Workshop N.6: A Protein Crystallographic Toolbox: CCP4 Software Suite and PDB Deposition Tools

IUCr 2005 Florence
23rd August 2005

Workshop Organisers

Maeri Howard (CCP4,, Peter Briggs (CCP4, & Judith Flippen-Anderson (RCSB PDB,



The Collaborative Computational Project Number 4 (CCP4) is a UK-based initiative which collates and distributes over 150 programs that encompass most aspects of macromolecular structure determination via X-ray crystallography. The Protein Data Bank (PDB) contains 3-dimensional structure data of biological macromolecules. The RCSB is one of the three sites of the wwPDB where structures are deposited to the PDB, and also provides a website with resources for related aspects of structural biology.

This full-day workshop will include an introduction to CCP4, the CCP4 package and associated software and the CCP4 data formats, which will be suitable for new or inexperienced users. It will then focus on a small number of specific programs (MOSFLM/SCALA, REFMAC5, CCP4 Molecular Graphics and COOT) in a way that will also be of interest to the more experienced crystallographer who is willing and able to delve deeper into the options available in these programs.

The RCSB Protein Data Bank ( has developed several tools to make structure deposition simple and easy. PDB_EXTRACT collects information from a variety of programs used in structure determination. These data are compiled into a file that can be uploaded into the deposition tool ADIT.

There will be presentations by CCP4 and RCSB PDB staff and developers as well as the opportunity for informal group or individual discussions and tutorials throughout the IUCr at the CCP4 and RCSB PDB booths in the exhibit hall.


The objective of this one-day workshop is not to teach crystallography but to teach people how to use some of the programs distributed with the CCP4 package to do protein crystallography, and how to get the best from the PDB when they deposit their structures.

Pre-registration through the IUCr is required for this workshop:

8:30am Introduction and Welcome
Morning session: General
8:45 An Introduction to the CCP4 Package: Utilities, Tricks and Tips Peter Briggs
9:30 Overview of using CCP4 for PX Martin Noble
10:30 Coffee
11:00 Data Processing and Reduction using MOSFLM & SCALA Gwyndaf Evans
12:30 Lunch
Afternoon session
13:30 TLS Refinement with REFMAC5 Martyn Winn
14:30 CCP4 Molecular Graphics: Pictures & Movies With CCP4MG Liz Potterton
15:00 Coffee
15:30 Coot And Graphical Model Building Tools Paul Emsley
16:00 Data Deposition And Validation Using RCSB PDB Tools Kyle Burkhardt
Summing Up
16:45 Summary, or: "if you don't remember anything else from today, remember this..."
Questions and Answers
17:00 Close