<div dir="ltr"><div><div>Benoît, since you don't mention what version of XQuartz you are using, I'll point out that the 11.1 build of coot requires version 2.7.9_rc2, which can be installed as described at <a href="https://xquartz.macosforge.org/trac/wiki/Releases">https://xquartz.macosforge.org/trac/wiki/Releases</a>. My apologies if this isn't your problem.<br><br></div>Best wishes<br></div>Kevin<br></div><div class="gmail_extra"><br><div class="gmail_quote">On Tue, Apr 26, 2016 at 1:41 AM, Benoît Masquida <span dir="ltr"><<a href="mailto:b.masquida@unistra.fr" target="_blank">b.masquida@unistra.fr</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div style="word-wrap:break-word">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><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo">-rwxr-xr-x 1 root wheel 535 24 mar 17:32 coot</div><div>Chown does not change solve the problem that the graphics do not appear.</div><div><br></div><div>Any help still welcome.</div><div><br></div><div>Best,</div><div><br></div><div>Benoit</div><div><br></div><div><br></div><div><br></div><div><br><div>
Benoît Masquida<br><a href="mailto:b.masquida@unistra.fr" target="_blank">b.masquida@unistra.fr</a><br>UMR 7156 GMGM<br>tel: <a href="tel:%2B33%203%2068%2085%2014%2081" value="+33368851481" target="_blank">+33 3 68 85 14 81</a><br>fax: <a href="tel:%2B33%203%2068%2085%2013%2065" value="+33368851365" target="_blank">+33 3 68 85 13 65</a><br>IPCB - Plateforme de Biologie<br>4 Allée Konrad Roentgen<br>67081 STRASBOURG Cedex
</div>
<br><div><blockquote type="cite"><div>Le 22 avr. 2016 à 17:40, Engin Özkan <<a href="mailto:eozkan@uchicago.edu" target="_blank">eozkan@uchicago.edu</a>> a écrit :</div><br><div>
<div bgcolor="#FFFFFF" text="#000000"><p>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->Graphics in
Phenix).<br>
</p>
Engin<br>
<br>
<div>On 4/22/16 4:24 AM, Benoît Masquida
wrote:<br>
</div>
<blockquote type="cite">
<div>Dear All,</div>
<div><br>
</div>
<div>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. </div>
<div><br>
</div>
<div>Thanks.</div>
<div><br>
</div>
<div>Benoit</div>
<div><br>
</div>
<div>
<div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo">mmdcd-img2:bin B.Masquida$
./coot</div>
<div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo">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"> 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">Spacegroup: P 1</div>
<div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo">initalize graphics
molecules...done.</div>
<div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo"><b>filter_fileselection_filenames_state
()</b></div>
<div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo"><b>get_active_map_drag_flag
()</b></div>
<div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo"><b>use_graphics_interface_state
()</b></div>
<div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo">INFO:: coot.py imported</div>
<div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo">INFO:: coot_python initialized</div>
<div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo">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">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"><b>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">Coot Python Scripting GUI code
found and loaded.</div>
<div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo">Coot Python Scripting GUI code
found and loaded.</div>
<div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo"><b>use_graphics_interface_state
()</b></div>
<div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo"><b>filter_fileselection_filenames_state
()</b></div>
<div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo"><b>get_active_map_drag_flag
()</b></div>
<div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo">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">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">mmdcd-img2:bin B.Masquida$ </div>
</div>
<div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo"><br>
</div>
<div><br>
</div>
<div><br>
</div>
<div><br>
</div>
<br>
<div>
Benoît Masquida<br>
<a href="mailto:b.masquida@unistra.fr" target="_blank">b.masquida@unistra.fr</a><br>
UMR 7156 GMGM<br>
tel: <a href="tel:%2B33%203%2068%2085%2014%2081" value="+33368851481" target="_blank">+33 3 68 85 14 81</a><br>
fax: <a href="tel:%2B33%203%2068%2085%2013%2065" value="+33368851365" target="_blank">+33 3 68 85 13 65</a><br>
IPCB - Plateforme de Biologie<br>
4 Allée Konrad Roentgen<br>
67081 STRASBOURG Cedex
</div>
<br>
<div>
<blockquote type="cite">
<div>Le 21 avr. 2016 à 17:10, Xiao Lei <<a href="mailto:xiaoleiusc@gmail.com" target="_blank"></a><a href="mailto:xiaoleiusc@gmail.com" target="_blank">xiaoleiusc@gmail.com</a>> a écrit :</div>
<br>
<div><p dir="ltr">Hi BM,</p><p dir="ltr">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" <<a href="mailto:b.masquida@unistra.fr" target="_blank">b.masquida@unistra.fr</a>>
wrote:<br type="attribution">
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Dear
Phenix,<br>
<br>
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>
<br>
Thanks for your help.<br>
<br>
BM<br>
<br>
--<br>
Benoît Masquida<br>
<a href="mailto:b.masquida@unistra.fr" target="_blank">b.masquida@unistra.fr</a><br>
UMR 7156 GMGM<br>
tel: <a href="tel:%2B33%203%2068%2085%2014%2081" value="+33368851481" target="_blank">+33 3 68 85 14 81</a><br>
fax: <a href="tel:%2B33%203%2068%2085%2013%2065" value="+33368851365" target="_blank">+33 3 68 85 13 65</a><br>
IPCB - Plateforme de Biologie<br>
4 Allée Konrad Roentgen<br>
67081 STRASBOURG Cedex<br>
<br>
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