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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