[phenixbb] b factors reporting

Nathaniel Echols nechols at lbl.gov
Thu Apr 21 15:43:07 PDT 2011


On Thu, Apr 21, 2011 at 3:23 PM, Maia Cherney <chern at ualberta.ca> wrote:
> 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

Your PYTHONPATH environment variable has been modified to include
CCP4's distribution of CCTBX, which uses a completely different build
of Python (resulting in the cryptic error message).  I don't know how
exactly this happens, but I suspect your .bashrc or .cshrc invokes
some CCP4 script that modifies PYTHONPATH.  At any rate, this is bad,
because it overrides the module search paths used by Phenix.

-Nat


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