[Chimera-users] Delaunay Tessellation

Elaine Meng meng at cgl.ucsf.edu
Tue Mar 23 11:43:03 PDT 2010

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  

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  

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.

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.

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

AD-ENM web server

Anisotropic Network Model web server

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

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