[Chimera-users] on contact surface and domain angle

Elaine Meng meng at cgl.ucsf.edu
Mon Apr 4 08:51:35 PDT 2016


Dear Smith,
It is not possible to give the whole exact commands because it depends on which atoms and which chains you want to use for the calculation.  However, to get you started, the commands to use would be

(A)  “measure buriedArea” 
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#buriedArea>

(B) “define plane” (once for each domain) and then “angle” on the resulting two planes
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/define.html#plane>
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/angle.html>

You’d have to specify the relevant sets of atoms as well as any other command options you might want to use.
I hope this helps,
Elaine
----------
Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco



> On Apr 4, 2016, at 2:23 AM, Smith Liu <smith_liu123 at 163.com> wrote:
> 
> Dear All,
> 
> Will you please tell me the command to calculate the contact surface area between 2 sub-units in the protein complex? Will you please also tell me the command to calculate the angle in degree between 2 domains in a subunit?
> 
> Smith 




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