VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Thu May 15 2014 - 17:30:12 CDT

On Thu, May 15, 2014 at 5:48 PM, Bokas George <bokas_at_wisc.edu> wrote:

> Hello all,
>
> I am attempting to create a script in order to open multiple molecules
> together with predefined default representations.
>
> I think that I am close enough but I have a small problem.
>
> When I am calling vmd from terminal I am using this command:
>
> vmd -m traj*
>
> So I am achieving to have about 100 different molecules imported at the
> vmd.
> The problem is that only the first one has the predefined representation I
> have set at the .vmdrc file.
>
> In particular I have added these three lines at the .vmdrc file:
>
> color Display Background white
> display projection Orthographic
> mol modstyle 0 0 CPK 1.000000 0.300000 10.000000 10.000000
>
> but only the first imported molecule appear with CPK representation.
>

​yes, because you only apply the modification to the first molecule.​

>
> I tried also:
> mol all modstyle 0 0 CPK 1.0000000 0.300000000 10.000000 10.000000
>

​no. that is not a valid syntax. please look it up in the VMD user's guide.

you should be using the "mol default" sub​command to change your default
settings, or put a little piece of script code into a "after idle" section
that loops over all molecules and changes/adds/deletes representations as
you want/need it.

axel.

>
> If anyone can help me I would appreciate it a much.
>
> Thank you very much in advance,
> GBokas
>
> 

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.