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CCP4 News

Martyn Winn, Sue Bailey, Alun Ashton and Peter Briggs

Daresbury Laboratory,
WA4 4AD, U.K.

Staff changes

In October, we said goodbye to Adam Ralph who moved to the Institute of Virology, Glasgow. We wish him well, and thank him for his many contributions to CCP4.

In March, Peter Briggs joined the Daresbury staff. Peter moved from the University of East Anglia, where he obtained a PhD in Theoretical Physics.

Release 3.4

Version 3.4 of the CCP4 suite was released on May 5th. In addition to a number of bug fixes and enhancements to existing programs, this release included the following new programs: There are also new versions of PROCHECK (3.5), REFMAC (3.3), RESTRAIN (4.6.9) and SCALA (2.4.2). There is a new script "duptree" for setting up multiple installations from a common source directory, and a preliminary installation procedure for the X-windows programs (at present, only for IRIX, OSF1 and LINUX). There has been significant progress on the linux/g77 installation, and most programs should now compile and run under g77.

Details of all the changes can be found in the CHANGES file in the top-level directory ($CCP4), and in $CCP4/html/CHANGESinV3_4.html.

On May 27th, there was a minor release 3.4.1 which included a few minor bug fixes to version 3.4. No distinction between 3.4 and 3.4.1 is made in program headers, etc. Subsequent problems will be reported on the Problems Page as usual.


The 1998 CCP4 Study Weekend on databases and their use by crystallographers was held in Reading on the 9th/10th of January 1998. The meeting aimed to introduce practising macromolecular crystallographers to the wide range of database resources available. The areas covered included sequence alignment, properties of heavy atoms, tools for characterising non-bonded interactions, and tools for analysing models of macromolecules. In between the main talks, there was a demonstration by Liz Potterton of the new Graphical User Interface to the CCP4 Suite, and a demonstration of their latest products by the Cambridge Crystallographic Data Centre. A list of URLs related to the talks can be found at Next year's Study Weekend will be at Sheffield and will be on Data Collection and Processing: more details in due course.

CCP4 and CCLRC Daresbury Laboratory hosted a workshop on Multiwavelength Anomalous Dispersion on 23 - 27 June. A combination of talks and hands-on practicals instructed participants on the planning and executing of a multiwavelength anomalous dispersion experiment up to the stage of obtaining an interpretable electron density map.

The next CCP4 workshop will be in Prague at the 18th European Crystallographic Meeting, and will be held prior to the main conference on Saturday August 15th. Introductory talks on the philosophy and use of the CCP4 Program Suite will be given in the morning, followed by practical sessions in the afternoon.

A joint CCP4-EBI workshop is to be held at the EBI (European Bioinformatics Institute, Hinxton, Cambridge) on 16th to 19th September, and is primarily aimed at software developers. There will be an introduction to the concept of automatic data harvesting during structure determination for deposition information. It is hoped to define and then accumulate the required information by "harvesting" output from existing packages. There will also be instruction on the use of the CCP4 libraries. These libraries are freely available, and it is hoped that their use by non-CCP4 software will aid standardisation of file formats and program usage. The workshop will also include an introduction to the new CCP4 working coordinate file format, CCIF, see below.

Future changes to the CCP4 working coordinate format

The macromolecular Crystallographic Information File (mmCIF) format was developed by a working group of the IUCr formed in 1990. It represents an extension of the CIF format used by small molecule crystallographers, and which is used for automatic submission to Acta Crystallographica C. mmCIF files are text files with a flexible format based around either <data_name> <data_value> pairs or a loop structure (works like a table). In particular, a wide variety of data items are supported (as defined in the mmCIF dictionary), and character data values may be lengthy and descriptive. This alleviates many of the restrictions of the traditional PDB format.

In view of the likely increasing importance of the mmCIF format, CCP4 intend to move an mmCIF-like format as the working format for coordinate data. Conversion programs will be provided to change between this working format and PDB, but the programs will no longer work directly with PDB files. Initially, we intend to use only a small subset of the full mmCIF format, which will mirror the current PDB format. Coordinate data files should not look too dissimilar from PDB files; in particular, the bulk of the file will remain as columns of atom data. As we gain experience with the format, and users become comfortable with it, we will probably increase the subset of mmCIF data items which can be used, thereby using making more use of the power of mmCIF. This extensibility is indeed one of the advantages of mmCIF over PDB.

The first version of the CCP4 suite to use the mmCIF-like format may appear towards the end of 1998. Releases before then will not include the new format. Precise details are still evolving, so watch this space. Background information on the full mmCIF format can be found at Details of the (still evolving!) CCP4 implementation can be found here.

Other developments

The Graphical User Interface to the CCP4 Suite is now reaching its final form, and it is hoped to make a public release later this year. Details can be found in Liz Potterton's article.

As mentioned above, the EBI Macromolecular Structure Database group are working on Data Harvesting, which involves the automatic collection of deposition information from programs used during structure determination (see here). CCP4 programs are currently being converted to output the information needed by the harvesting software.

Looking further into the future, we are investigating the new XML (Extensible Markup Language) as a way of handling complex information, e.g. more intelligent program documentation or program log files. An exmple of what can be done is provided by the Chemical Markup Language (CML).

And finally ... We have now settled on an official CCP4 logo. Many many thanks to all those who sent in suggestions, some of which were quite artistic. Our final choice is somewhat simpler, but we hope distinctive.

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