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.htm... 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@meduniwien.ac.at> To: Thomas Goddard <goddard@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