From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Mon Oct 29 2012 - 07:51:16 CDT

On Mon, Oct 29, 2012 at 12:57 PM, Aronica, Pietro
<pietro.aronica07_at_imperial.ac.uk> wrote:
> Hello,
> I was wondering if there was a way to set the representation a molecule from
> the command line. For example, given a .prmtop and a .restart file, I'd like
> VMD to automatically load the molecule with a specific residue in "licorice"
> representation and all atoms within 5 angstroms of that residue in "line"
> representation. I know how to do that from the graphical representation
> window, but can it be done from the command line?

yes, it can be done.

practically all GUI operation have a textmode/script equivalent.

you can just turn on logging and watch (or log to a file) and you
see the script command equivalents of your GUI operations.

axel

> Kind regards
> Pietro Aronica

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  http://goo.gl/1wk0
International Centre for Theoretical Physics, Trieste. Italy.