VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Aug 28 2002 - 15:05:35 CDT

Hi Marc,
  In thinking about this, if you have a disconnected set of points
and don't have any specific connectivity information, perhaps you can
turn it into a point cloud in VMD with the "draw" commands, or alternately
it might be possible to do something useful with a 3-D Delaunay triangulation
and some post-processing to remove internal facets, along the same lines
as this VMD script for displaying lipid membranes:
http://www.ks.uiuc.edu/Research/vmd/script_library/scripts/delaunay_triangulate/

On the other hand, if you know for sure the ordering of the points, and
can come up with some sort of connectivity data for them based on this
implicit ordering, you could probably re-sample the points onto a
regular grid and run an isosurface reconstruction on it, much like we do
with these volumetric data sets:
http://www.ks.uiuc.edu/Research/vmd/script_library/scripts/readedm/
http://www.ks.uiuc.edu/Research/vmd/script_library/volumetric.html

Those are the only immediate suggestions that come to mind based
on the information you provided in your email. You would have a lot
more options if you knew more specifics about the connectivity of the
points you're working with, their spacing, etc..

Thanks,
  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Aug 28, 2002 at 09:03:48AM +0100, Marc Baaden wrote:
>
> Hi,
>
> I got an analysis output consisting of points of a surface (no normals, etc).
> Is there a simple way to visualize this (eg make a mesh or a solid rendered
> surface out of it) with VMD ? I guess I will have to pre-process the data
> somehow ?
>
> I think the points are a priori ordered (eg each one lies on a grid and has an
> index), but some intermediate points are missing .. if that helps ..
>
> Thanks for any suggestions,
>
> Marc Baaden 

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