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Hopefully (he said plaintively), sometime soon I'll find the breathing space to flesh this out into a properly polished tool. For now, the approach Alexis outlined does work with a modicum of patience.</div>
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<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>From:</b> ChimeraX-users <chimerax-users-bounces@cgl.ucsf.edu> on behalf of Alexis Rohou <a.rohou@gmail.com><br>
<b>Sent:</b> 26 April 2021 19:12<br>
<b>To:</b> Tom Goddard <goddard@sonic.net><br>
<b>Cc:</b> chimeraX Users Help <chimerax-users@cgl.ucsf.edu><br>
<b>Subject:</b> Re: [chimerax-users] Adding amino acids to end of chain</font>
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<div class="" style="word-wrap:break-word; line-break:after-white-space">I hope Tristan won’t mind, but since the question is now on the list, below is the recipe that Tristan sent me directly. If it works, Tristan gets credit. If it doesn’t, then my bad for
sharing it - please don’t blame Tristan.
<div class="">It worked for me, but <insert standard lawyer speak to lower expectations and avoid future blame for your troubles>.</div>
<div class=""><br class="">
</div>
<div class="">Cheers,</div>
<div class="">Alexis<br class="">
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<blockquote type="cite" class="">
<div class="" style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:12pt">
You can add an amino acid to your chain using the following approach. First, select any atom from the residue you want to attach it to. Then in the shell:</div>
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m = session.isolde.selected_model</div>
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from chimerax.atomic import selected_residues</div>
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from chimerax.isolde.atomic.building.build_utils import add_amino_acid_residue</div>
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# if you're adding an ARG to the C-terminal end:</div>
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add_amino_acid_residue(m, 'ARG', prev_res=selected_residues(session)[0])</div>
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# if you're adding to the N-terminal end:</div>
<div class="" style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:12pt">
<span class="" style="margin:0px; font-size:12pt; background-color:rgb(255,255,255)">add_amino_acid_residue(m, 'ARG', next_res=selected_residues(session)[0])</span><br class="">
</div>
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<span class="" style="margin:0px; font-size:12pt; background-color:rgb(255,255,255)"><br class="">
</span></div>
<div class="" style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:12pt">
It currently makes no attempt to pre-optimise geometry so that'll be pretty crap, but it's usually good enough to easily settle into place (you might occasionally need to "isolde ignore" one or two residues for the first sim). There are a few known bugs:</div>
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<div class="" style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:12pt">
<ul class="">
<li class="">when adding into a gap, occasionally the "missing structure" pseudobonds will fail to update correctly, leaving the old pseudobond in place. This doesn't cause any immediate harm, but can mess up the structure on saving if not corrected. To do
so, select the atoms on either end of the offending pseudobond, then:</li></ul>
<div class="">pbg = m.pseudobond_group[m.PBG_MISSING_STRUCTURE, create_type=None)</div>
<div class="">from chimerax.atomic import selected_atoms</div>
<div class="">pbg.pseudobonds[pbg.pseudobonds.between_atoms(selected_atoms(session))].delete()</div>
<div class=""><br class="">
</div>
<div class="">
<ul class="">
<li class="">very occasionally, and for reasons that still remain mysterious, saving to mmCIF will lead to one or more of the new residues being duplicated - which can be really confusing at first because the coordinates for the new residue will be identical
to the old. If it happens, this can be fixed by taking advantage of the fact that the "extra" residue is not bonded to anything:</li></ul>
<div class="">m = session.isolde.selected_model</div>
<div class="">from collections import defaultdict</div>
<div class="">rmap = defaultdict(list)</div>
<div class="">for r in m.residues:</div>
<div class=""> sig = (r.chain_id, r.number, r.insertion_code)</div>
<div class=""> rmap[sig].append(r)</div>
<div class="">for rlist in rmap.values():</div>
