From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Fri Mar 12 2010 - 09:11:24 CST

On Thu, 2010-03-11 at 15:04 -0300, Alexandre Suman de Araujo wrote:

hi alexandre,
> >
> Like I said, the code using topotool worked perfectly, but to have a
> second option I tried to implement the code using mergestructs package.
> I changed the first code you propose to fit to your last message but I'm
> having a strange behavior.
> When I run the following script:
>
> #Load package
> package require mergestructs 1.0
> namespace import MergeStructs::*
>
> ::MergeStructs::mergeMolecules {caixa_membrana.psf caixa_membrana.pdb}
> {colesterol.psf colesterol.pdb} popc_1chol
>
> #Bye
> exit
>
> Using "vmd -dispdev text -e merge_strucs.tcl" I have the following error:
>
> invalid command name "psfcontext"
>
> When I run it with "vmd -e merge_strucs.tcl", everything works fine.
>
> I don´t know why this is happening. Maybe it is because when I run vmd
> in graphical mode there are packages that are loaded by default and in

exactly. the mergestructs plugin is not importing
the psfgen package like it should. in graphical mode
some other plugins (e.g. autopsf) will import it so
one doesn't notice. i guess the original author of
the plugin didn't expect people to use it in text mode,
since most people that know a little bit of using
psfgen would be able to write that kind of script
directly.

it is a trivial change and i'll see that it will be fixed
in the mean time just add a "package require psfgen"
to your script and then it should work in text mode, too.

cheers,
   axel.

> text mode not, but this is just a guess.
> Do you know what is really happening?
>
> Cheers
>
> >> 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.