Making multimers from monomers and PDB translation data

POSTMASTER at NBRF.GEORGETOWN.EDU POSTMASTER at NBRF.GEORGETOWN.EDU
Mon Mar 15 11:29:09 EST 1993


In message <9303150316.AA23839 at net.bio.net> Steven Brenner
(seb1005 at bio.cam.ac.uk) asks

> 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.  ...
> Does anyone know of such a program?

The translation-rotation matrices in the MATRX records are very easy to work
with.  They are usable by all the commercial molecular modeling programs I
know of.  A few lines of code from something like "Numerical Recipes in 
[C/FORTRAN]: The Art of Scientific Computing", W.H. Press, et al., Cambridge 
University Press, 1988, should give you what you need.

He continues:

> 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?

I think a more appropriate forum for this question would be the group
PROTEIN-CRYSTALLOGRAPHY at xtal-log at net.bio.net and the corresponding European
network address.  In that group your question could be addressed by a member of
the PDB staff and other crystallographers.
------------------------------------------------------------------------
                                 Dr. John S. Garavelli
                                 Database Coordinator
                                 Protein Information Resource
                                 National Biomedical Research Foundation
                                 Washington, DC  20007
                                 POSTMAST at GUNBRF.BITNET
                                 POSTMASTER at NBRF.GEORGETOWN.EDU



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