WK03: A Protein Crystallographic Toolbox: CCP4 Software Suite and PDB Deposition Tools

ACA 2004 Chicago
July 17th 2004




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. Structures are deposited to the PDB through any of the three sites of the wwPDB (the RCSB PDB, MSD-EBI and PDBj). Each site 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) 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 (www.pdb.org) 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 ACA 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 ACA is required for this workshop.

Timetable (draft)
8:30amIntroduction and Welcome
Morning session
8:35Introduction to CCP4 and the PDB Maeri Howard-Eales & Judith Flippen-Anderson
8:50The CCP4 Package: General Overview: Utilities, Tricks and Tips Peter Briggs
9:20Overview of using CCP4 for PX Martin Noble
10:40PDB_EXTRACT and CCP4 - making deposition easier Shuchismita Dutta
11:40Data collection & data reduction using MOSFLM and SCALA Gwyndaf Evans
12:20Lunch (provided onsite)
Afternoon session
13:00Data collection & data reduction using MOSFLM and SCALA (continued) Gwyndaf Evans
13:40Refinement using REFMAC5 Roberto Steiner
15:00CCP4 Molecular Graphics: what can it do for you? Stuart McNicholas
15:30Data deposition using ADIT Kyle Burkhardt
Summing Up
16:30Summary, or: "if you don't remember anything else from today, remember this..."
16:40Question and Answer Session