<div dir="ltr">Hi Shijun,<div><br></div><div><span style="color:rgb(34,34,34);font-family:arial,sans-serif;font-size:12.8px;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:400;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial;float:none;display:inline">"Threshold degrees for cis-peptide" is only used to determine if Pro is cis or trans. If you increase this value it is expected that some trans Pro will become labeled as cis. It does not influence the refinement directly. If you want to impose restraints and get more trans-Pro after refinement you may try to use apply_all_trans=True option. But the best would be to examine carefully the model and map and rebuild appropriate parts manually.</span><br></div><div><span style="color:rgb(34,34,34);font-family:arial,sans-serif;font-size:12.8px;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:400;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial;float:none;display:inline"><br></span></div><div><span style="color:rgb(34,34,34);font-family:arial,sans-serif;font-size:12.8px;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:400;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial;float:none;display:inline">Best regards,</span></div><div><span style="color:rgb(34,34,34);font-family:arial,sans-serif;font-size:12.8px;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:400;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial;float:none;display:inline">Oleg Sobolev.</span></div></div><div class="gmail_extra"><br><div class="gmail_quote">On Thu, Mar 1, 2018 at 11:35 PM, 张士军 <span dir="ltr"><<a href="mailto:21620150150550@stu.xmu.edu.cn" target="_blank">21620150150550@stu.xmu.edu.cn</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><p>Dear all </p>
<p> I am refining a structure which has cis-Pro and trans-Pro, the tans-Pro is gone when I set the "threshold degrees for cis-peptide " from default 45 to 65, but still has cis-Pro. While no significant change when I set it to 15. My question is how to set in phenix refinement in phenix GUI to clear the Pro residues in cis- or trans- conformations.</p>
<p>Best Regards </p>
<p>shijun </p>
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