[Chimera-users] measure crossing angles for axes

Thomas Goddard goddard at cgl.ucsf.edu
Tue Feb 9 11:52:50 PST 2010

Hi Tom,

   The Chimera capabilities to create axes and measure angles are still 
being developed.  I put a Python script called angle.py on our scripts 
web page that will report the angle between two axes created with the 
"measure rotation" command.


If the axes are model numbers 2 and 3 you would use the script by typing 
a command

	runscript /Users/goddard/angle.py #2 #3

The angle will be shown in the status line and in the reply log (menu 
Favorites / Reply Log).

   We have three different objects representing an axis in Chimera now: 
1) pairs of atoms, 2) a bond, 3) an axis object, and a variety of 
dialogs and commands that use axes

Structure Measurements dialog


Command "define axis"


Command "turn"


Command "measure rotation"


The axis objects are relatively new and we need to make all our tools 
that use axes follow uniform conventions.


> I have used the "measure rotation" command to create several axes. In
> each case, a marker set (to show the axis) is generated that consists of
> 2 pseudoatoms and 1 bond.
> Is there a simple way to measure the crossing angle between 2 such axes?
> If the marker set had 3 atoms, I could probably use the Axes/Planes
> tools to do this.
> Thanks,
> Tom

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