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

[Benoît Masquida]

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 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 22 avr. 2016 à 17:40, Engin Özkan <eozkan at 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 at unistra.fr <mailto: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 < <mailto:xiaoleiusc at gmail.com>xiaoleiusc at gmail.com <mailto: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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>> 
>> 
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