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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. <br>
</p>
<p>isolde restrain distances #1&(helix|strand)&backbone</p>
<p><img src="cid:part1.09p0uiHA.41fj6uxZ@biochem.uni-luebeck.de"
alt=""></p>
<p> What you get when using the gui is something like that:<br>
</p>
<p><img src="cid:part2.0mNP8JTc.JBo6Z60y@biochem.uni-luebeck.de"
alt=""></p>
<p>-- Guido<br>
</p>
<p><br>
</p>
<p><br>
</p>
<div class="moz-cite-prefix">Am 13.03.2022 um 16:07 schrieb Tristan
Croll:<br>
</div>
<blockquote type="cite"
cite="mid:FB5A6A5D-8204-4CFE-8EA2-B3919A0ABAFC@cam.ac.uk">
<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
<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"
moz-do-not-send="true" class="moz-txt-link-freetext">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>
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<div class="moz-signature">-- <br>
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<title>Re: email signature</title>
<br>
<div class="moz-signature"><font size="-1" color="#14738c"><b>PD
Dr. Guido Hansen</b></font><font size="-1"><br>
</font>
<div class="moz-signature"><font size="-1" color="#14738c">
Group Leader<br>
<br>
</font><font size="-1"> </font>
<div class="moz-signature"><font size="-1" color="#14738c"> </font>
<font size="-1"> </font> <img moz-do-not-send="true"
alt="Uni-Lübeck"
src="http://media.biochem.uni-luebeck.de/export/logo/Signaturbild.png"
width="187" height="54"> <font size="-1"> <font
color="#14738c"> </font> </font>
<p class="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="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="moz-txt-link-abbreviated
moz-txt-link-freetext"
href="mailto:hansen@biochem.uni-luebeck.de"
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