VMD-L Mailing List

From: Scazzocchio, Claudio (c.scazzocchio_at_imperial.ac.uk)
Date: Thu Apr 14 2016 - 06:12:42 CDT

Thanks, Cesar, I try it a little while

Claudio

Prof. Claudio Scazzocchio
Dept. of Microbiology,
Imperial College London
South Kensington Campus
Flowers Building
Armstrong Road
London SW7 2AZ.
UK
Tel int-44(0)20 7594 7409
c.scazzocchio_at_imperial.ac.uk

________________________________
From: Cesar Millan <pachequin_at_gmail.com>
Sent: 14 April 2016 13:02
To: Scazzocchio, Claudio
Cc: vmd-l_at_ks.uiuc.edu
Subject: Re: vmd-l: problems with ligands

If you use the selection: "resname 141" in the 3bdj structure you might be able to see your ligand. I just tried and it worked.

Cesar

############################
César Millán Pacheco
Facultad de Farmacia
Universidad Autonoma del Estado de Morelos
Tel: 777 3297020
Fax: 777 3207040
email: cmp_at_uaem.mx<mailto:cmp_at_uaem.mx>
          pachequin_at_gmail.com<mailto:pachequin_at_gmail.com>

On Thu, Apr 14, 2016 at 5:29 AM, Scazzocchio, Claudio <c.scazzocchio_at_imperial.ac.uk<mailto:c.scazzocchio_at_imperial.ac.uk>> wrote:

When I load some structures in VMD, some ligands are not visualised. For example, I loaded
3bdj.pdb and the inhibitor oxypurinol is not visualised nor it is recorded in the sequence viewer. Note that both cofactors FAD and MOCO are loaded and visualised.
If I load the same molecule in Swiss-PDviewer, oxypurinol is loaded and recorded in the control panel, as 141501.
Is there any way to solve this problem? I have had it before with non-standard ligands.

Another example:

I just looked for the binding of FMN in an oxydoreductase, fine, but when I want to look at the binding of alpha-ketoglutarate in a

di-oxygenase, it is not seen in VMD.

Could anyone help?
Claudio

Prof. Claudio Scazzocchio
Dept. of Microbiology,
Imperial College London
South Kensington Campus
Flowers Building
Armstrong Road
London SW7 2AZ.
UK
Tel int-44(0)20 7594 7409
c.scazzocchio_at_imperial.ac.uk<mailto:c.scazzocchio_at_imperial.ac.uk>