<html><head><meta http-equiv="Content-Type" content="text/html charset=us-ascii"><base href="x-msg://178/"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div>Hi Ajay,</div><div><br></div><div> 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.</div><div><br></div><span class="Apple-tab-span" style="white-space:pre"> </span><a href="http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#rotation">http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#rotation</a><div><br></div><div>Now that you've discovered the second ellipsoid is not needed the axis can be made with</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><span style="color: rgb(40, 40, 40); font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; ">turn 0.428,0.497,0.755 90 center #2 model #2 coord #2</span></div><div><font color="#282828" face="Calibri, Arial, Helvetica, sans-serif"><span style="font-size: 16px;"><span class="Apple-tab-span" style="white-space:pre"> </span> measure rotation #2 #1 color pink</span></font></div><div><font color="#282828" face="Calibri, Arial, Helvetica, sans-serif"><span style="font-size: 16px;"><br></span></font></div><div><font color="#282828" face="Calibri, Arial, Helvetica, sans-serif"><span style="font-size: 16px;">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).</span></font></div><div><font color="#282828" face="Calibri, Arial, Helvetica, sans-serif"><span style="font-size: 16px;"><br></span></font></div><div><font color="#282828" face="Calibri, Arial, Helvetica, sans-serif"><span style="font-size: 16px;"> 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.</span></font></div><div><font color="#282828" face="Calibri, Arial, Helvetica, sans-serif"><span style="font-size: 16px;"><br></span></font></div><div><font color="#282828" face="Calibri, Arial, Helvetica, sans-serif"><span style="font-size: 16px;"><span class="Apple-tab-span" style="white-space:pre"> </span>Tom</span></font></div><div><font color="#282828" face="Calibri, Arial, Helvetica, sans-serif"><span style="font-size: 16px;"><br></span></font><div><div><br></div><div><br></div><div>On Oct 16, 2013, at 3:31 AM, "Pande, Ajay K" wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div dir="ltr" tabindex="0" jquery17208790652769395031="515" aria-label="Message body" fpstyle="1" 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; outline: invert none medium; "><div name="divtagdefaultwrapper" id="divtagdefaultwrapper" style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; margin: 0px; "><div style="margin-top: 0px; margin-bottom: 0px; ">Hi Tom,</div><p class="owaPara" style="margin-top: 0px; margin-bottom: 0px; "> </p><div style="margin-top: 0px; margin-bottom: 0px; ">I was in fact surprised that the operations you described actually worked - I did not comprehend what I was doing!</div><p class="owaPara" style="margin-top: 0px; margin-bottom: 0px; "> </p><div style="margin-top: 0px; margin-bottom: 0px; ">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.</div><p class="owaPara" style="margin-top: 0px; margin-bottom: 0px; "> </p><div style="margin-top: 0px; margin-bottom: 0px; ">Thanks</div><p class="owaPara" style="margin-top: 0px; margin-bottom: 0px; "> </p><div style="margin-top: 0px; margin-bottom: 0px; ">Ajay</div><p class="owaPara" style="margin-top: 0px; margin-bottom: 0px; "> </p><p class="owaPara" style="margin-top: 0px; margin-bottom: 0px; "> </p><p class="owaP" style="margin-top: 0px; margin-bottom: 0px; "></p><div style="color: rgb(40, 40, 40); "><hr tabindex="-1" style="width: 868px; display: inline-block; "><div dir="ltr" id="divRplyFwdMsg"><font face="Calibri, sans-serif" style="font-size: 11pt; "><b>From:</b><span class="Apple-converted-space"> </span>Tom Goddard <goddard@sonic.net><br><b>Sent:</b><span class="Apple-converted-space"> </span>Tuesday, October 15, 2013 8:09 PM<br><b>To:</b><span class="Apple-converted-space"> </span>Pande, Ajay K<br><b>Cc:</b><span class="Apple-converted-space"> </span>chimera-users@cgl.ucsf.edu List<br><b>Subject:</b><span class="Apple-converted-space"> </span>Re: [Chimera-users] Normal to the plane of the aromatic ring at the centroid</font><div> </div></div><div>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><span><1a0m_ring_axis.jpg></span><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 dir="ltr" tabindex="0" style="widows: 2; text-transform: none; text-indent: 0px; font-style: normal; font-variant: normal; font-weight: normal; font-size: medium; line-height: normal; font-family: Helvetica; white-space: normal; orphans: 2; letter-spacing: normal; word-spacing: 0px; "><div id="divtagdefaultwrapper" name="divtagdefaultwrapper" style="margin: 0px; font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; ">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></div></div></div></div></div></div></div></blockquote></div><br></div></body></html>