[Chimera-users] External SAS calculation

Tom Goddard goddard at cgl.ucsf.edu
Mon Nov 9 15:51:58 PST 2009

Hi Yasser,

  Chimera uses the MSMS library from Michel Sanner at Scripps.  The 
Python routines in Chimera are in


If you are interested in surface areas you may also be interested in the 
Chimera "measure buriedArea" command


Python code for that is the buried_area() function in


These Python files are in your Chimera distribution.  On the Mac instead 
of "chimera/share" you would find them in


The MSMS code does not compute solvent accessible surface (SAS) 
triangulations, only solvent excluded surface (SES) triangulations.  The 
difference is that the former uses the center of a ball rolling over the 
molecule while the latter uses the contact point of a ball rolling over 
the molecule to define the surface.  The MSMS code does compute the SAS 
surface area even though it does not compute the triangles making up the 


-------- Original Message --------
Subject: [Chimera-users] External SAS calculation
From: Yasser
To: chimera-users
Date: 11/9/09 8:42 AM
> Hi all..
> In the Chimera source where is located the sources files for the 
> calculation of SAS. I'm writing a python script for calculate the SAS 
> and i want to call the Chimera's routines to do this task...
> Best regards

More information about the Chimera-users mailing list