VMD-L Mailing List

From: Mario Saavedra (mario.saavedra.torres_at_gmail.com)
Date: Thu Apr 29 2010 - 08:23:42 CDT

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/ <http://www.ks.uiuc.edu/%7Ejohns/>
> Fax: 217-244-6078
> 

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