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 https://xquartz.macosforge.org/trac/wiki/Releases. My apologies if this isn't your problem. Best wishes Kevin On Tue, Apr 26, 2016 at 1:41 AM, Benoît Masquida wrote:

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: -rwxr-xr-x 1 root wheel 535 24 mar 17:32 coot Chown does not change solve the problem that the graphics do not appear.

Any help still welcome.

Best,

Benoit

Benoît Masquida [email protected] UMR 7156 GMGM tel: +33 3 68 85 14 81 fax: +33 3 68 85 13 65 IPCB - Plateforme de Biologie 4 Allée Konrad Roentgen 67081 STRASBOURG Cedex

Le 22 avr. 2016 à 17:40, Engin Özkan a écrit :

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). Engin

On 4/22/16 4:24 AM, Benoît Masquida wrote:

Dear All,

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.

Thanks.

Benoit

mmdcd-img2:bin B.Masquida$ ./coot INFO:: Reading coordinate file: /Library/Coot/share/coot/standard-residues.pdb PDB file /Library/Coot/share/coot/standard-residues.pdb has been read. Spacegroup: P 1 initalize graphics molecules...done. *filter_fileselection_filenames_state ()* *get_active_map_drag_flag ()* *use_graphics_interface_state ()* INFO:: coot.py imported INFO:: coot_python initialized Running python script /Library/Coot/lib/python2.7/site-packages/coot/coot_load_modules.py Good Morning B.masquida, Welcome to Coot. 0.8.3-pre *set_display_intro_string ("Good Morning B.masquida, Welcome to Coot. 0.8.3-pre")* Coot Python Scripting GUI code found and loaded. Coot Python Scripting GUI code found and loaded. *use_graphics_interface_state ()* *filter_fileselection_filenames_state ()* *get_active_map_drag_flag ()* coot-bin: Fatal IO error 35 (Resource temporarily unavailable) on X server /private/tmp/com.apple.launchd.cTrzTueRvK/org.macosforge.xquartz:0. coot-bin: Fatal IO error 35 (Resource temporarily unavailable) on X server /private/tmp/com.apple.launchd.cTrzTueRvK/org.macosforge.xquartz:0. mmdcd-img2:bin B.Masquida$

Benoît Masquida [email protected] UMR 7156 GMGM tel: +33 3 68 85 14 81 fax: +33 3 68 85 13 65 IPCB - Plateforme de Biologie 4 Allée Konrad Roentgen 67081 STRASBOURG Cedex

Le 21 avr. 2016 à 17:10, Xiao Lei < [email protected]> a écrit :

Hi BM,

If it happens after you upgrade the system, you may try re-install the Xquartz. On Apr 21, 2016 6:48 AM, "Benoît Masquida" wrote:

...

Dear Phenix,

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)?

Thanks for your help.

BM

-- Benoît Masquida [email protected] UMR 7156 GMGM tel: +33 3 68 85 14 81 fax: +33 3 68 85 13 65 IPCB - Plateforme de Biologie 4 Allée Konrad Roentgen 67081 STRASBOURG Cedex

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