<div class=""> if len(rlist) > 1:</div>
<div class=""> for r in rlist:</div>
<div class=""> if len(r.neighbors) == 0:</div>
<div class=""> r.delete()</div>
</div>
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</blockquote>
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<blockquote type="cite" class="">
<div class="">On Apr 26, 2021, at 10:12 AM, Tom Goddard <<a href="mailto:goddard@sonic.net" class="">goddard@sonic.net</a>> wrote:</div>
<br class="x_Apple-interchange-newline">
<div class="">
<div class="" style="word-wrap:break-word; line-break:after-white-space">
<div class=""><font color="#0f1419" face="-apple-system, BlinkMacSystemFont, Segoe UI, Roboto, Helvetica, Arial, sans-serif" class=""><span class="" style="font-size:15px; white-space:pre-wrap">Alexis Rohou asked on Twitter</span></font></div>
<div class=""><font color="#0f1419" face="-apple-system, BlinkMacSystemFont, Segoe UI, Roboto, Helvetica, Arial, sans-serif" class=""><span class="" style="font-size:15px; white-space:pre-wrap"><br class="">
</span></font></div>
<span class="x_css-16my406 x_r-qvutc0 x_r-poiln3 x_css-901oao x_r-bcqeeo" style="border:0px solid black; box-sizing:border-box; color:rgb(15,20,25); display:inline; font-stretch:inherit; font-size:15px; line-height:inherit; margin:0px; padding:0px; white-space:pre-wrap; word-wrap:break-word; min-width:0px"><span class="x_Apple-tab-span" style="white-space:pre"></span>In
</span>
<div class="x_r-xoduu5 x_css-1dbjc4n" style="align-items:stretch; border:0px solid black; box-sizing:border-box; display:inline-flex; margin:0px; min-height:0px; min-width:0px; padding:0px; z-index:0; color:rgb(15,20,25); font-size:15px; white-space:pre-wrap">
<span class="x_r-18u37iz" style=""><a dir="ltr" href="https://twitter.com/UCSFChimeraX" role="link" class="x_css-18t94o4 x_css-16my406 x_r-1loqt21 x_r-qvutc0 x_css-4rbku5 x_r-bcqeeo x_css-901oao x_r-poiln3 x_r-1n1174f" style="color:rgb(27,149,224); font-family:inherit; font-size:inherit; font-style:inherit; font-variant-caps:inherit; font-stretch:inherit; line-height:inherit; list-style:none; margin:0px; text-align:inherit; text-decoration:none; border:0px solid black; box-sizing:border-box; display:inline; padding:0px; white-space:inherit; word-wrap:break-word; min-width:0px">@UCSFChimeraX</a></span></div>
<span class="x_css-16my406 x_r-qvutc0 x_r-poiln3 x_css-901oao x_r-bcqeeo" style="border:0px solid black; box-sizing:border-box; color:rgb(15,20,25); display:inline; font-stretch:inherit; font-size:15px; line-height:inherit; margin:0px; padding:0px; white-space:pre-wrap; word-wrap:break-word; min-width:0px">1.1.1
and </span><span class="x_r-18u37iz" style="color:rgb(15,20,25); font-size:15px; white-space:pre-wrap"><a dir="ltr" href="https://twitter.com/hashtag/Isolde?src=hashtag_click" role="link" class="x_css-18t94o4 x_css-16my406 x_r-1loqt21 x_r-qvutc0 x_css-4rbku5 x_r-bcqeeo x_css-901oao x_r-poiln3 x_r-1n1174f" style="color:rgb(27,149,224); font-family:inherit; font-size:inherit; font-style:inherit; font-variant-caps:inherit; font-stretch:inherit; line-height:inherit; list-style:none; margin:0px; text-align:inherit; text-decoration:none; border:0px solid black; box-sizing:border-box; display:inline; padding:0px; white-space:inherit; word-wrap:break-word; min-width:0px">#Isolde</a></span><span class="x_css-16my406 x_r-qvutc0 x_r-poiln3 x_css-901oao x_r-bcqeeo" style="border:0px solid black; box-sizing:border-box; color:rgb(15,20,25); display:inline; font-stretch:inherit; font-size:15px; line-height:inherit; margin:0px; padding:0px; white-space:pre-wrap; word-wrap:break-word; min-width:0px">
by </span>
<div class="x_r-xoduu5 x_css-1dbjc4n" style="align-items:stretch; border:0px solid black; box-sizing:border-box; display:inline-flex; margin:0px; min-height:0px; min-width:0px; padding:0px; z-index:0; color:rgb(15,20,25); font-size:15px; white-space:pre-wrap">
<span class="x_r-18u37iz" style=""><a dir="ltr" href="https://twitter.com/CrollTristan" role="link" class="x_css-18t94o4 x_css-16my406 x_r-1loqt21 x_r-qvutc0 x_css-4rbku5 x_r-bcqeeo x_css-901oao x_r-poiln3 x_r-1n1174f" style="color:rgb(27,149,224); font-family:inherit; font-size:inherit; font-style:inherit; font-variant-caps:inherit; font-stretch:inherit; line-height:inherit; list-style:none; margin:0px; text-align:inherit; text-decoration:none; border:0px solid black; box-sizing:border-box; display:inline; padding:0px; white-space:inherit; word-wrap:break-word; min-width:0px">@CrollTristan</a></span></div>
