[Chimera-users] Distance measurement in density map

Maarten Schledorn m.schledorn at gmail.com
Wed Jan 14 15:15:47 PST 2015

This is exactly the kind of solution I was looking for. Thank you so much
for your time and help!


On Wednesday, 14 January 2015, Elaine Meng <meng at cgl.ucsf.edu> wrote:

> 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
> <javascript:;>> 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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