From: Scazzocchio, Claudio (
Date: Thu Apr 14 2016 - 05:29:16 CDT

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?

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