VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Aug 28 2002 - 16:43:21 CDT

Hi Marc,
  Here are a couple of suggestions for the questions you asked below:

On Wed, Aug 28, 2002 at 10:35:10PM +0100, Marc Baaden wrote:
> I have checked out your first suggestion.
> It works out quite nicely. I might send you a modified
> dummy script 'hull_surface.tcl' if I manage to get some
> things smoothed out ..

That'd be great!

> Maybe you have some suggestions ..
> - is it possible to color the generated surface eg via the
> B-factor field (.. or other options) ?

In order to do this, you would need to have a tag for each point that
indicates what atom it corresponds to. Alternately, if you have a
spatial or volumetric property that could be evaluated, it should be
simple to color the geometry with a transfer function that maps the
chosen property to colors, evaluated at each source vertex/point in the
surface. This is how VMD applies its coloring methods to the surfaces
that are produced by Surf and MSMS, they keep an atom tag with the
various vertices, and this tag allows VMD to go in and re-color the
geometry with whatever it likes, based on the atom tags it gets from
Surf and MSMS.

> - part of the surface is quite curved and thus leads to
> 'ugly' results, the rest of it is nice, smooth and well
> interpolated.
> Is there a way to improve representation of the 'outliers'
> or if not eventually remove them (other than just excluding
> those points manually)

Without an example image I'm not sure what the cause of the high curvature
is. It could simply be that you need to generate a finer mesh, or that
you need to manually assign per-vertex normals (average of all facets
that include the vertex), which would give you much better shading
results.

> BTW .. what I did is put the points in a separate PDB file.
> As they are quite closely related, I get already a connectivity
> ('bonds') that quite well describes the surface as mesh ..
> an unwanted but very wellcome 'artefact' ..

Interesting.

Let me know if the things I wrote aren't described clearly enough.

Thanks,
  John Stone
  vmd_at_ks.uiuc.edu

> >>> John Stone said:
> >>
> >> 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 triangulati
> on
> >> 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_triangu
> late/
>
>
> --
> Dr. Marc Baaden - Laboratory of Molecular Biophysics, Oxford University
> mailto:baaden_at_smplinux.de - ICQ# 11466242 - http://www.marc-baaden.de
> FAX/Voice +49 697912 39550 - Tel: +44 1865 275380 or +33 609 843217
> 

-- 
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