Dear Tom, Here is the reply log when I used the 'measure buried' command in a modeled complex. What am I missing in the pdb file and how erroneous are the calculations? Please find the pdb file at the bottom to repeat the error. ______________________________________ Calculation of some surface components failed. Using only single surface component. This may give inaccurate areas if surfaces of either set of atoms or the combined set are disconnected. Buried solvent accessible surface area = 1333.97 (A1 = 10302.4, A2 = 7673.48, A12 = 15307.9) Buried solvent excluded surface area = 818.456 (A1 = 8044.45, A2 = 6390.68, A12 = 12798.2) ______________________________________ Sincerely, Hari On Aug 11, 2009, at 11:11 PM, Tom Goddard wrote:
Hi Hari,
open 1a0m measure buried :.A :.B
This measures the buried area between chains A and B. Here's the measure command documentation
http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html
and some info on how to specify different sets of atoms
http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/atom_spec.html
Tom
-------- Original Message -------- Subject: [Chimera-users] command 'buriedArea' From: Harinathachari Bahudhanapati To: chimera-users@cgl.ucsf.edu Date: 8/11/09 7:59 PM
Hi all, Could you explain the command 'measure buriedArea' ? I am trying yesterday's daily build. Could you give me an example how to use this command? I think I am mangling the command, somehow. Could you help me?
Thank you very much.
Sincerely, Hari