CCP4 News

Martyn Winn, Adam Ralph, Alun Ashton and Sue Bailey

Daresbury Laboratory,
Daresbury,
Warrington
WA4 4AD, U.K.
ccp4@dl.ac.uk

Latest release on its way ...

Version 3.3 of the CCP4 suite will be released in the near future. In addition to a number of bug fixes and enhancements to existing programs, we plan to include the following new programs:

ARPP: Automated Refinement Program from Victor Lamzin.
ARPP updates a model by removing poorly defined atoms and adding new atoms, and should be used in conjunction with a refinement program. Note that "arp" has been renamed "arpp" to avoid conflict with a unix command.
GETAX from Clemens Vonrhein.
Real space searching for rotation axis of a D<n> or C<n> multimer, given an initial map and a selfrotation function solution.
OMIT from Bauke Dijkstra and Fred Vellieux.
Calculate omit maps according to procedure of Bhat.
REVISE from Yao Jia-xing.
Program to generate normalised anomalous scattering factor magnitudes from MAD data.
wulff.ps added to 'aggregated' stuff, for generating Wulff net.

In addition, there will be a new version of SCALA, which now incorporates the functionality of both ROTAVATA and AGROVATA. Documentation for most of the main programs is now distributed in html format, in addition to the formatted versions. See Alun's article in this newsletter.

Versions of the CCP4 Suite up to 3.2 have used a pseudo-PDB format for holding coordinate data. In version 3.3, this will be updated to the current PDB Version 2.1 standard. The main additions will be the ANISOU record for anisotropic U factors, and an extention to the ATOM/HETATM record to include segment and element IDs at the end of the line.

Study Weekend 1998

The next CCP4 Study Weekend is to be held in Reading on the 9th/10th of January 1998. The topic is to be databases and their use by crystallographers.

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.

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 http://www.iucr.ac.uk/iucr-top/cif/mmcif/ndb/index.html.

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