VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Jan 27 2004 - 15:32:11 CST

Yusu,
  You can alter the transformation matrices to be identity matrices
by doing something like this:

proc make_transforms_identity {} {
  foreach mol [molinfo list] {
    foreach matrix {center_matrix rotate_matrix scale_matrix global_matrix} {
      molinfo $mol set $matrix { {{1 0 0 0} {0 1 0 0} {0 0 1 0} {0 0 0 1}} }
    }
  }
}

That should do what you want.

Enjoy,
  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Jan 27, 2004 at 01:21:30AM -0500, Yusu Wang wrote:
>
> It worked. Thanks a lot.
>
> However, the output stl is transformed and scaled. Is it possible to
> obtain it in the original coord-system? I know that if I use "save
> state" option, then vmd can output a file containing viewing infor.
> But I am not sure how exactly to get the transformation matrix from
> that file.
>
> Thanks,
> --Yusu
> --
> Yusu Wang, CS Dept. Duke University. Durham, NC, 27008-0129
> http://www.cs.duke.edu/~wys
>
> On Mon, 26 Jan 2004, John Stone wrote:
>
> > Dear Yusu,
> > VMD stores the output of both Surf and MSMS internally and doesn't
> > keep any of the output as a file. You can emit the surface triangulation
> > using the "STL" rendering method which writes a triangulated surface.
> > Alternately, you could run Surf or MSMS by hand and read their output
> > files directly. Within VMD though, using one of the "Render" options
> > is the easiest way to get a surface out. Before rendering, be sure
> > that the only geometry displayed in VMD is the surface you're interested in.
> >
> > Thanks,
> > John Stone
> > vmd_at_ks.uiuc.edu
> >
> > On Mon, Jan 26, 2004 at 03:23:42PM -0500, Yusu Wang wrote:
> > >
> > > I am a Mac user (mac OS X). I'd like to compute the triangulation
> > > of a molecular surface. I know that surf can do that. However, I
> > > don't know where vmd stores the tempary output file of that
> > > triangulation. Does any one have any idea? Thanks a million!
> > >
> > > --Yusu
> > > --
> > > Yusu Wang, CS Dept. Duke University. Durham, NC, 27008-0129
> > > http://www.cs.duke.edu/~wys
> >
> > --
> > 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
> > 

-- 
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