[Chimera-users] Question regarding Chimera Measurements

[Elaine Meng]

Hi Sarah,
The scale bar is based on the data coordinates, and simply uses the same units as those coordinates,
as mentioned in the Scale Bar documentation:
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/scalebar/scalebar.html>
When you change label name you are only changing the label text.

In Volume Viewer, if you choose "Coordinates" from the "Features" menu, the dialog will show
a number for Voxel size, which is the grid point spacing in the inherent distance units of your data, 
whatever those units may be.   My understanding (unfortunately our volume expert is away) is 
that whoever did the tomogram experiment would know the spacing of the grid points in their map
in terms of some standard distance unit such as Angstroms or nm.  I don't know if that is read 
from the file or not; it may depend on the format.  Anyway, if you do know this value, you can 
verify that that is what is shown as "Voxel size," or if not, you can edit that to the correct value 
to scale your data to those units.  I.e. if you know your map grid points are 1 nm apart you would 
enter 1 to have your scale bar in nm units, or 10 to have your scale bar in Angstrom units.
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/volumeviewer.html#coordinates>

Distance measurements are between two points.  You would need to define the two points somehow, 
which can be done by adding markers with Volume Tracer.  Documentation for this tool:
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/volumepathtracer/framevolpath.html>
Then you can measure the distance between the markers, since they are treated the much the same
as atoms in Chimera.

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 Aug 19, 2010, at 11:36 AM, Shahmoradian, Sarah H wrote:

> Hello,
> This is an urgent question and your help would be appreciated. I am trying to find a way to perform measurements in my tomogram volume file (.rec file). I tried using the "Distances" option under Tools --> Structure analysis, but this requires two "atoms." My tomogram does not depict at the atomic resolution and I would like to measure the distance between one area on my tomogram density and another area on the tomogram density. These measurements would be through a 3D section. Could you please let me know how I could do this?
> Furthermore, I have a question about the scale bar -- when the program generates a default scale bar, how does the program assign the default value to the scale bar size? Does it read the header info from my tomogram file? I am concerned because when I change the label name from Angstrom to nanometers, the scale bar size stays the same-- how then, would I be able to assign an accurate scale bar that would change accordingly with the alterations in scale (Angstrom to nm, etc)? Please let me know if I need to clarify further. Your assistance would be appreciated!
> Sincerely,
> Sarah Shahmoradian