VMD-L Mailing List
From: Yusu Wang (wys_at_cs.duke.edu)
Date: Tue Jan 27 2004 - 19:26:16 CST
- Next message: Saladino, Alex: "Helical Tilt Angle"
- Previous message: John Stone: "Re: OpenGL library loading"
- In reply to: John Stone: "Re: surf for mac"
- Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]
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 >
- Next message: Saladino, Alex: "Helical Tilt Angle"
- Previous message: John Stone: "Re: OpenGL library loading"
- In reply to: John Stone: "Re: surf for mac"
- Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]