[Chimera-users] calculate buried surface area
bala.biophysics at gmail.com
Thu Dec 5 12:03:32 PST 2013
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 ?
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.
> 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.
> >> <
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> > Chimera-users at cgl.ucsf.edu
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