id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 20421 ChimeraX bug report submission chimerax-bug-report@… "{{{ The following bug report has been submitted: Platform: Linux-6.8.0-117-generic-x86_64-with-glibc2.35 ChimeraX Version: 1.12rc202605142114 (2026-05-14 21:14:16 UTC) Description Replace this text with list of actions that caused this problem to occur Log: Startup Messages --- warning | GBM is not supported with the current configuration. Fallback to Vulkan rendering in Chromium. notes | CubeNTube: sphere eraser undo support enabled /home/junhe/.local/share/ChimeraX/1.12/lib/python3.11/site- packages/chimerax/clipper/__init__.py:29: UserWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81. import pkg_resources UCSF ChimeraX version: 1.12rc202605142114 (2026-05-14) © 2016-2026 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open run_class001.mrc Opened run_class001.mrc as #1, grid size 72,72,72, pixel 3.82, shown at level 0.529, step 1, values float32 > artiax start Using preset: ArtiaX / Artiax Default Preset expands to these ChimeraX commands: set bgColor black lighting depthCue false camera ortho > open /home/junhe/Desktop/warp-mt/relion-if- > bin2/Refine3D/job002/run_data.star format star Summary of feedback from opening /home/junhe/Desktop/warp-mt/relion-if- bin2/Refine3D/job002/run_data.star --- notes | Processed as relion Processed as relion Traceback (most recent call last): File ""/home/junhe/.local/share/ChimeraX/1.12/lib/python3.11/site- packages/chimerax/artiax/widgets/ArtiaxOpenDialog.py"", line 66, in _qt_safe run(session, ""open "" + "" "".join([FileNameArg.unparse(p) for p in paths]) + ("""" File ""/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/core/commands/run.py"", line 49, in run results = command.run(text, log=log, return_json=return_json) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/core/commands/cli.py"", line 3245, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/open_command/cmd.py"", line 138, in cmd_open models = Command(session, registry=registry).run(provider_cmd_text, log=log)[0] ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/core/commands/cli.py"", line 3245, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/open_command/cmd.py"", line 233, in provider_open models, status = collated_open(session, None, [data], data_format, _add_models, ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/open_command/cmd.py"", line 546, in collated_open return remember_data_format() ^^^^^^^^^^^^^^^^^^^^^^ File ""/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/open_command/cmd.py"", line 517, in remember_data_format models, status = func(*func_args, **func_kw) ^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/home/junhe/.local/share/ChimeraX/1.12/lib/python3.11/site- packages/chimerax/artiax/io/formats.py"", line 25, in open return open_particle_list(session, data, file_name, format_name=self.name, from_chimx=True) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/home/junhe/.local/share/ChimeraX/1.12/lib/python3.11/site- packages/chimerax/artiax/io/io.py"", line 104, in open_particle_list data = formats[format_name].particle_data( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/home/junhe/.local/share/ChimeraX/1.12/lib/python3.11/site- packages/chimerax/artiax/io/RELION/RELIONParticleData.py"", line 126, in __init__ super().__init__( File ""/home/junhe/.local/share/ChimeraX/1.12/lib/python3.11/site- packages/chimerax/artiax/io/ParticleData.py"", line 507, in __init__ self.read_file() File ""/home/junhe/.local/share/ChimeraX/1.12/lib/python3.11/site- packages/chimerax/artiax/io/RELION/RELIONParticleData.py"", line 252, in read_file if np.issubdtype(df.dtypes[key], np.number): ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/numpy/core/numerictypes.py"", line 417, in issubdtype arg1 = dtype(arg1).type ^^^^^^^^^^^ TypeError: Cannot interpret '' as a data type TypeError: Cannot interpret '' as a data type File ""/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/numpy/core/numerictypes.py"", line 417, in issubdtype arg1 = dtype(arg1).type ^^^^^^^^^^^ See log for complete Python traceback. > open /home/junhe/Desktop/warp-mt/relion-if- > bin2/Refine3D/job002/run_data.star Summary of feedback from opening /home/junhe/Desktop/warp-mt/relion-if- bin2/Refine3D/job002/run_data.star --- notes | Processed as relion Processed as relion Traceback (most recent call last): File ""/home/junhe/.local/share/ChimeraX/1.12/lib/python3.11/site- packages/chimerax/artiax/widgets/ArtiaxOpenDialog.py"", line 66, in _qt_safe run(session, ""open "" + "" "".join([FileNameArg.unparse(p) for p in paths]) + ("""" File ""/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/core/commands/run.py"", line 49, in run results = command.run(text, log=log, return_json=return_json) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/core/commands/cli.py"", line 3245, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/open_command/cmd.py"", line 138, in cmd_open models = Command(session, registry=registry).run(provider_cmd_text, log=log)[0] ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/core/commands/cli.py"", line 3245, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/open_command/cmd.py"", line 233, in provider_open models, status = collated_open(session, None, [data], data_format, _add_models, ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/open_command/cmd.py"", line 546, in collated_open return remember_data_format() ^^^^^^^^^^^^^^^^^^^^^^ File ""/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/open_command/cmd.py"", line 517, in remember_data_format models, status = func(*func_args, **func_kw) ^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/home/junhe/.local/share/ChimeraX/1.12/lib/python3.11/site- packages/chimerax/artiax/io/formats.py"", line 25, in open return open_particle_list(session, data, file_name, format_name=self.name, from_chimx=True) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/home/junhe/.local/share/ChimeraX/1.12/lib/python3.11/site- packages/chimerax/artiax/io/io.py"", line 104, in open_particle_list data = formats[format_name].particle_data( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/home/junhe/.local/share/ChimeraX/1.12/lib/python3.11/site- packages/chimerax/artiax/io/RELION/RELIONParticleData.py"", line 126, in __init__ super().__init__( File ""/home/junhe/.local/share/ChimeraX/1.12/lib/python3.11/site- packages/chimerax/artiax/io/ParticleData.py"", line 507, in __init__ self.read_file() File ""/home/junhe/.local/share/ChimeraX/1.12/lib/python3.11/site- packages/chimerax/artiax/io/RELION/RELIONParticleData.py"", line 252, in read_file if np.issubdtype(df.dtypes[key], np.number): ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/numpy/core/numerictypes.py"", line 417, in issubdtype arg1 = dtype(arg1).type ^^^^^^^^^^^ TypeError: Cannot interpret '' as a data type TypeError: Cannot interpret '' as a data type File ""/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/numpy/core/numerictypes.py"", line 417, in issubdtype arg1 = dtype(arg1).type ^^^^^^^^^^^ See log for complete Python traceback. Opened tomo186_7.65Apx.mrc as #2.1.1, grid size 1024,1024,400, pixel 7.65,7.65,7.65, shown at level 0.0272, step 1, values float32 > artiax clip off > artiax tomo #2.1.1 sliceDirection 0,0,1 > artiax view xy > open /home/junhe/Desktop/warp-mt/relion-if- > bin4/Refine3D/job005/run_data.star format star Summary of feedback from opening /home/junhe/Desktop/warp-mt/relion-if- bin4/Refine3D/job005/run_data.star --- notes | Processed as relion Processed as relion Traceback (most recent call last): File ""/home/junhe/.local/share/ChimeraX/1.12/lib/python3.11/site- packages/chimerax/artiax/widgets/ArtiaxOpenDialog.py"", line 66, in _qt_safe run(session, ""open "" + "" "".join([FileNameArg.unparse(p) for p in paths]) + ("""" File ""/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/core/commands/run.py"", line 49, in run results = command.run(text, log=log, return_json=return_json) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/core/commands/cli.py"", line 3245, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/open_command/cmd.py"", line 138, in cmd_open models = Command(session, registry=registry).run(provider_cmd_text, log=log)[0] ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/core/commands/cli.py"", line 3245, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/open_command/cmd.py"", line 233, in provider_open models, status = collated_open(session, None, [data], data_format, _add_models, ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/open_command/cmd.py"", line 546, in collated_open return remember_data_format() ^^^^^^^^^^^^^^^^^^^^^^ File ""/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/open_command/cmd.py"", line 517, in remember_data_format models, status = func(*func_args, **func_kw) ^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/home/junhe/.local/share/ChimeraX/1.12/lib/python3.11/site- packages/chimerax/artiax/io/formats.py"", line 25, in open return open_particle_list(session, data, file_name, format_name=self.name, from_chimx=True) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/home/junhe/.local/share/ChimeraX/1.12/lib/python3.11/site- packages/chimerax/artiax/io/io.py"", line 104, in open_particle_list data = formats[format_name].particle_data( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/home/junhe/.local/share/ChimeraX/1.12/lib/python3.11/site- packages/chimerax/artiax/io/RELION/RELIONParticleData.py"", line 126, in __init__ super().__init__( File ""/home/junhe/.local/share/ChimeraX/1.12/lib/python3.11/site- packages/chimerax/artiax/io/ParticleData.py"", line 507, in __init__ self.read_file() File ""/home/junhe/.local/share/ChimeraX/1.12/lib/python3.11/site- packages/chimerax/artiax/io/RELION/RELIONParticleData.py"", line 252, in read_file if np.issubdtype(df.dtypes[key], np.number): ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/numpy/core/numerictypes.py"", line 417, in issubdtype arg1 = dtype(arg1).type ^^^^^^^^^^^ TypeError: Cannot interpret '' as a data type TypeError: Cannot interpret '' as a data type File ""/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/numpy/core/numerictypes.py"", line 417, in issubdtype arg1 = dtype(arg1).type ^^^^^^^^^^^ See log for complete Python traceback. Array Excerpt (first 5 elements): [-0.00287437 0.00365448 0.00344086 0.00590515 0.015625 ] Basic Information: Shape: (400, 1024, 1024) Data type: float32 Size (number of elements): 419430400 Memory (bytes): 1677721600 Max value: 0.0784912109375 Min value: -0.1485595703125 Max value: 0.0784912109375 Min value: -0.1485595703125 Midpoint: -0.0350341796875 Inverted array (first 5 elements): [-0.06719398 -0.07372284 -0.07350922 -0.07597351 -0.08569336] Opened tomo186_7.65Apx_invert as #2.1.2, grid size 1024,1024,400, pixel 7.65,7.65,7.65, shown at level -0.0427, step 1, values float32 > artiax clip off Array Excerpt (first 5 