VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Mar 02 2012 - 15:47:41 CST

Hi,
  Yes, you should be able to use a simple VMD script to loop over trajectory
frames and export each frame as an STL file as-needed. I would suggest that
you have a look at some of the old movie rendering scripts as an example:
  http://www.ks.uiuc.edu/Research/vmd/script_library/scripts/trajectory_movie_short/trajectory_movie_short.tcl

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Sat, Mar 03, 2012 at 05:04:18AM +0800, Zhe Wu wrote:
> Hi John,
> Thank you very much for the reply. Yes, I got it working in this way. The
> STL output can be read readily with many softwares like Mathematica etc..
> It is really great!!!
> So my question now becomes whether there is way for me to render many
> snapshots (in a trajectory) at the same time (or maybe with a script in
> Python or Tcl). I am thinking about getting 100+ snapshots for analysis to
> get reasonable statics.
> Thank you again and again for your help!
> Zhe
> > Date: Thu, 1 Mar 2012 22:18:48 -0600
> > From: johns_at_ks.uiuc.edu
> > To: zephyrwuz_at_hotmail.com
> > CC: vmd-l_at_ks.uiuc.edu
> > Subject: Re: vmd-l: exporting marching cubes data from QuickSurf
> >
> > 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 1.0 00000 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 

-- 
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