From: Axel Kohlmeyer (
Date: Tue Apr 20 2010 - 19:18:09 CDT


thanks a lot for submitting a proper bug report.
in fact, it is a perfect example of how this should
be done. everybody else, please take note.

this way it took me only 5 minutes to identify and
correct the problem that you are seeing.

the issue is - as suspected - a bug in the pqr parser,
but has nothing to do with folding, but rather it was
mixing up columns due to some code that was making
unneeded (and partially wrong) assumptions about
the format of the file.
i was under the impression that pymol uses the same
plugins to read files, so it should suffer from the same
issue but perhaps not in this case here.

the bugfix should be in the next vmd alpha/beta release version.
if you are comfortable with compiling software for yourself,
i can send you the update file and what is needed to compile it.


2010/4/20 Knut Jørgen Bjuland <>:
> 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
> Version-Release number of selected component (if applicable):
> Latest stable
> How reproducible:
> Every time
> Steps to Reproduce:
> The pqr files were created using 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
> 2. Open 3IC0_without_chain_information.pqr
> 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
> Additional info:
> You can download the pqr files from these links
> and

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