VMD-L Mailing List

From: Eric H. Lee (ericlee_at_ks.uiuc.edu)
Date: Sun Mar 29 2009 - 14:22:18 CDT

You will have to make a new representation and selection for just the
protein, and one for just the drug. In other words, you will need two
representations - 1) protein as cartoon, and 2) the drug as bonds. It
is likely that the pdb already separates the drug and protein into
separate segments or chains, so you can just make the selection that
way. If you need to find out how the PDB named everything, just use a
text editor to view the PDB file.

-Eric

On Mar 29, 2009, at 1:59 PM, Francesco Pietra wrote:

> I would like to display the protein in 'ribbon' or 'cartoon' and the
> docked small drug in 'bonds'. Both are in the same pdb file.
> Superimposed is a vmd_plot.
>
> I guess i should select the protein and setting 'ribbon' or 'cartoon';
> then select the drug and set 'bonds' . Though, i did not succeed and
> was unable to find an example.
>
> thanks
> francesco pietra

Eric H. Lee
Medical Scholars Program
Theoretical and Computational Biophysics Group, UIUC
ericlee_at_ks.uiuc.edu