[phenixbb] error in the newer version of phenix
Nathaniel Echols
nechols at lbl.gov
Tue Mar 1 09:45:30 PST 2011
Delete the entire REMARK section at the start of the PDB file, and the
error should go away.
On Tue, Mar 1, 2011 at 8:39 AM, Maia Cherney <chern at ualberta.ca> wrote:
> Hi phenixers,
>
> I just installed the version phenix-1.7-650 on ubuntu 9.4 and tried a test
> run. My previous version runs fine. The new version gives me this error
>
> =============================== refinement start
> ==============================
>
> Traceback (most recent call last):
> File "/usr/local/phenix-1.7-650/phenix/phenix/command_line/refine.py", line
> 11, in <module>
> command_line.run(command_name="phenix.refine", args=sys.argv[1:])
> File "/usr/local/phenix-1.7-650/phenix/phenix/refinement/command_line.py",
> line 89, in run
> call_back_handler=call_back_handler)
> File "/usr/local/phenix-1.7-650/phenix/phenix/refinement/driver.py", line
> 1207, in run
> call_back_handler = call_back_handler)
> File "/usr/local/phenix-1.7-650/phenix/phenix/refinement/strategies.py",
> line 220, in refinement_machine
> xray_structure = model.xray_structure,)
> File "/usr/local/phenix-1.7-650/phenix/phenix/refinement/strategies.py",
> line 124, in extract_from_pdb_header
> xray_structure = xray_structure)
> File "/usr/local/phenix-1.7-650/cctbx_project/mmtbx/f_model.py", line 327,
> in __init__
> twin_law_xyz = sgtbx.rt_mx(symbol=self.twin_law, r_den=12, t_den=144)
> RuntimeError: cctbx Error: Parse error: unexpected character:
> NULL
> ^
> Please, take a look at the error and advise me how to fix it.
>
> Maia
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