[phenixbb] Joint X-ray/Neutron Refinement

Pavel Afonine pafonine at lbl.gov
Wed Oct 20 21:18:03 PDT 2010


  Hi Louis,

sorry for delayed reply - I was supposed to take this one but I was out 
of email for a few days...

A few suggestions:

1) Try the latest PHENIX nightly build to see if this problem is still 
there:

http://www.phenix-online.org/download/nightly_builds.cgi

2) If the problem persists then please send me the data and model and 
the exact command that leads to the crash. I will work on it once I have 
the data and I will let you know once the problem is fixed. If I have it 
tomorrow morning then the chances are that you will have a working 
solution by the end of the day.

Pavel.


On 10/20/10 12:17 PM, Louis Lazar wrote:
> Hello,
>
> Sorry for reposting, I am trying to get a better response with a more detailed subject line. I am seeing an internal error while trying to conduct joint x-ray/neutron refinement, and any help with the issue below would be greatly appreciated.
> Thank you very much in advance:
>
> ================================ ADP refinement===============================
>
> Traceback (most recent call last):
>    File
> "/sware/phenix-1.6.4-486/linux64/phenix-1.6.4-486/phenix/phenix/command_line/refine.py",
> line 11, in<module>
>      command_line.run(command_name="phenix.refine", args=sys.argv[1:])
>    File
> "/sware/phenix-1.6.4-486/linux64/phenix-1.6.4-486/phenix/phenix/refinement/command_line.py",
> line 89, in run
>      call_back_handler=call_back_handler)
>    File
> "/sware/phenix-1.6.4-486/linux64/phenix-1.6.4-486/phenix/phenix/refinement/driver.py",
> line 1182, in run
>      call_back_handler       = call_back_handler)
>    File
> "/sware/phenix-1.6.4-486/linux64/phenix-1.6.4-486/phenix/phenix/refinement/strategies.py",
> line 735, in refinement_machine
>      h_params               = h_params)
>    File
> "/sware/phenix-1.6.4-486/linux64/phenix-1.6.4-486/cctbx_project/mmtbx/refinement/adp_refinement.py",
> line 192, in __init__
>      all_params = all_params)
>    File
> "/sware/phenix-1.6.4-486/linux64/phenix-1.6.4-486/cctbx_project/mmtbx/refinement/adp_refinement.py",
> line 216, in refine_adp
>      model.set_refine_individual_adp()
>    File
> "/sware/phenix-1.6.4-486/linux64/phenix-1.6.4-486/cctbx_project/mmtbx/model.py",
> line 1035, in set_refine_individual_adp
>      iselection = selection_iso.iselection())
> RuntimeError: cctbx InternalError:
> /net/anaconda/scratch1/phenix/phenix-1.6.4-486/cctbx_project/cctbx/xray/scatterer_flags.h(417):
> CCTBX_ASSERT(f.use_u_iso()) failure.
>
>
>
> This error occurs during the 2nd macro cycle of refinement using this
> general command:
>
> phenix.refine model.pdb data_xray.hkl
> neutron_data.file_name=data_neutron.hkl
> input.xray_data.labels=FOBSx input.neutron_data.labels=FOBSn
>
>
>
> Thanks again.
>
> Regards,
>
> Louis
>
>
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://phenix-online.org/mailman/listinfo/phenixbb

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