Research: Shared Services

X-ray Crystallography: Useful Links

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

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

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)

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

This page was last updated on: July 15, 2008.