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Hi John,<br>
<br>
just to add to Oleg's reply.. This option will enable three types of
DNA specific restraints:<br>
<br>
- restraints to mimic hydrogen bonds between interacting base pairs;<br>
- planarity restraints for interacting base pairs;<br>
- parallelity restraints will gently enforce stacking bases to be
approximately parallel.<br>
<br>
Pavel<br>
<br>
<div class="moz-cite-prefix">On 9/12/14 3:10 PM, Oleg Sobolev wrote:<br>
</div>
<blockquote
cite="mid:CADd3otHSxCn+hiNEW0A37ionnE8JBL=vUo0B0MHV5hvqHaOtsw@mail.gmail.com"
type="cite">
<div dir="ltr">Dear John,
<div><br>
</div>
<div>Can you please try to use option�</div>
<div>"nucleic_acid_restraints.enabled=True"<br>
</div>
<div>if you run phenix.refine from command line. This is fairly
new option so you should have recent nightly build.�</div>
<div><br>
</div>
<div>Since the option is new, your feedback will be greatly
appreciated. If it does not do the job, I'll be happy to look
at your files (off list) and will try to solve the issue.</div>
<div><br>
</div>
<div>Best regards,</div>
<div>Oleg Sobolev.</div>
</div>
<div class="gmail_extra"><br>
<div class="gmail_quote">On Fri, Sep 12, 2014 at 2:42 PM, John
Lee <span dir="ltr"><<a moz-do-not-send="true"
href="mailto:jklee@umn.edu" target="_blank">jklee@umn.edu</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
<div dir="ltr"><span
style="font-family:arial,sans-serif;font-size:13px">Hi,</span>
<div><span
style="font-family:arial,sans-serif;font-size:13px"><br>
</span></div>
<div><span
style="font-family:arial,sans-serif;font-size:13px">I'm
refining a low resolution structure of a dna-protein
complex (3.7A) �& wondering if someone could help
me with setting restraints in Phenix to maintain the
base-pair planarity of the dna?</span>
<div style="font-family:arial,sans-serif;font-size:13px"><br>
</div>
<div style="font-family:arial,sans-serif;font-size:13px">With
the restraints I have, even with a reference model,
I'm getting 'puckering' of the base-pairs. Although
the h-bonding distances seem to hold over time, I
can't seem to find a way to keep the planarity intact.</div>
<div style="font-family:arial,sans-serif;font-size:13px"><br>
</div>
<div style="font-family:arial,sans-serif;font-size:13px">Thanks
in advance for your help.</div>
<span class="HOEnZb"><font color="#888888">
<div
style="font-family:arial,sans-serif;font-size:13px"><br>
</div>
<div
style="font-family:arial,sans-serif;font-size:13px">-John</div>
</font></span></div>
</div>
<br>
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</blockquote>
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<br>
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<br>
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