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Hi Jens,<br>
<br>
let us know if you manage to make it work. If not I can change
phenix.refine to not care about restraints at all if unrestrained
refinement is requested (currently it still constructs restraints no
matter what just to report geometry statistics such as bond/angle
rmsd etc; but this can be changed.). This may take me a day to do.<br>
<br>
Pavel<br>
<br>
<div class="moz-cite-prefix">On 12/18/18 18:54, Nigel Moriarty
wrote:<br>
</div>
<blockquote type="cite"
cite="mid:CANkP=2eMJVO89g4X4o+kdZ1EAA3vT0KQMAohS7Hrq9eWc2ds+g@mail.gmail.com">
<meta http-equiv="content-type" content="text/html; charset=utf-8">
<div dir="ltr">Jena
<div><br>
</div>
<div>UNK is, surprisingly, not a complete unknown. It is a
general amino acid used for unknown amino acids. Your model
contains a C81 atom which is not in the UNK restraints.</div>
<div><br>
</div>
<div>However, regardless of the existence of UNK or not, you
need to provide the refinement with a restraints file whether
automatically or user supplied. It is needed for the atom
types and non-bonded interactions so it should contain an atom
loop and a bond loop.</div>
<div><br clear="all">
<div>
<div dir="ltr" class="gmail_signature"
data-smartmail="gmail_signature">
<div dir="ltr">
<div>
<div dir="ltr">
<div dir="ltr">Cheers
<div><br>
</div>
<div>Nigel
<div><br>
</div>
<div>---</div>
<div>Nigel W. Moriarty<br>
Building 33R0349, Molecular Biophysics and
Integrated Bioimaging</div>
<div>Lawrence Berkeley National Laboratory<br>
Berkeley, CA 94720-8235<br>
Phone : 510-486-5709 Email :
<a class="moz-txt-link-abbreviated" href="mailto:NWMoriarty@LBL.gov">NWMoriarty@LBL.gov</a><br>
Fax : 510-486-5909 Web : <a
href="http://CCI.LBL.gov" target="_blank"
moz-do-not-send="true">CCI.LBL.gov</a></div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
<br>
</div>
</div>
<br>
<div class="gmail_quote">
<div dir="ltr">On Tue, Dec 18, 2018 at 3:01 PM Kaiser, Jens T.
<<a href="mailto:kaiser@caltech.edu" moz-do-not-send="true">kaiser@caltech.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 dir="ltr">
<div id="gmail-m_-8474023673322612364divtagdefaultwrapper"
style="font-size:12pt;color:rgb(0,0,0);font-family:Calibri,Helvetica,sans-serif"
dir="ltr">
<p style="margin-top:0px;margin-bottom:0px">Hi!</p>
<p style="margin-top:0px;margin-bottom:0px"> 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:0px;margin-bottom:0px"> 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:0px;margin-bottom:0px"> <br>
</p>
<p style="margin-top:0px;margin-bottom:0px">I tried
unchecking all references to geometry restraints in the
GUI, setting wc and wu to 0<br>
</p>
<p style="margin-top:0px;margin-bottom:0px"> 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:0px;margin-bottom:0px"> I also tried
the line from the phenix.refine documentation:</p>
<p style="margin-top:0px;margin-bottom:0px"><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:0px;margin-bottom:0px"><br>
</p>
<p style="margin-top:0px;margin-bottom:0px"> I'm using
phenix v 1.14-3260 from an sbgrid environment.</p>
<p style="margin-top:0px;margin-bottom:0px"><br>
</p>
<p style="margin-top:0px;margin-bottom:0px"> Any pointers
welcome.</p>
<p style="margin-top:0px;margin-bottom:0px"><br>
</p>
<p style="margin-top:0px;margin-bottom:0px">Cheers,</p>
<p style="margin-top:0px;margin-bottom:0px"><br>
</p>
<p style="margin-top:0px;margin-bottom:0px">Jens<br>
</p>
</div>
</div>
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