bryant at ray.nlm.nih.gov
Thu Feb 17 10:38:11 EST 1994
In response to Peter Murry-Rust's enquiry concering machine-readable space
I have put this into recent distributions of the PKB database suite. PKB uses
the S language to create macromolecular structure objects, by automatic parsing
of pdb-format files. It then provides a series of query functions that do
retrieval, data transformation and pattern-matching operations. One of these
functions is CRYSTAL.CONTACTS, which returns lists of packing contacts based
on the space group and cell dimension information included in the macromolecular
structure object. To do this transformation the function access an object
containing the space group symmetry operators Peter asks about.
If you have S it is simple to write out the rotation-translation matrices as
C or C++ structures, or formatted ascii files for that matter. If you don't
have S it possible to parse the ascii distribution format of the PKB object
SPACE.GROUP.SYMMETRY and get the needed information, though this is harder than
the first option. You can get a distribution of PKB by annonymous ftp to
ncbi.nlm.nih.gov. Look in the directory pub/pkb.
The list contains all the space groups in the international tables, identified
by number and by a string matching the space group codes that PDB uses. There
are some non-standard settings included at the end of the list, and these match
the codes PDB has used. It covers all of the pdb non-standard settings as of
a release or two ago. The list was made by S. Dasgupta, J. Bell and myself,
as part of a project to do some analysis on packing contacts. We're
responsible for any errors, so let me know if you find them!
There's also a word of warning I must give concerning use of CRYSTAL.CONTACTS
in PKB. The space group and cell information in the macromolecular structure
objects you get by LOAD("pdb.file.name") are taken directly from the PDB file.
This information is correct in the sense that you have a valid assymmetric
unit and orthogonal/fractional transformation for only about 2/3 of the files
in recent PDB distributions. This warning doesn't affect other uses of
the SPACE.GROUP.SYMMETRY object, but it means you have to double check the
information in the PDB file before trusting the output of CRYSTAL.CONTACTS.
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