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

Tom Goddard goddard at sonic.net
Fri Jan 3 14:17:51 PST 2014

Another approach is to use the Measure and Color Blobs.  You can click on the virus surface and it will draw a box around it and report the exact dimensions of the box.

The tricky part of this problem is deciding how you want to define "radius".  Radius to a 5-fold vertex may be larger than radius along a 3-fold symmetry axis.  And where do you define the surface of the virus, or do you measure to a maximum in density within the virus capsid along a radial line.  I'm not sure what the commonly used definitions of virus radius are -- probably everyone does something different so the numbers are only meaningful to within maybe 5%.


On Jan 3, 2014, at 1:25 PM, Elaine Meng  wrote:

> 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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