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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="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>
<br>
<div class="moz-cite-prefix">On 12/18/18 14:58, Kaiser, Jens T.
wrote:<br>
</div>
<blockquote type="cite"
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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>
<div><span style="font-family: "Courier
New",monospace;"><br>
HETATM�� 33� C81 UNK���� 1������ 3.117� 14.425� 18.765�
1.00� 1.45���������� C �</span><br>
</div>
<p style="margin-top:0;margin-bottom:0">� <br>
</p>
<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>
</p>
<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>
<p style="margin-top:0;margin-bottom:0"><br>
</p>
<p style="margin-top:0;margin-bottom:0">�I'm using phenix v
1.14-3260 from an sbgrid environment.</p>
<p style="margin-top:0;margin-bottom:0"><br>
</p>
<p style="margin-top:0;margin-bottom:0">� Any pointers welcome.</p>
<p style="margin-top:0;margin-bottom:0"><br>
</p>
<p style="margin-top:0;margin-bottom:0">Cheers,</p>
<p style="margin-top:0;margin-bottom:0"><br>
</p>
<p style="margin-top:0;margin-bottom:0">Jens<br>
</p>
</div>
</blockquote>
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