[Chimera-users] Command for volume and area calculation

[Elaine Meng]

Dear Zhiya,
There is no Chimera command to measure surface area or surface- 
enclosed volume, but there are keyboard shortcuts (Accelerators) to  
perform these measurements on the currently selected surface(s).

(1) turn on Accelerators (Tools... General Controls... Accelerators On)
(2) select the surface(s)
   - for many kinds of surface (molecular, multiscale, etc.), simply  
use Ctrl-click to select, Shift-Ctrl-click to add to selection
   - the only way I was able to select a volume surface for these  
measurements was to use the Model Panel (under Favorites): choose the  
volume surface on the left side of the Model Panel, click the  
"select" button on the right
(3) type the accelerator "ma" to measure area and "mv" to measure volume

For details, see:
http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/accelerators/ 
accelerators.html
http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/accelerators/ 
alist.html
http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/accelerators/ 
alist.html#measure

However, accelerators cannot be included in a Chimera command script,  
and you would still have to select the surface(s) interactively.

In the future we hope to have the surface calculations more  
integrated and available with Chimera commands, but it has not been  
done yet.

I hope this helps,
Elaine
-----
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
                      http://www.cgl.ucsf.edu/home/meng/index.html




On Dec 26, 2007, at 1:58 AM, "" <shengzhiya at nibs.ac.cn> wrote:

> Dear all,
>
> May I know if there is some command in chimera for measuring volume  
> and area like in the menus: “Tools…Surface/Binding Analysis…Measure  
> Volume and Area”? Thanks in advance!
>
> Happy new year and have a nice holiday!
>
> Zhiya