[Chimera-users] Chimera Surface Area/Volume

Elaine Meng meng at cgl.ucsf.edu
Wed Apr 27 13:28:52 PDT 2005

Hi Dieter,
Just a few add-ons to Tom's reply:

Another approach to getting the surface area of the receptor
buried by the ligand is to run Surface Area/Volume
(a) on the complex of ligand and receptor (must delete water
and anything else first).  Then use Attribute Calculator to
sum the surface areas of the receptor atoms only.
(b) after deleting ligand, run it again on the receptor.  
The total is all from the receptor, so it is not necessary to use 
Attribute Calculator.  Subtract the value from (a) from this value.

Tom gave a link to the development documentation, which is
slightly ahead of the Chimera version you have.  It is
almost the same, except that the Tools menu has been
reorganized.  Probably in the version you have, both Attribute
Calculator and Surface Area/Volume are in the Utilities submenu
of the Tools menu.  To get the documentation that goes with
your version, use the Help buttons on those dialogs or open
the User's Guide from the Help menu.

If you have the latest snapshot (1.2105, March) there is
an "Attributes" tutorial (Help... Tutorials).  Part 2 has one 
example of using Surface Area/Volume and Attribute Calculator.

Finally, if anything is confusing or hard to find in the
documentation, please feel free to complain to me!  8-)
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

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