[Chimera-users] Fwd: accessible surface area for electron density maps

David Chenoweth dchen at caltech.edu
Fri Mar 27 08:59:26 PDT 2009

Begin forwarded message:

> From: David Chenoweth <dchen at caltech.edu>
> Date: March 27, 2009 8:58:31 AM PDT
> To: Elaine Meng <meng at 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 at 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/measurevol.html
>> <http://www.cgl.ucsf.edu/chimera/current/docs/ContributedSoftware/pickblobs/pickblobs.html
>> I hope this helps,
>> Elaine
>> -----
>> 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
>>                     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
>> _______________________________________________
>> Chimera-users mailing list
>> Chimera-users at cgl.ucsf.edu
>> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users

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