[Chimera-users] calculate buried surface area

Tom Goddard goddard at sonic.net
Thu Dec 5 10:25:59 PST 2013


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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