A Part of the University of Maryland Medical Center

• Research

• News Briefs
• Find a Researcher
• Shared Services
• Cancer Center Membership
• Researchers' Toolkit
• Clinical Investigator Handbook
• NIH Grant Deadlines
• 
    Related Resources
• Cigarette Restitution Fund Program
• Clinical Trials

Research: Shared Services

X-ray Crystallography: Useful Links

Crystallization

• BMCD Biological Macromolecule Crystallization Database
• CRYSTOOL Computing of efficient screening conditions
• Hampton Research Crystallization products

Data Processing

• CrystalClear GUI for data collection and processing based on d*TREK
• Crytstal Twinning Server Merohedral twinning characterization
• HKL Package Denzo/Scalepack
• MOSFLM Data processing package

Phasing Packages

• CCP4 Collaborative Computational Project, Number 4 (software suite)
• CNS Crystallography & NMR System
• Phases Package of computer programs designed to compute phase angles for diffraction data from macromolecular crystals
• PHENIX Python-based Hierarchical ENvironment for Integrated Xtallography
• REPLACE Molecular replacement package
• SHARP Statistical Heavy Atom Refinement and Phasing, includes density modification and auto-tracing
• Shelx Software suite for heavy atom location and high-resolution refinement
• Shake-and-Bake Dual-space direct-methods procedure for determining crystal structures
• SOLVE Automated crystallographic structure solution for MIR, SAD, and MAD
• XtalView Crystallographic software package for fitting electron density maps and solving structures by MIR and MAD

Refinement

• Bias Removal Server Bias removal and map improvement
• CCP4 Collaborative Computational Project, Number 4 (software suite)
• CNS Crystallography & NMR System
• PHENIX Python-based Hierarchical ENvironment for Integrated Xtallography
• Shelx Software suite for heavy atom location, phasing, and high-resolution refinement
• TNT Least-squares structure refinement
• X-PLOR Structure determination and refinement

Structure Modeling

• BobScript MolScript with electron density functionality
• Coot Model building with real-space fitting
• GLR Graphical interface integrating Bob/MolScript, Raster3d, and POV-Ray for generation of figures
• Hic-Up Server Database of ligand, co-factor, etc. coordinates and topology files for O, CNS, X-PLOR, TNT
• MolScript Creates both detailed and schematic pictures of molecular 3D structures, in particular proteins
• O Model building
• PRODRG Server Converts coordinates for small molecules in PDB format to the following topology formats: GROMOS, GROMACS, WHAT IF, CNS, O, SHELX, HEX and MOL2
• RasMol Model viewer
• VMD Molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting
• XtalView Model building (Xfit program)

Structure Analysis

• Domain Movement Detects the domain movement from two homologous protein structures
• GRASP Display and manipulation of the surfaces of molecules and their electrostatic properties
• PARVATI Protein Anisotropic Refinement Validation and Analysis Tool
• PDB Structure Validation Server
• Richardsons' Validation Tools MolProbity
• SAVS Structure Analysis and Verification Server
• STAN Structure Analysis Server
• Uppsala Software Factory Various crystallographic tools
• WHATCHECK Structure validation
  

Tutorials

• Crystallography 101
• Fourier Transform
• Mike Sawaya's Tips
• MAD Phasing Ethan Merrit's Site
• MAD Phasing Bernhard Rupp's Site
• Structure Factors

Synchrotrons

• ALS Advanced Light Source
• APS Advanced Photon Source
• CHESS Cornell High Energy Synchrotron Source
• NSLS National Synchrotron Light Source
• SSRL Stanford Synchrotron Radiation Laboratory

This page was last updated on: January 21, 2010.

Please rate the quality of this article. Do you find this article to be helpful / informative?                Poor                                       Excellent Do you have any brief comments on this page: (up to 255 characters) Note: If you have a question, please contact Ask the Expert.

Email this Page                                                                     Print this Page