[Chimera-users] Delaunay Tessellation

[Elaine Meng]

Hi Forbes,
I'm hoping others will pipe up, since I don't have wonderful  
answers... I'm not aware of any work on directly interfacing either  
Delaunay tessellation or elastic network model calculations with  
Chimera.

For Delaunay tessellation, Qhull is freeware, and I even thought we  
were using it for something in Chimera, but I don't think it is in  
python.
<http://wareseeker.com/Home-Education/qhull-2010.1.zip/370b017fb>

Chimera does connect to the NIH Structools server to get atom- 
associated Voronoi volumes assigned as attributes (see Tools...  
Surface/Binding Analysis... Area/Volume from Web), but there is no  
display of the actual tessellation.
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/surfvol/surfvol.html 
 >

The CASTp pocket area/volume information that can be shown in Chimera  
is calculated using the weighted Delaunay triangulation, but you only  
get the results, again not the tessellation.
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/castp.html>

For ENM and similar, there are a number of web servers, but they do  
not provide output convenient for viewing in Chimera. Here are a few  
(and surely there are more):

elNemo elastic network model server
<http://www.igs.cnrs-mrs.fr/elnemo/start.html>

AD-ENM web server
<http://enm.lobos.nih.gov/>

Anisotropic Network Model web server
<http://ignmtest.ccbb.pitt.edu/cgi-bin/anm/anm1.cgi>

Best,
Elaine
-----
Elaine C. Meng, Ph.D.
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco


On Mar 23, 2010, at 10:32 AM, Forbes J. Burkowski wrote:

> Hi:
> Do you folks know if there is a Python Script to do Delaunay  
> Tessellation
> for proteins?
>
> I am also wondering if anyone has written code to handle Elastic  
> Normal
> Mode analysis.
>
> Any suggestions or pointers would be appreciated.
> Many thanks,
> Forbes Burkowski