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.htm...
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