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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Ok, now I can reproduce the problem: phenix.reduce model.pdb > modelH.pdb phenix.pdbtools occupancies.set=-0.36 modelH.pdb selection="element C or element H" phenix.refine modelH.pdb_modified.pdb data.mtz --overwrite which crashes: Traceback (most recent call last): File "/net/chevy/raid1/afonine/build/../sources/phenix/phenix/command_line/refine.py", line 11, in <module> command_line.run(command_name="phenix.refine", args=sys.argv[1:]) File "/net/chevy/raid1/afonine/sources/phenix/phenix/refinement/command_line.py", line 97, in run call_back_handler=call_back_handler) File "/net/chevy/raid1/afonine/sources/phenix/phenix/refinement/driver.py", line 1501, in run ncs_manager = self.ncs_manager) File "/net/chevy/raid1/afonine/sources/phenix/phenix/refinement/strategies.py", line 345, in refinement_machine model.show_occupancy_statistics(text = "Occupancies statistics", out=log) File "/net/chevy/raid1/afonine/sources/cctbx_project/mmtbx/model.py", line 868, in show_occupancy_statistics self.xray_structure.set_occupancies(value=0., selection = less_than_zero) File "/net/chevy/raid1/afonine/sources/cctbx_project/cctbx/xray/structure.py", line 480, in set_occupancies assert selection.size() == s.size() AssertionError Pavel On 2/27/12 10:33 AM, Nathaniel Echols wrote:

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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