<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div><div>On Mar 15, 2013, at 11:32 AM, Elaine Meng wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div>Forgot to mention the plane center and radius.<br><br><<a href="http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/define.html#plane">http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/define.html#plane</a>><br><br>"<b>The disk center is the non-mass-weighted centroid of the atoms; disk radius can be set to a fixed value as described below or set automatically to enclose the projections of the atoms </b>(default). An extra margin (padding, default 0.0 Å) can be added to the automatically determined radius, but is ignored if a fixed radius is supplied."<br><br>On Mar 15, 2013, at 11:25 AM, Elaine Meng wrote:<br><br><blockquote type="cite">Hi Steven,<br></blockquote><blockquote type="cite">I wouldn't go by any information for "ksdssp," as that is completely separate from Axes/Planes/Centroids calculations.<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Axes/Planes/Centroids:<br></blockquote><blockquote type="cite"><<a href="http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/structuremeas/structuremeas.html#axes">http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/structuremeas/structuremeas.html#axes</a>><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">"Each axis is anchored at the the centroid of the defining atomic coordinates and aligned with the principal component of the coordinates (prior to any helical correction)." There is also a choice of mass-weighting or not. If you choose the each-helix option, it is only using the backbone atoms N,CA,C.<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><b>The plane is the best-fit plane to the specified points (atoms). </b></blockquote></div></blockquote><br></div><div>To expand on the last bolded part: the centroid is subtracted from the atoms and then eigenvectors/values are computed. The eigenvector with the smallest eigenvalue is consider to be the normal to the plane (<i>i.e.</i> the two largest-valued eigenvectors define the plane). A point (centroid) and a normal defines a plane. The radius is as described in the first bolded section above.</div><div><br></div><div>--Eric</div><br><div>
<span class="Apple-style-span" style="border-collapse: separate; border-spacing: 0px 0px; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 16px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-align: auto; -khtml-text-decorations-in-effect: none; text-indent: 0px; -apple-text-size-adjust: auto; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; "><p style="margin: 0.0px 0.0px 0.0px 0.0px"><font face="Helvetica" size="5" style="font: 16.0px Helvetica"><span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>Eric Pettersen</font></p><p style="margin: 0.0px 0.0px 0.0px 0.0px"><font face="Helvetica" size="5" style="font: 16.0px Helvetica"><span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>UCSF Computer Graphics Lab</font></p><p style="margin: 0.0px 0.0px 0.0px 0.0px"><font face="Helvetica" size="5" style="font: 16.0px Helvetica"><span class="Apple-converted-space"> </span><a href="http://www.cgl.ucsf.edu">http://www.cgl.ucsf.edu</a></font></p><br class="Apple-interchange-newline"></span>
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