[Chimera-users] volume and area measurements

[Chinthaka Silva]

Thanks Elaine, it sure helped me understand what I am getting.

Thanks,
Chinthaka.
Postdoctoral, ORNL

On Tue, Jul 13, 2010 at 2:49 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:

> 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:
>
> <
> http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/measurevol/measurevol.html
> >
> <
> http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/volstats.html
> >
>
> 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
> ----------
> 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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