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<p style="margin-top:0;margin-bottom:0">Thanks, Pavel!</p>
<p style="margin-top:0;margin-bottom:0">I'll let you know how it goes.</p>
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<p style="margin-top:0;margin-bottom:0">Cheers,</p>
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<p style="margin-top:0;margin-bottom:0">Jens<br>
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<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>From:</b> Pavel Afonine <pafonine@lbl.gov><br>
<b>Sent:</b> Monday, January 28, 2019 4:58:22 PM<br>
<b>To:</b> Kaiser, Jens T.; phenixbb@phenix-online.org<br>
<b>Subject:</b> Re: [phenixbb] unrestrained refinement</font>
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<div style="background-color:#FFFFFF">Hi Jens,<br>
<br>
I re-enabled this functionality so that phenix.refine can continue if there is an unknown entity found in input model file.<br>
To run unrestrained refinement you can simply use "wc=0" which sets zero weight on geometry restraints (this is unrelated to above).<br>
<br>
A next available nightly build should have it:<br>
<br>
<a class="x_moz-txt-link-freetext" href="https://www.phenix-online.org/download/nightly_builds.cgi?show_all=1">https://www.phenix-online.org/download/nightly_builds.cgi?show_all=1</a><br>
<br>
Let me know of any issues!<br>
<br>
Good luck,<br>
Pavel<br>
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<div class="x_moz-cite-prefix">On 12/18/18 14:58, Kaiser, Jens T. wrote:<br>
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<p style="margin-top:0; margin-bottom:0">Hi!</p>
<p style="margin-top:0; margin-bottom:0"> I'm trying to do unrestrained refinement of a small molecule in phenix. I have done this many years ago, but it seems whatever I try, phenix.refine now complains about missing nonbonded energy type for all atoms.</p>
<p style="margin-top:0; margin-bottom:0"> The pdb file I supply has the following format (just one line)</p>
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HETATM 33 C81 UNK 1 3.117 14.425 18.765 1.00 1.45 C </span><br>
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<p style="margin-top:0; margin-bottom:0"> <br>
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<p style="margin-top:0; margin-bottom:0">I tried unchecking all references to geometry restraints in the GUI, setting wc and wu to 0<br>
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<p style="margin-top:0; margin-bottom:0"> I also started from a default .eff file and set all references to restraints to either True of False (depending what they said).</p>
<p style="margin-top:0; margin-bottom:0"> I also tried the line from the phenix.refine documentation:</p>
<p style="margin-top:0; margin-bottom:0"><span>phenix.refine ../cif_in/mkt_a.ent ../data/181119/proc/137C3/XDS_17000.HKL strategy=individual_sites wc=0 refinement.input.symmetry_safety_check=warning refinement.input.xray_data.r_free_flags.generate=True</span></p>
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<p style="margin-top:0; margin-bottom:0"> I'm using phenix v 1.14-3260 from an sbgrid environment.</p>
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<p style="margin-top:0; margin-bottom:0"> Any pointers welcome.</p>
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<p style="margin-top:0; margin-bottom:0">Cheers,</p>
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<p style="margin-top:0; margin-bottom:0">Jens<br>
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