[Chimera-users] Measure the cross section of an EM map

[Elaine Meng]

Hi Yangqi,
You could place markers on opposite sides of the density contour surface, then measure the distance between the markers.

For marker creation/placement, see Volume Tracer (in menu under Tools… Volume Data):
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumepathtracer/framevolpath.html>

For distance measurement, markers are treated the same as atoms.  One way to do the measurement is to Ctrl-click on one marker to select it, then Shift-Ctrl-doubleclick on the other one to also select it and show context menu with a choice to measure the distance.
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/structuremeas/structuremeas.html#distances>

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Aug 17, 2018, at 6:53 PM, BuddySphinx <yangqi.gu at yale.edu> wrote:
> 
> Dear Chimera users,
> I am trying to measure the diameter of my filament based on the EM volume. I am wondering which function I can use to measure the cross-section of it?
> Best,
> Yangqi
>