VMD-L Mailing List

From: Mario Saavedra (mario.saavedra.torres_at_gmail.com)
Date: Thu Apr 29 2010 - 13:47:24 CDT

Hi, again!

Great! It Works!, problem solved!

Thanks!!!

2010/4/29 John Stone <johns_at_ks.uiuc.edu>

>
> Hi,
> Try replacing the symmetrytool plugin in your VMD with the one
> I've attached to this email, and let me know if it cures your problem
> or not. You can find yours in the VMD installation directory, in
> the "plugins/noarch/tcl/symmetrytool1.2" subdirectory.
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
>
> On Thu, Apr 29, 2010 at 09:23:42AM -0400, Mario Saavedra wrote:
> > Thanks John,
> >
> > The problem is with any molecule. For example a simplest H20:
> >
> > ATOM 1 O HOH X 1 -0.228 0.232 -0.167 1.00
> > 0.00 O
> > ATOM 2 H HOH X 0 0.063 -0.601 -0.520 1.00
> > 0.00 H
> > ATOM 3 H HOH X 0 0.165 0.369 0.687 1.00
> > 0.00 H
> > END
> >
> > However, It seems that in the next release 1.8.8a3, this was fixed
> (??) (I
> > hope):
> >
> > "VMD 1.8.8a3 (September 22, 2009):
> > symmetrytool: Use correct scope for getargs function. (It is in
> > ::util::getargs)"
> >
> > So, i must wait the beta release.
> > Cheers,
> >
> > Mario.
> >
> > 2010/4/28 John Stone <johns_at_ks.uiuc.edu>
> >
> > Hi,
> > Can you send me the structure that you're analyzing with the
> Symmetry
> > Tool
> > so I can try and reproduce this problem?
> >
> > Cheers,
> > John Stone
> > vmd_at_ks.uiuc.edu
> > On Fri, Apr 23, 2010 at 05:41:06PM -0400, Mario Saavedra wrote:
> > > Dear VMD Users and Developers:
> > >
> > > When i guess the symmetry group, using the Symmetry Tool,
> return
> > the
> > > Group, but don't draw axis or planes:
> > >
> > > invalid command name "getargs"
> > > invalid command name "getargs"
> > > while executing
> > > "getargs $args "-color" orange3"
> > > (procedure "draw_symaxis" line 2)
> > > invoked from within
> > > "draw_symaxis $sel $center $axis -label "$i: C$order" -color
> > orange3"
> > > (procedure "draw_symmetry_elements" line 65)
> > > invoked from within
> > > "draw_symmetry_elements"
> > > (procedure "::Symmetry::guess" line 108)
> > > invoked from within
> > > "::Symmetry::guess $::Symmetry::sel $::Symmetry::tol"
> > > (procedure "::Symmetry::make_guess" line 7)
> > > invoked from within
> > > "::Symmetry::make_guess"
> > > invoked from within
> > > ".symmetry.guess.button invoke"
> > > ("uplevel" body line 1)
> > > invoked from within
> > > "uplevel #0 [list $w invoke]"
> > > (procedure "tk::ButtonUp" line 22)
> > > invoked from within
> > > "tk::ButtonUp .symmetry.guess.button"
> > > (command bound to event)
> > >
> > > And if i choose some axis, reflections or planes:
> > >
> > > expected integer but got ""
> > > expected integer but got ""
> > > while executing
> > > "graphics $canvaso replace $lastselectaxis"
> > > (procedure "::Symmetry::select_axis" line 8)
> > > invoked from within
> > > "::Symmetry::select_axis [.symmetry.ele.axes.list.list
> > curselection]"
> > > (command bound to event)
> > >
> > > I dont know, why or something is wrong. Any help is
> appreciated.
> > >
> > > Best
> > > Mario Saavedra
> > > Universidad Andres Bello, Chile.
> >
> > --
> > NIH Resource for Macromolecular Modeling and Bioinformatics
> > Beckman Institute for Advanced Science and Technology
> > University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> > Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
> > WWW: http://www.ks.uiuc.edu/~johns/> Fax: 217-244-6078
> >
> > --
> > Mario Saavedra Torres
> > Doctorado en Fisicoquimica Molecular
> > Universidad Andres Bello
> > Santiago, Chile
>
> --
> NIH Resource for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
> WWW: http://www.ks.uiuc.edu/~johns/ <http://www.ks.uiuc.edu/%7Ejohns/>
> Fax: 217-244-6078
> 

-- 
Mario Saavedra Torres
Doctorado en Fisicoquimica Molecular
Universidad Andres Bello
Santiago, Chile