[Chimera-users] Using Chimera to measure voxel densities

Elaine Meng meng at cgl.ucsf.edu
Fri Jan 30 14:36:06 PST 2015


Hi Alex,
Sure!  There is a “Values at Atom Positions” tool to get the values, interpolating as needed, and to assign them as atom attributes.  Then you can do various things with the attributes: label the atoms with the values, color the atoms to show the values, etc.

The tool is in the menu under Tools… Volume Data.
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/density/density.html>

Clicking the Histogram button in the Values at Atom Positions dialog opens Render/Select by Attribute to allow coloring or selecting atoms based on the corresponding local density values.  Render/Select also shows the name that was assigned to this new atom attribute (which is based on the name of your density map) so that you could refer to it in the commands mentioned below.

<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/render/render.html>

The coloring could also be done with the “rangecolor” command, and labeling with “labelopt” (or menu Actions… Label… other). With labelopt you can specify a format so that you don’t get a ridiculous number of decimal places, for example, something like the following except with your specific attribute name:

labelopt info %(value_name_of_map).3f

<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/labelopt.html>

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 30, 2015, at 1:33 PM, Noble, Alex <ajn10d at fsu.edu> wrote:

> Hi all,
> I have a pdb fit into an EM density in Chimera and I would like to be able to see what the nearest voxel densities are at specific atomic coordinates. Is there any way to do this in Chimera?
> Best,
> -Alex Noble




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