<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div><div>On Dec 12, 2008, at 10:40 AM, Tom Goddard wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: -webkit-monospace; font-size: 14px; 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: 0; ">Hi David,<br><br> Ok I see now, it's a matter of choosing the size of each ellipsoid to<span class="Apple-converted-space"> </span><br>have a 50% chance of finding the atom in that volume. This shouldn't be<span class="Apple-converted-space"> </span><br>too hard but I'll let Eric tackle it if he has time.</span></blockquote><br></div><div>Hi David,</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>This is one of those things that I'll endeavor to get into Chimera's production version of thermal ellipsoids, but that I can't spare the time for until then. My guess is that the eigenvectors/values of the U matrix are at the 50% probability level, but verifying that would require some research. If you do look into and find that that's not the case, just change the setting of the 'scale' variable of the start of the script to change the ellipsoid sizes to whatever size encloses 50%.<br></div><div><br></div><div>--Eric</div><div><br></div><br></body></html>