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

Billy Poon bkpoon at lbl.gov
Fri Feb 12 00:52:45 PST 2016


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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