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<span style="font-size:12pt"><span style="font-family:Arial, Helvetica, sans-serif">Steven,</span></span>
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<div style="font-size:12pt"><span style="font-family:Arial, Helvetica, sans-serif">The `bond` command is available in the ChimeraX daily build.</span><span style="font-family:Arial, Helvetica, sans-serif"> They've also added this capability to the 'Build Structure'
tool in the daily build.</span></div>
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<div style="font-size:12pt"><span style="font-family:Arial, Helvetica, sans-serif">I can't speak to why you're getting an error in Chimera - maybe Chimera is still interpreting the input as two separate models? Based on your example command, one of the molecules
(#0.1) is a child of the other (#0), which would technically be a separate model. I don't work with PDB files too often, but look out for MODEL/ENDMDL in your file. If those are present, they'll define separate models.
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<div style="font-size:12pt"><span style="font-family:Arial, Helvetica, sans-serif">If you're bent on doing this in ChimeraX 1.1, my SEQCROW bundle has a bond editor tool (Tools -> Structure Editing -> Bond Editor). You just select the atoms you want bonded
and click 'draw bonds between selected atoms'. With the </span><code><span style="font-family:Arial, Helvetica, sans-serif">bond</span></code><span style="font-family:Arial, Helvetica, sans-serif"> command imminent, I didn't bother adding my own command.
It just made sense to have that capability on that tool.</span><span style="font-family:Arial, Helvetica, sans-serif"> The atoms will still need to be on the same model.
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<div style="font-size:12pt"><span style="font-family:Arial, Helvetica, sans-serif">Depending on how much you're adding, you might also be able to use SEQCROW to attach monosaccharides to residues or each other as 'substituents'.
<span>SEQCROW cannot put an added substituent in its own residue (yet). I can imagine this limitation might make using SEQCROW for this pretty awkward.</span> You'll also have to add your saccharides to the list of substituents SEQCROW knows about. The process
for this would look something like:</span></div>
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<li><span style="font-family:Arial, Helvetica, sans-serif">open/build a saccharide</span></li><li><span style="font-family:Arial, Helvetica, sans-serif">open Tools -> AaronTools -> Add to Personal Library</span><br>
<span style="font-family:Arial, Helvetica, sans-serif"></span></li><li><span style="font-family:Arial, Helvetica, sans-serif">select everything except the OH of
</span><span style="font-family:Arial, Helvetica, sans-serif">whatever is going to be linked to another residue<br>
</span></li><li><span style="font-family:Arial, Helvetica, sans-serif">enter a name on the tool</span></li><ol style="list-style-type:lower-alpha">
<li><span style="font-family:Arial, Helvetica, sans-serif">ignore conformer stuff, it's only used by a different program</span></li></ol>
<li><span style="font-family:Arial, Helvetica, sans-serif">click 'add current selection to library'</span></li></ol>
<div><span style="font-family:Arial, Helvetica, sans-serif">To add this substituent to a SER residue, for example:</span></div>
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<li><span style="font-family:Arial, Helvetica, sans-serif">select the SER's H</span><span style="font-family:Arial, Helvetica, sans-serif"> on the hydroxyl group</span><span><br>
</span></li><li><span style="font-family:Arial, Helvetica, sans-serif">add the saccharide using the command:</span><span><br>
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<li><span style="font-family:Arial, Helvetica, sans-serif">run `substitute sel substituent <your saccharide's name> [other options]`</span></li></ol>
<li><span style="font-family:Arial, Helvetica, sans-serif">or using the tool (Tools -> Structure Editing -> Change Substituents</span><span></span></li><ol style="list-style-type:lower-alpha">
<li><span style="font-family:Arial, Helvetica, sans-serif">enter your saccharide substituent's name on the 'Change Substituents' tool</span></li><li><span style="font-family:Arial, Helvetica, sans-serif">check/uncheck any other options</span></li><li><span style="font-family:Arial, Helvetica, sans-serif">click 'substitute current selection'</span></li></ol>
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<div style="font-size:12pt"><span style="font-family:Arial, Helvetica, sans-serif">Best,</span></div>
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<div style="font-size:12pt"><span style="font-family:Arial, Helvetica, sans-serif">Tony</span><br>
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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 Steven Truong <sdt45@cam.ac.uk><br>
<b>Sent:</b> Wednesday, March 24, 2021 11:55 PM<br>
<b>To:</b> ChimeraX Users Help <chimerax-users@cgl.ucsf.edu><br>
<b>Subject:</b> [chimerax-users] Making New Bonds between two molecules in ChimeraX</font>
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<div class="" style="word-wrap:break-word; line-break:after-white-space"><font color="BA0C2F">[EXTERNAL SENDER - PROCEED CAUTIOUSLY]</font><br>
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<div>Dear ChimeraX Admins and Elaine,
<div class=""><br class="">
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<div class="">Hello, I was wondering if ChimeraX now has a “bond” command. I saw an inquiry like this in the mailing list archives (<a href="https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2020-April/001029.html" class="">https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2020-April/001029.html</a>),
but it seems like bond is still not an official functionality. When I switched over to Chimera and tried using the “bond” command, I get the error “Cannot form covalent bond joining two molecules,” even though I’ve saved all of the molecules into one PDB
file. Is it because Chimera still sees these two sub-models as un-joinable? My command looks something like: "<b class="">bond #0:61.A@ND2 #0.1:1222.X@C1</b>”.</div>
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<div class="">For further context, we are trying to script orienting/bonding residues to glycans. We’ve been able to figure out aligning and orienting the glycans quite well with the scripts alone (.py scripts), but it seems like we’ll have to find another
way to make bonds between the proteins/glycans. Do you have any suggestions? Ideally, we’d also keep as much of the pipeline in ChimeraX, but if it’s necessary, we could further pursue the ChimeraX+Chimera route.</div>
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<div class="">Thank you for your help!</div>
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<div class="">Many thanks,</div>
<div class="">Steven Truong</div>
<div class=""><a href="mailto:sdt45@cam.ac.uk" class="">sdt45@cam.ac.uk</a></div>
<div class="">Cambridge University</div>
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