<html xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:w="urn:schemas-microsoft-com:office:word" xmlns:m="http://schemas.microsoft.com/office/2004/12/omml" xmlns="http://www.w3.org/TR/REC-html40">
<head>
<meta http-equiv="Content-Type" content="text/html; charset=Windows-1252">
<meta name="Generator" content="Microsoft Word 15 (filtered medium)">
<style><!--
/* Font Definitions */
@font-face
{font-family:Helvetica;
panose-1:0 0 0 0 0 0 0 0 0 0;}
@font-face
{font-family:"Cambria Math";
panose-1:2 4 5 3 5 4 6 3 2 4;}
@font-face
{font-family:Calibri;
panose-1:2 15 5 2 2 2 4 3 2 4;}
@font-face
{font-family:"Malgun Gothic";
panose-1:2 11 5 3 2 0 0 2 0 4;}
@font-face
{font-family:"\@Malgun Gothic";}
/* Style Definitions */
p.MsoNormal, li.MsoNormal, div.MsoNormal
{margin:0in;
font-size:10.0pt;
font-family:"Calibri",sans-serif;}
a:link, span.MsoHyperlink
{mso-style-priority:99;
color:blue;
text-decoration:underline;}
span.apple-converted-space
{mso-style-name:apple-converted-space;}
.MsoChpDefault
{mso-style-type:export-only;
font-size:10.0pt;}
@page WordSection1
{size:8.5in 11.0in;
margin:1.0in 1.0in 1.0in 1.0in;}
div.WordSection1
{page:WordSection1;}
--></style>
</head>
<body lang="EN-US" link="blue" vlink="purple" style="word-wrap:break-word;-webkit-nbsp-mode: space;line-break:after-white-space">
<div class="WordSection1">
<p class="MsoNormal"><span style="font-size:11.0pt">Thank you all (Elaine, Tom, Eric).<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">"align #2-100/X:1@ca,o,c,n to #1/X:1@ca,o,c,n each structure"
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">worked perfectly!<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">Best,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">Doo Nam<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<div style="border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0in 0in 0in">
<p class="MsoNormal" style="margin-bottom:12.0pt"><b><span style="font-size:12.0pt;color:black">From:
</span></b><span style="font-size:12.0pt;color:black">Eric Pettersen <pett@cgl.ucsf.edu><br>
<b>Date: </b>Monday, November 28, 2022 at 2:32 PM<br>
<b>To: </b>Kim, Doo Nam <doonam.kim@pnnl.gov><br>
<b>Cc: </b>chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu><br>
<b>Subject: </b>Re: [chimerax-users] Align with specific atoms (but against all other molecules)<o:p></o:p></span></p>
</div>
<div style="border:none;border-left:solid #D77600 6.0pt;padding:0in 0in 0in 0in;font-size:1.15rem">
<p class="MsoNormal" align="center" style="text-align:center;background:#F7E3CC">
<span style="font-size:11.0pt;font-family:"Arial",sans-serif;color:black">Check twice before you click! This email originated from outside PNNL.</span><span style="font-size:11.0pt;font-family:"Arial",sans-serif"><o:p></o:p></span></p>
</div>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt">Hi Doo Nam, <o:p></o:p></span></p>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt">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.<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
</div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt">--Eric<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt">Eric Pettersen<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt">UCSF Computer Graphics Lab<o:p></o:p></span></p>
</div>
</div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt"><br>
<br>
<o:p></o:p></span></p>
<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
<div>
<p class="MsoNormal"><span style="font-size:11.0pt">On Nov 26, 2022, at 1:49 PM, Kim, Doo Nam via ChimeraX-users <</span><a href="mailto:chimerax-users@cgl.ucsf.edu"><span style="font-size:11.0pt">chimerax-users@cgl.ucsf.edu</span></a><span style="font-size:11.0pt">>
wrote:<o:p></o:p></span></p>
</div>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt">Hi,<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt"> <o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt">I’ve used<span class="apple-converted-space"> </span><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt"> <o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt">align #2/X:1 @CA,O,C,N to #1/X:1 @CA,O,C,N<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt">align #3/X:1 @CA,O,C,N to #1/X:1 @CA,O,C,N<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt">align #4/X:1 @CA,O,C,N to #1/X:1 @CA,O,C,N<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt">…<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt"> <o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt">to align<span class="apple-converted-space"> </span><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt">#2 molecule against #1 molecule with backbone atoms<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt">#3 molecule against #1 molecule with backbone atoms<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt">#4 molecule against #1 molecule with backbone atoms<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt">etc…<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt"> <o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt"> <o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt">However, how can I align all rest molecules (e.g. #2~#100) against #1 molecule<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt">with backbone atoms<span class="apple-converted-space"><b><u> </u></b></span><b><u>at once<span class="apple-converted-space"> </span></u></b>in chimeraX?<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt"> <o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt"> <o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt">I’ve used<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt">align all toAtoms #1 matchAtomNames true<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt">align all toAtoms #1 matchNumbering true<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt"> <o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt">to align all molecules to #1 molecule<span class="apple-converted-space"> </span><b><u>at once</u></b>.<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt">However, with this command, I cannot specify to use backbone atoms (e.g. CA,O,C,N) only when aligning.<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt"> <o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt"> <o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt">I think that there should a 1 line command that aligns all molecules with specific atoms only<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt">or there is chimeraX equivalent python script as<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt"> <o:p></o:p></span></p>
</div>
<div style="margin-left:.5in">
<p class="MsoNormal"><span style="font-size:11.0pt">from chimera import runCommand as rc # use 'rc' as shorthand for runCommand<o:p></o:p></span></p>
</div>
<div style="margin-left:.5in">
<p class="MsoNormal"><span style="font-size:11.0pt">from chimera import replyobj # for emitting status messages<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt"> <o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt">Best,<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt">Doo Nam<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt"> <o:p></o:p></span></p>
</div>
<p class="MsoNormal"><span style="font-size:9.0pt;font-family:Helvetica">_______________________________________________<br>
ChimeraX-users mailing list<br>
</span><a href="mailto:ChimeraX-users@cgl.ucsf.edu"><span style="font-size:9.0pt;font-family:Helvetica">ChimeraX-users@cgl.ucsf.edu</span></a><span style="font-size:9.0pt;font-family:Helvetica"><br>
Manage subscription:<br>
</span><a href="https://gcc02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.rbvi.ucsf.edu%2Fmailman%2Flistinfo%2Fchimerax-users&data=05%7C01%7Cdoonam.kim%40pnnl.gov%7Ceae8b899c9064cc3f98e08dad19065a5%7Cd6faa5f90ae240338c0130048a38deeb%7C0%7C0%7C638052715367370676%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=CoT5qldSz2ofWkwUBb9tKVXUpmxtytXBcr3VnpT80qk%3D&reserved=0"><span style="font-size:9.0pt;font-family:Helvetica">https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users</span></a><span style="font-size:11.0pt"><o:p></o:p></span></p>
</div>
</blockquote>
</div>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
</div>
</div>
</div>
</body>
</html>