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

[acyang]

Hi, Billy

It works, after I added the flags in that file.
I also created a patch file.
Please check the attach file.
Just put it in the root folder of PHENIX, and type
"patch -p0 < install_base_packages.py.patch"

Thanks for your help.

By A.C.

2016-02-15 16:34 GMT+08:00 Billy Poon <bkpoon at lbl.gov>:

> Hi,
>
> Since you are installing from source, the easiest way would be to edit the
> Python script that installs all the base dependencies. To do so,
>
> 1) Open install_base_packages.py located in
> phenix-installer-dev-2306-source/modules/cctbx_project/libtbx/auto_build
> 2) Add 'configure_args.append("--enable_unicode=ucs4")' after line 644.
> That section just adds our flags to the configure step for installing
> Python. After editing, your section should look like,
>
> configure_args.append("--enable-shared")
> configure_args.append("--enable-unicode=ucs4")
> configure_args.append("LDFLAGS=-Wl,-rpath=\$$ORIGIN/../lib")
>
> 3) Just run the Phenix install program (./install --prefix=<installation
> directory>) like normal and Python will be compiled with your new flag.
>
> Let me know if you have any issues. Thanks!
>
> --
> 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 Sun, Feb 14, 2016 at 5:55 PM, acyang <acyang0903 at gmail.com> wrote:
>
>> 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
>>>>
>>>>
>>>> _______________________________________________
>>>> phenixbb mailing list
>>>> phenixbb at phenix-online.org
>>>> http://phenix-online.org/mailman/listinfo/phenixbb
>>>> Unsubscribe: phenixbb-leave at phenix-online.org
>>>>
>>>
>>>
>>
>
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