elements): [-0.06719398 -0.07372284 -0.07350922 -0.07597351 -0.08569336] Basic Information: Shape: (400, 1024, 1024) Data type: float32 Size (number of elements): 419430400 Memory (bytes): 1677721600 Max value: 0.0784912109375 Min value: -0.1485595703125 Max value: 0.0784912109375 Min value: -0.1485595703125 Midpoint: -0.0350341796875 Inverted array (first 5 elements): [-0.00287437 0.00365448 0.00344086 0.00590515 0.015625 ] Opened tomo186_7_invert as #2.1.3, grid size 1024,1024,400, pixel 7.65,7.65,7.65, shown at level 0.0272, step 1, values float32 > artiax clip off [Repeated 1 time(s)] > open /home/junhe/Desktop/warp-mt/relion-if- > bin4/Refine3D/job005/run_data.star format star Summary of feedback from opening /home/junhe/Desktop/warp-mt/relion-if- bin4/Refine3D/job005/run_data.star --- notes | Processed as relion Processed as relion Traceback (most recent call last): File ""/home/junhe/.local/share/ChimeraX/1.12/lib/python3.11/site- packages/chimerax/artiax/widgets/ArtiaxOpenDialog.py"", line 66, in _qt_safe run(session, ""open "" + "" "".join([FileNameArg.unparse(p) for p in paths]) + ("""" File ""/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/core/commands/run.py"", line 49, in run results = command.run(text, log=log, return_json=return_json) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/core/commands/cli.py"", line 3245, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/open_command/cmd.py"", line 138, in cmd_open models = Command(session, registry=registry).run(provider_cmd_text, log=log)[0] ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/core/commands/cli.py"", line 3245, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/open_command/cmd.py"", line 233, in provider_open models, status = collated_open(session, None, [data], data_format, _add_models, ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/open_command/cmd.py"", line 546, in collated_open return remember_data_format() ^^^^^^^^^^^^^^^^^^^^^^ File ""/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/open_command/cmd.py"", line 517, in remember_data_format models, status = func(*func_args, **func_kw) ^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/home/junhe/.local/share/ChimeraX/1.12/lib/python3.11/site- packages/chimerax/artiax/io/formats.py"", line 25, in open return open_particle_list(session, data, file_name, format_name=self.name, from_chimx=True) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/home/junhe/.local/share/ChimeraX/1.12/lib/python3.11/site- packages/chimerax/artiax/io/io.py"", line 104, in open_particle_list data = formats[format_name].particle_data( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/home/junhe/.local/share/ChimeraX/1.12/lib/python3.11/site- packages/chimerax/artiax/io/RELION/RELIONParticleData.py"", line 126, in __init__ super().__init__( File ""/home/junhe/.local/share/ChimeraX/1.12/lib/python3.11/site- packages/chimerax/artiax/io/ParticleData.py"", line 507, in __init__ self.read_file() File ""/home/junhe/.local/share/ChimeraX/1.12/lib/python3.11/site- packages/chimerax/artiax/io/RELION/RELIONParticleData.py"", line 252, in read_file if np.issubdtype(df.dtypes[key], np.number): ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/numpy/core/numerictypes.py"", line 417, in issubdtype arg1 = dtype(arg1).type ^^^^^^^^^^^ TypeError: Cannot interpret '' as a data type TypeError: Cannot interpret '' as a data type File ""/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/numpy/core/numerictypes.py"", line 417, in issubdtype arg1 = dtype(arg1).type ^^^^^^^^^^^ See log for complete Python traceback. Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/core/triggerset.py"", line 149, in invoke return self._func(self._name, data) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/ui/widgets/item_chooser.py"", line 464, in _items_change self.set_value(next_val, delayed=True) File ""/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/ui/widgets/item_chooser.py"", line 404, in set_value _when_all_updated(self, self.value_changed.emit) File ""/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/ui/widgets/item_chooser.py"", line 534, in _when_all_updated timer, old_func = self._wau_timer_info ^^^^ NameError: name 'self' is not defined Error processing trigger ""add models"": NameError: name 'self' is not defined File ""/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/ui/widgets/item_chooser.py"", line 534, in _when_all_updated timer, old_func = self._wau_timer_info ^^^^ See log for complete Python traceback. Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/core/triggerset.py"", line 149, in invoke return self._func(self._name, data) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/ui/widgets/item_chooser.py"", line 464, in _items_change self.set_value(next_val, delayed=True) File ""/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/ui/widgets/item_chooser.py"", line 404, in set_value _when_all_updated(self, self.value_changed.emit) File ""/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/ui/widgets/item_chooser.py"", line 534, in _when_all_updated timer, old_func = self._wau_timer_info ^^^^ NameError: name 'self' is not defined Error processing trigger ""remove models"": NameError: name 'self' is not defined File ""/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/ui/widgets/item_chooser.py"", line 534, in _when_all_updated timer, old_func = self._wau_timer_info ^^^^ See log for complete Python traceback. > artiax add tomo #1 Opened