<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div><div>On Jul 7, 2009, at 10:09 AM, Dipl.-Ing. Thomas Mitterfellner wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div>Hello again!<br><br><blockquote type="cite">Currently it works only using the information in ANISOU records of PDB<br></blockquote><blockquote type="cite">files. You would just open the PDB file as usual, then use the Thermal<br></blockquote><blockquote type="cite">Ellipsoids tool (under Tools... Structure Analysis). It is fairly<br></blockquote><blockquote type="cite">self-explanatory, but there is also documentation -- just click the Help<br></blockquote><blockquote type="cite">button on the dialog or see the copy at our site:<br></blockquote><blockquote type="cite"><<a href="http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/thermal/thermal.html">http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/thermal/thermal.html</a>><br></blockquote><br>I'm very happy to see this working!<br><br>At the risk of sounding ungrateful -- I'd like to request two features.<br><br>The first one: it is quite common to plot thermal ellipsoids on some <br>probability level (e.g. 30% or 50%). Unfortunately, I don't know how <br>these Values correspond to the scaling factor that currently controls <br>the size of the ellipsoids. Could you implement this kind of scaling as <br>a feature or point out, if/how these two measures correspond to each other?<br></div></blockquote><div><br></div>We intend to implement a probability-to-scaling-factor calculator in the interface, but haven't gotten there yet. We felt that the tool was useful enough as is to put it out in what we consider to be an incomplete state. As a stopgap for you, the scaling factor for 30% is 1.1932 and for 50% is 1.5382.</div><div><br><blockquote type="cite"><div>The second one: could you possibly implement it as a feature, that the <br>lines resulting from the intersection of the main planes (xy, xz, yz) <br>with the surface of the ellipsoid (the principal ellipses) can be <br>displayed ?</div></blockquote><br></div><div>Given the way the underlying ellipsoid depiction is generated, it won't be easy. Nonetheless, I do think it should happen but it will take awhile. One thing that would be easy for me to do would be to actually show the ellipsoid axes (as lines). Would this help any if I put it in there?</div><div><br></div><div>--Eric</div><div><br class="webkit-block-placeholder"></div><div><span class="Apple-style-span" style="border-collapse: separate; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 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; -webkit-text-decorations-in-effect: none; text-indent: 0px; -webkit-text-size-adjust: auto; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Helvetica" size="5" style="font: normal normal normal 16px/normal Helvetica; "> Eric Pettersen</font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Helvetica" size="5" style="font: normal normal normal 16px/normal Helvetica; "> UCSF Computer Graphics Lab</font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Helvetica" size="5" style="font: normal normal normal 16px/normal Helvetica; "> <a href="http://www.cgl.ucsf.edu">http://www.cgl.ucsf.edu</a></font></div><br class="Apple-interchange-newline"></div></span></div><br><div></div></body></html>