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@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@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@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.maxunicode
1114111

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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