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<div class="moz-cite-prefix">Hi Nigel,</div>
<div class="moz-cite-prefix"><br>
</div>
<div class="moz-cite-prefix">yes, I did follow the instructions and
afitt is running. Path is set. It should be properly installed.</div>
<div class="moz-cite-prefix"> The afitt gui works to write inputs
for refmac and calls also refmac. The afitt gui prepares also the
input files for phenix but phenix.refine fails then with the error
below. <br>
</div>
<div class="moz-cite-prefix"><br>
</div>
<div class="moz-cite-prefix">"Sorry: Unknown command line parameter
definition: use_afitt = True"</div>
<div class="moz-cite-prefix"><br>
</div>
<div class="moz-cite-prefix">Same in the command line or if I try
afitt.run_tests. It looks as if phenix does not recognize the
keyword use_afitt=True.</div>
<div class="moz-cite-prefix"><br>
</div>
<div class="moz-cite-prefix"><br>
</div>
<div class="moz-cite-prefix">PS: There must be also a typo on the
instructions page: <br>
</div>
<div class="moz-cite-prefix">The example on the page for the command
is :<br>
<pre class="literal-block">phenix.refine mymodel.pdb mymodel.mtz myligand.cif use_afitt=True
afitt.ligand_file=myligand.cif afitt.ligand_names=UNL,BCL
</pre>
</div>
<blockquote type="cite"
cite="mid:CANkP=2cDXkk9G551MqZtxhp2HNVAx4t69FrRT-XhdotuhGVvPQ@mail.gmail.com">
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<p>Below in the list of required keywords it is <br>
</p>
<p> "afitt.ligand_file_name" <br>
</p>
<p>Anyhow this is not the cause for the error. <br>
</p>
<p>I guess I overlook some detail. I will test some older versions
and the latest builds. <br>
</p>
<p>I wish you have some relaxing days! Season Greetings and best
wishes, Guenter</p>
<p>PPS there is absolutely no hurry for this,cheers<br>
</p>
<p><br>
</p>
<blockquote type="cite"
cite="mid:CANkP=2cDXkk9G551MqZtxhp2HNVAx4t69FrRT-XhdotuhGVvPQ@mail.gmail.com">
<div dir="ltr">
<div dir="ltr">AFITT is still supported and tested nightly.
<div><br>
</div>
<div>Did you follow the instructions here?</div>
<div><br>
</div>
<div><a
href="https://www.phenix-online.org/documentation/reference/afitt.html"
moz-do-not-send="true">https://www.phenix-online.org/documentation/reference/afitt.html</a><br>
</div>
<div><br clear="all">
<div>
<div dir="ltr" class="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>
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<br>
<div class="gmail_quote">
<div dir="ltr">On Fri, Dec 21, 2018 at 2:55 AM Guenter Fritz
<<a href="mailto:guenter.fritz.phenix.ccp4@gmail.com"
moz-do-not-send="true">guenter.fritz.phenix.ccp4@gmail.com</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">Dear
phenix developers,<br>
<br>
I am trying to run phenix.refine with afitt (phenix 1.14 3260,
afitt <br>
2.4.1.2). However, I receive the an error:<br>
<br>
"Sorry: Unknown command line parameter definition: use_afitt =
True"<br>
<br>
This I get on my mac or on my linux box. Is support for afitt
discontinued?<br>
<br>
Any help is appreciated. Thanks and best regards,<br>
<br>
Guenter<br>
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