<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="">Okay, I have opened an enhancement-request ticket in out bug-tracking database for this (<a href="https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/8323" class="">https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/8323</a>). It may take awhile before it gets implemented -- it is competing against quite a few other development priorities.<div class=""><br class=""></div><div class="">--Eric<br class=""><div><br class=""><blockquote type="cite" class=""><div class="">On Jan 12, 2023, at 2:31 PM, Vorländer,Matthias Kopano 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: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span lang="EN-US" class="">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 class=""></o:p></span></div><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span lang="EN-US" class="">Many thanks,<o:p class=""></o:p></span></div><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span lang="EN-US" class="">Matthias<o:p class=""></o:p></span></div><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span class=""><o:p class=""> </o:p></span></div><div style="border-style: solid none none; border-top-width: 1pt; border-top-color: rgb(181, 196, 223); padding: 3pt 0cm 0cm;" class=""><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><b class=""><span style="font-size: 12pt;" class="">From:<span class="Apple-converted-space"> </span></span></b><span style="font-size: 12pt;" class="">Eric Pettersen <<a href="mailto:pett@cgl.ucsf.edu" style="color: blue; text-decoration: underline;" class="">pett@cgl.ucsf.edu</a>><br class=""><b class="">Reply to:<span class="Apple-converted-space"> </span></b>ChimeraX Users Help <<a href="mailto:chimerax-users@cgl.ucsf.edu" style="color: blue; text-decoration: underline;" class="">chimerax-users@cgl.ucsf.edu</a>><br class=""><b class="">Date:<span class="Apple-converted-space"> </span></b>Thursday, 12. January 2023 at 18:49<br class=""><b class="">To:<span class="Apple-converted-space"> </span></b>"Vorländer,Matthias Kopano" <<a href="mailto:matthias.vorlaender@imp.ac.at" class="">matthias.vorlaender@imp.ac.at</a>><br class=""><b class="">Cc:<span class="Apple-converted-space"> </span></b>ChimeraX Users Help <<a href="mailto:chimerax-users@cgl.ucsf.edu" class="">chimerax-users@cgl.ucsf.edu</a>><br class=""><b class="">Subject:<span class="Apple-converted-space"> </span></b>Re: [chimerax-users] Feature request: replace residues in model with residues from other model<o:p class=""></o:p></span></div></div><div class=""><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div></div><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">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 class=""></o:p></div><div class=""><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div></div><div class=""><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">If ISOLDE doesn't, it doesn't seem like something that would be excessively hard to implement.<o:p class=""></o:p></div><div class=""><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div></div><div class=""><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">--Eric<o:p class=""></o:p></div><div class=""><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><br class=""><br class=""><o:p class=""></o:p></div><blockquote style="margin-top: 5pt; margin-bottom: 5pt;" class=""><div class=""><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">On Jan 12, 2023, at 9:34 AM, Vorländer,Matthias Kopano via ChimeraX-users <<a href="mailto:chimerax-users@cgl.ucsf.edu" style="color: blue; text-decoration: underline;" class="">chimerax-users@cgl.ucsf.edu</a>> wrote:<o:p class=""></o:p></div></div><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><div class=""><div class=""><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span lang="EN-US" class="">Hi Eric,</span><o:p class=""></o:p></div></div><div class=""><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span lang="EN-US" class=""> </span><o:p class=""></o:p></div></div><div class=""><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span lang="EN-US" class="">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 class=""></o:p></div></div><div class=""><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span lang="EN-US" class=""> </span><o:p class=""></o:p></div></div><ol start="1" type="1" style="margin-bottom: 0cm; margin-top: 0cm;" class=""><li class="MsoListParagraph" style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;"><span lang="EN-US" style="font-family: Courier;" class="">delete #1/A:1-10</span><o:p class=""></o:p></li><li class="MsoListParagraph" style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;"><span lang="EN-US" style="font-family: Courier;" class="">select #2/A:1-10</span><span lang="EN-US" class="">, save a pdb file with only the selected residues<span class="apple-converted-space"> </span></span><o:p class=""></o:p></li><li class="MsoListParagraph" style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;"><span lang="EN-US" class="">Open this new PDB file (model #3)</span><o:p class=""></o:p></li><li class="MsoListParagraph" style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;"><span lang="EN-US" style="font-family: Courier;" class="">combine #1,3</span><o:p class=""></o:p></li><li class="MsoListParagraph" style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;"><span lang="EN-US" class="">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 class=""></o:p></li><li class="MsoListParagraph" style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;"><span lang="EN-US" class="">The I would use the<span class="apple-converted-space"> </span></span><span lang="EN-US" style="font-family: Courier;" class="">command changechains #4/B A<span class="apple-converted-space"> </span></span><span lang="EN-US" class="">and this would yield the result that I want</span><o:p class=""></o:p></li></ol><div class=""><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class=""> <o:p class=""></o:p></div></div><div class=""><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span lang="EN-US" class="">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 class=""></o:p></div></div><div class=""><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span lang="EN-US" class=""> </span><o:p class=""></o:p></div></div><div class=""><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span lang="EN-US" class="">I hope that made it clearer?