Re: [phenixbb] b factors reporting

Hi Maia, I think all you need to do is make sure phenix_env (or phenix_env.sh) is sourced after the ccp4 setup. Apparently you invoked the "phenix.pdbtools" command that comes with CCP4, and apparently the CCP4 installation isn't internally consistent. CCP4 bundles the cctbx libraries (which includes mmtbx) mainly because some parts of it are required for the compilation of phaser. I'm not surprised that the Python-based commands don't work; to my knowledge they aren't actually used in CCP4. Ralf

________________________________ From: Maia Cherney To: [email protected] Sent: Thursday, April 21, 2011 3:23 PM Subject: Re: [phenixbb] b factors reporting

To: PHENIX user mailing list Date: Thu, 21 Apr 2011 15:09:19 -0600 Subject: Re: [phenixbb] B factor for DNA and Protein Pavel Afonine wrote:

...

  Yes, this trivial combination of two commands will do it:

  phenix.pdbtools model.pdb keep=protein output.file_name=protein_only.pdb   phenix.pdbtools model.pdb keep=rna output.file_name=rna_only.pdb   phenix.pdbtools model.pdb keep=water output.file_name=water_only.pdb

Dear Pavel,

These commands did not work for me (version 1.7-650). I need to report average b factors separately for the protein, water, several ligands and ions, all of them in one chain A.

Traceback (most recent call last): File "/raid/programs/linux/ccp4-6.1.0/ccp4-6.1.3/lib/cctbx/cctbx_sources/mmtbx/mmtbx/command_line/pdbtools.py", line 3, in<module>   from mmtbx import pdbtools File "/raid/programs/linux/ccp4-6.1.0/ccp4-6.1.3/lib/cctbx/cctbx_sources/mmtbx/mmtbx/__init__.py", line 3, in<module>   import cctbx.array_family.flex File "/raid/programs/linux/ccp4-6.1.0/ccp4-6.1.3/lib/cctbx/cctbx_sources/cctbx/cctbx/array_family/flex.py", line 1, in<module>   import scitbx.array_family.flex File "/raid/programs/linux/ccp4-6.1.0/ccp4-6.1.3/lib/cctbx/cctbx_sources/scitbx/scitbx/array_family/flex.py", line 2, in<module>   import boost.optional File "/raid/programs/linux/ccp4-6.1.0/ccp4-6.1.3/lib/cctbx/cctbx_sources/boost_adaptbx/boost/optional.py", line 1, in<module>   import boost.python File "/raid/programs/linux/ccp4-6.1.0/ccp4-6.1.3/lib/cctbx/cctbx_sources/boost_adaptbx/boost/python.py", line 45, in<module>   ext = import_ext("boost_python_meta_ext") File "/raid/programs/linux/ccp4-6.1.0/ccp4-6.1.3/lib/cctbx/cctbx_sources/boost_adaptbx/boost/python.py", line 24, in import_ext   + ["  "+p for p in sys.path])) ImportError: __import__("boost_python_meta_ext"): /raid/programs/linux/ccp4-6.1.0/ccp4-6.1.3/src/phaser/phaser-2.1.4/build/intel-linux/lib/libboost_python.so: undefined symbol: PyUnicodeUCS2_AsWideChar sys.path:   /raid/programs/linux/ccp4-6.1.0/ccp4-6.1.3/lib/cctbx/cctbx_sources/mmtbx/mmtbx/command_line   /raid/programs/linux/ccp4-6.1.0/ccp4-6.1.3/lib/cctbx/cctbx_sources/mmtbx   /raid/programs/linux/ccp4-6.1.0/ccp4-6.1.3/lib/cctbx/cctbx_sources/iotbx   /raid/programs/linux/ccp4-6.1.0/ccp4-6.1.3/lib/cctbx/cctbx_sources/PyCifRW   /raid/programs/linux/ccp4-6.1.0/ccp4-6.1.3/src/phaser/source/phaser   /raid/programs/linux/ccp4-6.1.0/ccp4-6.1.3/lib/cctbx/cctbx_sources/cctbx   /raid/programs/linux/ccp4-6.1.0/ccp4-6.1.3/lib/cctbx/cctbx_sources/scitbx   /raid/programs/linux/ccp4-6.1.0/ccp4-6.1.3/lib/cctbx/cctbx_sources/boost_adaptbx   /raid/programs/linux/ccp4-6.1.0/ccp4-6.1.3/lib/cctbx/cctbx_sources/libtbx   /raid/programs/linux/ccp4-6.1.0/ccp4-6.1.3/src/phaser/phaser-2.1.4/build/intel-linux/lib   /raid/programs/linux/ccp4-6.1.0/ccp4-6.1.3/share/python   /usr/lib/python2.6   /usr/lib/python2.6/plat-linux2   /usr/lib/python2.6/lib-tk   /usr/lib/python2.6/lib-old   /usr/lib/python2.6/lib-dynload   /usr/lib/python2.6/dist-packages   /usr/lib/python2.6/dist-packages/Numeric   /usr/lib/python2.6/dist-packages/PIL   /usr/lib/python2.6/dist-packages/gst-0.10   /var/lib/python-support/python2.6   /usr/lib/python2.6/dist-packages/gtk-2.0   /var/lib/python-support/python2.6/gtk-2.0   /usr/local/lib/python2.6/dist-packages

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