<html><head><meta http-equiv="Content-Type" content="text/html; charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">Hi Hernando,<div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>This old chimera-users message shows how to find the alignment in Python and save it: <a href="http://plato.cgl.ucsf.edu/pipermail/chimera-users/2014-June/010017.html" class="">[Chimera-users] easy way to make alignments in chimera</a>. You can’t do it in nogui mode since the MAV window has the alignment data. You would be able to do it in nogui mode in ChimeraX, but the code would be significantly different of course.</div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>Anyway, if you are doing this in a loop you may want to call mav.Quit() after saving your alignment in order to quit MAV and conserve memory.</div><div class=""><br class=""></div><div class="">—Eric<br class=""><div class="">
<div style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; text-decoration: none;" class=""><span class="Apple-tab-span" style="white-space: pre;"><br class="Apple-interchange-newline"> </span>Eric Pettersen</div><div style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; text-decoration: none;" class=""><span class="Apple-tab-span" style="white-space: pre;"> </span>UCSF Computer Graphics Lab</div><div style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; text-decoration: none;" class=""><br class=""></div><br class="Apple-interchange-newline">
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<div><br class=""><blockquote type="cite" class=""><div class="">On May 3, 2019, at 2:03 PM, Hernando J Sosa <<a href="mailto:hernando.sosa@einstein.yu.edu" class="">hernando.sosa@einstein.yu.edu</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div class="">Dear Chimera,<br class=""><br class=""> Is there a command option to save a sequence alignment (after executing matchmaker) or a way to do it in a python script? <br class=""><br class="">Thanks<br class=""><br class="">H.<br class=""><br class=""><br class=""><br class=""><br class=""><br class="">_______________________________________________<br class="">Chimera-users mailing list: <a href="mailto:Chimera-users@cgl.ucsf.edu" class="">Chimera-users@cgl.ucsf.edu</a><br class="">Manage subscription: <a href="http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users" class="">http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users</a><br class=""></div></div></blockquote></div><br class=""></div></body></html>