run_class001.mrc as #2.1.4, grid size 72,72,72, pixel 3.82, shown at level 0.529, step 1, values float32 > artiax clip off > artiax tomo #2.1.4 sliceDirection 0,0,1 > artiax view xy > open /home/junhe/Desktop/warp-mt/relion-if- > bin2/Refine3D/job002/run_it000_data-new.star format star Summary of feedback from opening /home/junhe/Desktop/warp-mt/relion-if- bin2/Refine3D/job002/run_it000_data-new.star --- notes | Processed as relion Traceback (most recent call last): File ""/home/junhe/.local/share/ChimeraX/1.12/lib/python3.11/site- packages/chimerax/artiax/widgets/ArtiaxOpenDialog.py"", line 66, in _qt_safe run(session, ""open "" + "" "".join([FileNameArg.unparse(p) for p in paths]) + ("""" File ""/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/core/commands/run.py"", line 49, in run results = command.run(text, log=log, return_json=return_json) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/core/commands/cli.py"", line 3245, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/open_command/cmd.py"", line 138, in cmd_open models = Command(session, registry=registry).run(provider_cmd_text, log=log)[0] ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/core/commands/cli.py"", line 3245, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/open_command/cmd.py"", line 233, in provider_open models, status = collated_open(session, None, [data], data_format, _add_models, ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/open_command/cmd.py"", line 546, in collated_open return remember_data_format() ^^^^^^^^^^^^^^^^^^^^^^ File ""/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/open_command/cmd.py"", line 517, in remember_data_format models, status = func(*func_args, **func_kw) ^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/home/junhe/.local/share/ChimeraX/1.12/lib/python3.11/site- packages/chimerax/artiax/io/formats.py"", line 25, in open return open_particle_list(session, data, file_name, format_name=self.name, from_chimx=True) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/home/junhe/.local/share/ChimeraX/1.12/lib/python3.11/site- packages/chimerax/artiax/io/io.py"", line 104, in open_particle_list data = formats[format_name].particle_data( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/home/junhe/.local/share/ChimeraX/1.12/lib/python3.11/site- packages/chimerax/artiax/io/RELION/RELIONParticleData.py"", line 126, in __init__ super().__init__( File ""/home/junhe/.local/share/ChimeraX/1.12/lib/python3.11/site- packages/chimerax/artiax/io/ParticleData.py"", line 507, in __init__ self.read_file() File ""/home/junhe/.local/share/ChimeraX/1.12/lib/python3.11/site- packages/chimerax/artiax/io/RELION/RELIONParticleData.py"", line 252, in read_file if np.issubdtype(df.dtypes[key], np.number): ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/numpy/core/numerictypes.py"", line 417, in issubdtype arg1 = dtype(arg1).type ^^^^^^^^^^^ TypeError: Cannot interpret '' as a data type TypeError: Cannot interpret '' as a data type File ""/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/numpy/core/numerictypes.py"", line 417, in issubdtype arg1 = dtype(arg1).type ^^^^^^^^^^^ See log for complete Python traceback. > open /home/junhe/Desktop/warp-mt/relion-if- > bin2/Refine3D/job002/test_artiax_min.star format star Summary of feedback from opening /home/junhe/Desktop/warp-mt/relion-if- bin2/Refine3D/job002/test_artiax_min.star --- notes | Processed as relion Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/core/triggerset.py"", line 149, in invoke return self._func(self._name, data) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/ui/widgets/item_chooser.py"", line 464, in _items_change self.set_value(next_val, delayed=True) File ""/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/ui/widgets/item_chooser.py"", line 404, in set_value _when_all_updated(self, self.value_changed.emit) File ""/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/ui/widgets/item_chooser.py"", line 534, in _when_all_updated timer, old_func = self._wau_timer_info ^^^^ NameError: name 'self' is not defined Error processing trigger ""model id changed"": NameError: name 'self' is not defined File ""/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/ui/widgets/item_chooser.py"", line 534, in _when_all_updated timer, old_func = self._wau_timer_info ^^^^ See log for complete Python traceback. Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/core/triggerset.py"", line 149, in invoke return self._func(self._name, data) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/ui/widgets/item_chooser.py"", line 464, in _items_change self.set_value(next_val, delayed=True) File ""/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/ui/widgets/item_chooser.py"", line 404, in set_value _when_all_updated(self, self.value_changed.emit) File ""/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/ui/widgets/item_chooser.py"", line 534, in _when_all_updated timer, old_func = self._wau_timer_info ^^^^ NameError: name 'self' is not defined Error processing trigger ""add models"": NameError: name 'self' is not defined File ""/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/ui/widgets/item_chooser.py"", line 534, in _when_all_updated timer, old_func = self._wau_timer_info ^^^^ See log for complete Python traceback. > artiax clip off Opened Particle list test_artiax_min.star with 2 particles. Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/core/triggerset.py"", line 149, in invoke return self._func(self._name, data) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/ui/widgets/item_chooser.py"", line 464, in _items_change self.set_value(next_val, delayed=True) File ""/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/ui/widgets/item_chooser.py"", line 404, in set_value _when_all_updated(self, self.value_changed.emit) File ""/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/ui/widgets/item_chooser.py"", line 534, in _when_all_updated timer, old_func = self._wau_timer_info ^^^^ NameError: name 'self' is not defined Error processing trigger ""add models"": NameError: name 'self' is not defined File ""/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/ui/widgets/item_chooser.py"", line 534, in _when_all_updated timer, old_func = self._wau_timer_info ^^^^ See log for complete Python traceback. Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/core/triggerset.py"", line 149, in invoke return self._func(self._name, data) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/ui/widgets/item_chooser.py"", line 464, in _items_change self.set_value(next_val, delayed=True) File ""/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/ui/widgets/item_chooser.py"", line 404, in set_value _when_all_updated(self, self.value_changed.emit) File ""/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/ui/widgets/item_chooser.py"", line 534, in _when_all_updated timer, old_func = self._wau_timer_info ^^^^ NameError: name 'self' is not defined Error processing trigger ""remove models"": NameError: name 'self' is not defined File ""/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/ui/widgets/item_chooser.py"", line 534, in _when_all_updated timer, old_func = self._wau_timer_info ^^^^ See log for complete Python traceback. > open /home/junhe/Desktop/warp-mt/relion-if- > bin2/Refine3D/job002/test_artiax_min.star format star Summary of feedback from opening /home/junhe/Desktop/warp-mt/relion-if- bin2/Refine3D/job002/test_artiax_min.star --- notes | Processed as relion Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/core/triggerset.py"", line 149, in invoke return self._func(self._name, data) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/ui/widgets/item_chooser.py"", line 464, in _items_change self.set_value(next_val, delayed=True) File ""/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/ui/widgets/item_chooser.py"", line 404, in set_value _when_all_updated(self, self.value_changed.emit) File ""/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/ui/widgets/item_chooser.py"", line 534, in _when_all_updated timer, old_func = self._wau_timer_info ^^^^ NameError: name 'self' is not defined Error processing trigger ""model id changed"": NameError: name 'self' is not defined File ""/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/ui/widgets/item_chooser.py"", line 534, in _when_all_updated timer, old_func = self._wau_timer_info ^^^^ See log for complete Python traceback. Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/core/triggerset.py"", line 149, in invoke return self._func(self._name, data) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/ui/widgets/item_chooser.py"", line 464, in _items_change self.set_value(next_val, delayed=True) File ""/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/ui/widgets/item_chooser.py"", line 404, in set_value _when_all_updated(self, self.value_changed.emit) File ""/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/ui/widgets/item_chooser.py"", line 534, in _when_all_updated timer, old_func = self._wau_timer_info ^^^^ NameError: name 'self' is not defined Error processing trigger ""add models"": NameError: name 'self' is not defined File ""/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/ui/widgets/item_chooser.py"", line 534, in _when_all_updated timer, old_func = self._wau_timer_info ^^^^ See log for complete Python traceback. > artiax clip off Opened Particle list test_artiax_min.star with 2 particles. Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/core/triggerset.py"", line 149, in invoke return self._func(self._name, data) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/ui/widgets/item_chooser.py"", line 464, in _items_change self.set_value(next_val, delayed=True) File ""/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/ui/widgets/item_chooser.py"", line 404, in set_value _when_all_updated(self, self.value_changed.emit) File ""/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/ui/widgets/item_chooser.py"", line 534, in _when_all_updated timer, old_func = self._wau_timer_info ^^^^ NameError: name 'self' is not defined Error processing trigger ""add models"": NameError: name 'self' is not defined File ""/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/ui/widgets/item_chooser.py"", line 534, in _when_all_updated timer, old_func = self._wau_timer_info ^^^^ See log for complete Python traceback. Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/core/triggerset.py"", line 149, in invoke return self._func(self._name, data) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/ui/widgets/item_chooser.py"", line 464, in _items_change self.set_value(next_val, delayed=True) File ""/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/ui/widgets/item_chooser.py"", line 404, in set_value _when_all_updated(self, self.value_changed.emit) File ""/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/ui/widgets/item_chooser.py"", line 534, in _when_all_updated timer, old_func = self._wau_timer_info ^^^^ NameError: name 'self' is not defined Error processing trigger ""remove models"": NameError: name 'self' is not defined File ""/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/ui/widgets/item_chooser.py"", line 534, in _when_all_updated timer, old_func = self._wau_timer_info ^^^^ See log for complete Python traceback. > open /home/junhe/Desktop/warp-mt/relion-if- > bin4/Refine3D/job005/run_data.star format star Summary of feedback from opening /home/junhe/Desktop/warp-mt/relion-if- bin4/Refine3D/job005/run_data.star --- notes | Processed as relion Processed as relion Traceback (most recent call last): File ""/home/junhe/.local/share/ChimeraX/1.12/lib/python3.11/site- packages/chimerax/artiax/widgets/ArtiaxOpenDialog.py"", line 66, in _qt_safe run(session, ""open "" + "" "".join([FileNameArg.unparse(p) for p in paths]) + ("""" File ""/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/core/commands/run.py"", line 49, in run results = command.run(text, log=log, return_json=return_json) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/core/commands/cli.py"", line 3245, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/open_command/cmd.py"", line 138, in cmd_open models = Command(session, registry=registry).run(provider_cmd_text, log=log)[0] ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/core/commands/cli.py"", line 3245, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/open_command/cmd.py"", line 233, in provider_open models, status = collated_open(session, None, [data], data_format, _add_models, ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/open_command/cmd.py"", line 546, in collated_open return remember_data_format() ^^^^^^^^^^^^^^^^^^^^^^ File ""/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/open_command/cmd.py"", line 517, in remember_data_format models, status = func(*func_args, **func_kw) ^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/home/junhe/.local/share/ChimeraX/1.12/lib/python3.11/site- packages/chimerax/artiax/io/formats.py"", line 25, in open return open_particle_list(session, data, file_name, format_name=self.name, from_chimx=True) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/home/junhe/.local/share/ChimeraX/1.12/lib/python3.11/site- packages/chimerax/artiax/io/io.py"", line 104, in open_particle_list data = formats[format_name].particle_data( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/home/junhe/.local/share/ChimeraX/1.12/lib/python3.11/site- packages/chimerax/artiax/io/RELION/RELIONParticleData.py"", line 126, in __init__ super().__init__( File ""/home/junhe/.local/share/ChimeraX/1.12/lib/python3.11/site- packages/chimerax/artiax/io/ParticleData.py"", line 507, in __init__ self.read_file() File ""/home/junhe/.local/share/ChimeraX/1.12/lib/python3.11/site- packages/chimerax/artiax/io/RELION/RELIONParticleData.py"", line 252, in read_file if np.issubdtype(df.dtypes[key], np.number): ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/numpy/core/numerictypes.py"", line 417, in issubdtype arg1 = dtype(arg1).type ^^^^^^^^^^^ TypeError: Cannot interpret '' as a data type TypeError: Cannot interpret '' as a data type File ""/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/numpy/core/numerictypes.py"", line 417, in issubdtype arg1 = dtype(arg1).type ^^^^^^^^^^^ See log for complete Python traceback. > open /home/junhe/Desktop/warp-mt/relion-if- > bin4/Refine3D/job005/run_data.star format star Summary of feedback from opening /home/junhe/Desktop/warp-mt/relion-if- bin4/Refine3D/job005/run_data.star --- notes | Processed as relion Processed as relion Traceback (most recent call last): File ""/home/junhe/.local/share/ChimeraX/1.12/lib/python3.11/site- packages/chimerax/artiax/widgets/ArtiaxOpenDialog.py"", line 66, in _qt_safe run(session, ""open "" + "" "".join([FileNameArg.unparse(p) for p in paths]) + ("""" File ""/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/core/commands/run.py"", line 49, in run results = command.run(text, log=log, return_json=return_json) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/core/commands/cli.py"", line 3245, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/open_command/cmd.py"", line 138, in cmd_open models = Command(session, registry=registry).run(provider_cmd_text, log=log)[0] ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/core/commands/cli.py"", line 3245, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/open_command/cmd.py"", line 233, in provider_open models, status = collated_open(session, None, [data], data_format, _add_models, ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/open_command/cmd.py"", line 546, in collated_open return remember_data_format() ^^^^^^^^^^^^^^^^^^^^^^ File ""/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/open_command/cmd.py"", line 517, in remember_data_format models, status = func(*func_args, **func_kw) ^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/home/junhe/.local/share/ChimeraX/1.12/lib/python3.11/site- packages/chimerax/artiax/io/formats.py"", line 25, in open return open_particle_list(session, data, file_name, format_name=self.name, from_chimx=True) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/home/junhe/.local/share/ChimeraX/1.12/lib/python3.11/site- packages/chimerax/artiax/io/io.py"", line 104, in open_particle_list data = formats[format_name].particle_data( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/home/junhe/.local/share/ChimeraX/1.12/lib/python3.11/site- packages/chimerax/artiax/io/RELION/RELIONParticleData.py"", line 126, in __init__ super().