Molecular replacement
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CCP4 6.2 – New and enhanced software for Protein Crystallography. Visit us at Exhibition Booth #47. About CCP4. CCP4 Mission Statement. CCP4 Today. Produce a comprehensive software suite for macromolecular crystallography Develop cutting edge approaches to structure solution

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Molecular Replacement

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Molecular replacement

CCP4 6.2 – New and enhanced software for Protein Crystallography

Visit us at Exhibition Booth #47

About CCP4

CCP4 Mission Statement

CCP4 Today

  • Produce a comprehensive software suite for macromolecular crystallography

  • Develop cutting edge approaches to structure solution

  • Community-based resource – reach out to academic, non-profit and for-profit organisations

  • Provide education and training in structural biology

  • Encourage the wide dissemination of new ideas, techniques and practice.

  • Funded by BBSRC and MRC in the UK, and coordinated by STFC

  • Core group based at the Research Complex at Harwell

  • Supports software developers in the UK and further afield

  • Annual Study Weekend in January - next on “Data Collection and Processing at Synchrotrons” at Warwick University, UK

  • Teaching workshops worldwide

A little history

  • CCP4 is the Collaborative Computational Project No. 4

  • Set up in the late 1970’s in the UK to bring together developers of PX software

  • Goal was to assemble a comprehensive collection of software, based around standard file formats

Refinement, Model Building and Molecular Graphics

The CCP4 Software Suite 6.2.x


  • REFMAC 5.6

    • Refine against SIRAS data

    • Jelly body refinement

    • Occupancy group refinement

    • Restrain to reference structures

    • Regularised map sharpening

    • Automatic and local NCS restraints



Data Processing, Experimental Phasing and Molecular Replacement

Molecular Replacement

Data processing with iMOSFLM:

Determine Laue group and spacegroup with POINTLESS:

COOT 0.6.2:

  • Linked with SBase - idealised coordinates for all monomer types in PDB.

  • InterfacesProDRG(soon in CCP4) for generation of restraints

Phase improvement with DM/PIRATE/PARROT

Automated model building with BUCCANEER

Automated data processing from images to |F| for multi-wedge, multi-pass, multiwavelength data

  • "Cut-glass" transparent surface effect

Experimental Phasing


  • jLIGAND:

  • Graphical interface for linking ligands and creating link descriptions

  • Creation of library descriptions for single ligands

Phasing via Molecular Replacement and/or SAD

Quaternary structure prediction with PISA:

R. Keegan1, J. Bibby3, C. Ballard1, E. Krissinel1, D. Waterman1, A. Lebedev1, M. Winn2, D. Rigden3

1 Research Complex at Harwell, STFC Rutherford Appleton Laboratory, UK

2 STFC Daresbury Laboratory, UK, 3 School of Biological Sciences, University of Liverpool, UK

Qt-based version of CCP4mg:






pipelines (using Molrep/Phaser)

homologous structures positioned in cell

target sequence

Future Developments

Related Developments

  • DIMPLE: Difference map pipeline for high speed automated processing of structures with potentially bound ligands

Data Structure Solution by Molecular Replacement using ab initio protein models


Our method employs ab initio polyalanine models (or ‘decoys’), produced in large numbers then clustered based on the presence of similar core structures. The largest of these clusters is likely to be closest to the native structure [2]. Such ab initio modelling may result in an accurate prediction of the structural core of the target, but with inaccurate loops and termini.

  • New graphical viewer for reflection data.

  • Supports most of widely used file formats: MTZ, SHELX, XDS, Saint and Scalepack

  • Make PDF and postscript outputs


  • Aimless– replacement for Scala and Pointless with increased functionality

  • Sculptor & Ensembler – tools for preparing search models for Molecular Replacement

  • Prosmart- structural comparison of protein chains

  • Zanuda – checking refinement results, e.g. Checking for false origins in the presence of pseudo translation

This pipeline will be made freely available, and may ultimately require only the input of the protein sequence along with the experimental data. Unlike other computationally intensive methods [3], this method is suitable for modest hardware, allowing for broader adoption.

Collaborative Computational Project Number 4

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