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
b.masquida@unistra.fr
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 <eozkan@uchicago.edu> 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
b.masquida@unistra.fr
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 <xiaoleiusc@gmail.com> 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" <b.masquida@unistra.fr> 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
b.masquida@unistra.fr
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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