VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Mar 01 2012 - 22:18:48 CST

Hi,
  If you turn off the VMD axes (and any other non-QuickSurf representations)
and then use the File->Render menu, you can export the QuickSurf
surface mesh to STL or one of the other easy-to-parse text scene file
formats. If you want to preserve the original molecular coordinate
system (no rotation/translation/scaling applied to coordinates),
you can run these commands prior to the export:

set identityvpts {
  {{1.000000 0.000000 0.000000 0.000000}
   {0.000000 1.000000 0.000000 0.000000}
   {0.000000 0.000000 1.000000 0.000000}
   {0.000000 0.000000 0.000000 1.000000}}
  {{1.000000 0.000000 0.000000 0.000000}
   {0.000000 1.000000 0.000000 0.000000}
   {0.000000 0.000000 1.000000 0.000000}
   {0.000000 0.000000 0.000000 1.000000}}
  {{1.000000 0.000000 0.000000 0.000000}
   {0.000000 1.000000 0.000000 0.000000}
   {0.000000 0.000000 1.000000 0.000000}
   {0.000000 0.000000 0.000000 1.000000}}
  {{1.000000 0.000000 0.000000 0.000000}
   {0.000000 1.000000 0.000000 0.000000}
   {0.000000 0.000000 1.000000 0.000000}
   {0.000000 0.000000 0.000000 1.000000}}
  }

molinfo top set {center_matrix rotate_matrix scale_matrix global_matrix} $identityvpts

Give that a try and let me know how it works for you.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Fri, Mar 02, 2012 at 11:40:11AM +0800, Zhe Wu wrote:
> Hi,
> The QuickSurf drawing method in VMD is really cool! From the output
> message, it shows the marching cube algorithm. I wonder whether I can
> export the marching cubes data (the triangle positions) so I can further
> analysis the resulting surface such as curvatures.
> I am using the VMD version of 1.9.1 and I am trying to analysis a
> block-copolymer morphology as its micro-phase interface.
> Thank you in advanced for your help!
> Thanks,
> Zhe
> 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/       Fax: 217-244-6078