[phenixbb] Error while updating water

[Pavel Afonine]

Engin,

it's actually me.. I'm rewriting some parts of phenix.refine, slowly, so 
some accidental glitches (that were not caught by our test) are possible 
in nightly builds. Sorry.

Pavel

On 7/1/13 1:58 PM, Engin Özkan wrote:
> For the error you got with dev-1418, I thought I would beat Nat to the 
> punch, and tell you that the ordered_solvent modes have recently 
> changed. So, you just have to go to All parameters -> Ordered solvent, 
> and set the mode.
>
> Engin
>
> On 7/1/13 3:09 PM, Subhani Bandara wrote:
>> Dear all,
>>
>> I am refining a protein structure at 2.5 A.
>>
>> After running some refinements with water update option on, I 
>> manually added water to some positions and ran without water update 
>> option as it removes those water from the sites and show green 
>> density around.    Then after some refinements like this, I tried to 
>> use water update option to add water to some newly appeared density.
>>
>> When I check the option to update water using dev 1418 version it 
>> stops with the following error.  Also  when not using water update 
>> option, refinement statistics got worse when I used 1418 compared 
>> to 1.8.2-1309 with refinements using same inputs and options.
>>
>> R work-0.1988 compared to 0.1920 with 1.8.2-1309
>> Rfree-0.2623 compared to 0.2490 with 1.8.2-1309
>>
>> Traceback:
>>
>> File 
>> "/Applications/PHENIX-dev-1418/Contents/phenix-dev-1418/cctbx_project/libtbx/thread_utils.py", 
>> line 236, in run
>>
>> return_value = self._target(self._args, self._kwargs, self._c)
>>
>>
>> File 
>> "/Applications/PHENIX-dev-1418/Contents/phenix-dev-1418/cctbx_project/libtbx/runtime_utils.py", 
>> line 94, in __call__
>>
>> result = self.target()
>>
>>
>> File 
>> "/Applications/PHENIX-dev-1418/Contents/phenix-dev-1418/cctbx_project/libtbx/runtime_utils.py", 
>> line 73, in __call__
>>
>> result = self.run()
>>
>>
>> File 
>> "/Applications/PHENIX-dev-1418/Contents/phenix-dev-1418/phenix/phenix/refinement/runtime.py", 
>> line 69, in run
>>
>> refine_object = self._run(args, callback)
>>
>>
>> File 
>> "/Applications/PHENIX-dev-1418/Contents/phenix-dev-1418/phenix/phenix/refinement/runtime.py", 
>> line 85, in _run
>>
>> call_back_handler=callback)
>>
>>
>> File 
>> "/Applications/PHENIX-dev-1418/Contents/phenix-dev-1418/phenix/phenix/refinement/command_line.py", 
>> line 161, in run
>>
>> call_back_handler=call_back_handler)
>>
>>
>> File 
>> "/Applications/PHENIX-dev-1418/Contents/phenix-dev-1418/phenix/phenix/refinement/driver.py", 
>> line 1630, in run
>>
>> ncs_manager             = self.ncs_manager).result
>>
>>
>> File 
>> "/Applications/PHENIX-dev-1418/Contents/phenix-dev-1418/phenix/phenix/refinement/strategies.py", 
>> line 155, in __init__
>>
>> neutron_refinement2 = self.neutron_refinement2)
>>
>>
>> File 
>> "/Applications/PHENIX-dev-1418/Contents/phenix-dev-1418/phenix/phenix/refinement/task_table.py", 
>> line 26, in __init__
>>
>> self.__call__()
>>
>>
>> File 
>> "/Applications/PHENIX-dev-1418/Contents/phenix-dev-1418/phenix/phenix/refinement/task_table.py", 
>> line 36, in __call__
>>
>> self.__getattribute__(method_name)()
>>
>>
>> File 
>> "/Applications/PHENIX-dev-1418/Contents/phenix-dev-1418/phenix/phenix/refinement/task_table.py", 
>> line 106, in run_sol
>>
>> mc   = self.macro_cycle)
>>
>>
>> File 
>> "/Applications/PHENIX-dev-1418/Contents/phenix-dev-1418/phenix/phenix/refinement/task_table.py", 
>> line 79, in _need_to_run
>>
>> else: raise RuntimeError("Not a valid mode: %s"%mode)
>>
>>
>> Thanks in advance for any help
>>
>> Subhani
>>
>>
>>
>>
>> _______________________________________________
>> phenixbb mailing list
>> phenixbb at phenix-online.org
>> http://phenix-online.org/mailman/listinfo/phenixbb
>
>
> -- 
> Engin Özkan
> Post-doctoral Scholar
> Laboratory of K. Christopher Garcia
> Howard Hughes Medical Institute
> Dept of Molecular and Cellular Physiology
> 279 Campus Drive, Beckman Center B173
> Stanford School of Medicine
> Stanford, CA 94305
> w ph: (650)-498-7111
> cell: (650)-862-8563
>
>
> _______________________________________________
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> phenixbb at phenix-online.org
> http://phenix-online.org/mailman/listinfo/phenixbb

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