Fwd: accessible surface area for electron density maps
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
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
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@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
_______________________________________________ Chimera-users mailing list Chimera-users@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@afmb.univ-mrs.fr Web: http://www.pangea.org/mol/spip.php?rubrique2 -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean.
Hi everybody, What Miguel describes is how to make the displayed molecular surface look more like a solvent-accessible surface by moving it 1.4 A outward, even though it is really calculated as a solvent-excluded surface. However, it is not necessary to do that if you are interested in the area values rather than the display: areas are reported and assigned as attributes for both types of surface even though only the solvent- excluded one is shown. In fact, if you will be using the area values, you should NOT perform those adjustments, because the area of that displayed surface (which is now expanded from the solvent-excluded surface but is still not exactly the solvent-accessible surface) will be reported as the solvent-excluded area, and even bigger values reported as the solvent- accessible areas. Also in agreement with what Miguel said, the surface calculation does not use density, it only uses atomic positions and radii. Best, Elaine ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) 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 10:35 AM, Miguel Ortiz Lombardia wrote:
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
participants (3)
-
David Chenoweth -
Elaine Meng -
Miguel Ortiz Lombardia