Hi Tom, I was in fact surprised that the operations you described actually worked - I did not comprehend what I was doing! But, my normal to the plane (cylinder) had a large unseemly diameter and too long a length. How can I control those? In the picture you attached, they look very nice. I also don't necessarily need the normal on both sides of the plane. Thanks Ajay ________________________________ From: Tom Goddard <goddard@sonic.net> Sent: Tuesday, October 15, 2013 8:09 PM To: Pande, Ajay K Cc: chimera-users@cgl.ucsf.edu List Subject: Re: [Chimera-users] Normal to the plane of the aromatic ring at the centroid 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! Tom [cid:4366A083-E964-4CE7-A651-B1F68AA4A781@cgl.ucsf.edu] 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@cgl.ucsf.edu<mailto:Chimera-users@cgl.ucsf.edu> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
