VMD-L Mailing List

From: Peter Schellenberg (peter.schellenberg_at_ipht-jena.de)
Date: Tue Jul 12 2005 - 02:36:11 CDT

Hi

there are certain pdb files which contain variations of a structure, like different
isomerization states of a chromophore and correspondingly more than one
structure for neighboring amino acids, for example the structures of photoactive
yellow protein: 1s1y.pdb

The different structures are distinguished in the pdb file by an A resp.B prior to
the amino acid (and chromophore) name, for example:
ATOM 1021 OG1ATHR A 101 ....
ATOM 1022 OG1BTHR A 101 ....
ATOM 1023 CG2ATHR A 101 ....
ATOM 1024 CG2BTHR A 101 etc.

Unfortunately VMD draws bonds not only within A and B but also between all
atoms within the bond radius that belong to the different representations. Is there
an easy workaround ? Something like select ATHR and BTHR does not work!
The only way was to select all atoms belonging to one structure, which is quite
some work and looks odd.

Many thanks in advance Peter
   
Dr. Peter Schellenberg
Institute for Physical High Technology Jena
Dept. of Biotechnical Microsystems
Albert -Einstein -Str. 9
D-07745 Jena