[Chimera-users] Place markers

Elaine Meng meng at cgl.ucsf.edu
Wed Jan 9 11:06:28 PST 2013


Hi Kim,
If it needs to be a "marker" (created by Volume Tracer), then sorry, I don't know an easy way to do what you describe. The marker creation options don't include centering on some set of atoms:
<http://www.cgl.ucsf.edu/home/meng/docs/ContributedSoftware/volumepathtracer/volumepathtracer.html#mousemode>

However, there are two other approaches that can easily generate a sphere centered on a given residue:

(a) command "define centroid" or tool: Axes/Planes/Centroids
The centroid object is a sphere and you can control its size and color, and use it in distance measurements.  However, it is not implemented as an atom, so you can't use it for all the same stuff as atoms or markers.
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/define.html>
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/structuremeas/structuremeas.html#axes>

example: define centroid color magenta radius 2.5 #0:25.a
(non-mass-weighted centroid of residue 25 in chain A of model 0)

(b) command "shape sphere" in this case generating a spherical surface of controllable size and color
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/shape.html>

One other idea is just to use the alpha-carbons of the existing structure, i.e. hide the other atoms, show the alpha-carbons (@ca) as spheres, increase their "VDW" radii if you want (see command "vdwdefine"). 
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/vdwdefine.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 9, 2013, at 7:56 AM, Kim Fong wrote:

> Hello,
> Is there an easy way to select a single residue along a chain and center a new marker on that selected residue?
> Thanks!
> Kim




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