<html><head><meta http-equiv="Content-Type" content="text/html charset=us-ascii"><base href="x-msg://54/"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi Ajay,<div><br></div><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><div><br></div><div><span class="Apple-tab-span" style="white-space:pre"> </span>measure inertia sel</div><div><br></div><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><div><br></div><div><span class="Apple-tab-span" style="white-space:pre"> </span>measure inertia sel</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>turn 0.428,0.497,0.755 90 center #2 model #2 coord #2</div> <span class="Apple-tab-span" style="white-space:pre"> </span>measure rotation #1 #2 color pink<div><br></div><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><div><br></div><div><span class="Apple-tab-span" style="white-space:pre"> </span>Tom</div><div><br></div><div><br></div><div><img height="857" width="900" apple-width="yes" apple-height="yes" id="c719096f-143c-42ab-a6ed-6d745bdbe5bb" src="cid:4366A083-E964-4CE7-A651-B1F68AA4A781@cgl.ucsf.edu"><br><div><div><span class="Apple-tab-span" style="white-space:pre"> </span></div><div><br></div><div><br><div><div>On Oct 14, 2013, at 2:10 PM, "Pande, Ajay K" wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div tabindex="0" aria-label="Message body" fpstyle="1" dir="ltr" style="font-family: Helvetica; font-size: medium; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><div name="divtagdefaultwrapper" id="divtagdefaultwrapper" style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; margin: 0px; ">How would I draw a normal to the plane of an aromatic ring, at its centroid?<br><br>Thanks<br><br>Ajay Pande<br></div>_______________________________________________<br>Chimera-users mailing list<br><a href="mailto:Chimera-users@cgl.ucsf.edu">Chimera-users@cgl.ucsf.edu</a><br><a href="http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users">http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users</a></div></blockquote></div><br></div></div></div></body></html>