X-Ray Crystallography Facility

Ab Initio Protein Modeling

Ab initio protein modeling is performed using a variety of software. A Mac Pro graphics workstation contains all of the necessary crystallographic software.

Mac Pro graphics workstation

Uses

  • Data processing with HKL2000
  • Electron density fitting with the Coot program
  • X-ray refinement with the Phoenix package

Specifications

  • Equipped with stereo graphics and stereo glasses for 3-D visualization of macromolecular structures


Licensed software provided for 3D structure determination and analysis

Coot

A tool for macromolecular model building, model completion and validation, particularly suitable for protein modelling using X-ray data.

Coot displays maps and models, and allows model manipulations such as:

  • Idealization
  • Real space refinement
  • Manual rotation/translation
  • Rigid-body fitting
  • Ligand search
  • Solvation
  • Mutations
  • Rotamers
  • Ramachandran plots
  • Skeletonization
  • Non-crystallographic symmetry and more

PHENIX

A software suite for the automated determination of macromolecular structures using X-ray crystallography methods.

CCP4

A suite of programs covering all aspects of crystallographic structure determination, refinement and analysis.

SHELX

A set of programs for direct structure solution and refinement with high-resolution diffraction data.

SOLVE

An automated system for phase determination from MIR and MAD data.

HKL2000

A tool for processing X-ray data collected by the Rigaku Saturn 944+ CCD detector.