VMD-L Mailing List

From: Zhe Wu (zephyrwuz_at_hotmail.com)
Date: Fri Mar 02 2012 - 15:04:18 CST

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 1.000000 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