VMD-L Mailing List

From: Joaquim Rui de Castro Rodrigues (joaquim.rodrigues_at_ipleiria.pt)
Date: Wed Nov 28 2012 - 10:50:30 CST

Hi,

The square brackets mean "optional". According to the link you've found, "the optional selection string defines how atoms for each frame have to be selected. If not given, as selection string of "user > 0" is assumed."

In your case, this should reproduce the default behaviour:
topo writevarxyz "test.xyz" selmod "user > 0"

If you use "all", you will constant number of atoms.

HTH,
Rui Rodrigues

________________________________________
De: owner-vmd-l_at_ks.uiuc.edu [owner-vmd-l_at_ks.uiuc.edu] Em Nome De Philippe Bopp / temporary [philippebopp_at_yahoo.com]
Enviado: quarta-feira, 28 de Novembro de 2012 15:02
Para: vmd-l_at_ks.uiuc.edu
Assunto: vmd-l: not very helpful documentation

 Hi everybody

Quastion: what is 'selmod' ?

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

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

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.

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)
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