[Chimera-users] Shape complementarity

Elaine Meng meng at cgl.ucsf.edu
Wed Aug 7 10:23:17 PDT 2013


Hi Hernando,
Chimera does include many ways to evaluate protein-protein interfaces, but nothing like the "shape complementarity" calculation done by that Sc program, sorry.

As you may already know, the things you could do in Chimera include:

- calculating H-bonds and contacts
- showing molecular surfaces of the contact regions and calculating the surface area
   <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#buriedArea>
- showing "interface surface" with Intersurf tool
   <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/intersurf/intersurf.html>
- coloring surfaces by hydrophobicity, electrostatic potential, and even concavity/convexity
   <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/surfprop.html>
   <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/attributes.html#part2>

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 Aug 7, 2013, at 8:47 AM, Hernando J Sosa wrote:

> Dear Chimera,
> Is there a way to evaluate protein-protein interfaces (e.g. using a program like CCP4 Sc)  within chimera?. 
> Thanks 
> Hernando 



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