[Chimera-users] Normal to the plane of the aromatic ring at the centroid

Tom Goddard goddard at sonic.net
Tue Oct 15 17:09:44 PDT 2013

Hi Ajay,

  Ok, I have a totally twisted way to do this in Chimera.  Select the ring atoms, say with the mouse (shift ctrl click each atom).  Then

	measure inertia sel

This shows an inertia ellipsoid centered on the atoms.  Then how about just stretching the ellipsoid perpendicular to the plane and squeezing it in the plane to make a cigar?  I thought I could do that with the sop transform command, but no such luck.  So instead make a second inertia ellipsoid, rotate it, then show the rotation axis:

	measure inertia sel
	turn 0.428,0.497,0.755 90 center #2 model #2 coord #2
 	measure rotation #1 #2 color pink

In the turn command I used the axis taken from the reply log given by the measure inertia command (v3, axis with largest inertia).  Picture attached.  Ok, this should be easier in Chimera!



On Oct 14, 2013, at 2:10 PM, "Pande, Ajay K" wrote:

> How would I draw a normal to the plane of an aromatic ring, at its centroid?
> Thanks
> Ajay Pande
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

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