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

Pande, Ajay K apande at albany.edu
Wed Oct 16 03:31:41 PDT 2013


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 at sonic.net>
Sent: Tuesday, October 15, 2013 8:09 PM
To: Pande, Ajay K
Cc: chimera-users at 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 at 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
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