Software Section - Daresbury Laboratory
Collaborative Software Projects (CCPs)

Coordination and Collaborations

The Collaborative Computational Projects (CCPs), assist universities in developing, maintaining and distributing computer programs and promoting the best computational methods. Each focuses on a specific area of research and is funded by the UK's EPSRC, PPARC or BBSRC Research Councils. Many of them receive scientific support from the Daresbury Computing Department. The list below shows those projects which may be relevant to some area of crystallography.

• CCP1 The electronic structure of molecules
• CCP2 Continuum states of atoms and molecules
• CCP3 Surface Science - Simulation of physical and electronic properties of surfaces and interfaces
• CCP4 Protein Crystallography
• CCP5 Computer simulation of condensed phases
• CCP9 Computational studies of the electronic structure of solids
• CCP11 Biosequence and structure analysis
• CCP12 High performance Computing in Engineering
• CCP13 Fibre and Polymer diffraction
• CCP14 Powder and small molecule single crystal diffraction

They mostly have web pages describing their activities.
Start from http://www.dci.clrc.ac.uk/Home/ and look for the particular CCP of interest. Reports on some of these have been published in 'Crystallography News'; there is an update to CCP4 below. Previously it was Sept 97. We had a description of CCP14 in March 1996 with an update in June 97

The CCP4 Program Suite for Protein Crystallography

The Collaborative Computational Project No. 4 (CCP4) is an initiative of the UK Biotechnology and Biological Sciences Research Council. A major part of the remit of CCP4 is the development, maintenance and distribution of a software suite for protein crystallography. Applications cover most aspects of protein crystallography including data reduction, various scaling programs, Patterson search and refinement, isomorphous and molecular replacement, MAD phasing, phase improvement (density modification), structure refinement and presentation of results. The suite is ported to most UNIX systems, including LINUX, as well as VMS. Since the CCP4 project was established in 1979, the suite has continued to grow, both in the number of programs included and in the number of users. At the latest count, the Suite included 130 programs, and was used at around 400 sites worldwide.

Programs are contributed to the suite by practising crystallographers from many groups and countries. Integration of diverse programs into a single package is handled by central staff at Daresbury Laboratory, who also govern the distribution of the suite to users. Active development of the suite is also pursued in a number of UK protein crystallography groups. This mechanism means that program authors have access to a large user base, while users have easy access to state of the art software. Contributions to the suite are always welcome, and interested program authors should contact the Daresbury staff, see below. In addition, a central part of the suite is a library of routines commonly used in crystallographic applications and these may be useful in non-CCP4 programs (see http://www.dl.ac.uk/CCP/CCP4/dev/templates/templates.html).

New releases of the suite are made once or twice a year, as the number of additions and changes to the suite warrant. Version 3.4 was released in May 1998 and it is hoped to release Version 3.5 in the near future. The latter will contain the following new programs:

• DYNDOM: Program to Determine Domains, Hinge Axes and Hinge Bending Residues in Proteins where Two Conformations are Available (Steve Hayward).
• MTZMADMOD: Jiffy for converting between F+/F- and F/D
• FINDNCS: Find out NCS operations from heavy atom sites (Guoguang Lu).
• WATNCS: Pick waters which follow NCSs and sort out to NCS asymmetric unit (Guoguang Lu).
• TOP: An automatic structure comparison program and Web server (Guoguang Lu).

In addition, there are major new versions of the maximum likelihood refinement program REFMAC, which now includes individual anisotropic atomic refinement, and of the density modification package DM. The latter program now produces log files which contain HTML links to targets within the log file and to targets in the program documentation. This reflects a continuing trend to make the purpose and output of programs as clear as possible.

Following soon after Version 3.5 of the main suite, will be the first public release of the Graphical User Interface developed by Liz Potterton at York. The GUI will work as an additional layer on top of the traditional Suite. In addition to providing a user-friendly environment for running the suite, the GUI will include additional functionality for project management and the analysis of results.

The suite is available free to non-profit institutions, subject to a completed license form being returned to the CCP4 secretary. A charge is made to commercial users who should contact the CCP4 secretary at [email protected] to make arrangements. Please note that all charges for the suite are used to fund CCP4 activities. Further details on obtaining the Suite can be found on the CCP4 web site http://www.dl.ac.uk/CCP/CCP4/main.html

Enquiries may be sent to the staff at Daresbury Laboratory
(Martyn Winn, Alun Ashton, Peter Briggs and Sue Bailey) email: [email protected]

Martyn Winn, Daresbury

Page last updated 12 Mar 1999

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