0.1
My commentary on the ABC transporter debacle that led to the retraction of 5 papers recently (3 of them from Science).
Molbio Facility Page now "live".
Some changes to the look-and-feel of these pages to make it similar to my Molbio Facility Page
Backups of all Unix user space are now active and run at least weekly
Tutorials added: Presentation Graphics; Streak Seeding; MAD examples are under way. Numerous updates to guides and tutorials.
X-ray safety/SOP info updated, more SOPs added for hardware processes

Safety

Public Safety - 8-3134
Princeton EHS website and 8-5294
Cornell MSDS site.
SIRI MSDS site.

Hardware-related Issues

Standard Operating Procedure for Raxis IV++ system.
Procedure for generator startup/shutdown.
Minimal Procedure for generator startup.
How to program the Oxford Cryostream.
Cryo controller EvapT issues.
Procedure for testing X-ray Facility interlocks.
Protocol for changing the filament
Protocol for pumpdown of Oxford cryo head
Supplies - Convenience list of frequently-ordered supplies for xtaln and xray work.
Phil's notes on Setting Up the Linux/RedHat Servers from MSKCC
Phil's notes on Setting Up the Linux/RedHat Graphics Workstations from MSKCC
Phil's notes on Setting Up the Linux/RedHat Laptop from MSKCC
Phil's notes on Setting Up the OS X Server at MSKCC
Phil's notes on Setting Up the OS X Server at Princeton
Phil's brief notes on OS X for crystallography
Useful: MacOSXLabs project and their webcasts
Phil's notes on Cloning and restoring SGI Root disks
Phil's notes on compression and backups
Useful external link for Advanced IRIX Sysadmin for Scientists from Daresbury lab.
MacResearch.org - Mac OSX in Science

Synchrotron Issues

BNL Gate Access Form and User Registration pages.
BNL User Admin is (631) 344-7976 (8am-5pm M-F).
BNL Housing is (631) 344-2541 (or 2551) (8am-midnight M-F, 4pm-12pm Sun).
Packing - Synchrotron packing list.
Directions to BNL and CHESS.
Summary of synchrotron beamlines of interest to us (in preparation).
Brookhaven (NSLS) beamline X29
Brookhaven (NSLS) beamline X25
Phil's primer on backing up data at BNL (old version here).
Brookhaven beam status.
Brookhaven Ring Status
Brookhaven Operating Schedules
Macromolecular Protein Crystallography at the NSLS.
CHESS and MacCHESS pages
APS (Argonne) home page, APS user info (registration etc)
NE-CAT beamlines at Argonne
8BM - notes on Argonne beamline 8BM
How to collect data from crystals with long unit cell axes
Library of beamlines and methods used to solve structures

Software-related Issues

Summary of crystallographic software installed or at least under consideration.
Xray0 SHARP server (registered users only; tell Phil if the server is down)
Unix crib sheet - Basic commands and features of Unix.
Cygwin - Unix environment for Windows.
External: Unix for Beginners from Uppsala.
Mac OSX screen capture hints.

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
Buster-TNT - map improvement.
CCP4.
CCP4mg - molecular graphics project
CE - combanitorial extension 3D alignment program
CHARMM - relatively ancient molecular dynamics package
CHIMERA - UCSF modeling package
CNS.
DALI server at EBI.
DINO - molecular graphics.
Dunbrack rotamer libraries - backbone-dependent libraries
openEPMR - a new version of the Genetic Algorithm program for molecular replacement
ELVES - automated crystallography tasks.
FREEHELIX - DNA bending parameters
GROMOS molecular dynamics package
HBPLUS - hydrogen bond calculator
HELANAL - alpha-helix geometry
HKL (Denzo and Scalepack).
HKL2MAP (Thomas Scheider's GUI for SHELX)
HOLE - holes through molecular structures of ion channels.
IUCr Crystallography online
LigPlot - ligand plotting software
MAID (auto chain tracing).
MIFit from Rigaku/MSC - son of XtalView ?
MMTK - molecular modeling toolkit
Molscript.
MolviewX.
MSMS - molecular surface computation
NACCESS - Atomic Solvent Accessible Area
NAMD molecular graphics
Alwyn's O site and the one from Morten
ORTEP - flexible and arcane molecular graphics
PDB validation suite - as used by ADIT, the bane of our existence
PDB format v2.2 description.
PHASER for molecular replacement
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 (part of CCP4)
RIBBONS - Mike Carson's molecular graphics programs
Shake and Bake.
SHARP.
SHELX.
SOLVE/RESOLVE.
SPOCK - molecular graphics
SQUID - early implementation of auto-building.
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.
VMD (Visual Molecular Dynamics).
XDS - X-ray data processing software from Wolfgang Kabsch
X-PLOR.
XtalView.
Kevin Cowtan's CLIPPER C++ libraries for crystallographic computing.
CCTBX - the Computational Crystallography Toolbox.

