VMD-L Mailing List

From: Knut Jørgen Bjuland (knutjorgen_at_gmail.com)
Date: Tue Apr 20 2010 - 09:58:35 CDT

I hope I got all information that is need in this email.

Description of problem:
VMD does not display pqr files with chain correctly. The pqr files was
created by the use of http://pdb2pqr-1.wustl.edu/pdb2pqr/.

Version-Release number of selected component (if applicable):
Latest stable

How reproducible:
Every time

Steps to Reproduce:

The pqr files were created using http://pdb2pqr-1.wustl.edu/pdb2pqr/
using default values and the pH were set to 7. The difference between
the two file is that chain information which is removed from the files
without chain information. The files without chain information is
displayed correct in vmd but with chain information is is displayed as
it is in unfolded state. To be sure I also check the file in pymol to
see if the pdb2pqr had given me an incorrect file. I use vmd because I
need to display charge and pymol lacks some feature that I need.

1. Open 3IC0_with_chain_information.pqr in vmd
http://www.knutjorgen.com/vmd/3ICO_with_chain.jpg
2. Open 3IC0_without_chain_information.pqr
http://www.knutjorgen.com/vmd/3ICO_without_chain_info.jpg
3.

Actual results:
The two file display different image as shown in attach file

Expected results:
VMD should display the same picture ,or this picture
http://www.knutjorgen.com/vmd/3CIO_with_chain_information_in_pymol.jpg
Additional info:
You can download the pqr files from these links
http://www.knutjorgen.com/vmd/3IC0_with_chain_information.pqr and
http://www.knutjorgen.com/vmd/3IC0_without_chain_information.pqr