Useful Links

Crystallization

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

Data Processing

Phasing Packages

  • CCP4 Collaborative Computational Project, Number 4 (software suite)
  • PHENIX Python-based Hierarchical ENvironment for Integrated Xtallography
  • 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

  • CCP4 Collaborative Computational Project, Number 4 (software suite)
  • 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
  • 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

Structure Analysis

Tutorials

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
         
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