This is the methods home page of the Macromolecular Crystallography Core Facility in the Dept. of Molecular Biology at Princeton University. This page was created by and is managed by the Crystallography Facility Manager - Phil Jeffrey - to assist in the nuts and bolts of working on crystal structures. There's a more official Molbio Crystallography Core Facility Home Page that will be of more use to you if you're looking for information about services. These pages contain a lot of utilitarian data intended for use by crystallographers during structure determination - 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 219 or preferably via EMAIL.

The crystallography core facility is dedicated to providing services for crystallization, X-ray data collection and data analysis. Our equipment includes a Rigaku 007HF-MR microfocus rotating anode generator and Dectris Pilatus3 R 300K detector, and an Art Robbins Phoenix crystallization robot. We can collect data and solve structures for both macromolecular and small molecule samples. Our services also include consultation on difficult structures - hopefully with the current software tools and perhaps even the pages/links below you can determine straightforward structures yourself, but of the 100+ structures I've solved over the years quite a few have been less than simple.

Some links will be broken at the moment - I rapidly reconstituted this site over here on the facility pages after OIT disconnected the original xray0 without informing anyone. Most links have been converted, but there will be inconsistencies as well as the usual "link rot" for references to older software and sites.

 

What's New?

• Local interest: Molbio Structural Biology email list - intra-departmental email list for cryo EM and crystallography
• A new Rigaku MicroMax 007HF/Varimax HF/Pilatus 300K system replaces the old RuH3R/Xenocs/RAXIS IV++ system as of June 2017 - small molecule and macromolecular structure determination at a rapid rage
• Video: ProteinaseK_xtal7.mp4 - a video of a total of 90° of data collection on our old RuH3R-RAXISIV++ system on a Proteinase K crystal (~150µm) at 120 secs/0.5° frames. This data goes clean off the edge of the detector at 100mm and has a 23.6% outer-shell Rmeas at 1.6 Å resolution. Nice crystal ! Converted to JPEG via Andy Arvai's adxv (adxv -sa file.osc file.jpg) and from JPEG to MP4 using ffmpeg (ffmpeg -f image2 -i Eval-ProteinaseK_crystal7_1_%4d.jpg test.mp4).
• Under development: references for theory and practice.
• X-ray Facility publications list now available, also the molbio facility structures page. It's always a little out of date.
• How-to's on operating our Art Robbins Phoenix crystallization robot can be obtained from Phil - they are not linked here yet
• Intranet reference: the Hughson lab has a new home page that marks the migration away from the old one.
• The Molbio Facility Page now updated to reflect the more recent publications.
• I particularly like An idea whose time has gone - Prof. Greg Petsko's commentary on the Protein Structure Initiative.
• Data Wrangling v0.1
• My commentary on the ABC transporter debacle that led to the retraction of 5 papers (3 of them from Science).

 

Safety

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

 

Hardware-related

• X-ray generator/detector - now (mostly) updated to reflect the new generator system
  • Standard Operating Procedure for Rigaku 007HF/Pilatus 300K system.
  • Procedure for generator startup/shutdown.
  • Minimal Procedure for generator startup.
  • Using HKL3000 for Data Collection (and very little else)
  • Use of XG Control software to change generator power and check for alerts
  • More detailed description of the new Rigaku hardware
  • Procedure for testing X-ray Facility interlocks - ADMIN ONLY - this must be done every 6 months
  • Protocol for changing the filament on older RuH3R/Ru200 machines
• Cryo:
  • Oxford Model 700: How to program the Oxford Cryostream for a typical experiment.
  • Oxford Model 600: How to program the Oxford Cryostream for a typical experiment.
  • Protocol for pumpdown of Oxford cryo head
• Art Robbins Phoenix crystallization robot guide
• Linux admin:
  • 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
• Mac OSX admin:
  • 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
• Phil's notes on Cloning and restoring SGI Root disks
• Phil's notes on compression and backups
• MacResearch.org - Mac OSX in Science

 

Synchrotron Issues

• Mitegen's summary of synchrotrons with crystallography beamlines.
• My X-ray Data Collection and X-ray Data Processing guides
• Packing - Synchrotron packing list.
• How to collect data from crystals with long unit cell axes
• BNL Gate Access Form and User Registration pages.
• BNL User Admin at the newer Guest/User/Visitor Center is (631) 344-3333 (7am-5pm M-F; badging closes 1pm Fridays), guvcenter@bnl.gov in building 400
• BNL Housing is (631) 344-2541 (or 2551) (8am-midnight M-F, 4pm-12pm Sun). Don't assume you can simply book for the next day - sometimes the dorms fill up.
• Directions to BNL and CHESS.
• 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
• 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.

 

Crystallography/Lab Methods, Tuturials and Guides

Look further down the page for software and servers.

