VMD-L Mailing List

From: Eduard Schreiner (eduard.schreiner_at_theochem.ruhr-uni-bochum.de)
Date: Tue Jul 12 2005 - 11:01:24 CDT

Peter Schellenberg wrote:
> 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
>
>
>
Hey Peter,

I took a look into this pdb file and viewed it in vmd.
It seems that VMD does not distinguish for example

C ATOM 305 CG AGLN A 41 16.955 -25.627 2.450 0.77 15.70
         C ATOM 306 CG BGLN A 41 16.921 -25.587 2.464 0.23
16.79

Within VMD both atoms have the resname GLN, belong to the same chain etc.
The two possibilities I see are either to select by index or to change
the pdb file in order to make these atoms different, i.e. one could give
them different chain id (C,D), and then select by chain id.

Eddi 

-- 
--
=======================================================================
Eduard Schreiner                        e-mail: eduard.schreiner_at_rub.de
Lehrstuhl fuer Theoretische Chemie          Phone: ++49 (0)234/32-22121
Ruhr-Universitaet Bochum - NC 03/52         Fax:   ++49 (0)234/32-14045
D-44780 Bochum                               http://www.theochem.rub.de
=======================================================================