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


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


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

Licensed software provided for 3D structure determination and analysis


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


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


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


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


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