VMD-L Mailing List

From: Yusu Wang (wys_at_cs.duke.edu)
Date: Tue Jan 27 2004 - 19:26:16 CST

  I see. This seems to work. Really appreciate it!

  --Yusu 

--
Yusu Wang, CS Dept. Duke University. Durham, NC, 27008-0129
http://www.cs.duke.edu/~wys
On Tue, 27 Jan 2004, John Stone wrote:
>
> 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
>