[phenixbb] Using PyMOL-1.8 with PHENIX-dev-2306

[acyang]

Hi Billy

Thanks for your reply.
I installed phenix from source (phenix-installer-dev-2306-source.tar.gz).
And I used scientific linux 7.1 for my workstation.
I noticed that SCONS is adopted in the installation of phenix, and phenix
will download a modified version of python (python_2.7.8_cci).
I think the problem can be solved by adding a flag "--enable-unicode=ucs4"
in configuring Python-2.7.8_cci.

I'd appreciate if you can tell me how to modify the SCONS script file.

by A.C.


2016-02-12 16:52 GMT+08:00 Billy Poon <bkpoon at lbl.gov>:

> Hi,
>
> Are you installing phenix from source or from a binary distribution? And
> which operating system are you using? I can give you the flags (in addition
> to the --prefix flag for installing into the base directory) for the
> configure step for either OS X or Linux.
>
> You can basically install Phenix normally, and then recompile our Python
> from scratch with our regular flags and your extra flag.
>
> --
> Billy K. Poon
> Research Scientist, Molecular Biophysics and Integrated Bioimaging
> Lawrence Berkeley National Laboratory
> 1 Cyclotron Road, M/S 33R0345
> Berkeley, CA 94720
> Tel: (510) 486-5709
> Fax: (510) 486-5909
> Web: https://phenix-online.org
>
> On Wed, Feb 3, 2016 at 3:05 AM, acyang <acyang0903 at gmail.com> wrote:
>
>> Hi everyone
>>
>> I've installed pymol and phenix on my scientific linux7.1 workstation.
>> I can launch pymol via the launching script($PYMOL_HOME/pymol) normally.
>> But when I launched pymol in phenix GUI, I got some error as followed:
>>
>> *********************************************************************************************************************************
>> Traceback (most recent call last):
>>   File "/opt/PyMOL/modules/pymol/__init__.py", line 71, in <module>
>>     import pymol
>>   File "/opt/PyMOL/modules/pymol/__init__.py", line 521, in <module>
>>     import pymol._cmd
>> ImportError: /opt/PyMOL/modules/pymol/_cmd.so: undefined symbol:
>> PyUnicodeUCS4_SetDefaultEncoding
>>
>> *********************************************************************************************************************************
>> After STFW*, *I knew the problem is about unicode variant (UCS2, UCS4).
>> I also checked the configuration of two python.
>> For /bin/python (adopted by pymol)
>>
>> >>> import sys>>> print sys.maxunicode1114111
>>
>> And for $PHENIX_HOME/base/bin/python (adopted by phenix)
>> >>> import sys
>> >>> print sys.maxunicode
>> 65535
>>
>> My question is : How do I add the flag --enable-unicode=ucs4 in configuring Python-2.7.8_cci.
>>
>>
>> I'd appreciate if any reply on this.
>>
>> acyang
>>
>>
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>>
>
>
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