VMD-L Mailing List

From: Zhe Wu (zephyrwuz_at_hotmail.com)
Date: Wed Mar 21 2012 - 10:02:16 CDT

Dear John,
Thank you so much for the reply! The script works great! May I ask one more question related to this topic?
Can VMD calculates Gaussian/mean curvature of the surface (for different regions around a particular point) I got from QuickSurf? Maybe I am expecting too much from VMD. But since VMD has applied a smoothing scheme to the surface, it should have done such calculation for the surface. I want to VMD to output those numbers if possible. (I can also cut the surface into small pieces so the curvature is relatively simple.) Or is there any script I can use to do that in VMD? I just ask to see the possibility because I sew some picture looks like the outcome from VMD and is colored for different regions with respect to their Gaussian/mean curvature.
Thank you again and again for your help!
Thanks,Zhe

> Date: Fri, 2 Mar 2012 15:47:41 -0600
> From: johns_at_ks.uiuc.edu
> To: zephyrwuz_at_hotmail.com; vmd-l_at_ks.uiuc.edu
> Subject: Re: vmd-l: exporting marching cubes data from QuickSurf
>
>
> 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