Friends, I have a dimer protein (say monomers 1,2). I have calculated the electrostatic potential of monomer 1 using apbs. I used volume viewer to display the electrostatic surface. I see that the elect. surface of one monomer 1, touches the vdw surface of monomer 2 at a contour level of 1. I want to calculate the total surface area of monomer 2 that is exposed/buried within the elec. surface of monomer 1. Is there any simple. If not suggestion how i can do it with a python script perhaps. Thanks, Bala -- C. Balasubramanian
Hi Bala, I can't think of any (noncoding) way in Chimera for looking at surfaces geometrically and getting the area of the monomer 2 molecular surface that is inside the ESP isosurface from monomer 1. However, it sounds like it just boils down to getting the surface area of monomer 2 at which the ESP from monomer 1 is above (or below) some value. In that case, you could color the monomer 2 molecular surface by the ESP from monomer 1 and then use the script that was posted yesterday to get surface area based on color. <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2013-December/009401.html> Since in this case you want the coloring to reflect the ESP right at the surface instead of 1.4 angstroms outward, when coloring be sure to turn OFF the option for "Surface offset" in Electrostatic Surface Coloring. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/surfcolor/surfcolo...> I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Dec 5, 2013, at 7:58 AM, Bala subramanian <bala.biophysics@gmail.com> wrote:
Friends,
I have a dimer protein (say monomers 1,2). I have calculated the electrostatic potential of monomer 1 using apbs. I used volume viewer to display the electrostatic surface.
I see that the elect. surface of one monomer 1, touches the vdw surface of monomer 2 at a contour level of 1. I want to calculate the total surface area of monomer 2 that is exposed/buried within the elec. surface of monomer 1. Is there any simple. If not suggestion how i can do it with a python script perhaps.
Thanks, Bala
Or, maybe you do want the values 1.4 angstroms outward. Either way, be aware of how it works and make a conscious decision about which values you want the coloring to reflect. Elaine On Dec 5, 2013, at 9:12 AM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Since in this case you want the coloring to reflect the ESP right at the surface instead of 1.4 angstroms outward, when coloring be sure to turn OFF the option for "Surface offset" in Electrostatic Surface Coloring. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/surfcolor/surfcolo...>
Hi Bala, One more little detail about using the redarea command to do this measurement. The command measures the area of the surface points where the red color component is greater than or equal to the blue color component. So you should use the surface color dialog to color the molecular surface by volume where it is red at values above a certain potential, e.g. above 5, and blue below 5. To do this you would use two colors for example blue with level 4.999 and red with level 5.001. If you choose other colors like white and red, then every surface point will have the red component greater than or equal to the blue component and you won't measure what you want. Tom On Dec 5, 2013, at 9:25 AM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Or, maybe you do want the values 1.4 angstroms outward. Either way, be aware of how it works and make a conscious decision about which values you want the coloring to reflect. Elaine
On Dec 5, 2013, at 9:12 AM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Since in this case you want the coloring to reflect the ESP right at the surface instead of 1.4 angstroms outward, when coloring be sure to turn OFF the option for "Surface offset" in Electrostatic Surface Coloring. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/surfcolor/surfcolo...>
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Elaine, Tom, Thank you for the information. Just a clarification, I coloured the surface of monomer 2 with the electrostatic potential of monomer 1 with a threshold of -0.5 to 0.5 and the colour range goes from red-white-blue. What i see is that some portion of monomer 2 surface is out of this colour range (and are coloured in dim gray). Does it mean this portion is out of the electrostatic grid of monomer 1 ? Thanks, Bala On Thu, Dec 5, 2013 at 7:25 PM, Tom Goddard <goddard@sonic.net> wrote:
Hi Bala,
One more little detail about using the redarea command to do this measurement. The command measures the area of the surface points where the red color component is greater than or equal to the blue color component. So you should use the surface color dialog to color the molecular surface by volume where it is red at values above a certain potential, e.g. above 5, and blue below 5. To do this you would use two colors for example blue with level 4.999 and red with level 5.001. If you choose other colors like white and red, then every surface point will have the red component greater than or equal to the blue component and you won't measure what you want.
Tom
On Dec 5, 2013, at 9:25 AM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Or, maybe you do want the values 1.4 angstroms outward. Either way, be aware of how it works and make a conscious decision about which values you want the coloring to reflect. Elaine
On Dec 5, 2013, at 9:12 AM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Since in this case you want the coloring to reflect the ESP right at
the surface instead of 1.4 angstroms outward, when coloring be sure to turn OFF the option for "Surface offset" in Electrostatic Surface Coloring.
< http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/surfcolor/surfcolo...
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
-- C. Balasubramanian
Probably: the "color outside volume" is one of the options in the Surface Color (Electrostatic Surface Coloring) dialog. Elaine On Dec 5, 2013, at 12:03 PM, Bala subramanian <bala.biophysics@gmail.com> wrote:
Elaine, Tom,
Thank you for the information. Just a clarification, I coloured the surface of monomer 2 with the electrostatic potential of monomer 1 with a threshold of -0.5 to 0.5 and the colour range goes from red-white-blue. What i see is that some portion of monomer 2 surface is out of this colour range (and are coloured in dim gray). Does it mean this portion is out of the electrostatic grid of monomer 1 ?
Thanks, Bala
On Thu, Dec 5, 2013 at 7:25 PM, Tom Goddard <goddard@sonic.net> wrote: Hi Bala,
One more little detail about using the redarea command to do this measurement. The command measures the area of the surface points where the red color component is greater than or equal to the blue color component. So you should use the surface color dialog to color the molecular surface by volume where it is red at values above a certain potential, e.g. above 5, and blue below 5. To do this you would use two colors for example blue with level 4.999 and red with level 5.001. If you choose other colors like white and red, then every surface point will have the red component greater than or equal to the blue component and you won't measure what you want.
Tom
On Dec 5, 2013, at 9:25 AM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Or, maybe you do want the values 1.4 angstroms outward. Either way, be aware of how it works and make a conscious decision about which values you want the coloring to reflect. Elaine
On Dec 5, 2013, at 9:12 AM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Since in this case you want the coloring to reflect the ESP right at the surface instead of 1.4 angstroms outward, when coloring be sure to turn OFF the option for "Surface offset" in Electrostatic Surface Coloring. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/surfcolor/surfcolo...>
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participants (3)
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Bala subramanian -
Elaine Meng -
Tom Goddard