Thanks a lot Ralf, Running cctbx.python allows the sgtbx and uctbx modules to get imported. I think I see what needs to be done to use these modules in other programs , which is what the SuperSym plugin does from within pymol... Thank you Hari On Mon, Nov 2, 2009 at 2:37 PM, Ralf W. Grosse-Kunstleve wrote:

Does this work?

cctbx.python from cctbx import sgtbx

The setpaths scripts only add one entry to PATH and leave the shell environment unmodified otherwise. This is the only way to avoid bad interferrences with other Python-based systems, among other things.

cctbx.python is a small shell script (automatically generated) that updates PYTHONPATH and LD_LIBRARAY_PATH "just in time" before calling the actual python executable. You should never have to manually set PYTHONPATH for the cctbx modules. more cctbx_build/bin/cctbx.python to see how it works.

You can set PYTHONPATH to point to other (non-cctbx) packages and it will be preserved when you run cctbx.python.

You could also source setpaths_debug.sh to set PYTHONPATH and LD_LIBRARY_PATH for the cctbx packages permanently in your environment, but in my experience this can cause a lot of confusion.

Ralf

----- Original Message ---- From: hari jayaram To: [email protected] Sent: Mon, November 2, 2009 8:53:45 AM Subject: [cctbxbb] using cctbx and sgtbx module

Hi I am trying to use a Python plugin SuperSymExample which has cctbx modules sgtbx and uctbx as dependencies.

I wanted to build these modules for my system python 2.5.2  on ubuntu hardy heron 8.04 64 bit linux.

I downloaded the selfx file for the cctbx alone ( without Python) and then had the build complete fully. I used the setpaths utility and then modifies m,y PYTHONPATH.

Now after I add the appropriate directories to my PYTHONPATH , if I import sgtbx and uctbx  in a python interactive session I get an error ( see below)

My PYTHONPATH has:

export PYTHONPATH="$PYTHONPATH:/rawdata12/cctbx_standalone/cctbx_sources:/rawdata12/cctbx_standalone/cctbx_sources/boost_adaptbx"

The error I get when I say from cctbx import sgtbx , uctbx:

ImportError: __import__("boost_python_meta_ext"): libboost_python.so: undefined symbol: PyUnicodeUCS2_FromEncodedObject

What can I do to avoid the error and use the Plugin correctly. Thanks Hari

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from cctbx import sgtbx,uctbx Traceback (most recent call last):  File "<stdin>", line 1, in <module>  File "/rawdata12/cctbx_standalone/cctbx_sources/cctbx/sgtbx/__init__.py",

Detailed error message: hari@charlie:/rawdata12/cctbx_auto/cctbx_build/lib$ python Python 2.5.2 (r252:60911, Jul 22 2009, 15:33:10) [GCC 4.2.4 (Ubuntu 4.2.4-1ubuntu3)] on linux2 Type "help", "copyright", "credits" or "license" for more information. line 2, in <module>    from cctbx import uctbx  File "/rawdata12/cctbx_standalone/cctbx_sources/cctbx/uctbx/__init__.py", line 1, in <module>    from cctbx.array_family import flex  File "/rawdata12/cctbx_standalone/cctbx_sources/cctbx/array_family/flex.py", line 1, in <module>    import scitbx.array_family.flex  File "/rawdata12/cctbx_standalone/cctbx_sources/scitbx/array_family/flex.py", line 1, in <module>    import boost.optional  File "/rawdata12/cctbx_standalone/cctbx_sources/boost_adaptbx/boost/optional.py", line 1, in <module>    import boost.python  File "/rawdata12/cctbx_standalone/cctbx_sources/boost_adaptbx/boost/python.py", line 45, in <module>    ext = import_ext("boost_python_meta_ext")  File "/rawdata12/cctbx_standalone/cctbx_sources/boost_adaptbx/boost/python.py", line 24, in import_ext    + ["  "+p for p in sys.path])) ImportError: __import__("boost_python_meta_ext"): libboost_python.so: undefined symbol: PyUnicodeUCS2_FromEncodedObject  sys.path:

   /usr/lib/python2.5/site-packages    /rawdata12/wx-widgets-read-only/wxPython    /home/hari/ccp4-6.0.99e/share/python    /rawdata12/cctbx_auto/cctbx_build/lib    /home/hari    /rawdata12/cctbx_standalone/cctbx_sources    /rawdata12/cctbx_standalone/cctbx_sources/boost_adaptbx    /usr/lib/python25.zip    /usr/lib/python2.5    /usr/lib/python2.5/plat-linux2    /usr/lib/python2.5/lib-tk    /usr/lib/python2.5/lib-dynload    /usr/local/lib/python2.5/site-packages    /usr/lib/python2.5/site-packages    /usr/lib/python2.5/site-packages/Numeric    /usr/lib/python2.5/site-packages/PIL    /home/hari/djtrunk    /usr/lib/python2.5/site-packages/kodos    /usr/lib/python2.5/site-packages/gst-0.10    /var/lib/python-support/python2.5    /usr/lib/python2.5/site-packages/gtk-2.0    /var/lib/python-support/python2.5/gtk-2.0    /usr/lib/python2.5/site-packages/wx-2.8-gtk2-unicode _______________________________________________ cctbxbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/cctbxbb

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