[Chimera-users] calculate buried surface area

Elaine Meng meng at cgl.ucsf.edu
Thu Dec 5 12:08:28 PST 2013


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 at 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 at 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 at 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 at 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/surfcolor.html>
> >
> >
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> 
> 
> 
> 
> -- 
> C. Balasubramanian
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