Making multimers from monomers and PDB translation data

Steven Brenner seb1005 at bio.cam.ac.uk
Sun Mar 14 19:13:52 EST 1993


The Protein Databank files frequently contain the structure only a
single chain of a homo-multimer but provide records describing how to
translate the coordinates for that monomer in order to produce the
entire protein.  For much work (for example, on solvent accessibility)
it is essential to work with the entire protein rather than with just
the monomeric chain.

I imagine it would be simple enough to write a little program to do
the translations to generate the complete protein, but it would be
even simpler to use one that has already been written.  Does anyone
know of such a program?

Two caveats:

1) I have been told that many of the translation records are
systematically incorrect as a result of a bug in an early
crystallographic program.  Is this true?  If so, is there a program
(or at least an algorithm) to convert the erroneous translation
records to correct ones?

2) I would like to be able to automate the process, since I will be
analyzing all of the proteins in the PDB.  Therefore, I would rather
use a program which can be called from the command-line than an
interactive one.  However, information about any programs that will do
the job would be appreciated.

Thanks in advance

-Steven
--
Steven E. Brenner               |  Internet    seb1005 at mbfs.bio.cam.ac.uk
Department of Biochemistry      |  JANET       seb1005 at uk.ac.cam.bio.mbfs
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