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<p class="MsoNormal"><span lang="EN-US" style="mso-fareast-language:EN-US">Exactly! I am not aware of ISOLDE having this functionality, but wouyld be very greatful if it could be implemented in either ChimeraX or ISOLDE : )<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="mso-fareast-language:EN-US">Many thanks,<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="mso-fareast-language:EN-US">Matthias
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<p class="MsoNormal"><span style="mso-fareast-language:EN-US"><o:p> </o:p></span></p>
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<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 18:49<br>
<b>To: </b>"Vorländer,Matthias Kopano" <matthias.vorlaender@imp.ac.at><br>
<b>Cc: </b>ChimeraX Users Help <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>
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<p class="MsoNormal">So it nukes the target residues, copies the source residues as is (conformation and position) into the chain where the target residues were, gives them the target chain ID and adds the connecting polymeric bonds to the target chain? This
seems like something that the ISOLDE plugin would do already, but I'm not sure about that.<o:p></o:p></p>
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<p class="MsoNormal">If ISOLDE doesn't, it doesn't seem like something that would be excessively hard to implement.<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">--Eric<o:p></o:p></p>
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<p class="MsoNormal">On Jan 12, 2023, at 9:34 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>
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<p class="MsoNormal"><span lang="EN-US">Hi Eric,</span><o:p></o:p></p>
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<p class="MsoNormal"><span lang="EN-US"> </span><o:p></o:p></p>
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<p class="MsoNormal"><span lang="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</span><o:p></o:p></p>
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<p class="MsoNormal"><span lang="EN-US"> </span><o:p></o:p></p>
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<span lang="EN-US" style="font-family:Courier">delete #1/A:1-10</span><o:p></o:p></li><li class="MsoListParagraph" style="margin-top:0cm;margin-bottom:0cm;mso-list:l0 level1 lfo1">
<span lang="EN-US" style="font-family:Courier">select #2/A:1-10</span><span lang="EN-US">, save a pdb file with only the selected residues<span class="apple-converted-space"> </span></span><o:p></o:p></li><li class="MsoListParagraph" style="margin-top:0cm;margin-bottom:0cm;mso-list:l0 level1 lfo1">
<span lang="EN-US">Open this new PDB file (model #3)</span><o:p></o:p></li><li class="MsoListParagraph" style="margin-top:0cm;margin-bottom:0cm;mso-list:l0 level1 lfo1">
<span lang="EN-US" style="font-family:Courier">combine #1,3</span><o:p></o:p></li><li class="MsoListParagraph" style="margin-top:0cm;margin-bottom:0cm;mso-list:l0 level1 lfo1">
<span lang="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><o:p></o:p></li><li class="MsoListParagraph" style="margin-top:0cm;margin-bottom:0cm;mso-list:l0 level1 lfo1">
<span lang="EN-US">The I would use the<span class="apple-converted-space"> </span></span><span lang="EN-US" style="font-family:Courier">command changechains #4/B A<span class="apple-converted-space"> </span></span><span lang="EN-US">and this would yield the
result that I want</span><o:p></o:p></li></ol>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal"><span lang="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.</span><o:p></o:p></p>
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<p class="MsoNormal"><span lang="EN-US"> </span><o:p></o:p></p>
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<p class="MsoNormal"><span lang="EN-US">I hope that made it clearer?</span><o:p></o:p></p>
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<p class="MsoNormal"><span lang="EN-US"> </span><o:p></o:p></p>
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<p class="MsoNormal"><span lang="EN-US">Thanks a lot,</span><o:p></o:p></p>
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<p class="MsoNormal"><span lang="EN-US">Matthias</span><o:p></o:p></p>
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<p class="MsoNormal"><b><span style="font-size:12.0pt">From:<span class="apple-converted-space"> </span></span></b><span style="font-size:12.0pt">Eric Pettersen <<a href="mailto:pett@cgl.ucsf.edu">pett@cgl.ucsf.edu</a>><br>
<b>Reply to:<span class="apple-converted-space"> </span></b>ChimeraX Users Help <<a href="mailto:chimerax-users@cgl.ucsf.edu">chimerax-users@cgl.ucsf.edu</a>><br>
<b>Date:<span class="apple-converted-space"> </span></b>Thursday, 12. January 2023 at 18:17<br>
<b>To:<span class="apple-converted-space"> </span></b>"Vorländer,Matthias Kopano" <<a href="mailto:matthias.vorlaender@imp.ac.at">matthias.vorlaender@imp.ac.at</a>><br>
<b>Cc:<span class="apple-converted-space"> </span></b>"<a href="mailto:chimerax-users@cgl.ucsf.edu">chimerax-users@cgl.ucsf.edu</a>" <<a href="mailto:chimerax-users@cgl.ucsf.edu">chimerax-users@cgl.ucsf.edu</a>><br>
<b>Subject:<span class="apple-converted-space"> </span></b>Re: [chimerax-users] Feature request: replace residues in model with residues from other model</span><o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal">Hi Matthias,<o:p></o:p></p>
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<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>
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<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>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal">--Eric<o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal">Eric Pettersen<o:p></o:p></p>
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<p class="MsoNormal">UCSF Computer Graphics Lab<o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal"><br>
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<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>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal"><span lang="EN-US">Dear ChimeraX team,<span class="apple-converted-space"> </span></span><o:p></o:p></p>
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<p class="MsoNormal"><span lang="EN-US"> </span><o:p></o:p></p>
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<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>
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<p class="MsoNormal"><span lang="EN-US"> </span><o:p></o:p></p>
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<p class="MsoNormal"><span lang="EN-US">Many thanks in advance,</span><o:p></o:p></p>
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<p class="MsoNormal"><span lang="EN-US">Matthias</span><o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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