From: Axel Kohlmeyer (
Date: Sun Apr 18 2010 - 18:50:33 CDT

On Sun, 2010-04-18 at 22:26 +0200, Knut Jørgen Bjuland wrote:
> Hi


> VMD does VMD does not visualize pqr file with
> chainID correctly. It is not even related to 2OB0, any pqr file with
> chainID will experience such a problem in VMD. However, there is no such
> a problem with other visualization programs like PyMOL. However I forced
> the vmd to read the file as pdb it produce a 3d structure with the right
> folds.

thanks for not helping to track this down.

in the mean time i suggest an occasional look at:
it may not 100% applicable in this case, but
the general drift is going into the right direction.

> Please take a look ate file with both pymol and vmd.

i might have looked into the issue, but i have no interest
to spend the additional effort to install pymol and figure
out how you have been using pdb2pqr only to get to a point
where i could by already have been, had you been a bit
more cooperative. since pymol seems to be working for you
and nobody else has yet been confirming the issue, i suggest
you enjoy pymol and i'll wait until somebody else confirms
and provides the required means to reproduce the issue.

have a nice day,

Dr. Axel Kohlmeyer
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.