VMD-L Mailing List

From: Stephen Cox (stephen.cox.10_at_ucl.ac.uk)
Date: Mon Mar 07 2011 - 13:28:41 CST

hi

the i've been using the clonerep plugin for a while now and it works pretty
well. I was just wondering how I could make a movie out of all the frames i
have loaded in as separate files (or more accurately, render each frame as I
can deal with making a movie once I have these). I tried the script below:

foreach f [lsort [glob *.xyz]] {
    mol new $f type xyz waitfor all
        pbc set {47.51 41.14 58.0323395}
        pbc box -width 5 -color yellow
* render POV3 $f.pov*
}
package require clonerep

which kind of works, but obviously I haven't changed any of the graphical
representations. Is there a way I could load in the graphical
representations in the script and then render the image as above? Or is
there a better way, making use of the clonerep plugin?

thanks in advance for any help,

steve

On Sun, Feb 6, 2011 at 9:43 PM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:

> hi steve,
>
> [...]
>
>
> > However, it would be nice to change the graphical representations of all
> the
> > loaded frames, so that for example Carbon atoms (name C) are "VDW 1.000
> > 23.000", Oxygens (name OW) are "VDW 0.800 23.00" and Hydrogens (name HW)
> are
> > "VDW 0.500 23.000". I tried adding something like
>
> the clonerep plugin is your friend.
>
> http://www.ks.uiuc.edu/Research/vmd/plugins/clonerep/
>
> just visualize one of the molecules and clone it to the
> rest of the frames.
>
> let me know, if you need help or run into problems.
>
> cheers,
> axel.
>
> >
> > foreach f [lsort [glob *.xyz]] {
> > mol new $f type xyz waitfor all
> > mol modselect 0 0 name OW
> > mol modstyle 0 0 VDW 0.800 23.000
> > addrep 0
> > .... ....
> > }
> >
> > Which I took from logging the commands to a console, but it only works
> for
> > the first frame... I think I need to loop over the second "0" over all
> > molecules but I'm not too familiar with Tcl, so any help would be
> > appreciated.
> >
> > Cheers,
> >
> > Steve
> >
>
>
>
> --
> Dr. Axel Kohlmeyer
> akohlmey_at_gmail.com http://goo.gl/1wk0
>
> Institute for Computational Molecular Science
> Temple University, Philadelphia PA, USA.
>