VMD-L Mailing List

From: Marc Baaden (baaden_at_smplinux.de)
Date: Wed Aug 28 2002 - 16:35:10 CDT

Hi John,

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 ..

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

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' ..

Cheers,
Marc

>>> 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
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