<html><body><div style="color:#000; background-color:#fff; font-family:Courier New, courier, monaco, monospace, sans-serif;font-size:10pt"><div><span>Hi Maia,</span></div><div><br><span></span></div><div><span>I think all you need to do is make sure phenix_env (or phenix_env.sh) is sourced after the ccp4 setup.</span></div><div><span><br></span></div><div><span>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.<br></span></div><div><br><span></span></div><div><span>Ralf<br></span></div><div><br><blockquote style="border-left: 2px solid rgb(16, 16, 255); margin-left: 5px; padding-left: 5px;"><div style="font-family: Courier
New, courier, monaco, monospace, sans-serif; font-size: 10pt;"><div style="font-family: times new roman, new york, times, serif; font-size: 12pt;"><font face="Arial" size="2"><hr size="1"><b><span style="font-weight:bold;">From:</span></b> Maia Cherney <chern@ualberta.ca><br><b><span style="font-weight: bold;">To:</span></b> phenixbb@phenix-online.org<br><b><span style="font-weight: bold;">Sent:</span></b> Thursday, April 21, 2011 3:23 PM<br><b><span style="font-weight: bold;">Subject:</span></b> Re: [phenixbb] b factors reporting<br></font><br>
<br>To: PHENIX user mailing list<<a ymailto="mailto:phenixbb@phenix-online.org" href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a>><br>Date: Thu, 21 Apr 2011 15:09:19 -0600<br>Subject: Re: [phenixbb] B factor for DNA and Protein<br>Pavel Afonine wrote:<br>> <br>> Yes, this trivial combination of two commands will do it:<br>> <br>> phenix.pdbtools model.pdb keep=protein output.file_name=protein_only.pdb<br>> phenix.pdbtools model.pdb keep=rna output.file_name=rna_only.pdb<br>> phenix.pdbtools model.pdb keep=water output.file_name=water_only.pdb<br>> <br>Dear Pavel,<br><br>These commands did not work for me (version 1.7-650). I need to report<br>average b factors separately for the protein, water, several ligands<br>and ions, all of them in one chain A.<br><br>Traceback (most recent call last):<br> File
"/raid/programs/linux/ccp4-6.1.0/ccp4-6.1.3/lib/cctbx/cctbx_sources/mmtbx/mmtbx/command_line/pdbtools.py",<br>line 3, in<module><br> from mmtbx import pdbtools<br> File "/raid/programs/linux/ccp4-6.1.0/ccp4-6.1.3/lib/cctbx/cctbx_sources/mmtbx/mmtbx/__init__.py",<br>line 3, in<module><br> import cctbx.array_family.flex<br> File "/raid/programs/linux/ccp4-6.1.0/ccp4-6.1.3/lib/cctbx/cctbx_sources/cctbx/cctbx/array_family/flex.py",<br>line 1, in<module><br> import scitbx.array_family.flex<br> File "/raid/programs/linux/ccp4-6.1.0/ccp4-6.1.3/lib/cctbx/cctbx_sources/scitbx/scitbx/array_family/flex.py",<br>line 2, in<module><br> import boost.optional<br> File "/raid/programs/linux/ccp4-6.1.0/ccp4-6.1.3/lib/cctbx/cctbx_sources/boost_adaptbx/boost/optional.py",<br>line 1, in<module><br> import boost.python<br> File
"/raid/programs/linux/ccp4-6.1.0/ccp4-6.1.3/lib/cctbx/cctbx_sources/boost_adaptbx/boost/python.py",<br>line 45, in<module><br> ext = import_ext("boost_python_meta_ext")<br> File "/raid/programs/linux/ccp4-6.1.0/ccp4-6.1.3/lib/cctbx/cctbx_sources/boost_adaptbx/boost/python.py",<br>line 24, in import_ext<br> + [" "+p for p in sys.path]))<br>ImportError: __import__("boost_python_meta_ext"):<br>/raid/programs/linux/ccp4-6.1.0/ccp4-6.1.3/src/phaser/phaser-2.1.4/build/intel-linux/lib/libboost_python.so:<br>undefined symbol: PyUnicodeUCS2_AsWideChar<br> sys.path:<br> /raid/programs/linux/ccp4-6.1.0/ccp4-6.1.3/lib/cctbx/cctbx_sources/mmtbx/mmtbx/command_line<br> /raid/programs/linux/ccp4-6.1.0/ccp4-6.1.3/lib/cctbx/cctbx_sources/mmtbx<br> /raid/programs/linux/ccp4-6.1.0/ccp4-6.1.3/lib/cctbx/cctbx_sources/iotbx<br> /raid/programs/linux/ccp4-6.1.0/ccp4-6.1.3/lib/cctbx/cctbx_sources/PyCifRW<br>
/raid/programs/linux/ccp4-6.1.0/ccp4-6.1.3/src/phaser/source/phaser<br> /raid/programs/linux/ccp4-6.1.0/ccp4-6.1.3/lib/cctbx/cctbx_sources/cctbx<br> /raid/programs/linux/ccp4-6.1.0/ccp4-6.1.3/lib/cctbx/cctbx_sources/scitbx<br> /raid/programs/linux/ccp4-6.1.0/ccp4-6.1.3/lib/cctbx/cctbx_sources/boost_adaptbx<br> /raid/programs/linux/ccp4-6.1.0/ccp4-6.1.3/lib/cctbx/cctbx_sources/libtbx<br> /raid/programs/linux/ccp4-6.1.0/ccp4-6.1.3/src/phaser/phaser-2.1.4/build/intel-linux/lib<br> /raid/programs/linux/ccp4-6.1.0/ccp4-6.1.3/share/python<br> /usr/lib/python2.6<br> /usr/lib/python2.6/plat-linux2<br> /usr/lib/python2.6/lib-tk<br> /usr/lib/python2.6/lib-old<br> /usr/lib/python2.6/lib-dynload<br> /usr/lib/python2.6/dist-packages<br> /usr/lib/python2.6/dist-packages/Numeric<br> /usr/lib/python2.6/dist-packages/PIL<br> /usr/lib/python2.6/dist-packages/gst-0.10<br>
/var/lib/python-support/python2.6<br> /usr/lib/python2.6/dist-packages/gtk-2.0<br> /var/lib/python-support/python2.6/gtk-2.0<br> /usr/local/lib/python2.6/dist-packages<br><br><br>_______________________________________________<br>phenixbb mailing list<br><a ymailto="mailto:phenixbb@phenix-online.org" href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a><br>http://phenix-online.org/mailman/listinfo/phenixbb<br><br><br></div></div></blockquote></div></div></body></html>