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<p class="owaPara">Hi Tom,</p>
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<p class="owaPara">I was in fact surprised that the operations you described actually worked - I did not comprehend what I was doing!</p>
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<p class="owaPara">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.</p>
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<p class="owaPara">Thanks</p>
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<p class="owaPara">Ajay</p>
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<div dir="ltr" id="divRplyFwdMsg"><font style="FONT-SIZE: 11pt" color="#000000" face="Calibri, sans-serif"><b>From:</b> Tom Goddard <goddard@sonic.net><br>
<b>Sent:</b> Tuesday, October 15, 2013 8:09 PM<br>
<b>To:</b> Pande, Ajay K<br>
<b>Cc:</b> chimera-users@cgl.ucsf.edu List<br>
<b>Subject:</b> Re: [Chimera-users] Normal to the plane of the aromatic ring at the centroid</font>
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<div>Hi Ajay,
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<div> 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</div>
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<div><span style="WHITE-SPACE: pre" class="Apple-tab-span"></span>measure inertia sel</div>
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<div>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:</div>
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<div><span style="WHITE-SPACE: pre" class="Apple-tab-span"></span>measure inertia sel</div>
<div><span style="WHITE-SPACE: pre" class="Apple-tab-span"></span>turn 0.428,0.497,0.755 90 center #2 model #2 coord #2</div>
<span style="WHITE-SPACE: pre" class="Apple-tab-span"> </span>measure rotation #1 #2 color pink
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<div>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!</div>
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<div><span style="WHITE-SPACE: pre" class="Apple-tab-span"></span>Tom</div>
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<div>On Oct 14, 2013, at 2:10 PM, "Pande, Ajay K" wrote:</div>
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How would I draw a normal to the plane of an aromatic ring, at its centroid?<br>
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Thanks<br>
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Ajay Pande<br>
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