• Introductory:
  • X-ray Crystallography 101 v1.0 , Jan 2007.
  • External: Bernhard Rupp's Crystallography 101
  • External: MRC/Cambridge Crystallography Course, especially basic diffraction.
  • External: Kevin Cowtan's Interactive Structure Factor tutorial
  • External: Kevin Cowtan's Book of Fourier
  • External: Bragg's Law applet
  • External: MAXINF - teaching macromolecular crystallography.
  • External: CCP4 wiki crystallography theory.
• 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.
  • External: Cambridge: crystallization theory and practice.
  • External: pictorial library of crystallization drop phenomena.
  • External: xtal protocols by Johan Zeelen.
  • External: Hampton Research crystallization tips
  • External: Cambridge crystallization course
  • External: Xtalbase crystallization Database.
  • External: Biological Macromolecule Crystallization Database (BMCD) v4.
  • External: High-throughput crystallization at HWI (free or for a fee).
  • External: Brandeis Flash-cooling: A practical guide
  • External: CCP4wiki: crystal cryo
• Data collection and processing:
  • X-ray Data Collection Course, v0.3, Jan 2007.
  • X-ray Data Processing Guide, v1.0, Oct 2006.
  • Data Wrangling v0.1, Jan 2007
  • phenix.xtriage mydata_truncate.mtz residues=1204 by way of example
  • External: Cambridge: structure factor statistics
  • External: Bart Hazes's Data Collection tutorial
  • External: Todd Yeates' Crystal Twinning tutorial (and server)
• Computers:
  • Newrest: Simple Unix scripting or older version.
  • Unix Quick Reference
• External: CCP4 community wiki.
• Solving a structure by molecular replacement:
  • Molecular Replacement Guide v1.0, Sept 2005.
  • External: Cambridge: Molecular Replacement.
  • 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: 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.
  • External: Cambridge: Experimental phasing by maximum likelihood
  • 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).
  • Notes on picking heavy atoms.
  • A little local Heavy Atom database.
  • External: Heavy atom notes from IMCA-CAT - 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.
• Density modification and averaging:
  • Phil's notes on Averaging.
  • External: Averaging - local density correlation.
  • External: Cambridge: density modification
• Refinement:
  • External: Notes from a refinement workshop archived at St. Andrews.
  • External: Randy Read's notes on Maximum Likelihood for refinement, maps, and practical considerations
  • External: Cambridge: Fitting, refinement and validation
  • Where to find topology/parameter files for ligands and hetero groups.
• Validation:
  • External: Gerard Kleywegt's Braille for Pugilists (making the most out of your model).
  • External: Gerard Kleywegt's model validation tutorial.
  • External: Ethan Merritt's PARVATI - Anisotropic Validation and Analysis.
• Graphics:
  • 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: HTML version of "O for Morons".
  • External: HTML version of "O for the Structurally Challenged" (text only).
  • External: 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:
  • External: Introduction to Direct Methods
  • External: UCLA Lab Tutorials
  • Phil's Peek2 manual.
  • Phil's Annotate manual.
  • Phil's Predict4 manual (data collection strategy for X9A).
  • Phil's report on the Gordon Conference on Diffraction Methods in 2002.
• External: High Resolution X-ray Diffraction
• External: Interactive Diffraction Tutorial
• External: Difference Patterson Tutorial

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

 

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 - vanished ??
• Buster-TNT - map improvement.
• 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.
• DINO - molecular graphics.
• DSSP - protein secondary structure determination.
• 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 parametersy
• 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.
• 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 and the more recent one for v3.2.
• 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 (included as part of CCP4)
• RIBBONS - Mike Carson's molecular graphics programs.
• Shake and Bake.
• 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.
• VMD (Visual Molecular Dynamics).
• XDS - X-ray data processing software from Wolfgang Kabsch
• X-PLOR - the predecessor to CNS sharing much the same functionality.
• XtalView - crystal structure package, not maintained post-2003.
• Kevin Cowtan's CLIPPER C++ libraries for crystallographic computing.
• CCTBX - the Computational Crystallography Toolbox.

This list curated August 2010.

 

Bioinformatics Software and Database Search Sites

• BARTON group home page - a lot of bioinformatics software
• Searches: BLAST at NCBI
• Searches: 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: TIGR BLAST for Unfinished Microbial Genomes
• 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: 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/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-MC multiple structure alignment
• Str Alignment: Multi-Prot multiple structure alignment
• Str Alignment: Mammoth-Mult multiple structure alignment
• 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: 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: 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 - (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: 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: 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
• 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.

Programming Tutorials (C-shell, C, Fortran etc)

• Simple Unix C shell scripting or old version.
• 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.
• Learn Python The Hard Way.
• Online Python Tutor.
• 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 .
• 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.

Manufacturers/Vendors

Some of them we use, some of them we do not. Inclusion in this list doesn't mean that we recommend them, just that we are aware of them. There's a fair amount of overlap: mutliple vendors offer Mitegen mounts and Spearlab foam dewars, for example.

• Crystallization:
  • Hampton Research - one of the earliest supplies of crystallization screens.
  • Jena bioscience
  • Emerald BioSystems - Wizard Screen(s) etc.
  • Molecular Dimensions, another manufacturer of crystallization screens and some cryocrystallography mounting items.
• 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
  • Oxford Instruments Cryojet - despite name similarities these are not affiliated with the more established Oxford Cryosystems
• 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).
• Robotics
  • Douglas Instruments Oryx robots
  • Art Robbins Gryphon and Phoenix
  • Innovadyne screen making and crystallization robots
  • Rigaku have quite a large array of automation systems for crystallization
  • ... and also have one of the few commercial crystal mounting robots
• 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)