Begin forwarded message:
From: David Chenoweth <dchen@caltech.edu> Date: March 27, 2009 8:58:31 AM PDT To: Elaine Meng <meng@cgl.ucsf.edu> Subject: Re: [Chimera-users] accessible surface area for electron density maps
Hi Elaine and Murali,
I have a similar problem that I've been trying to resolve. Calculating the accessible surface or solvent accessible surface is also something I've been interested in doing with Chimera but I don't think the area of the molecular surface is the same as the solvent accessible surface area. I believe that accessible surface comes from the locus of the center of a spherical probe as it rolls over the Van der Waals surface of a molecule. The molecular surface uses the locus of the inward facing spherical probe. They both depend on the spherical probe size which is set to the appropriate solvent molecule. Can you tell me which of these two methods Chimera is using when it calculates the area (if either)? Is there a way to calculate the solvent accessible surface area of a molecule with Chimera or some way to manipulate the current area calculator to give this value? I also think that depending on the quality of the electron density map one could get very different results for this calculation (especially if there is missing electron density or at different map contour values). If anyone has any advice for the best way to calculate solvent accessible surface area I would really appreciate the help.
Thanks, Dave Chenoweth
********************************************** David M. Chenoweth California Institute of Technology Division of Chemistry and Chemical Engineering Mail Code: 164-30 1200 California Boulevard, 91125 Pasadena California, USA
Phone: 626-395-6074 Email: dchen@caltech.edu **********************************************
On Mar 27, 2009, at 8:14 AM, Elaine Meng wrote:
Hi Murali, If I understand correctly, you want to get the area of a contour surface of the density shown using the Volume Viewer tool. If you want the total surface area, even of multiple separate blobs, use "Measure Volume and Area." If you want to measure the area of different blobs individually, use "Measure and Color Blobs."
These can be started from the Tools menu of the Volume Viewer dialog, and also from the main Chimera Tools menu (Tools... Volume Data... [name of tool]).
For more details on how to use a tool, press the Help button on the dialog. That opens the documentation included with your download. Our web site also has copies of the documentation: <http://www.cgl.ucsf.edu/chimera/current/docs/ContributedSoftware/measurevol/...
<http://www.cgl.ucsf.edu/chimera/current/docs/ContributedSoftware/pickblobs/p...
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html
On Mar 27, 2009, at 7:42 AM, Murali Ayaluru wrote:
Dear Chimera users, I want to calculate the accessible surface area for an electron density map (mrc format) that I am working on. Can anyone, who knows how to do this, tell me how to do this? Thanks in advance for your reply, Regards, Murali
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