<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 Doo Nam,<div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>You should be able to use "align #2-100/X:1@ca,o,c,n to #1/X:1@ca,o,c,n each structure" to do this.</div><div class=""><br class=""></div><div class=""><div class="">--Eric</div><div class=""><br class=""></div><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><div class=""><br class=""><div><br class=""><blockquote type="cite" class=""><div class="">On Nov 26, 2022, at 1:49 PM, Kim, Doo Nam via ChimeraX-users <<a href="mailto:chimerax-users@cgl.ucsf.edu" class="">chimerax-users@cgl.ucsf.edu</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div class="WordSection1" style="page: WordSection1; caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;"><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;" class="">Hi,<o:p class=""></o:p></div><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;" class="">I’ve used<span class="Apple-converted-space"> </span><o:p class=""></o:p></div><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;" class="">align #2/X:1 @CA,O,C,N to #1/X:1 @CA,O,C,N<o:p class=""></o:p></div><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;" class="">align #3/X:1 @CA,O,C,N to #1/X:1 @CA,O,C,N<o:p class=""></o:p></div><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;" class="">align #4/X:1 @CA,O,C,N to #1/X:1 @CA,O,C,N<o:p class=""></o:p></div><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;" class="">…<o:p class=""></o:p></div><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;" class="">to align<span class="Apple-converted-space"> </span><o:p class=""></o:p></div><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;" class="">#2 molecule against #1 molecule with backbone atoms<o:p class=""></o:p></div><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;" class="">#3 molecule against #1 molecule with backbone atoms<o:p class=""></o:p></div><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;" class="">#4 molecule against #1 molecule with backbone atoms<o:p class=""></o:p></div><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;" class="">etc…<o:p class=""></o:p></div><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;" class="">However, how can I align all rest molecules (e.g. #2~#100) against #1 molecule<o:p class=""></o:p></div><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;" class="">with backbone atoms<b class=""><u class=""><span class="Apple-converted-space"> </span>at once<span class="Apple-converted-space"> </span></u></b>in chimeraX?<o:p class=""></o:p></div><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;" class="">I’ve used<o:p class=""></o:p></div><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;" class="">align all toAtoms #1 matchAtomNames true<o:p class=""></o:p></div><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;" class="">align all toAtoms #1 matchNumbering true<o:p class=""></o:p></div><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;" class="">to align all molecules to #1 molecule<span class="Apple-converted-space"> </span><b class=""><u class="">at once</u></b>.<o:p class=""></o:p></div><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;" class="">However, with this command, I cannot specify to use backbone atoms (e.g. CA,O,C,N) only when aligning.<o:p class=""></o:p></div><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;" class="">I think that there should a 1 line command that aligns all molecules with specific atoms only<o:p class=""></o:p></div><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;" class="">or there is chimeraX equivalent python script as<o:p class=""></o:p></div><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><div style="margin: 0in 0in 0in 0.5in; font-size: 11pt; font-family: Calibri, sans-serif;" class="">from chimera import runCommand as rc # use 'rc' as shorthand for runCommand<o:p class=""></o:p></div><div style="margin: 0in 0in 0in 0.5in; font-size: 11pt; font-family: Calibri, sans-serif;" class="">from chimera import replyobj # for emitting status messages<o:p class=""></o:p></div><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;" class="">Best,<o:p class=""></o:p></div><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;" class="">Doo Nam<o:p class=""></o:p></div><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div></div><span style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;" class="">_______________________________________________</span><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; 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