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.
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/measurev...> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/volsta...> 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.
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@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/measurev...
< http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/volsta...
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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Elaine Meng