__init__( File ""/home/junhe/.local/share/ChimeraX/1.12/lib/python3.11/site- packages/chimerax/artiax/io/ParticleData.py"", line 507, in __init__ self.read_file() File ""/home/junhe/.local/share/ChimeraX/1.12/lib/python3.11/site- packages/chimerax/artiax/io/RELION/RELIONParticleData.py"", line 252, in read_file if np.issubdtype(df.dtypes[key], np.number): ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/numpy/core/numerictypes.py"", line 417, in issubdtype arg1 = dtype(arg1).type ^^^^^^^^^^^ TypeError: Cannot interpret '' as a data type TypeError: Cannot interpret '' as a data type File ""/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/numpy/core/numerictypes.py"", line 417, in issubdtype arg1 = dtype(arg1).type ^^^^^^^^^^^ See log for complete Python traceback. > open /home/junhe/Desktop/warp-mt/relion-if- > bin2/Refine3D/job002/test_artiax_min.star format star Summary of feedback from opening /home/junhe/Desktop/warp-mt/relion-if- bin2/Refine3D/job002/test_artiax_min.star --- notes | Processed as relion Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/core/triggerset.py"", line 149, in invoke return self._func(self._name, data) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/ui/widgets/item_chooser.py"", line 464, in _items_change self.set_value(next_val, delayed=True) File ""/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/ui/widgets/item_chooser.py"", line 404, in set_value _when_all_updated(self, self.value_changed.emit) File ""/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/ui/widgets/item_chooser.py"", line 534, in _when_all_updated timer, old_func = self._wau_timer_info ^^^^ NameError: name 'self' is not defined Error processing trigger ""model id changed"": NameError: name 'self' is not defined File ""/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/ui/widgets/item_chooser.py"", line 534, in _when_all_updated timer, old_func = self._wau_timer_info ^^^^ See log for complete Python traceback. Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/core/triggerset.py"", line 149, in invoke return self._func(self._name, data) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/ui/widgets/item_chooser.py"", line 464, in _items_change self.set_value(next_val, delayed=True) File ""/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/ui/widgets/item_chooser.py"", line 404, in set_value _when_all_updated(self, self.value_changed.emit) File ""/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/ui/widgets/item_chooser.py"", line 534, in _when_all_updated timer, old_func = self._wau_timer_info ^^^^ NameError: name 'self' is not defined Error processing trigger ""add models"": NameError: name 'self' is not defined File ""/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/ui/widgets/item_chooser.py"", line 534, in _when_all_updated timer, old_func = self._wau_timer_info ^^^^ See log for complete Python traceback. > artiax clip off Opened Particle list test_artiax_min.star with 2 particles. OpenGL version: 3.3.0 NVIDIA 580.159.03 OpenGL renderer: NVIDIA GeForce RTX 3080/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation Python: 3.11.13 Locale: en_US.UTF-8 Qt version: PyQt6 6.10.2, Qt 6.10.0 Qt runtime version: 6.10.1 Qt platform: xcb XDG_SESSION_TYPE=x11 DESKTOP_SESSION=ubuntu XDG_SESSION_DESKTOP=ubuntu XDG_CURRENT_DESKTOP=ubuntu:GNOME DISPLAY=:1 Manufacturer: Supermicro Model: Super Server OS: Ubuntu 22.04 Architecture: 64bit ELF Virtual Machine: none CPU: 192 AMD EPYC 7642 48-Core Processor Cache Size: 512 KB Memory: total used free shared buff/cache available Mem: 251Gi 20Gi 67Gi 9.9Gi 163Gi 218Gi Swap: 2.0Gi 17Mi 2.0Gi Graphics: 03:00.0 VGA compatible controller [0300]: ASPEED Technology, Inc. ASPEED Graphics Family [1a03:2000] (rev 52) DeviceName: ASPEED Video AST2600 Subsystem: Super Micro Computer Inc ASPEED Graphics Family [15d9:1c22] Installed Packages: accessible-pygments: 0.0.5 aiohappyeyeballs: 2.6.1 aiohttp: 3.13.1 aiosignal: 1.4.0 alabaster: 1.0.0 annotated-doc: 0.0.4 annotated-types: 0.7.0 anyio: 4.13.0 appdirs: 1.4.4 asttokens: 3.0.1 attrs: 26.1.0 autocommand: 2.2.2 babel: 2.18.0 backports.tarfile: 1.2.0 beautifulsoup4: 4.13.5 blockdiag: 3.0.0 blosc2: 4.2.0 bs4: 0.0.2 build: 1.3.0 certifi: 2026.4.22 cftime: 1.6.5 charset-normalizer: 3.4.7 ChimeraX-AddCharge: 1.5.20 ChimeraX-AddH: 2.2.8 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.6.2 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 3.2 ChimeraX-AlphaFold: 1.0.1 ChimeraX-AltlocExplorer: 1.2 ChimeraX-AmberInfo: 1.0 ChimeraX-Animations: 1.0 ChimeraX-Aniso: 1.3.2 ChimeraX-Arrays: 1.1 ChimeraX-ArtiaX: 0.6.0 ChimeraX-Atomic: 1.67.1 ChimeraX-AtomicLibrary: 14.4 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.3 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 3.0.0 ChimeraX-Boltz: 1.1 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.2 ChimeraX-BuildStructure: 2.13.