<span class="x_css-16my406 x_r-qvutc0 x_r-poiln3 x_css-901oao x_r-bcqeeo" style="border:0px solid black; box-sizing:border-box; color:rgb(15,20,25); display:inline; font-stretch:inherit; font-size:15px; line-height:inherit; margin:0px; padding:0px; white-space:pre-wrap; word-wrap:break-word; min-width:0px">is
there an easy way to add aa residues to the end of a chain?</span>
<div class=""><span class="x_css-16my406 x_r-qvutc0 x_r-poiln3 x_css-901oao x_r-bcqeeo" style="border:0px solid black; box-sizing:border-box; color:rgb(15,20,25); display:inline; font-stretch:inherit; font-size:15px; line-height:inherit; margin:0px; padding:0px; white-space:pre-wrap; word-wrap:break-word; min-width:0px"><br class="">
</span></div>
<div class=""><span class="x_css-16my406 x_r-qvutc0 x_r-poiln3 x_css-901oao x_r-bcqeeo" style="border:0px solid black; box-sizing:border-box; display:inline; font-stretch:inherit; line-height:inherit; margin:0px; padding:0px; word-wrap:break-word; min-width:0px; font-size:15px; white-space:pre-wrap"><font color="#0f1419" face="-apple-system, BlinkMacSystemFont, Segoe UI, Roboto, Helvetica, Arial, sans-serif" class=""><a href="https://twitter.com/AlexisRohou/status/1386171500604977152" class=""><span class="x_Apple-tab-span" style="white-space:pre"></span>https://twitter.com/AlexisRohou/status/1386171500604977152</a></font></span></div>
<div class=""><span class="x_css-16my406 x_r-qvutc0 x_r-poiln3 x_css-901oao x_r-bcqeeo" style="border:0px solid black; box-sizing:border-box; display:inline; font-stretch:inherit; line-height:inherit; margin:0px; padding:0px; word-wrap:break-word; min-width:0px; font-size:15px; white-space:pre-wrap"><font color="#0f1419" face="-apple-system, BlinkMacSystemFont, Segoe UI, Roboto, Helvetica, Arial, sans-serif" class=""><br class="">
</font></span></div>
<div class=""><span class="x_css-16my406 x_r-qvutc0 x_r-poiln3 x_css-901oao x_r-bcqeeo" style="border:0px solid black; box-sizing:border-box; display:inline; font-stretch:inherit; line-height:inherit; margin:0px; padding:0px; word-wrap:break-word; min-width:0px; font-size:15px; white-space:pre-wrap"><font color="#0f1419" face="-apple-system, BlinkMacSystemFont, Segoe UI, Roboto, Helvetica, Arial, sans-serif" class="">Elaine
says:</font></span></div>
<div class=""><span class="x_css-16my406 x_r-qvutc0 x_r-poiln3 x_css-901oao x_r-bcqeeo" style="border:0px solid black; box-sizing:border-box; display:inline; font-stretch:inherit; line-height:inherit; margin:0px; padding:0px; word-wrap:break-word; min-width:0px; font-size:15px; white-space:pre-wrap"><font color="#0f1419" face="-apple-system, BlinkMacSystemFont, Segoe UI, Roboto, Helvetica, Arial, sans-serif" class=""><br class="">
</font></span></div>
<div class=""><span class="x_css-16my406 x_r-qvutc0 x_r-poiln3 x_css-901oao x_r-bcqeeo" style="border:0px solid black; box-sizing:border-box; display:inline; font-stretch:inherit; line-height:inherit; margin:0px; padding:0px; word-wrap:break-word; min-width:0px; white-space:pre-wrap; font-size:15px"><span class="" style="white-space:normal">There
isn't an "add amino acid" yet in ChimeraX, only Chimera.... unless ISOLDE can do it (I don't know). So maybe it's an ISOLDE question.</span><br class="" style="white-space:normal">
<br class="" style="white-space:normal">
<span class="" style="white-space:normal">ChimeraX itself has building peptides from scratch but not sticking them on to the end of an existing peptide.</span><br class="" style="white-space:normal">
<br class="" style="white-space:normal">
<span class="" style="white-space:normal">Build Structure, Start Structure: peptide</span><br class="" style="white-space:normal">
<span class="" style="white-space:normal"><</span><a href="https://rbvi.ucsf.edu/chimerax/docs/user/tools/buildstructure.html#start" class="" style="white-space:normal">https://rbvi.ucsf.edu/chimerax/docs/user/tools/buildstructure.html#start</a><span class="" style="white-space:normal">></span><br class="" style="white-space:normal">
<br class="" style="white-space:normal">
<span class="" style="white-space:normal">or command "build start peptide"</span><br class="" style="white-space:normal">
<span class="" style="white-space:normal"><</span><a href="https://rbvi.ucsf.edu/chimerax/docs/user/commands/build.html#start" class="" style="white-space:normal">https://rbvi.ucsf.edu/chimerax/docs/user/commands/build.html#start</a><span class="" style="white-space:normal">></span><br class="" style="white-space:normal">
<br class="" style="white-space:normal">
<span class="" style="white-space:normal">Elaine</span></span></div>
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