Martyn Winn, Adam Ralph, Alun Ashton and Sue Bailey
WA4 4AD, U.K.
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
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
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
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