[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.


More information about the phenixbb mailing list