<div dir="ltr">Glad to hear it! <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 : NWMoriarty@LBL.gov<br>Fax : 510-486-5909 Web : <a href="http://CCI.LBL.gov" target="_blank">CCI.LBL.gov</a></div></div></div></div></div></div></div></div><br></div></div><br><div class="gmail_quote"><div dir="ltr">On Sun, Dec 30, 2018 at 2:25 AM Guenter Fritz <<a href="mailto:guenter.fritz.phenix.ccp4@gmail.com">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">
<div bgcolor="#FFFFFF">
<div class="gmail-m_-7667865525518494306moz-cite-prefix">Hi Nigel,</div>
<div class="gmail-m_-7667865525518494306moz-cite-prefix"><br>
</div>
<div class="gmail-m_-7667865525518494306moz-cite-prefix">some days off do wonders :). <br>
</div>
<div class="gmail-m_-7667865525518494306moz-cite-prefix">I made a mistake and had a conflict in
setting the variables. I had in my .bash_profile</div>
<div class="gmail-m_-7667865525518494306moz-cite-prefix">export OE_EXE='/usr/local/bin/flynn'</div>
<div class="gmail-m_-7667865525518494306moz-cite-prefix"><br>
</div>
<div class="gmail-m_-7667865525518494306moz-cite-prefix">but in the .openeyerc.bash I had it
again but with an additional "e" in "usr"<br>
</div>
<div class="gmail-m_-7667865525518494306moz-cite-prefix">export OE_EXE='/user/local/bin/flynn'</div>
<div class="gmail-m_-7667865525518494306moz-cite-prefix"><br>
</div>
<div class="gmail-m_-7667865525518494306moz-cite-prefix">This messed things up. <br>
</div>
<div class="gmail-m_-7667865525518494306moz-cite-prefix"><br>
</div>
<div class="gmail-m_-7667865525518494306moz-cite-prefix">Thanks a lot and already now Happy New
Year!<br>
</div>
<div class="gmail-m_-7667865525518494306moz-cite-prefix">Guenter<br>
</div>
<blockquote type="cite">
<div dir="ltr">
<div dir="ltr">What is the value of $<span style="color:rgb(0,0,0);font-family:Verdana,Helvetica,Arial,sans-serif;font-size:14.4px">OE_EXE?</span></div>
<div dir="ltr"><span style="color:rgb(0,0,0);font-family:Verdana,Helvetica,Arial,sans-serif;font-size:14.4px"><br>
</span></div>
<div><font face="Verdana, Helvetica, Arial, sans-serif" color="#000000"><span style="font-size:14.4px">BTW. I don't
think it's a typo as PHIL will match a keyword if the
search finds a unique match which I believe is the case
this time.</span></font></div>
<div dir="ltr"><br>
</div>
<div dir="ltr">
<div>
<div>
<div dir="ltr" class="gmail-m_-7667865525518494306gmail_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="gmail-m_-7667865525518494306moz-txt-link-abbreviated" href="mailto:NWMoriarty@LBL.gov" target="_blank">NWMoriarty@LBL.gov</a><br>
Fax : 510-486-5909 Web : <a href="http://CCI.LBL.gov" target="_blank">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 25, 2018 at 3:13 PM Guenter Fritz
<<a href="mailto:guenter.fritz.phenix.ccp4@gmail.com" target="_blank">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">
<div bgcolor="#FFFFFF">
<div class="gmail-m_-7667865525518494306gmail-m_-8857844668402906691moz-cite-prefix">Hi
Nigel,</div>
<div class="gmail-m_-7667865525518494306gmail-m_-8857844668402906691moz-cite-prefix"><br>
</div>
<div class="gmail-m_-7667865525518494306gmail-m_-8857844668402906691moz-cite-prefix">yes,
I did follow the instructions and afitt is running. Path
is set. It should be properly installed.</div>
<div class="gmail-m_-7667865525518494306gmail-m_-8857844668402906691moz-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="gmail-m_-7667865525518494306gmail-m_-8857844668402906691moz-cite-prefix"><br>
</div>
<div class="gmail-m_-7667865525518494306gmail-m_-8857844668402906691moz-cite-prefix">"Sorry:
Unknown command line parameter definition: use_afitt =
True"</div>
<div class="gmail-m_-7667865525518494306gmail-m_-8857844668402906691moz-cite-prefix"><br>
</div>
<div class="gmail-m_-7667865525518494306gmail-m_-8857844668402906691moz-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="gmail-m_-7667865525518494306gmail-m_-8857844668402906691moz-cite-prefix"><br>
</div>
<div class="gmail-m_-7667865525518494306gmail-m_-8857844668402906691moz-cite-prefix"><br>
</div>
<div class="gmail-m_-7667865525518494306gmail-m_-8857844668402906691moz-cite-prefix">PS:
There must be also a typo on the instructions page: <br>
</div>
<div class="gmail-m_-7667865525518494306gmail-m_-8857844668402906691moz-cite-prefix">The
example on the page for the command is :<br>
<pre class="gmail-m_-7667865525518494306gmail-m_-8857844668402906691literal-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"> </blockquote>
<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">
<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" target="_blank">https://www.phenix-online.org/documentation/reference/afitt.html</a><br>
</div>
<div><br clear="all">
<div>
<div dir="ltr" class="gmail-m_-7667865525518494306gmail-m_-8857844668402906691gmail_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="gmail-m_-7667865525518494306gmail-m_-8857844668402906691moz-txt-link-abbreviated" href="mailto:NWMoriarty@LBL.gov" target="_blank">NWMoriarty@LBL.gov</a><br>
Fax : 510-486-5909 Web :
<a href="http://CCI.LBL.gov" target="_blank">CCI.LBL.gov</a></div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
<br>
</div>
</div>
</div>
<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" target="_blank">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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</blockquote>
</div>
</blockquote>
<p><br>
</p>
</div>
</blockquote>
</div>
</div>
</blockquote>
<p><br>
</p>
</div>
</blockquote></div>