Re: [phenixbb] Phenix Error while running refinement

Did the model you tested this on contain hydrogens? What about the model that actually crashed the program? -Nat On Mon, Feb 27, 2012 at 10:24 AM, Pavel Afonine wrote:

I just tried this

phenix.pdbtools occupancies.set=-0.36 model.pdb selection="element C"

and then

phenix.refine model.pdb_modified.pdb data.mtz --overwrite

and it runs fine. So there must be something more specific about your refinement run or input file or commands you used or all of them. Yes, sending us the reproducer (all inputs necessary to reproduce the problem) will help to debug this.

Pavel

On 2/27/12 10:15 AM, Nathaniel Echols wrote:

...

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  wrote:

...

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

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