<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=utf-8">
<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:Courier;
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;}
/* Style Definitions */
p.MsoNormal, li.MsoNormal, div.MsoNormal
{margin:0cm;
font-size:11.0pt;
font-family:"Calibri",sans-serif;}
a:link, span.MsoHyperlink
{mso-style-priority:99;
color:blue;
text-decoration:underline;}
p.MsoListParagraph, li.MsoListParagraph, div.MsoListParagraph
{mso-style-priority:34;
margin-top:0cm;
margin-right:0cm;
margin-bottom:0cm;
margin-left:36.0pt;
font-size:11.0pt;
font-family:"Calibri",sans-serif;}
span.apple-converted-space
{mso-style-name:apple-converted-space;}
span.EmailStyle20
{mso-style-type:personal-reply;
font-family:"Calibri",sans-serif;
color:windowtext;}
.MsoChpDefault
{mso-style-type:export-only;
font-size:10.0pt;}
@page WordSection1
{size:612.0pt 792.0pt;
margin:72.0pt 72.0pt 72.0pt 72.0pt;}
div.WordSection1
{page:WordSection1;}
/* List Definitions */
@list l0
{mso-list-id:942803038;
mso-list-type:hybrid;
mso-list-template-ids:614728658 134807569 134807577 134807579 134807567 134807577 134807579 134807567 134807577 134807579;}
@list l0:level1
{mso-level-text:"%1\)";
mso-level-tab-stop:none;
mso-level-number-position:left;
text-indent:-18.0pt;}
@list l0:level2
{mso-level-number-format:alpha-lower;
mso-level-tab-stop:none;
mso-level-number-position:left;
text-indent:-18.0pt;}
@list l0:level3
{mso-level-number-format:roman-lower;
mso-level-tab-stop:none;
mso-level-number-position:right;
text-indent:-9.0pt;}
@list l0:level4
{mso-level-tab-stop:none;
mso-level-number-position:left;
text-indent:-18.0pt;}
@list l0:level5
{mso-level-number-format:alpha-lower;
mso-level-tab-stop:none;
mso-level-number-position:left;
text-indent:-18.0pt;}
@list l0:level6
{mso-level-number-format:roman-lower;
mso-level-tab-stop:none;
mso-level-number-position:right;
text-indent:-9.0pt;}
@list l0:level7
{mso-level-tab-stop:none;
mso-level-number-position:left;
text-indent:-18.0pt;}
@list l0:level8
{mso-level-number-format:alpha-lower;
mso-level-tab-stop:none;
mso-level-number-position:left;
text-indent:-18.0pt;}
@list l0:level9
{mso-level-number-format:roman-lower;
mso-level-tab-stop:none;
mso-level-number-position:right;
text-indent:-9.0pt;}
ol
{margin-bottom:0cm;}
ul
{margin-bottom:0cm;}
--></style>
</head>
<body lang="en-AT" link="blue" vlink="purple" style="word-wrap:break-word">
<div class="WordSection1">
<p class="MsoNormal"><span lang="EN-US" style="mso-fareast-language:EN-US">Hi Eric,
<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="mso-fareast-language:EN-US">Thanks for getting back to me! Perhaps it is clearer with an example. Lets assume I am working on a model, and I have two different PDB files of the same molecule. In model 1, residues
1:10 are wrongly built and need to be changed, but the remainder of chain A(say #11-100) is correct, so I want to replace residues #1/A:1-10 with the same residues in a different PDB file where they are correct (#2/A:1-10). So I would
<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<ol style="margin-top:0cm" start="1" type="1">
<li class="MsoListParagraph" style="margin-left:0cm;mso-list:l0 level1 lfo1"><span lang="EN-US" style="font-family:Courier;mso-fareast-language:EN-US">delete #1/A:1-10</span><span style="font-family:Courier;mso-fareast-language:EN-US"><o:p></o:p></span></li><li class="MsoListParagraph" style="margin-left:0cm;mso-list:l0 level1 lfo1"><span lang="EN-US" style="font-family:Courier;mso-fareast-language:EN-US">select #2/A:1-10</span><span lang="EN-US" style="mso-fareast-language:EN-US">, save a pdb file with only the
selected residues </span><span style="mso-fareast-language:EN-US"><o:p></o:p></span></li><li class="MsoListParagraph" style="margin-left:0cm;mso-list:l0 level1 lfo1"><span lang="EN-US" style="mso-fareast-language:EN-US">Open this new PDB file (model #3)</span><span style="mso-fareast-language:EN-US"><o:p></o:p></span></li><li class="MsoListParagraph" style="margin-left:0cm;mso-list:l0 level1 lfo1"><span lang="EN-US" style="font-family:Courier;mso-fareast-language:EN-US">combine #1,3
</span><span style="font-family:Courier;mso-fareast-language:EN-US"><o:p></o:p></span></li><li class="MsoListParagraph" style="margin-left:0cm;mso-list:l0 level1 lfo1"><span lang="EN-US" style="mso-fareast-language:EN-US">Now ChimeraX will change the chain ID that used to be #A/1-10 and create a new chain B in model #4</span><span style="mso-fareast-language:EN-US"><o:p></o:p></span></li><li class="MsoListParagraph" style="margin-left:0cm;mso-list:l0 level1 lfo1"><span lang="EN-US" style="mso-fareast-language:EN-US">The I would use the
</span><span lang="EN-US" style="font-family:Courier;mso-fareast-language:EN-US">command changechains #4/B A
</span><span lang="EN-US" style="mso-fareast-language:EN-US">and this would yield the result that I want</span><span style="mso-fareast-language:EN-US"><o:p></o:p></span></li></ol>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="mso-fareast-language:EN-US">What I am hoping for is that there would be a command that would achieve this in one go. Essentially it would just replace the lines in the PDB file from one file with those in another.
<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="mso-fareast-language:EN-US">I hope that made it clearer?<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="mso-fareast-language:EN-US">Thanks a lot,
<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="mso-fareast-language:EN-US">Matthias<o:p></o:p></span></p>
<div style="border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0cm 0cm 0cm">
<p class="MsoNormal"><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>Reply to: </b>ChimeraX Users Help <chimerax-users@cgl.ucsf.edu><br>
<b>Date: </b>Thursday, 12. January 2023 at 18:17<br>
<b>To: </b>"Vorländer,Matthias Kopano" <matthias.vorlaender@imp.ac.at><br>
<b>Cc: </b>"chimerax-users@cgl.ucsf.edu" <chimerax-users@cgl.ucsf.edu><br>
<b>Subject: </b>Re: [chimerax-users] Feature request: replace residues in model with residues from other model<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<p class="MsoNormal">Hi Matthias,<o:p></o:p></p>
<div>
<p class="MsoNormal">I not familiar with "replace fragment", so I have a few questions. Is it always the same number of residues in source and target? Is it always polymeric residues, and the same type of polymer (amino acids, nucleic acids)? I assume you
have to use the backbone conformation of the target. Are the side chain angles preserved in any way?<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">It's possible this could be implemented as sort of a macro around multiple swapaa/swapna commands.<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<div>
<p class="MsoNormal">--Eric<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal">Eric Pettersen<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">UCSF Computer Graphics Lab<o:p></o:p></p>
</div>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
<div>
<p class="MsoNormal"><br>
<br>
<o:p></o:p></p>
<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
<div>
<p class="MsoNormal">On Jan 12, 2023, at 4:24 AM, Vorländer,Matthias Kopano via ChimeraX-users <<a href="mailto:chimerax-users@cgl.ucsf.edu">chimerax-users@cgl.ucsf.edu</a>> wrote:<o:p></o:p></p>
</div>
<p class="MsoNormal"><o:p> </o:p></p>
<div>
<div>
<p class="MsoNormal"><span lang="EN-US">Dear ChimeraX team,<span class="apple-converted-space"> </span></span><o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><span lang="EN-US"> </span><o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><span lang="EN-US">Thanks a lot for developing the amazing tool that is ChimeraX! I use it extensively for model building, and would like to request a functionality to replace a residue selection in one model from residues in another model
(similar to what is possible in coot via the replace fragment functionality). I am aware that this currently possible by a combination of delete, combine, and changechains, but it would be great if this could be shortcutted.</span><o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><span lang="EN-US"> </span><o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><span lang="EN-US">Many thanks in advance,</span><o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><span lang="EN-US">Matthias</span><o:p></o:p></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://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users"><span style="font-size:9.0pt;font-family:Helvetica">https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users</span></a><o:p></o:p></p>
</div>
</blockquote>
</div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
</div>
</body>
</html>