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

[Pande, Ajay K]

Thank you very much. It worked beautifully!!



Ajay











________________________________
From: Tom Goddard <goddard at sonic.net>
Sent: Wednesday, October 16, 2013 1:03 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,

  The example commands were if your molecule was model #0 and the two inertia ellipsoids were #1 and #2.  But I see that if your molecule was #1 and the ellipsoids were #2 and #3 it still works but gives a fat long axis cylinder!  You don't end up even using the second ellipsoid.  The axis comes out fat and long because its size is based on the first model in the "measure rotation #1 #2" comand and that was your molecule model, instead of the much smaller ellipsoid model.  As mentioned in the documentation on measure rotation it makes the axis length equal the size of the first model and the axis diameter equal 5% of that size.

http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#rotation

Now that you've discovered the second ellipsoid is not needed the axis can be made with

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

where we assume #1 is your molecule model and #2 is the inertia ellipsoid model.  Substitute the correct model numbers for your case by checking the numbers in Model Panel (Favorites menu).

  And here's a better explanation of this bit of trickery.  Measure inertia shows an ellipsoid surface that matches the inertia of the selected ring atoms and that surface is a new model.  Then the turn command rotates the ellipsoid about the axis perpendicular to the ring with center being the center of the ellipsoid, and it rotates only the ellipsoid, not the molecule, and the axis is specified in the coordinate system of the ellipsoid, and we rotate 90 degrees (although an non-zero angle will work).  Then the measure rotation command shows the rotation axis for one model that is rotated relative to another.

Tom



On Oct 16, 2013, at 3:31 AM, "Pande, Ajay K"  wrote:

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


<1a0m_ring_axis.jpg>


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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