From: Cesar Millan (pachequin_at_gmail.com)
Date: Thu Apr 14 2016 - 06:02:29 CDT

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
          pachequin_at_gmail.com

On Thu, Apr 14, 2016 at 5:29 AM, Scazzocchio, Claudio <
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
>