[Chimera-users] Connolly surface and Triangulation

Elaine Meng meng at cgl.ucsf.edu
Mon Sep 25 09:46:01 PDT 2006

Hi Nihshanka,
Messages to this list might not appear immediately if the moderator  
has to approve them.

Currently, molecular surfaces in Chimera are calculated by the MSMS  
package, as mentioned in this man page:

There is some description of surfaces there, but if you want more  
details you could get the reference cited therein and/or follow the  
"MSMS package" link to that software's home page.  I believe the  
algorithm includes some heuristics to make it faster.  Regardless of  
the algorithm, a molecular surface would never contain a point that  
is at the same position as an atom, because the atom will generally  
have a nonzero radius - the surface touches the surface of the atom,  
not its center.

I hope this helps,

On Sep 23, 2006, at 2:39 PM, Nihshanka Debroy wrote:

> Hi,
>      Not sure if this went the first time, so sending it again:
> ---------------------------------------------------------------------- 
> -------------------------
>     I have been using Chimera to generate the Connolly surface for  
> several different proteins and saving the surface information in  
> X3D format. I was wondering what algorithms are used in the  
> Connolly surface generation. Is it the same approach that Michael  
> Connolly had come up with in his 1983 paper on Analytical Molecular  
> Surface Calculation, or is it a variation of that algorithm?
>     Also, when the surface information is saved by Chimera in X3D,  
> it breaks the surface into triangular faces. I noticed that the   
> coordinates of the points comprising the triangles are completely  
> different from the atomic coordinates. I am interested in learning  
> more about how the triangulation is created.
>     If you could direct me to a link or paper that would help me  
> better understand the algorithms involved in these two processes,  
> that would be great!
> Thanks.
> Sincerely,
> Nihshanka
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users

Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

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