[phenixbb] b factors reporting

[Maia Cherney]

To: PHENIX user mailing list<phenixbb at phenix-online.org>
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