[Chimera-users] buried surface area

Thomas Goddard goddard at cgl.ucsf.edu
Wed Apr 27 13:06:36 PDT 2005

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


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.


> 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

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