[phenixbb] phenix.refine crashed

[Pavel Afonine]

Hi Jianghai,
could you please tell which command you are running? I need to have some 
more context to see where the problem comes from. Also it would be 
helpful if you could briefly explain what you are trying to refine. Does 
you model have H atoms?

Thank you,
Pavel.

Jianghai Zhu wrote:
> Hi,
>
> In my refinement phenix.refine crashed with the following errors.
>
> ================================ xyz refinement 
> ===============================
>
> Traceback (most recent call last):
>   File 
> "/nfs/home/jzhu/cci_apps_sources/phenix/phenix/command_line/refine.py", 
> line 5, in <module>
>     command_line.run(command_name="phenix.refine", args=sys.argv[1:])
>   File 
> "/nfs/home/jzhu/cci_apps_sources/phenix/phenix/refinement/command_line.py", 
> line 78, in run
>     call_back_after_monitor_collect=call_back_after_monitor_collect)
>   File 
> "/nfs/home/jzhu/cci_apps_sources/phenix/phenix/refinement/driver.py", 
> line 1310, in run
>     log                     = log)
>   File 
> "/nfs/home/jzhu/cci_apps_sources/phenix/phenix/refinement/strategies.py", 
> line 733, in refinement_machine
>     h_params                 = h_params)
>   File 
> "/nfs/home/jzhu/cci_apps_sources/mmtbx/mmtbx/refinement/minimization.py", 
> line 136, in __init__
>     ignore_line_search_failed_step_at_lower_bound = True))
>   File "/nfs/home/jzhu/cci_apps_sources/scitbx/scitbx/lbfgs.py", line 
> 242, in run
>     log)
>   File "/nfs/home/jzhu/cci_apps_sources/scitbx/scitbx/lbfgs.py", line 
> 121, in run_c_plus_plus
>     f, g = target_evaluator.compute_functional_and_gradients()
>   File 
> "/nfs/home/jzhu/cci_apps_sources/mmtbx/mmtbx/refinement/minimization.py", 
> line 369, in compute_functional_and_gradients
>     u_iso_refinable_params = u_iso_refinable_params)
>   File 
> "/nfs/home/jzhu/cci_apps_sources/mmtbx/mmtbx/refinement/minimization.py", 
> line 224, in compute_target
>     sf_v3d_sel = sf_v3d.set_selected(self.hd_selection, [0,0,0])
> RuntimeError: scitbx Internal Error: 
> /net/sharptail/scratch1/rwgk/auto_build/sources/scitbx/include/scitbx/array_family/boost_python/flex_wrapper.h(473): 
> SCITBX_ASSERT(a.accessor() == flags.accessor()) failure.
>
>
> What happened here?  Thanks.
>
> Jianghai
>
> +++++++++++++++++++++++++++++++
> Jianghai Zhu, Ph.D
> CBR Institute for Biomedical Research
> Department of Pathology
> Harvard Medical School
> 200 Longwood Ave., Boston, MA 02115
> Ph: 617-278-3211
> Fx: 618-278-3232
> +++++++++++++++++++++++++++++++
>
>
>
> ------------------------------------------------------------------------
>
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