[phenixbb] Error while updating water

Engin Özkan eozkan at stanford.edu
Mon Jul 1 13:58:47 PDT 2013


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
>
>
>
>
> _______________________________________________
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> phenixbb at phenix-online.org
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-- 
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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