It's a bug. It looks like it's triggered by occupancies that are less
than zero, but it looks to me like the code is doing something it
shouldn't. (If you are starting out with negative occupancies in the
PDB file, correcting these may avoid the problem - I'm not sure if
it's possible for them to refine to negative values.) Could you
please send me the input files (including .eff file) off-list so I can
make sure I fix it?
thanks,
Nat
On Mon, Feb 27, 2012 at 10:06 AM, Subhani Bandara
Hi everyone,
I am getting following error while running phenix refinement for a protein cocrystalized with a metal chelator complex. What could be the problem.
AssertionError :
Traceback:
File "/Applications/PHENIX-1.7.3-928/Contents/phenix-1.7.3-928/cctbx_project/libtbx/thread_utils.py", line 229, in run
return_value = self._target(self._args, self._kwargs, self._c)
File "/Applications/PHENIX-1.7.3-928/Contents/phenix-1.7.3-928/cctbx_project/libtbx/runtime_utils.py", line 72, in __call__
result = self.target()
File "/Applications/PHENIX-1.7.3-928/Contents/phenix-1.7.3-928/phenix/phenix/refinement/runtime.py", line 67, in __call__
call_back_handler=callback)
File "/Applications/PHENIX-1.7.3-928/Contents/phenix-1.7.3-928/phenix/phenix/refinement/command_line.py", line 97, in run
call_back_handler=call_back_handler)
File "/Applications/PHENIX-1.7.3-928/Contents/phenix-1.7.3-928/phenix/phenix/refinement/driver.py", line 1478, in run
ncs_manager = self.ncs_manager)
File "/Applications/PHENIX-1.7.3-928/Contents/phenix-1.7.3-928/phenix/phenix/refinement/strategies.py", line 344, in refinement_machine
model.show_occupancy_statistics(text = "Occupancies statistics", out=log)
File "/Applications/PHENIX-1.7.3-928/Contents/phenix-1.7.3-928/cctbx_project/mmtbx/model.py", line 868, in show_occupancy_statistics
self.xray_structure.set_occupancies(value=0., selection = less_than_zero)
File "/Applications/PHENIX-1.7.3-928/Contents/phenix-1.7.3-928/cctbx_project/cctbx/xray/structure.py", line 480, in set_occupancies
assert selection.size() == s.size()
Thanks
Subhani
_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb