VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Mar 21 2012 - 10:39:17 CDT

Hi,

On Wed, Mar 21, 2012 at 11:02:16PM +0800, Zhe Wu wrote:
> Dear John,
> Thank you so much for the reply! The script works great! May I ask one
> more question related to this topic?

Sure.

> 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.

VMD doesn't apply any smoothing scheme to the surface after-the-fact.
At present, the surface that is extracted is the isosurface extracted
directly from the summed Gaussian density map, for a particular user-defined
atom radius scaling factor, isovalue, and grid spacing. Computing the
local surface curvature of the resulting mesh would make the algorithm
much slower, and since we don't need it for the visualization use of
QuickSurf, we don't do such a calculation at present. You could certainly
compute this for yourself by various means, by postprocessing the mesh
and/or the input data and parameters.

> 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.

It is possible that someone made such a picture, but they would have
computed the curvature independently of the mesh that QuickSurf generated.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

> 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 r! ender ma
> ny
> > > 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 0.000! 000 0.00 0000}
> > > > {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 

-- 
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