X-Ray Crystallography Facility

Access to The Protein Data Bank

The Protein Data Bank is the single worldwide repository for the processing and distribution of 3-D structure data of large molecules of proteins and nucleic acids.

We can visualize and analyze structures deposited in this database using a range of software.

Licensed software 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.


Licensed software for molecular graphics and structure visualization

PyMOL

A free and open-source molecular graphics system for visualization, animation, editing, and publication-quality imagery. PyMOL is scriptable and can be extended using the Python language. It supports Windows, Mac OSX, Unix, and Linux.

RasMol

A free viewing system for PDB coordinate files that runs on Mac PPC, Windows, Unix, and Linux systems. Open source versions are also available.

Swiss PDB viewer

A 3D graphics and molecular modeling program for the simultaneous analysis of multiple models and for model-building into electron density maps.