<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div>Eric,</div><div><br></div><div>For small molecule/high resolution work an ortep type representation would be as shown below (all three clips are from the same molecule). The ellipsoid, it's three axis and a shaded octant. </div><div><br></div><div>I understand the octant is the hardest part. As you can see the addition of thermal ellipsoid information adds a lot to the rendering. My small molecule users are very excited about the addition of thermal ellipsoids to Chimera and we're doing hundreds of structures per year.</div><div><br></div><img height="263" width="234" apple-width="yes" apple-height="yes" src="cid:8C98A312-B21F-4BD3-9BDF-AE4F965AB860@caltech.edu"> <img height="214" width="202" apple-width="yes" apple-height="yes" src="cid:EF0943D5-02D5-4AA2-B1CF-D3DC8FD53334@caltech.edu"> <img height="258" width="221" apple-width="yes" apple-height="yes" src="cid:B9EAC148-CBC6-46FA-B9E9-C6DCC04B14D7@caltech.edu"><div><br><div apple-content-edited="true"> <span class="Apple-style-span" style="font-family: 'Bradley Hand ITC TT'; font-size: 20px; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div><div><div><div><div><div><div>Cheers,</div><div>Mike</div><div><br></div><div><<< ------------------------------------------------------------------------>>></div><div>Dr. Michael W. Day</div><div>Director - X-ray Crystallography Lab & Molecular Observatory</div><div>California Institute of Technology</div><div>Mail Code 139-74</div><div>Pasadena, CA 91125</div><div><br></div><div><>< <>< <>< <>< <>< <>< <>< <>< <>< <><</div><div><br></div><div>Beckman Institute, Room 116</div><div>Phone: (626) 395-2734</div><div>Fax: (626) 449-4159</div><div>e-mail: <a href="mailto:mikeday@caltech.edu">mikeday@caltech.edu</a></div><div><<< ------------------------------------------------------------------------>>></div></div></div></div></div></div></div></div></span> </div><br><div><div>On Jul 8, 2009, at 9:56 AM, Eric Pettersen wrote:</div><br class="Apple-interchange-newline"><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi David,<div><span class="Apple-tab-span" style="white-space:pre"> </span>I guess my question is how important is fancy5 and fancy6? Those will be the hard ones for me to do. Keep in mind that "display of ... major ellipses" will look like fancy3 except that you will be able to see the arcs of the major ellipses without using a transparent ellipsoid. The other "fancy modes" are not difficult to do.</div><div><br></div><div>--Eric<br><div apple-content-edited="true"> <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; "><div style="word-wrap: break-word; -khtml-nbsp-mode: space; -khtml-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: 16.0px Helvetica"><span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>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: 16.0px Helvetica"><span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>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: 16.0px Helvetica"><span class="Apple-converted-space"> </span><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>On Jul 8, 2009, at 8:29 AM, David Chenoweth wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div>Eric and Elaine,<br><br>The display of axes and major ellipses as well as a probability-level-to-scaling-factor calculator will be a great addition to Chimera and I think more small molecule people and Organic chemists will start to use the program. I'm really excited about this feature being added to Chimera and I wanted to pass along some ideas for displaying the axes as well as octants. The program RASTEP (Raster3D Thermal Ellipsoid Program) has some very nice rendering features that would be great options to have in chimera. I attached an example below.<br><br>Thanks to the Chimera team for working on this feature,<br>Dave Chenoweth<br></div></blockquote><br></div><span><Thermal_ellipsoid_representations.tiff></span></div></div>_______________________________________________<br>Chimera-users mailing list<br><a href="mailto:Chimera-users@cgl.ucsf.edu">Chimera-users@cgl.ucsf.edu</a><br>http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users<br></div><br></div></body></html>