VMD-L Mailing List

From: Bokas George (bokas_at_wisc.edu)
Date: Thu May 15 2014 - 17:58:52 CDT

Dear Axel,

First of all I would like to thank you very much for your quick reply.

I forgot to mention that I have used also the mol default command with no success.

But the after idle method work like a charm.

So thank you very much for your help.

Best,
GBokas

On May 15, 2014, at 17:30, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:

>
>
>
> 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.