[Chimera-users] How to measure the radius of density map

Elaine Meng meng at cgl.ucsf.edu
Fri Jan 3 13:25:27 PST 2014


Hi Jian,
Well, this idea is also partly manual: using Volume Tracer to place two markers (fake atoms) on the surface and then measuring the distance between them.

(1) use Volume Tracer to place "markers" on the density map isosurface (Volume Tracer menu: Mouse... Place markers on surfaces, turn off other Mouse options).  The manual part is where you click on the surface, and it might be tricky to put the markers where you want them.  Maybe clip the surface so that it is cut across where you want to measure it, then try to put the markers on opposite sides of the rim.

Volume Tracer:
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumepathtracer/framevolpath.html>

(2) measure distance between the two markers, just like for atoms, e.g. Ctrl-click one, Shift-Ctrl-doubleclick on the other, choose "show distance" from the resulting context menu.

Happy New Year to you too,
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 Jan 3, 2014, at 11:08 AM, Jian Guan wrote:

> Hi all,
> I have density map of virus (mrc format) and want to measure the radius of
> it. I tried measure command, High-order structure-->Icosahedron surface.
> Both of them need me to measure it manually by eye. Are there any tools to
> measure the radius by chimera, so we can get more accurate result? Or does
> anybody know how to measure it accurately? Thank you so much.
> Sincerely yours,
> Happy New Year.
> Jian




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