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

Billy Poon bkpoon at lbl.gov
Mon Feb 15 00:34:34 PST 2016


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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