[phenixbb] error with phenix.refinine

[Pavel Afonine]

Hi Maxime,

I'm sorry for the problem! I'm keen to address it asap. For that could 
you please send me all inputs (off list, to me directly) so that I can 
reproduce this error myself and then fix it?

Thanks,
Pavel

On 11/8/15 12:09, Maxime Cuypers wrote:
> hi,
>
> i have the following error refining a neutron structure (no xrays 
> data) with the latest builds (dev and official):
> it used to work perfectly and now it says:
> tried many things with my pdb yet to no avail. even archived runs do 
> not work anymore.
>
> ====================== ADP refinement (reciprocal space) 
> ======================
>
>
>                  ----------Individual ADP refinement----------
>
>     R-FACTORS      <Bi-Bj>  <B>   WEIGHT TARGETS
>  work  free  delta                           data restr
> 19.38 23.49   4.11  1.665  13.405 32.138    0.039
> Traceback (most recent call last):
>   File 
> "/usr/local/phenix-1.10.1-2155/build/../modules/phenix/phenix/command_line/refine.py", 
> line 11, in <module>
>     command_line.run(command_name="phenix.refine", args=sys.argv[1:])
>   File 
> "/usr/local/phenix-1.10.1-2155/modules/phenix/phenix/refinement/command_line.py", 
> line 162, in run
>     call_back_handler=call_back_handler)
>   File 
> "/usr/local/phenix-1.10.1-2155/modules/phenix/phenix/refinement/driver.py", 
> line 1532, in run
>     call_back_handler       = call_back_handler).result
>   File 
> "/usr/local/phenix-1.10.1-2155/modules/phenix/phenix/refinement/strategies.py", 
> line 201, in __init__
>     ion_placement_manager = ion_placement_manager)
>   File 
> "/usr/local/phenix-1.10.1-2155/modules/phenix/phenix/refinement/macro_cycle.py", 
> line 117, in __init__
>     self.call(self.adp,      "ADP refinement (reciprocal space)")
>   File 
> "/usr/local/phenix-1.10.1-2155/modules/phenix/phenix/refinement/macro_cycle.py", 
> line 143, in call
>     func(prefix = prefix)
>   File 
> "/usr/local/phenix-1.10.1-2155/modules/phenix/phenix/refinement/macro_cycle.py", 
> line 396, in adp
>     log                      = self.log)
>   File 
> "/usr/local/phenix-1.10.1-2155/modules/phenix/phenix/refinement/adp.py", 
> line 62, in run
>     h_params               = h_params)
>   File 
> "/usr/local/phenix-1.10.1-2155/modules/cctbx_project/mmtbx/refinement/adp_refinement.py", 
> line 232, in __init__
>     nproc                 = nproc)
>   File 
> "/usr/local/phenix-1.10.1-2155/modules/cctbx_project/mmtbx/refinement/adp_refinement.py", 
> line 337, in __init__
>     result = self.try_weight(weight, print_stats=True)
>   File 
> "/usr/local/phenix-1.10.1-2155/modules/cctbx_project/mmtbx/refinement/adp_refinement.py", 
> line 427, in try_weight
>     minimized = self.minimize()
>   File 
> "/usr/local/phenix-1.10.1-2155/modules/cctbx_project/mmtbx/refinement/adp_refinement.py", 
> line 496, in minimize
>     self.model.set_refine_individual_adp()
>   File 
> "/usr/local/phenix-1.10.1-2155/modules/cctbx_project/mmtbx/model.py", 
> line 1523, in set_refine_individual_adp
>     iselection = selection_iso.iselection())
> RuntimeError: cctbx Internal Error: 
> /home/builder/slave/phenix-nightly-intel-linux-2_6-x86_64-centos5/modules/cctbx_project/cctbx/xray/scatterer_flags.h(417): 
> CCTBX_ASSERT(f.use_u_iso()) failure.
>
>
> any clue what is happening?
>
> thank you for your help,
>
> Maxime Cuypers
>
>
>
>
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