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    <div class="moz-cite-prefix">Hi Nigel,</div>
    <div class="moz-cite-prefix"><br>
    </div>
    <div class="moz-cite-prefix">some days off do wonders :). <br>
    </div>
    <div class="moz-cite-prefix">I made a mistake and had a  conflict in
      setting the variables. I had in my .bash_profile</div>
    <div class="moz-cite-prefix">export OE_EXE='/usr/local/bin/flynn'</div>
    <div class="moz-cite-prefix"><br>
    </div>
    <div class="moz-cite-prefix">but in the .openeyerc.bash I had it
      again but with an additional "e" in "usr"<br>
    </div>
    <div class="moz-cite-prefix">export OE_EXE='/user/local/bin/flynn'</div>
    <div class="moz-cite-prefix"><br>
    </div>
    <div class="moz-cite-prefix">This messed things up. <br>
    </div>
    <div class="moz-cite-prefix"><br>
    </div>
    <div class="moz-cite-prefix">Thanks a lot and already now Happy New
      Year!<br>
    </div>
    <div class="moz-cite-prefix">Guenter<br>
    </div>
    <blockquote type="cite"
cite="mid:CANkP=2dFb1-TC8-hiFQY4bSuKSVHOF=gQ565q3p5bs8nM6VknQ@mail.gmail.com">
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        <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>
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                <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>
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        <div class="gmail_quote">
          <div dir="ltr">On Tue, Dec 25, 2018 at 3:13 PM Guenter Fritz
            &lt;<a href="mailto:guenter.fritz.phenix.ccp4@gmail.com"
              moz-do-not-send="true">guenter.fritz.phenix.ccp4@gmail.com</a>&gt;
            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">
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              <div class="gmail-m_-8857844668402906691moz-cite-prefix">Hi
                Nigel,</div>
              <div class="gmail-m_-8857844668402906691moz-cite-prefix"><br>
              </div>
              <div class="gmail-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_-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_-8857844668402906691moz-cite-prefix"><br>
              </div>
              <div class="gmail-m_-8857844668402906691moz-cite-prefix">"Sorry:
                Unknown command line parameter definition: use_afitt =
                True"</div>
              <div class="gmail-m_-8857844668402906691moz-cite-prefix"><br>
              </div>
              <div class="gmail-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_-8857844668402906691moz-cite-prefix"><br>
              </div>
              <div class="gmail-m_-8857844668402906691moz-cite-prefix"><br>
              </div>
              <div class="gmail-m_-8857844668402906691moz-cite-prefix">PS:
                There must be also a typo on the instructions page: <br>
              </div>
              <div class="gmail-m_-8857844668402906691moz-cite-prefix">The
                example on the page for the command is :<br>
                <pre class="gmail-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" moz-do-not-send="true">https://www.phenix-online.org/documentation/reference/afitt.html</a><br>
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                          class="gmail-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_-8857844668402906691moz-txt-link-abbreviated"
                                        href="mailto:NWMoriarty@LBL.gov"
                                        target="_blank"
                                        moz-do-not-send="true">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 &lt;<a
                      href="mailto:guenter.fritz.phenix.ccp4@gmail.com"
                      target="_blank" moz-do-not-send="true">guenter.fritz.phenix.ccp4@gmail.com</a>&gt;
                    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>
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