Protein Crystallography Structure Solution

Experimental Data: Processing/Data Analysis

Adxv - A program to display X-Ray diffraction images (Andy Arvai; Scripps)
d*TREK - Device independent software suite for processing single crystal diffraction images.
Diffraction Anisotropy Server - Ellipsoidal truncation and anisotropic scaling.
HKL and HKL 2000 - Data processing and scaling suite from HKL Research, Inc.
LABELIT - Auto-indexing server.
Merohedral Crystal Twinning Server - Checks protein diffraction data for merohedral twinning.
MOSFLM - Data processing and scaling from the CCP4 Suite of crystallographic software.
TARDIS - Archiving and sharing of X-ray images from the Australian protein cryst. community.
XDS - Reduction of 2D images obtained from crystals irradiated with monochromatic X-rays.
X-GEN - Documentation for the X-GEN data processing package.

General Packages
Auto-Rickshaw - Automated macromolecular crystal structure determination pipeline.
CNS - Crystallography & NMR System.
CCP4 - Collaborative software for macromolecular X-Ray crystallography.
FORTRAN programs for crystallography - Crystallography and Modelling
Phenix - Software suite for the automated determination of macromolecular structures.
Sesame - LIMS system to support high-throughput protein structure-function investigations.
SHELX - Program suite for phasing and refinement.
XTRACK - A web-based notebook for tracking crystallographic projects.

Phasing

BALBES  - An automated molecular replacement (MR) pipeline. Server   Download
COMO - Combined Molecular Replacement (Liang Tong).
CASPr - An automated approach to molecular replacement.
EPMR - Open-source molecular replacement program for protein crystallography.
HKL2MAP - a graphical user-interface for macromolecular phasing with Shelx programs (Thomas Pape &
Thomas R. Schneider).
MOLREP - an automated program for molecular replacement.
Mr Bump - Automated molecular replacement.
Phaser - Phasing with maximum likelihood methods; Phaser Manual   Difficult Cases
Queen of Spades - Molecular replacement.
SHARP/autoSHARP - Phasing and density modification.
SnB - Dual-space direct-methods procedure (Shake and Bake); SnB User Guide.
SOLVE/RESOLVE - Crystallographic structure solution for MIR, SAD, and MAD.
Superflip -    ab initio procedure for the determination of protein crystal structures using diffraction data
at atomic resolution; heavy atom or anomalous scatterers substructure determination from isomorphous
or anomalous differences.
X-ray Anomalous Scattering -  Database, Tutorial, MAD Phasing from Univ. of Washington.

Model Building
ARP/wARP - Automatic construction and refinement of macromolecular models.
AutoBuild - automated model building starting from scratch.
Chemdoodle - chemical sketcher
COOT - Main website for model building program; COOT Manual
eLBOW electronic Ligand Builder and Optimisation Workbench (Phenix)
JLigand - Allows ligands to be linked on- screen and a link description to be created.
Ligand Expo - provides chemical and structural information about small molecules within the structure
entries of the Protein Data Bank.
MAID - Automatic fitting of protein X-Ray crystallographic electron density maps.
Make NA Server - Automation of making nucleic acid helices by NAB.
MIFIT+ - Crystallographic model building.
O - Crystallographic model building; This site describes how to get the O distribution, how to install the
program, and how to configure it to work the way you want.
PRODRG-2 Server - Generate ligand PDB and cif file for refinement of bound ligand.
RAPPER - An ab initio conformational search algorithm for restraint-based protein modelling.  Useful for
modelling poorly defined loops.
SPASM Server - Server will find similar motifs based in a database derived from the PDB.  Useful in
modelling poorly defined loops.
TURBO-FRODO - Crystallographic model building.
Xpleo -  Inserts missing fragments into a partially complete protein model; Xpleo References

Refinement

Parvati -  Protein Anisotropic Refinement Validation and Analysis Tool
PURY - Database and server of geometric restraints of hetero compounds for use in refinement of
macromolecular structures.
REFMAC - Rigid body, TLS, restrained or unrestrained refinement against Xray data. Manual.
REFMAC Ligands List - Ligand dictionary.
RSRef - real space refinement of atomic models into electron density maps.
TLSMD - Inference of TLS motion from single crystal structures.  Useful for selecting TLS domains for
refinement.
TNT - Crystallographic refinement package.

Useful Papers to Aid Structure Solution
Surprises and pitfalls arising from (pseudo)symmetry Peter H. Zwart,a* Ralf W. Grosse-Kunstleve,b
Andrey A. Lebedev,c Garib N. Murshudov,c and Paul D. Adamsab

Crystallographic Source Code Libraries

CCTBX - Computational Crystallography Toolbox

CLIPPER - A set of object-oriented libraries for the organisation of crystallographic data and the
performance of crystallographic computation.
Provided as a service to the community by the Rigaku Life Science Group, All rights reserved.
Informative Reference Material

Surprises and pitfalls arising from (pseudo)symmetry: P. H. Zwart, R. W. Grosse-Kunstleve, A. A. Lebedev, G. N.
Murshudov and P. D. Adams

Brian Matthew's short commentary on the handling of anomalous-scattering data:   Matthews, B.W. (2007) Five retracted
structure reports: Inverted or incorrect?  Protein Sci. 16, 1013-1016.

X-ray Damage to Biological Crystalline Samples  - A collection of papers on radiation damage, including James Horton's
"Beginner's Guide to Radiation Damage"

Metal Sites in Proteins - MESPEUS database - (Marjorie M Harding's server)

Model-building strategies for low-resolution X-ray crystallographic data. A. M. Karmali, T. L. Blundell and N. Furnham.