From: Axel Kohlmeyer (
Date: Sun Apr 18 2010 - 11:14:01 CDT

On Sun, 2010-04-18 at 07:55 +0200, Knut Jørgen Bjuland wrote:


the quality of help you can get largely depends on the quality
of your problem report. unfortunately, you are not very specific,
so people can only guess, which in turn will make it difficult to
solve your problem and discourage people to reply in the first place.

> The problem is that vmd does not display the 3d strcuture in a right
> manner. When I keep the chain information when I am making a pqr by

what is 'right' or 'wrong' in this context is often a matter
of opinion or habit. it is an old joke that people in search
of the truth should consider studying philosophy instead of
doing computer simulations. it would be better if you describe
what you expect and compare it to what you get instead. since
your problem is "visual" a couple of screenshots are probably
the best way to show the difference.

> using pdb2pqr. If I chose not to include the chain vmd does display
> the protein in folded state, but when chain information is prsent vmd
> display the protein as unfoldes protein. I used 2OB0 as test case
> since it is polypetid with chain A,B and C.

again, this i very unspecific. it would be better, if you provide
the exact command lines and program versions that you were using,
as this would enable somebody else to _exactly_ reproduce what
you have done, without having to be an expert in your special area
of expertise. you have to keep in mind that .pdb and .pqr files are
read by different file reader plugins and since those were not always
written by the same people, they may chose differently in case there
is ambiguous data.


> Den 17.04.2010 21:33, skrev Rodrigo Silveira:

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