<html>
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8">
</head>
<body dir="auto">
<div dir="ltr"></div>
<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>
<div dir="ltr"><br>
</div>
<div dir="ltr">isolde restrain distances #1&(helix|strand)&backbone</div>
<div dir="ltr">isolde restrain torsions #1&(helix|strand) sidechain false</div>
<div dir="ltr"><br>
</div>
<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>
<div dir="ltr"><br>
</div>
<div dir="ltr">— Tristan </div>
<div dir="ltr"><br>
On 13 Mar 2022, at 14:42, Guido Hansen via ChimeraX-users <<a href="mailto:chimerax-users@cgl.ucsf.edu">chimerax-users@cgl.ucsf.edu</a>> wrote:<br>
<br>
</div>
<blockquote type="cite">
<div dir="ltr">
<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="moz-signature">
<div class="moz-signature"><img src="http://media.biochem.uni-luebeck.de/export/logo/Signaturbild.png" alt="Uni-Lübeck" width="187" height="54">
<span><span style="color: #14738c;"></span></span>
<p class="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="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="moz-txt-link-abbreviated" href="mailto:hansen@biochem.uni-luebeck.de">
hansen@biochem.uni-luebeck.de</a><br>
<a class="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="MsoNormal"><span style="color: #14738c;">Ratzeburger Allee 160<br>
</span><span style="color: #145a6e; mso-fareast-language: DE;"><span style="color: #14738c;">23562 Lübeck
</span><span><br>
</span><br>
</span></p>
</div>
</div>
</div>
</blockquote>
<blockquote type="cite">
<div dir="ltr"><span>_______________________________________________</span><br>
<span>ChimeraX-users mailing list</span><br>
<span><a href="mailto:ChimeraX-users@cgl.ucsf.edu">ChimeraX-users@cgl.ucsf.edu</a></span><br>
<span>Manage subscription:</span><br>
<span><a href="https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users">https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users</a></span><br>
</div>
</blockquote>
</body>
</html>