VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Wed Mar 10 2010 - 07:57:38 CST

On Wed, 2010-03-10 at 09:03 -0300, Alexandre Suman de Araujo wrote:
> Hi Axel

hi alexandre,

> The second suggestion worked very well.

thanks, that is very good to know. please check carefully.
since the topotools package is still fairly new and bugs
tend to surface occasionally. i tried hard to write conservative
code, but there is always a good chance that somebody tries
something that i never had throught of before.

> But the use of mergestructs package resulted in problems. When I try to
> use the following command:
>
> mergestructs {file1.psf file1.pdb} {file2.psf file2.pdb} file3
>
> I have the following error
>
> wrong # args: should be "mergestructs"
>
>
> When I try to call mergestructs without parameters, the GUI interface is
> opened.
> I tried to find the correct syntax but I have not success.
> Do you mind what is happening?

yes. this was of course a cunning plan to promote my plugin. ;-)

in reality, it was my fault. i made a mistake when looking up
the script code for mergestructs. what you have to call is
::MergeStructs::mergeMolecules instead of mergestructs

if you look closely at the tcl/tk code for the mergstructs plugin,
then you'll see that the majority of it is just to generate the GUI.
the "real" code is just this one function and it is a fairly
short one. in any case, i think it is good to have multiple
options.

cheers,
   axel.

>
> Cheers
>
> **************************************************************
> Alexandre Suman de Araujo *
> Faculdade de Ciências Farmacêuticas de Ribeirão Preto *
> Universidade de São Paulo *
> Dep. de Física e Química *
> Grupo de Física Biológica * e-mail: asaraujo_at_fcfrp.usp.br*
> Av. do Café, s/n° * e-mail: ale.suman_at_gmail.com *
> CEP: 14040-903 * Phone: +55 (16) 3602-4172 *
> Ribeirão Preto, SP, Brasil * Phone: +55 (16) 3602-4222 *
> **************************************************************
>
>
>
> Axel Kohlmeyer escreveu:
> > hi alexandre,
> >
> > On Tue, Mar 9, 2010 at 1:24 PM, Alexandre Suman de Araujo
> > <asaraujo_at_if.sc.usp.br> wrote:
> >
> >> Hi all.
> >>
> >> Is it possible to use MergeStructs plugin in Tk console or scripts?
> >>
> >
> > yes.
> >
> >
> >> If yes, which is the sintax should I use?
> >>
> >
> > package require megstructs 1.0
> > namespace import Mergestructs::*
> >
> > mergestructs {file1.psf file1.pdb} {file2.psf file2.pdb} file3
> >
> > that would require having the two molecules as external files.
> >
> > if you want to do this with internal data (perhaps after modifying
> > bonding or atom types/names/coordinates) you can also try
> >
> > package require topotools 1.0
> > namespace import TopoTools::mergemols
> >
> > set newmol [mergemols {0 1 2}]
> >
> > animate write psf file3.psf $newmol
> > animate write pdb file3.pdb $newmol
> >
> > there are a few small improvements in the topotools package
> > since vmd 1.8.7, so if you don't want to update to the latest
> > VMD alpha version, you can download the updated package
> > by itself from
> >
> > https://sites.google.com/site/akohlmey/software/topotools
> >
> > mergestructs uses psfgen and topotools uses the internal
> > information that VMD has after loading a psf or similar topology
> > format. so depending on what you are doing one of the two
> > may be the better solution.
> >
> > cheers,
> > axel.
> >
> >
> >> Cheers
> >>
> >> --
> >> **************************************************************
> >> Alexandre Suman de Araujo *
> >> Faculdade de Ciências Farmacêuticas de Ribeirão Preto *
> >> Universidade de São Paulo *
> >> Dep. de Física e Química *
> >> Grupo de Física Biológica * e-mail: asaraujo_at_fcfrp.usp.br*
> >> Av. do Café, s/n° * e-mail: ale.suman_at_gmail.com *
> >> CEP: 14040-903 * Phone: +55 (16) 3602-4172 *
> >> Ribeirão Preto, SP, Brasil * Phone: +55 (16) 3602-4222 *
> >> **************************************************************
> >>
> >>
> >
> >
> >
> > 

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com
http://sites.google.com/site/akohlmey/
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.