<html><head><meta http-equiv="Content-Type" content="text/html charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">Hi Oliver,<div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>Whereas the default Needleman-Wunsch algorithm is implemented in Python, the Smith-Waterman one is implemented in C++, so the latter will be much faster. I don’t know if the results will be better or worse though. In ChimeraX I will have both algorithms implemented in C++ so hopefully the issue will be moot. Nonetheless I will keep your suggestion in mind in case it turns out not to be moot!</div><div class=""><br class=""></div><div class="">—Eric</div><div class=""><br class=""><div class="">
<div style="color: rgb(0, 0, 0); letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div class=""><span class="Apple-tab-span" style="white-space: pre;"> </span>Eric Pettersen</div><div class=""><span class="Apple-tab-span" style="white-space: pre;"> </span>UCSF Computer Graphics Lab</div></div><br class="Apple-interchange-newline">
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<br class=""><div><blockquote type="cite" class=""><div class="">On May 12, 2016, at 12:01 PM, Oliver Clarke <<a href="mailto:olibclarke@gmail.com" class="">olibclarke@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class=""><div class=""><div class="">Hi, Matchmaker takes a *really* long time when dealing with long chains, particularly if it has been (unwisely/accidentally) directed to find the best matching pair of chains. <br class=""><br class="">This is as expected, but as Chimera is unresponsive while this happens, if the wrong matchmaker parameters are accidentally selected, there is no way to recover the session except by waiting for the operation to complete or force-quitting the app. If feasible, maybe in ChimeraX it would be useful to execute this operation in a manner that allows for cancelling a structural alignment in progress? And perhaps displaying an estimate of time to completion in the taskbar?<br class=""><br class=""></div>Cheers,<br class=""></div>Oli.<br class=""></div>
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