Crystallography/Lab Methods and Guides

External: CCP4 community wiki.
Simple protocol for running a crystal on a gel to determine its composition.
Phil's Streak Seeding protocol.
Simple Unix scripting v0.1, Mar 2007.
X-ray Crystallography 101 v1.0 , Jan 2007.
X-ray Data Collection Course in preparation, Jan 2007, incomplete .
X-ray Data Processing Guide v1.0, Oct 2006.
Data Wrangling v0.1, Jan 2007
Molecular Replacement Guide v1.0, Sept 2005.
MAD structure determination example v0.2, Oct 2006.
Presentation Graphics Guide v1.0, June 2005
PyMol for Dummies v0.000000000001, Feb 2006
C for Crystallographers Guide v0.01, Feb 2006 - in the very early stages of being written.
Primer on working with GL_RENDER and POVRAY .
Phil's primer on how to show sequence conservation in GRASP .
Bill (Barton) and Phil's primer on GRASP .
Where to find topology/parameter files for ligands and hetero groups.
Notes on picking heavy atoms.
A little local Heavy Atom database.
External: Heavy atom notes from IMCA-CAT - has useful info as well as beamline procedural stuff.
External: Imperial College Heavy Atom Database
External: HATODAS Heavy Atom Database
External-PDF: Hampton Research's documentation for their heavy atom screen contains some useful general info.
mmtbx.xtriage mydata_truncate.mtz residues=1204 by way of example
Phil's Peek2 manual.
Phil's Annotate manual.
Phil's Predict4 manual (data collection strategy for X9A).
Phil's Notes on O (very much under construction).
Phil's notes on Averaging.
External: Averaging - local density correlation.
External: Alwyn Jones' O essentials command summary.
External: Alwyn Jones' A-Z of O manual for O.
External: Alwyn Jones' How to O method reference.
External: O migration: v9 release notes
External: HTML version of "O for Morons".
External: HTML version of "O for the Structurally Challenged" (text only).
External: pictorial library of crystallization drop phenomena.
External: xtal protocols by Johan Zeelen.
External: Hampton Research crystallization course
External: Xtalbase crystallization Database.
External: Biological Macromolecule Crystallization Database (BMCD).
External: High-throughput crystallization at HWI (free or for a fee).
External: Bernhard Rupp's Crystallography 101
External: MRC/Cambridge Crystallography Course - URL now corrected
External: Kevin Cowtan's Interactive Structure Factor tutorial
External: Kevin Cowtan's Book of Fourier
External: Bragg's Law applet
External: Ethan Merritt's Anomalous Scattering pages
External: 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).
External: Brandeis Flash-cooling: A practical guide
Phil's notes for MAD data collection
External: High Resolution X-ray Diffraction
External: Bart Hazes's Data Collection tutorial
External: Interactive Diffraction Tutorial
External: Todd Yeates' Crystal Twinning tutorial (and server)
External: Difference Patterson Tutorial
External: Molecular Replacement course from Cambridge - URL updated.
External: Molecular Replacement course from Birkbeck.
External: Molecular Replacement course from Southampton.
External: Gerard Kleywegt's making the most of your molecular replacement model
External: Notes from a refinement workshop archived at St. Andrews.
External: Introduction to Direct Methods
External: Randy Read's notes on Maximum Likelihood for refinement, maps, and practical considerations
External: UCLA Lab Tutorials
External: Gerard Kleywegt's Braille for Pugilists (making the most out of your model).
Phil's report on the Gordon Conference on Diffraction Methods in 2002.
External: Ethan Merritt's PARVATI - Anisotropic Validation and Analysis.
External: Gerard Kleywegt's model validation tutorial.
External: MAXINF - teaching macromolecular crystallography.

