VMD-L Mailing List

From: amin sagar (aamin.sagar_at_gmail.com)
Date: Sat Aug 11 2018 - 03:14:12 CDT

Hello,
A new selection with

same residue as (protein within 3 of resname ligand)

should do it.

Best,
Amin.

On Sat, 11 Aug 2018 at 10:03 AM, Graham Jackson <graham.jackson_at_uct.ac.za>
wrote:

> Hi
>
> I am looking for the best way to display the interaction between a ligand
> (neuropeptide) and its receptor.
>
> I have a transmembrane receptor, to which I have docked a neuropeptide.
> The receptor is imbedded in a POPC membrane. At the moment I am not
> displaying the POPC or the water molecules. I display the receptor in
> ribbon form and the ligand as VDW. I now want to display those receptor
> residues near the ligand as CPK. I only seem to be able to select atoms
> near the ligand but not the whole residue. How do I select/display the
> whole residue?
>
>
>
> Also what is the best way of displaying the surface of the receptor so
> that you can see the ligand docked?
>
>
>
> Thanks
>
>
>
> Graham
>
>
>
> --
>
> Graham Jackson
>
> Professor Emeritus
>
> Department of Chemistry
>
> University of Cape Town
>
> Graham.jackson_at_uct.ac.za
>
> Tel +27 650 2531
>
>
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