[phenixbb] Coot does not start up with OS 10.11 El Capitan

Benoît Masquida b.masquida at unistra.fr
Fri Apr 22 02:24:30 PDT 2016


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 at 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 at 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 at unistra.fr <mailto:b.masquida at 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 at unistra.fr <mailto:b.masquida at unistra.fr>
> UMR 7156 GMGM
> tel: +33 3 68 85 14 81 <tel:%2B33%203%2068%2085%2014%2081>
> fax: +33 3 68 85 13 65 <tel:%2B33%203%2068%2085%2013%2065>
> IPCB - Plateforme de Biologie
> 4 Allée Konrad Roentgen
> 67081 STRASBOURG Cedex
> 
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