VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Fri May 20 2011 - 09:07:14 CDT

On Fri, May 20, 2011 at 9:31 AM, George Tzotzos <gtzotzos_at_me.com> wrote:
> Hi everybody,
>
> I'm new to VMD and would be grateful for any help you may provide.
>
> I've loaded and amber topology and trajectory file. The trajectory relates to a ligand bound on a protein of 137 residues.
>
> I can select the ligand from Selected Atomos with (resid 138) drawing method CPK
>
> I'm trying to visualise both the protein and the ligand. When I use (resid 138) and (protein) both molecules disappear from the display.
>
> Likewise when I try to select (resid X) and (resid 138) the effect is the same.

the "and" in the selection language is a 'logical and', i.e. condition
1 _and_ condition 2
have to be met. you, however, want to just part 1 "plus" part 2. that
is done with a
"logical or", that is you have to replace "and" with "or".

> I followed the basic tutorial but to no avail.

check out the user's guide on the details of the atom selection
language instead.

cheers,
   axel.

>
> Your advice will be greatly appreciated.
>
> Best regards
>
> George
>
> 

-- 
Dr. Axel Kohlmeyer
akohlmey_at_gmail.com  http://goo.gl/1wk0
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.