[Chimera-users] measure rotation rod

Tom Goddard goddard at cgl.ucsf.edu
Tue May 25 09:25:40 PDT 2010

The "measure rotation" command makes a rod composed of two atoms and a 
bond.  So commands that work to color and change the size of atoms and 
bonds will do what you want.  Assuming the rod model number is 2 (get 
model number from Favorites / Model Panel

   color red #2
   setattr a radius 5 #2
   setattr b radius 5 #2

These command set the color, atom radius and bond radius.  You can also 
use menus and dialogs.  Select an atom (ctrl-click), press up-arrow key 
to select whole rod, menu Actions / Color / red to color it.  Select 
rod, menu Actions / Inspect, and atom and radius in type in fields.

   Making the bond longer is a bit more obscure.  There is no command 
that I know of.  Use menu Tools / Structure Editing / Build Structure, 
use the Set Bond Length tab, select the bond, type in a new bond 
length.  It doesn't have a mode where it extends equally in both 
directions.  Instead extend by some in one direction ("move atoms on 
smaller side"), then extend again in the other direction ("move atoms on 
larger side").  You can also get this dialog by ctrl-double-click on the 
bond and choose set bond length.


> Hi all,
> I have used measure rotation to draw a rod down an axis of symmetry. 
> Does anyone know a way of altering the diameter, length and color of 
> the rod?
> Many thanks

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