Thanks!!
--
Paul Rigor
http://www.ics.uci.edu/~prigor <http://www.ics.uci.edu/%7Eprigor>
On Tue, Jan 18, 2011 at 6:47 AM, Robert Campbell <[email protected]
> wrote:
> Hi Paul,
>
> On Mon, 17 Jan 2011 19:00:09 -0800 Paul Rigor <[email protected]> wrote:
>
> > Hi gang,
> > Just wondering if anyone has experienced some weird rendering issues, ie,
> > aberrant bonds between atoms. I've attached a sample pdbqt file which
> > contains 4 molecules which are outputs of autodock vina. Can someone try
> > loading and visualizing it?
> >
> > I'm currently using the educational version 1.3. I've tried on linux and
> mac
> > os x. The nvideo cards include both ATI and NVidia.
>
> It isn't really a rendering issue, but a bonding issue (or an atom-ordering
> issue -- the structures in this multi-model file do not have the same atoms
> in the same order). You need to load the structures in this multi-model
> file
> with the discrete flag turned on. This will force PyMOL to construct a
> bonding-table for each model separately.
>
> load top4fix.pdbqt, discrete=1
>
> Cheers,
> Rob
> --
> Robert L. Campbell, Ph.D.
> Senior Research Associate/Adjunct Assistant Professor
> Botterell Hall Rm 644
> Department of Biochemistry, Queen's University,
> Kingston, ON K7L 3N6 Canada
> Tel: 613-533-6821 Fax: 613-533-2497
> <[email protected]>
> http://pldserver1.biochem.queensu.ca/~rlc<http://pldserver1.biochem.queensu.ca/%7Erlc>
>
>
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