[Chimera-users] volume and area measurements

Elaine Meng meng at cgl.ucsf.edu
Tue Jul 13 11:49:26 PDT 2010

Hi Chinthaka,
If you choose a tool from the menu, then you can click the Help button on the tool dialog to show its documentation.  Here's what you would get for those tools, which give the answers to your questions:


However, I'll also try to provide an answer here.

Measure Volume and Area applies to a surface.  If you are using Volume Viewer, it is probably the contour surface (isosurface) of the volume data that you are currently displaying.  The tool reports the surface area and the physical volume enclosed inside that surface.  You have to specify in the dialog which surface you want, if there is more than one. 

Volume Mean, SD, RMS gives standard deviation and root-mean-square deviation from zero of the *values* in a volume data set. A volume data set is something like a density map where there are values on the points on a grid.

I hope this helps,
Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Jul 13, 2010, at 11:31 AM, Chinthaka Silva wrote:

> Hi,
> Could you please tell me what is the difference between the values we get from the following two options?
> Volume Viewer:
> Tools --> Measure Volume and Area
> Tools --> Volume Mean, SD, RMS
> Is SD means standard deviation? What is RMS? 
> In the 2nd option, we get 'Surface V and A'. What does 'Surface' mean in here?
> Thanks,
> Chinthaka.

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