From: Knut Jørgen Bjuland (knutjorgen_at_gmail.com)
Date: Sun Apr 18 2010 - 00:55:54 CDT

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
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.

Den 17.04.2010 21:33, skrev Rodrigo Silveira:
> Knut,
>
> When a PQR file is loaded into VMD, bond distances are inferred from
> the PQR radii. These radii were chosen for continuum electrostatics
> calculations, not visualization, and therefore some of the radii are
> artificially small. Don't worry if some of the bonds appear a bit strange.
>
> --
> Rodrigo
>
> 2010/4/17 Knut Jørgen Bjuland <knutjorgen_at_gmail.com
> <mailto:knutjorgen_at_gmail.com>>
>
> When I use vmd to view pqr files with include chain from a
> polypetid vmd can not show the file correct. I have seen the file
> correct in pymol. I used pdb2pqr to add charge to a ph=8.5. For my
> experiment I used 2OB0.
>
> Knut J
>
>
>
>
>