[Chimera-users] Place markers

Tom Goddard goddard at sonic.net
Wed Jan 9 15:33:34 PST 2013

Hi Kim,

  Here's a command that puts marker at the center of mass of residue 24

	measure center #0:24 mark true color blue radius 2

If instead you hand select the residue with ctrl-click use the command

	measure center sel mark true

Here's documentation for the measure center command


  Another way to place a marker at the center of selected atoms is to use the (undocumented) keyboard shortcut "mC".  You would select the atoms and then use the command "ac mC".  Or if you had keyboard shortcuts enabled (using command "ac") then you would just type mC.  This places the marker at the geometric center (average atom coordinate without mass weighting).  I'll add mC to the shortcut documentation.


On Jan 9, 2013, at 11:06 AM, Elaine Meng  wrote:

> 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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