From: Josh Vermaas (
Date: Thu May 15 2014 - 17:49:51 CDT

See the manual
( You need
to set the default. mol modstyle only does it to the current molecule.
"mol default" changes the defaults, and those defaults would work for
all 100 molecules. I don't remember the exact syntax past that, but you
can figure it out. :) One potential issue is that file loading happens
BEFORE reading the vmdrc file. Put the commands in a separate script and
load the script, since those are executed before loading files (I
think). Your final command would look something like:

vmd -m traj* -e scriptfile.tcl

Good luck!
On 05/15/2014 05:48 PM, Bokas George 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.
> I tried also:
> mol all modstyle 0 0 CPK 1.0000000 0.300000000 10.000000 10.000000
> If anyone can help me I would appreciate it a much.
> Thank you very much in advance,
> GBokas