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

Fri Mar 27 10:35:31 PDT 2009

Hi,

My understanding is that the solvent accessible surface is not (yet)  
available in Chimera. However, Elaine showed me once how to get more  
or less such a surface:

1. Before calculating the surface issue the chimera command:

	vdwdefine +1.4

which adds 1.4 A (roughly the usual radius for the water probe) to all  
atom radii

2. Show the surface

3. On the Model Panel, select the surface and under "attributes"  
change the probe radius to 0.5 It should be 0.0 but this is not  
possible. This means that intersections of atom spheres will be  
smoothed slightly. Still, the surface represents almost correctly the  
solvent accessible one.

The error on this surfaces doesn't depend directly on the quality of  
the electron density but on the accuracy of the atoms positions. Which  
of course depends on the data...

I hope it helps,

Miguel

Le 27 mars 09 à 16:59, David Chenoweth a écrit :

>
>
> 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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--
Miguel Ortiz Lombardía
Architecture et Fonction des Macromolécules Biologiques
UMR6098 ( CNRS, U. de Provence, U. de la Méditerranée )
Case 932
163 Avenue de Luminy
13288 Marseille cedex 9
France
Tel : +33(0) 491 82 55 93
Fax: +33(0) 491 26 67 20
e-mail: miguel.ortiz-lombardia at afmb.univ-mrs.fr
Web: http://www.pangea.org/mol/spip.php?rubrique2

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