<html><head><meta http-equiv="Content-Type" content="text/html charset=windows-1252"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">Following the suggestion from Engin, I indicate which installer I used to install coot, Coot-0.8.3-pre-5936_64bit_10.11.3.pkg found on Bill Scott’s website. Installation creates the following executable in the /bin directory:<div class=""><div style="margin: 0px; font-size: 11px; line-height: normal; font-family: Menlo;" class="">-rwxr-xr-x&nbsp; 1 root&nbsp; &nbsp; &nbsp; &nbsp; wheel &nbsp; &nbsp; 535 24 mar 17:32 coot</div><div class="">Chown does not change solve the problem that the graphics do not appear.</div><div class=""><br class=""></div><div class="">Any help still welcome.</div><div class=""><br class=""></div><div class="">Best,</div><div class=""><br class=""></div><div class="">Benoit</div><div class=""><br class=""></div><div class=""><br class=""></div><div class=""><br class=""></div><div class=""><br class=""><div apple-content-edited="true" class="">
Benoît Masquida<br class=""><a href="mailto:b.masquida@unistra.fr" class="">b.masquida@unistra.fr</a><br class="">UMR 7156 GMGM<br class="">tel: +33 3 68 85 14 81<br class="">fax: +33 3 68 85 13 65<br class="">IPCB - Plateforme de Biologie<br class="">4 Allée Konrad Roentgen<br class="">67081 STRASBOURG Cedex
</div>
<br class=""><div><blockquote type="cite" class=""><div class="">Le 22 avr. 2016 à 17:40, Engin Özkan &lt;<a href="mailto:eozkan@uchicago.edu" class="">eozkan@uchicago.edu</a>&gt; a écrit :</div><br class="Apple-interchange-newline"><div class="">
  
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  <div bgcolor="#FFFFFF" text="#000000" class=""><p class="">As far as I know, there are no issues with Coot/Phenix on El
      Capitan. You may need to give more info on how you actually
      installed Coot (and which Coot you are invoking from Phenix, which
      you may have set in Coot path under Preferences-&gt;Graphics in
      Phenix).<br class="">
    </p>
    Engin<br class="">
    <br class="">
    <div class="moz-cite-prefix">On 4/22/16 4:24 AM, Benoît Masquida
      wrote:<br class="">
    </div>
    <blockquote cite="mid:29AC065E-9893-4CB5-BD35-9BE9BE74104F@unistra.fr" type="cite" class="">
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      <div class="">Dear All,</div>
      <div class=""><br class="">
      </div>
      <div class="">I re-installed Quartz as suggested. Then I have more
        verbose messages upon launching coot from the shell (See below).
        I don’t know if it is a general problem or a problem related to
        the configuration of my machine.&nbsp;</div>
      <div class=""><br class="">
      </div>
      <div class="">Thanks.</div>
      <div class=""><br class="">
      </div>
      <div class="">Benoit</div>
      <div class=""><br class="">
      </div>
      <div class="">
        <div style="margin: 0px; font-size: 11px; line-height: normal;
          font-family: Menlo;" class="">mmdcd-img2:bin B.Masquida$
          ./coot</div>
        <div style="margin: 0px; font-size: 11px; line-height: normal;
          font-family: Menlo;" class="">INFO:: Reading coordinate file:
          /Library/Coot/share/coot/standard-residues.pdb</div>
        <div style="margin: 0px; font-size: 11px; line-height: normal;
          font-family: Menlo;" class="">&nbsp;PDB file
          /Library/Coot/share/coot/standard-residues.pdb has been read.</div>
        <div style="margin: 0px; font-size: 11px; line-height: normal;
          font-family: Menlo;" class="">Spacegroup: P 1</div>
        <div style="margin: 0px; font-size: 11px; line-height: normal;
          font-family: Menlo;" class="">initalize graphics
          molecules...done.</div>
        <div style="margin: 0px; font-size: 11px; line-height: normal;
          font-family: Menlo;" class=""><b class="">filter_fileselection_filenames_state
            ()</b></div>
        <div style="margin: 0px; font-size: 11px; line-height: normal;
          font-family: Menlo;" class=""><b class="">get_active_map_drag_flag
            ()</b></div>
        <div style="margin: 0px; font-size: 11px; line-height: normal;
          font-family: Menlo;" class=""><b class="">use_graphics_interface_state
            ()</b></div>
        <div style="margin: 0px; font-size: 11px; line-height: normal;
          font-family: Menlo;" class="">INFO:: coot.py imported</div>
        <div style="margin: 0px; font-size: 11px; line-height: normal;
          font-family: Menlo;" class="">INFO:: coot_python initialized</div>
        <div style="margin: 0px; font-size: 11px; line-height: normal;
          font-family: Menlo;" class="">Running python script
          /Library/Coot/lib/python2.7/site-packages/coot/coot_load_modules.py</div>
        <div style="margin: 0px; font-size: 11px; line-height: normal;
          font-family: Menlo;" class="">Good Morning B.masquida, Welcome
          to Coot. 0.8.3-pre</div>
        <div style="margin: 0px; font-size: 11px; line-height: normal;
          font-family: Menlo;" class=""><b class="">set_display_intro_string
            ("Good Morning B.masquida, Welcome to Coot. 0.8.3-pre")</b></div>
        <div style="margin: 0px; font-size: 11px; line-height: normal;
          font-family: Menlo;" class="">Coot Python Scripting GUI code
          found and loaded.</div>
        <div style="margin: 0px; font-size: 11px; line-height: normal;
          font-family: Menlo;" class="">Coot Python Scripting GUI code
          found and loaded.</div>
        <div style="margin: 0px; font-size: 11px; line-height: normal;
          font-family: Menlo;" class=""><b class="">use_graphics_interface_state
            ()</b></div>
        <div style="margin: 0px; font-size: 11px; line-height: normal;
          font-family: Menlo;" class=""><b class="">filter_fileselection_filenames_state
            ()</b></div>
        <div style="margin: 0px; font-size: 11px; line-height: normal;
          font-family: Menlo;" class=""><b class="">get_active_map_drag_flag
            ()</b></div>
        <div style="margin: 0px; font-size: 11px; line-height: normal;
          font-family: Menlo;" class="">coot-bin: Fatal IO error 35
          (Resource temporarily unavailable) on X server
          /private/tmp/com.apple.launchd.cTrzTueRvK/org.macosforge.xquartz:0.</div>
        <div style="margin: 0px; font-size: 11px; line-height: normal;
          font-family: Menlo;" class="">coot-bin: Fatal IO error 35
          (Resource temporarily unavailable) on X server
          /private/tmp/com.apple.launchd.cTrzTueRvK/org.macosforge.xquartz:0.</div>
        <div style="margin: 0px; font-size: 11px; line-height: normal;
          font-family: Menlo;" class="">mmdcd-img2:bin B.Masquida$&nbsp;</div>
      </div>
      <div style="margin: 0px; font-size: 11px; line-height: normal;
        font-family: Menlo;" class=""><br class="">
      </div>
      <div class=""><br class="">
      </div>
      <div class=""><br class="">
      </div>
      <div class=""><br class="">
      </div>
      <br class="">
      <div apple-content-edited="true" class="">
        Benoît Masquida<br class="">
        <a moz-do-not-send="true" href="mailto:b.masquida@unistra.fr" class="">b.masquida@unistra.fr</a><br class="">
        UMR 7156 GMGM<br class="">
        tel: +33 3 68 85 14 81<br class="">
        fax: +33 3 68 85 13 65<br class="">
        IPCB - Plateforme de Biologie<br class="">
        4 Allée Konrad Roentgen<br class="">
        67081 STRASBOURG Cedex
      </div>
      <br class="">
      <div class="">
        <blockquote type="cite" class="">
          <div class="">Le 21 avr. 2016 à 17:10, Xiao Lei &lt;<a moz-do-not-send="true" href="mailto:xiaoleiusc@gmail.com" class=""></a><a class="moz-txt-link-abbreviated" href="mailto:xiaoleiusc@gmail.com">xiaoleiusc@gmail.com</a>&gt; a écrit :</div>
          <br class="Apple-interchange-newline">
          <div class=""><p dir="ltr" class="">Hi BM,</p><p dir="ltr" class="">If it happens after you upgrade the
              system, you may try re-install the Xquartz.</p>
            <div class="gmail_quote">On Apr 21, 2016 6:48 AM, "Benoît
              Masquida" &lt;<a moz-do-not-send="true" href="mailto:b.masquida@unistra.fr" class="">b.masquida@unistra.fr</a>&gt;
              wrote:<br type="attribution" class="">
              <blockquote class="gmail_quote" style="margin:0 0 0
                .8ex;border-left:1px #ccc solid;padding-left:1ex">Dear
                Phenix,<br class="">
                <br class="">
                The graphic window of coot does not open either launch
                from the shell or from Phenix GUI. Has anyone
                experienced (and solved) this problem on El Capitan
                (from Apple)?<br class="">
                <br class="">
                Thanks for your help.<br class="">
                <br class="">
                BM<br class="">
                <br class="">
                --<br class="">
                Benoît Masquida<br class="">
                <a moz-do-not-send="true" href="mailto:b.masquida@unistra.fr" class="">b.masquida@unistra.fr</a><br class="">
                UMR 7156 GMGM<br class="">
                tel: <a moz-do-not-send="true" href="tel:%2B33%203%2068%2085%2014%2081" value="+33368851481" class="">+33 3 68 85 14 81</a><br class="">
                fax: <a moz-do-not-send="true" href="tel:%2B33%203%2068%2085%2013%2065" value="+33368851365" class="">+33 3 68 85 13 65</a><br class="">
                IPCB - Plateforme de Biologie<br class="">
                4 Allée Konrad Roentgen<br class="">
                67081 STRASBOURG Cedex<br class="">
                <br class="">
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