<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><br><div><div>On Mar 15, 2013, at 10:42 PM, Eric Pettersen wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><span class="Apple-style-span" style="border-collapse: separate; font-family: Helvetica; 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-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; font-size: medium; "><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></span><br class="Apple-interchange-newline"></blockquote></div><div><br></div><div>Thanks for the quick responses. I think I got it, but just to clarify, let me know if this is correct:</div><div><br></div><div>The atoms in the selected residues are taken into consideration, and their coordinates are converted into a non-mass weighted centroid system. Then the principal axes are determined with the smallest vector considered normal to the plane defined by the other two axes.</div><div><br></div><div>If this is correct, my only other question is: Which atoms are used in the calculation? Is it just N,CA,C like for helices?</div><div><br></div><div>Thanks again for all the help.</div><br><div>
<span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; font-size: medium; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: medium; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div><span class="Apple-style-span" style="font-size: 12px; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div><div>******</div><div>Steven Andrew Waldauer Ph.D.</div><div>Postdoctoral Fellow, Hamm Group</div><div><br></div><div><span class="Apple-style-span" style="font-size: medium; ">Universität Zürich<br>Physikalisch-Chemisches Institut<br>Winterthurerstr. 190, CH-8057 Zürich<br><br></span></div><div><span class="Apple-style-span" style="font-size: medium; ">Tel: +41 (0)44 635 44 66</span></div><div><span class="Apple-style-span" style="font-size: medium; ">Fax: +41 (0)44 635 68 38</span></div><div><span class="Apple-style-span" style="font-size: medium; ">E-Mail: <a href="mailto:waldauer@pci.uzh.ch">waldauer@pci.uzh.ch</a></span></div><div><br class="webkit-block-placeholder"></div></div></div></span><br class="Apple-interchange-newline"></div></span><br class="Apple-interchange-newline"></div></span><br class="Apple-interchange-newline"></div></div></span><br class="Apple-interchange-newline"></span><br class="Apple-interchange-newline">
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