From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Wed Nov 28 2012 - 10:40:12 CST

On Wed, Nov 28, 2012 at 4:02 PM, Philippe Bopp / temporary
<philippebopp_at_yahoo.com> wrote:
>
> Hi everybody
>
> Quastion: what is 'selmod' ?

just a name.

> This term appears in the entire VMD documentations
> (according to Google and
> http://www.ks.uiuc.edu/Research/vmd/'s own search)
> exactly 2 (two) times on:
>
> http://www.ks.uiuc.edu/Research/vmd/plugins/topotools/
>
> in the string
>
> writevarxyz <file name> [selmod <sel>] [first|last|step <frame]
>
> VERY INFORMATIVE!
>
> So what is it?
>
> I tried
>
> topo writevarxyz "test.xyz" [selmod all]
> topo writevarxyz "test.xyz" [selmod "all"]
> topo writevarxyz "test.xyz" [all]
> topo writevarxyz "test.xyz" ["all"]
>
> which just generated a choice of obscure error meessages

yes. you didn't follow the VMD documentation conventions
(which are borrowed from unix manpages).

everything placed in square brackets is optional,
everything separated by a pipe sign are alternatives,
everything in angular brackets is a description of
what should be specified in its place.

thus the three following variants would be correct:

topo writevarxyz "test.xyz" selmod all
topo writevarxyz "test.xyz" selmod "all"
topo writevarxyz "test.xyz" selmod {all}

(mind you, using 'all' doesn't make much
sense, as you can just write out that file
directly from the GUI or with "animate write xyz")

> and finally
> topo writevarxyz "test.xyz" [top]
> which crashed VMD (reproducibly)

interesting. which version of VMD and topotools?
what OS?

> Everything else even vaguely plausible
>
> topo writevarxyz 'test.xyz' [atomselect top "name H"]
> topo writevarxyz 'test.xyz' [current]
> topo writevarxyz 'test.xyz' [selmod $atomselect0]
> .......
> fails.

sure. this is all because the square brackets
are a Tcl syntax element to evaluate the enclosed
list as a Tcl command and replace it with the output
of that command (like backticks in shell script).

ciao,
    axel.

>
> Looking into the file topovarxyz.tcl (which is exactly what one
> would want to avoid) didn't shed any light on 'selmod'
> either.
>
>
> cheers
>
> Philippe
>
>
>
> -----------------
> Philippe A. Bopp
>
> philippebopp AT yahoo.com (private)
> Philippe.Bopp AT u-bordeaux1.fr (office)
> -----------------
>
>

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