[Chimera-users] Distance measurement in density map

Elaine Meng meng at cgl.ucsf.edu
Wed Jan 14 10:58:08 PST 2015


Dear Maarten,
You can place “markers” (dummy atoms) on the surfaces with the Volume Tracer tool, then measure the distances between markers as if they were atoms.

Volume Tracer is in the volume viewer Tools menu and the main menu under Tools…Volume Data.
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumepathtracer/framevolpath.html>

The Mouse menu in Volume Tracer controls how markers are created and with which mouse button.  You can choose “Place markers on surfaces” to  add a marker at the nearest surface point under the cursor when the assigned button is clicked.

One way to measure atom-atom (or marker-marker) distances is to Ctrl-click one to select it, then Shift-Ctrl-doubleclick to select the second and then choose “Show Distance" from the resulting context menu.
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/structuremeas/structuremeas.html#distances>

There is also a “measure distance” command, but it finds the closest distance between two different surfaces and/or atoms, not between surface points of your choosing… so I believe the marker approach is what you want.  
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#distance>

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 Jan 14, 2015, at 2:55 AM, Maarten Schledorn <m.schledorn at gmail.com> wrote:

> Dear reader,
> I'm looking at EM tomography data summarised in *.mrc density files. Since there are no atoms defined in these files, the usual distance measurement tool is inappropriate (I suppose). Is there another way to assess the dimensions of the oligomerised protein I'm looking at?
> With my sincere thanks in advance,
> Maarten



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