</span><o:p class=""></o:p></div></div><div class=""><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span lang="EN-US" class=""> </span><o:p class=""></o:p></div></div><div class=""><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span lang="EN-US" class="">Thanks a lot,</span><o:p class=""></o:p></div></div><div class=""><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span lang="EN-US" class="">Matthias</span><o:p class=""></o:p></div></div><div style="border-style: solid none none; border-top-width: 1pt; border-top-color: rgb(181, 196, 223); padding: 3pt 0cm 0cm;" class=""><div class=""><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><b class=""><span style="font-size: 12pt;" class="">From:<span class="apple-converted-space"> </span></span></b><span style="font-size: 12pt;" class="">Eric Pettersen <<a href="mailto:pett@cgl.ucsf.edu" style="color: blue; text-decoration: underline;" class="">pett@cgl.ucsf.edu</a>><br class=""><b class="">Reply to:<span class="apple-converted-space"> </span></b>ChimeraX Users Help <<a href="mailto:chimerax-users@cgl.ucsf.edu" style="color: blue; text-decoration: underline;" class="">chimerax-users@cgl.ucsf.edu</a>><br class=""><b class="">Date:<span class="apple-converted-space"> </span></b>Thursday, 12. January 2023 at 18:17<br class=""><b class="">To:<span class="apple-converted-space"> </span></b>"Vorländer,Matthias Kopano" <<a href="mailto:matthias.vorlaender@imp.ac.at" style="color: blue; text-decoration: underline;" class="">matthias.vorlaender@imp.ac.at</a>><br class=""><b class="">Cc:<span class="apple-converted-space"> </span></b>"<a href="mailto:chimerax-users@cgl.ucsf.edu" style="color: blue; text-decoration: underline;" class="">chimerax-users@cgl.ucsf.edu</a>" <<a href="mailto:chimerax-users@cgl.ucsf.edu" style="color: blue; text-decoration: underline;" class="">chimerax-users@cgl.ucsf.edu</a>><br class=""><b class="">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 class=""></o:p></div></div></div><div class=""><div class=""><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class=""> <o:p class=""></o:p></div></div></div><div class=""><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">Hi Matthias,<o:p class=""></o:p></div></div><div class=""><div class=""><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">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 class=""></o:p></div></div></div><div class=""><div class=""><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">It's possible this could be implemented as sort of a macro around multiple swapaa/swapna commands.<o:p class=""></o:p></div></div></div><div class=""><div class=""><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class=""> <o:p class=""></o:p></div></div></div><div class=""><div class=""><div class=""><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">--Eric<o:p class=""></o:p></div></div></div><div class=""><div class=""><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class=""> <o:p class=""></o:p></div></div></div><div class=""><div class=""><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">Eric Pettersen<o:p class=""></o:p></div></div></div><div class=""><div class=""><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">UCSF Computer Graphics Lab<o:p class=""></o:p></div></div></div></div><div class=""><div class=""><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class=""> <o:p class=""></o:p></div></div><div class=""><div class=""><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><br class=""><br class=""><br class=""><o:p class=""></o:p></div></div><blockquote style="margin-top: 5pt; margin-bottom: 5pt;" class=""><div class=""><div class=""><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">On Jan 12, 2023, at 4:24 AM, Vorländer,Matthias Kopano via ChimeraX-users <<a href="mailto:chimerax-users@cgl.ucsf.edu" style="color: blue; text-decoration: underline;" class="">chimerax-users@cgl.ucsf.edu</a>> wrote:<o:p class=""></o:p></div></div></div><div class=""><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class=""> <o:p class=""></o:p></div></div><div class=""><div class=""><div class=""><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span lang="EN-US" class="">Dear ChimeraX team,<span class="apple-converted-space"> </span></span><o:p class=""></o:p></div></div></div><div class=""><div class=""><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span lang="EN-US" class=""> </span><o:p class=""></o:p></div></div></div><div class=""><div class=""><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span lang="EN-US" class="">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 class=""></o:p></div></div></div><div class=""><div class=""><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span lang="EN-US" class=""> </span><o:p class=""></o:p></div></div></div><div class=""><div class=""><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span lang="EN-US" class="">Many thanks in advance,</span><o:p class=""></o:p></div></div></div><div class=""><div class=""><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span lang="EN-US" class="">Matthias</span><o:p class=""></o:p></div></div></div><div class=""><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span style="font-size: 9pt; font-family: Helvetica;" class="">_______________________________________________<br class="">ChimeraX-users mailing list<br class=""></span><a href="mailto:ChimeraX-users@cgl.ucsf.edu" style="color: blue; 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