<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 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>
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