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

[Kevin Jude]

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 <b.masquida at unistra.fr>
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
> 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
> 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>
> 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> 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
>> 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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>
>
>
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