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. http://plato.cgl.ucsf.edu/trac/chimera/wiki/Scripts 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 http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/structuremeas/struc... Command "define axis" http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/define.html Command "turn" http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/turn.html Command "measure rotation" http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#rotation The axis objects are relatively new and we need to make all our tools that use axes follow uniform conventions. Tom

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