[Chimera-users] buried surface area

[Thomas Goddard]

Hi Dieter,

  The surface area / volume tool (menu entry Tools -> Utilities ->
Surface Area / Volume) could give buried surface areas if you ran it
for the unbound receptor, unbound ligand, and then the complex, and
then calculated

   { Area(receptor) + Area(ligand) - Area(receptor+ligand) } / 2

When you use this tool it reports the total area to the Reply Log
(menu entry Favorites / Reply Log) and atoms are assigned an attribute
saying how much area they contribute.  It is a bit of a pain to run it 3
times and do the math yourself.  The surface area is calculated by a
web server as described in the Chimera User's Guide

  http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/surfvol/surfvol.html

so you will need an internet connection to use it.
  
  The Chimera User's Guide is only available in HTML as far as I know.
It is written in HTML.

   Tom


> From: "Dieter Blaas" <dieter.blaas at meduniwien.ac.at>
> To: Thomas Goddard <goddard at cgl.ucsf.edu>
> Date: Wed, 27 Apr 2005 21:38:46 +0200
> Subject: buried surface area
> 
> Hi Tom,
>    two quick questions: 1/ can Chimera calculate/display 
> the surface area buried by e.g. a ligand when bound on 
> a receptor? 2/ is there a documentation other than htlm 
> (e.g. pdf file)?
> Thanx, Dieter
>