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Oops! My bad - was responding on the move, and forgetting my own implementation. You're right, the "isolde restrain distances" command works on a per-residue basis, so sidechain atoms will be included regardless. On the other hand, the "isolde release distances"
command works per-atom, so after the restrain command you can selectively release the sidechain restraints with:</div>
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isolde release distances #1&sideonly</div>
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<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>From:</b> Guido Hansen <hansen@biochem.uni-luebeck.de><br>
<b>Sent:</b> 15 March 2022 16:20<br>
<b>To:</b> Tristan Croll <tic20@cam.ac.uk><br>
<b>Cc:</b> chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu><br>
<b>Subject:</b> Re: [chimerax-users] ISOLDE and secondary structure restraints</font>
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<p>Thanks for your suggestions. However, I think that when applying distance restraints using the command below also distances of mainchain atoms of secondary structure elements to nearby sidechain atoms get restrainted.
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<p>isolde restrain distances #1&(helix|strand)&backbone</p>
<p><img alt="" data-outlook-trace="F:1|T:1" src="cid:part1.09p0uiHA.41fj6uxZ@biochem.uni-luebeck.de"></p>
<p> What you get when using the gui is something like that:<br>
</p>
<p><img alt="" data-outlook-trace="F:1|T:1" src="cid:part2.0mNP8JTc.JBo6Z60y@biochem.uni-luebeck.de"></p>
<p>-- Guido<br>
</p>
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<div class="x_moz-cite-prefix">Am 13.03.2022 um 16:07 schrieb Tristan Croll:<br>
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<div dir="ltr">Not the hard-coded helix and beta-sheet restraints, I’m afraid. But you can get a very similar (probably better, TBH) result with something like:</div>
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<div dir="ltr">isolde restrain distances #1&(helix|strand)&backbone</div>
<div dir="ltr">isolde restrain torsions #1&(helix|strand) sidechain false</div>
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<div dir="ltr">The advantage of those is that (a) they’ll work a bit better when the true conformation isn’t *perfect* helix or strand, and (b) they have a lot more flexibility in terms of your ability to fine-tune their behaviour (for models fetched from the
Alphafold DB, try adding the argument “adjustForConfidence true” to automatically take the pLDDT and PAE values into account).</div>
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<div dir="ltr">— Tristan </div>
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On 13 Mar 2022, at 14:42, Guido Hansen via ChimeraX-users <<a href="mailto:chimerax-users@cgl.ucsf.edu" class="x_moz-txt-link-freetext">chimerax-users@cgl.ucsf.edu</a>> wrote:<br>
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<p>Hi all,</p>
<p>I just started model building in cryoEM maps and get great results using ISOLDE on AlphaFold2-derived initial models. I have a question which is mainly directed to Tristan I guess:</p>
<p>Is is possible to use the command line/script to apply secondary structure restraints in ISOLDE? I would like to restrain the initial secondary structure assignment from Alphafold especially at resolution worse than 3.5 A. At the moment I select each and
every residue range assigned to helix, parallel or antiparallel beta-strand one after the other and turn on the corresponding restrains in the ISOLDE GUI. Is there a better way via command line of script?<br>
<br>
</p>
<p>Cheers,<br>
Guido</p>
<p>-- </p>
<p><span style="color:#14738c"><strong>PD Dr. Guido Hansen<br>
</strong></span><span style="color:#14738c">Group Leader</span></p>
<div class="x_moz-signature">
<div class="x_moz-signature"><img alt="Uni-Lübeck" width="187" height="54" src="http://media.biochem.uni-luebeck.de/export/logo/Signaturbild.png">
<span><span style="color:#14738c"></span></span>
<p class="x_MsoNormal"><span style="color:#14738c"><strong>Universität zu Lübeck</strong><br>
<strong>Institut für Biochemie</strong></span></p>
<span><span style="color:#14738c"></span></span>
<p class="x_MsoNormal"><span style="color:#14738c">Tel +49 451 3101 3122<br>
</span><span style="color:#14738c">Fax +49 451 3101 3104<br>
E-Mail <a class="x_moz-txt-link-abbreviated x_moz-txt-link-freetext" href="mailto:hansen@biochem.uni-luebeck.de">
hansen@biochem.uni-luebeck.de</a><br>
<a class="x_moz-txt-link-abbreviated" href="http://www.biochem.uni-luebeck.de">www.biochem.uni-luebeck.de</a><br>
</span></p>
<span><span style="color:#14738c"></span></span>
<p class="x_MsoNormal"><span style="color:#14738c">Ratzeburger Allee 160<br>
</span><span style="color:#145a6e"><span style="color:#14738c">23562 Lübeck </span>
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<div dir="ltr"><span>_______________________________________________</span><br>
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<div class="x_moz-signature">-- <br>
<br>
<div class="x_moz-signature"><font size="-1" color="#14738c"><b>PD Dr. Guido Hansen</b></font><font size="-1"><br>
</font>
<div class="x_moz-signature"><font size="-1" color="#14738c">Group Leader<br>
<br>
</font><font size="-1"></font>
<div class="x_moz-signature"><font size="-1" color="#14738c"></font><font size="-1"></font><img alt="Uni-Lübeck" width="187" height="54" src="http://media.biochem.uni-luebeck.de/export/logo/Signaturbild.png">
<font size="-1"><font color="#14738c"></font></font>
<p class="x_MsoNormal"><font size="-1" color="#14738c"><b>Universität zu Lübeck</b><br>
<b>Institut für Biochemie</b></font></p>
<font size="-1"><font color="#14738c"></font></font>
<p class="x_MsoNormal"><font size="-1" color="#14738c">Tel +49 451 3101 3122<br>
</font><font size="-1" color="#14738c">Fax +49 451 3101 3104<br>
E-Mail <a class="x_moz-txt-link-abbreviated x_moz-txt-link-freetext" href="mailto:hansen@biochem.uni-luebeck.de">
hansen@biochem.uni-luebeck.de</a><br>
<a class="x_moz-txt-link-abbreviated" href="http://www.biochem.uni-luebeck.de">www.biochem.uni-luebeck.de</a><br>
</font></p>
<font size="-1"><font color="#14738c"></font></font>
<p class="x_MsoNormal"><font size="-1" color="#14738c">Ratzeburger Allee 160<br>
</font><span style="color:#145A6E"><font size="-1" color="#14738c">23562 Lübeck </font>
<font size="-1"><br>
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