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

Bioinformatics Software and Database Search Sites

BARTON group home page - lotsa software
Searches: BLAST at NCBI
Searches: WU-BLAST at EBI/Hinxton
Searches: WU-BLAST at WUSTL
Searches: BLAST the Mouse genome project at Jackson Labs
Searches: BLAST the Drosophila genome project at Berkeley
Searches: BLAST the Plasmodium genome project
Searches: BLAST the S.cerevisiae genome project at Stanford
Searches: BLAST the Leishmania genome project
Searches: TIGR BLAST for Unfinished Microbial Genomes
Searches: HMMER (Hidden Markov Models) for finding domains/motifs in sequence space
Searches: SMART HMM software for finding domains/motifs in sequence space
Searches: ELM - functional sites in proteins
Searches: Protein Prospector - mining sequence databases from mass spec. results
Searches: OWL - composite protein sequence database
Searches: SwissProt - protein sequence annotations
Validation: Molprobity
Validation: ValLigURL - ligand validation with probably the most contrived URL of all time
Str Alignment: CE-MC multiple structure alignment
Str Alignment: Multi-Prot multiple structure alignment
Str Alignment: Mammoth-Mult multiple structure alignment
Alignment: ClustalW server at EBI
Alignment: EMBOSS - open source software for molecular biology
Alignment: DOTLET for finding sequence repeats
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: ESPript - sequence alignment (w/ annotation) figure preparation
Alignment: ClustalW - alignment server via the web
Alignment: ClustalX/ClustalW binaries for OSX
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 Search: SSM
Structure Search: MATRAS
Structure Search: DALI server at EBI - (the default for "what does my protein look like").
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: PredictProtein secondary structure predictions (now a pay site - no longer recommended)
SecStr Prediction: NPS@ - Network protein sequence @nalysis from IBCP, France
SecStr Prediction: PSIPred server
SecStr Prediction: JPRED:TNG - 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
Geometry: Metal coordination sites in proteins
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
Syrrx nanovolume crystallization service.

Structural Genomics

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
Adventures in capitalism #2: StructuralGenomix (SGX)
Syrrx nanovolume crystallization service.
Search Google for other "structural genomics" hits.

Programming Tutorials (C, Fortran etc)

Programming in C .
University of Strathclyde's C Programming .
Eskimo.com C Programming .
Eskimo.com Intermediate C Programming
University of Leicester Introduction to C Programming .
Brian Kernighan's old K&R style Programming in C: A Tutorial .
C optimisation 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 .
Stanford University Fortran Tutorial .
A whole host of links on Fortran programming .
Introductory online Java tutorial .
Webmonkey HTML Tutorial
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.

Manufacturers

Hampton Research have become the de-facto suppliers of a whole raft of crystallization supplies and crystal mounting tools for crystallography. They were quite pivotal in the standardization of cryo-crystallography apparatus too.
Emerald BioSystems make the Wizard Screen(s) and certain other screens.
Molecular Dimensions, another manufacturer of crystallization screens and some cryocrystallography mounting items.
MiteGen make a bunch of polymer-based crystal mounts and tools that are probably extremely useful for small xtals in synchrotron applications.
Rigaku/MSC are probably the leading supplier of in-house X-ray diffraction equipment at the moment including the ubiquitous Rigaku generators and Raxis-IV series detectors.
ADSC detectors are by far the most numerous CCD detectors found at synchrotrons (Quantum 4, Quantum 210, Quantum 315).
MAR research Inc also make CCD detectors for synchrotrons, still produce the venerable Mar345 image plate detector, and have a new robotic arm for mounting crystals.
Xenocs make multilayer X-ray optics comparable to the same sort of thing from the more established Osmic (now part of Rigaku).
Charles Supper Co. make an interesting set of extended arc goniometer heads and some other crystallographic equipment.
The Polycrystal Book Service is supposedly resurrected as polycbs.com, with a startlingly uninformative web page. Email polycbs@polycbs.com or call 888-628-5611
Probably other companies should go here....suggest some