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<span style="font-family: Arial, Helvetica, sans-serif;">Noor,</span></div>
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<span style="font-family: Arial, Helvetica, sans-serif;">My SEQCROW plugin can technically do this, but Eric and Elaine's methods are probably easier for this type of thing.
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<span style="font-family: Arial, Helvetica, sans-serif;">You have to add the 2MR side chain to the substituent library:</span></div>
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<li><span style="font-family: Arial, Helvetica, sans-serif;">Tools -> AaronTools -> Add to Personal Library</span></li><li><span style="font-family: Arial, Helvetica, sans-serif;">select side chain of a 2MR residue<br>
</span></li><li><span style="font-family: Arial, Helvetica, sans-serif;">give it a name, ignore conformer stuff (it's only used by another program)<br>
</span></li><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;">Before you do this, you might also need to set a directory for SEQCROW to store substituents. This is called 'Personal AaronTools library folder' in the 'SEQCROW' section of ChimeraX's settings.
Then, chain a residue into 2MR with SEQCROW's change substituent tool:</span></div>
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<li><span style="font-family: Arial, Helvetica, sans-serif;">Tools -> Structure Editing -> Change Substituents</span></li><li><span style="font-family: Arial, Helvetica, sans-serif;">select beta carbon on the residue</span></li><li><span style="font-family: Arial, Helvetica, sans-serif;">if you're worried about steric clashing, check 'relax substituent'</span></li><li><span style="font-family: Arial, Helvetica, sans-serif;">enter a new residue name</span></li><li><span style="font-family: Arial, Helvetica, sans-serif;">click 'substitute current selection'</span></li></ol>
<div><span style="font-family: Arial, Helvetica, sans-serif;">The atoms will have the wrong names. I've been playing around with making SEQCROW aware of proximity names, so it'll automatically use CB, CG, CD, etc. If you want to try that, you can get SEQCROW
from the dev branch on GitHub:</span></div>
<div><a href="https://github.com/QChASM/SEQCROW/tree/dev" id="LPlnk"><span style="font-family: Arial, Helvetica, sans-serif;">https://github.com/QChASM/SEQCROW/tree/dev</span></a></div>
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<div><span style="font-family: Arial, Helvetica, sans-serif;">If you scroll down on that page, there's instructions on how to install it. Note that this version only works with recent daily builds of ChimeraX. You'll also have to check 'use distance labels'
on the change substituents tool. <br>
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<div><span style="font-family: Arial, Helvetica, sans-serif;">Best,</span></div>
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<div><span style="font-family: Arial, Helvetica, sans-serif;">Tony</span><br>
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<div id="divRplyFwdMsg" dir="ltr"><font style="font-size:11pt" face="Calibri, sans-serif" color="#000000"><b>From:</b> ChimeraX-users <chimerax-users-bounces@cgl.ucsf.edu> on behalf of anaa2 <anaa2@mrc-mbu.cam.ac.uk><br>
<b>Sent:</b> Tuesday, February 9, 2021 8:29 PM<br>
<b>To:</b> chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu><br>
<b>Subject:</b> [chimerax-users] Replacing regular residues with unusual ones</font>
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<div class="PlainText">[EXTERNAL SENDER - PROCEED CAUTIOUSLY]<br>
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Hi,<br>
<br>
In ChimeraX can a regular residue be replaced with an unusual one using<br>
the swapaa function(pdb code 2MR)?<br>
<br>
Best wishes,<br>
Noor<br>
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