<div dir="ltr">Hi,<div><br></div><div>The strategy depends also on the resolution of the data, so if you could tell us that, we can give suggestions. Also the type of data, I guess X-ray diffraction?</div><div><br></div><div>Out of curiosity, how do model quality metrics look like (clashscore, ramachandran, etc) at this point? If you keep coordinates fixed, they won't improve in refinement. </div><div><br></div><div>Best wishes,</div><div><br></div><div>Dorothee</div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Fri, Aug 7, 2020 at 2:52 PM Joey Farrell <<a href="mailto:jpfarrell@uchicago.edu">jpfarrell@uchicago.edu</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div lang="EN-US">
<div class="gmail-m_851941004520673753WordSection1">
<p class="MsoNormal"><span lang="EN-GB" style="font-size:11pt">Hello,<u></u><u></u></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:11pt"><u></u> <u></u></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:11pt">I am trying to design a set of input parameters that I will be passing through the phenix.refine function. The structures<u></u><u></u></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:11pt">that I am working with have already had their X,Y, and Z orthogonal Å coordinates optimised via separate protocol.<u></u><u></u></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:11pt">I am looking for advice on which strategies and parameter values to use with phenix.refine to improve the crystallographic R-factors<u></u><u></u></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:11pt">of such structures while preserving their earlier optimisation in real space.<u></u><u></u></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:11pt"><u></u> <u></u></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:11pt">I have been having some success using “strategy = tls+individual_adp+occupancies” (where tls = “chain A”, tls = “chain B”, etc.) as
<u></u><u></u></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:11pt">well as adjusting the wxu_scale value until R-work and R-free are minimised. Are there other strategies or phenix.refine functionalities
<u></u><u></u></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:11pt">that may also prove helpful with this end in mind? I believe there may be ways to further improve R-work and R-free with this software<u></u><u></u></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:11pt">that I am not yet aware of.<u></u><u></u></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:11pt"><u></u> <u></u></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:11pt">Thank you for your help!<u></u><u></u></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:11pt"><u></u> <u></u></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:11pt">Best,<u></u><u></u></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:11pt">Joey<u></u><u></u></span></p>
</div>
</div>
_______________________________________________<br>
phenixbb mailing list<br>
<a href="mailto:phenixbb@phenix-online.org" target="_blank">phenixbb@phenix-online.org</a><br>
<a href="http://phenix-online.org/mailman/listinfo/phenixbb" rel="noreferrer" target="_blank">http://phenix-online.org/mailman/listinfo/phenixbb</a><br>
Unsubscribe: <a href="mailto:phenixbb-leave@phenix-online.org" target="_blank">phenixbb-leave@phenix-online.org</a></blockquote></div><br clear="all"><div><br></div>-- <br><div dir="ltr" class="gmail_signature"><div dir="ltr"><div>Project Scientist, Molecular Biophysics and Integrated Bioimaging<br></div><div>Lawrence Berkeley National Laboratory</div><div>1 Cyclotron Road, M/S 33R0345</div><div>Berkeley, CA 94720</div><div>Tel: (510) 486-5709</div><div>Fax: (510) 486-5909</div><div>Web: <a href="https://phenix-online.org/" style="color:rgb(17,85,204)" target="_blank">https://phenix-online.org</a></div></div></div>