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.6.0 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.4.1 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.5 ChimeraX-ChemGroup: 2.0.2 ChimeraX-Clashes: 2.4 ChimeraX-Clipper: 0.23.0 ChimeraX-Cluster: 1.0 ChimeraX-ColorActions: 1.0.5 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.8 ChimeraX-CommandLine: 1.3.1 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.12rc202605142114 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.5 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-CubeNTube: 1.1.0 ChimeraX-DataFormats: 1.2.4 ChimeraX-Dicom: 1.2.7 ChimeraX-DistMonitor: 1.4.2 ChimeraX-DockPrep: 1.2.1 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ESMFold: 1.0 ChimeraX-FileHistory: 1.0.1 ChimeraX-FunctionKey: 1.0.1 ChimeraX-Geometry: 1.3 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.4.1 ChimeraX-Hbonds: 2.5.3 ChimeraX-Help: 1.3 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.4 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-KVFinder: 1.8.2 ChimeraX-Label: 1.5 ChimeraX-LightingGUI: 1.0 ChimeraX-LinuxSupport: 1.0.1 ChimeraX-ListInfo: 1.3.1 ChimeraX-locscalesurfer: 0.1.4 ChimeraX-Log: 1.2.2 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.3 ChimeraX-Map: 1.3 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0.1 ChimeraX-MapFilter: 2.0.1 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1.1 ChimeraX-Markers: 1.0.1 ChimeraX-Mask: 1.0.2 ChimeraX-MatchAlign: 1.1 ChimeraX-MatchMaker: 2.4 ChimeraX-MCopy: 1.0 ChimeraX-MCPServer: 0.2.0 ChimeraX-MDcrds: 2.19 ChimeraX-MedicalToolbar: 1.1 ChimeraX-Meeting: 1.0.1 ChimeraX-Minimize: 1.3.8 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.16 ChimeraX-MMTF: 2.2 ChimeraX-ModelArchive: 1.0 ChimeraX-Modeller: 1.5.23 ChimeraX-ModelPanel: 1.6.1 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0.3 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.2 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0.1 ChimeraX-MutationScores: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.2 ChimeraX-NMRSTAR: 1.0.2 ChimeraX-NRRD: 1.2 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.15.4 ChimeraX-OpenFold: 1.0 ChimeraX-OrthoPick: 1.0.1 ChimeraX-PDB: 2.7.13 ChimeraX-PDBBio: 1.0.1 ChimeraX-PDBLibrary: 1.0.5 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1.4 ChimeraX-ProfileGrids: 1.6 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.8.2 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.3.3 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 4.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.2 ChimeraX-Scenes: 0.3.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.3 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-Segmentations: 3.5.12 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.18 ChimeraX-Shape: 1.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.2.1 ChimeraX-ShowSequences: 1.0.3 ChimeraX-SideView: 1.0.1 ChimeraX-SimilarStructures: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SNFG: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.19.3 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.2.1 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.5.3 ChimeraX-TapeMeasure: 1.0 ChimeraX-TaskManager: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.2.4 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.50.6 ChimeraX-Umap: 1.0 ChimeraX-uniprot: 2.3.2 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDock: 1.6.2 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-vrml: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.5 ChimeraX-Zone: 1.0.1 click: 8.4.0 colorama: 0.4.6 comm: 0.2.3 contourpy: 1.3.3 coverage: 7.14.0 cxservices: 1.2.3 cycler: 0.12.1 Cython: 3.2.4 debugpy: 1.8.20 decorator: 5.3.0 distro: 1.9.0 docutils: 0.21.2 einops: 0.8.2 executing: 2.2.1 filelock: 3.19.1 fonttools: 4.63.0 frozenlist: 1.8.0 fsspec: 2026.4.0 funcparserlib: 2.0.0a0 geomdl: 5.4.0 glfw: 2.10.0 grako: 3.16.5 h11: 0.16.0 h5py: 3.16.0 hf-xet: 1.5.0 html2text: 2025.4.15 httpcore: 1.0.9 httpx: 0.28.1 httpx-sse: 0.4.3 huggingface_hub: 1.15.0 idna: 3.15 ihm: 2.2 imagecodecs: 2024.6.1 imagesize: 2.0.0 importlib_metadata: 8.0.0 inflect: 7.3.1 iniconfig: 2.3.0 ipykernel: 7.1.0 ipython: 9.9.0 ipython_pygments_lexers: 1.1.1 jaraco.collections: 5.1.0 jaraco.context: 5.3.0 jaraco.functools: 4.0.1 jaraco.text: 3.12.1 jedi: 0.19.2 Jinja2: 3.1.6 jsonschema: 4.26.0 jsonschema-specifications: 2025.9.1 jupyter_client: 8.8.0 jupyter_core: 5.9.1 kiwisolver: 1.5.0 line_profiler: 5.0.0 lxml: 6.0.2 lz4: 4.3.2 Markdown: 3.8.2 markdown-it-py: 4.2.0 MarkupSafe: 3.0.3 matplotlib: 3.10.7 matplotlib-inline: 0.2.2 mcp: 1.18.0 mdurl: 0.1.2 more-itertools: 10.3.0 mpmath: 1.3.0 mrcfile: 1.5.4 msgpack: 1.1.1 multidict: 6.7.1 narwhals: 2.21.2 ndindex: 1.10.1 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.14.1 numpy: 1.26.4 nvidia-cublas-cu12: 12.8.4.1 nvidia-cuda-cupti-cu12: 12.8.90 nvidia-cuda-nvrtc-cu12: 12.8.93 nvidia-cuda-runtime-cu12: 12.8.90 nvidia-cudnn-cu12: 9.10.2.21 nvidia-cufft-cu12: 11.3.3.83 nvidia-cufile-cu12: 1.13.1.3 nvidia-curand-cu12: 10.3.9.90 nvidia-cusolver-cu12: 11.7.3.90 nvidia-cusparse-cu12: 12.5.8.93 nvidia-cusparselt-cu12: 0.7.1 nvidia-nccl-cu12: 2.27.5 nvidia-nvjitlink-cu12: 12.8.93 nvidia-nvjitlink-cu12: 12.9.86 nvidia-nvshmem-cu12: 3.3.20 nvidia-nvtx-cu12: 12.8.90 OpenMM: 8.4.0 OpenMM-CUDA-12: 8.4.0 openvr: 1.26.701 packaging: 25.0 packaging: 24.2 pandas: 3.0.3 ParmEd: 4.2.2 parso: 0.8.7 pep517: 0.13.1 pexpect: 4.9.0 pickleshare: 0.7.5 pillow: 11.3.0 pip: 25.2 pkginfo: 1.12.1.2 platformdirs: 4.9.6 platformdirs: 4.2.2 plotly: 6.7.0 pluggy: 1.6.0 prompt_toolkit: 3.0.52 propcache: 0.5.2 psutil: 7.0.0 ptyprocess: 0.7.0 pure_eval: 0.2.3 py-cpuinfo: 9.0.0 pyarrow: 24.0.0 pybind11: 3.0.1 pycollada: 0.8 pydantic: 2.13.4 pydantic-settings: 2.14.1 pydantic_core: 2.46.4 pydata-sphinx-theme: 0.17.1 pydicom: 2.4.4 Pygments: 2.18.0 pynmrstar: 3.5.1 pynrrd: 1.0.0 PyOpenGL: 3.1.10 PyOpenGL-accelerate: 3.1.10 pyopenxr: 1.1.4501 pyparsing: 3.3.2 pyproject_hooks: 1.2.0 PyQt6: 6.10.2 PyQt6-Qt6: 6.10.1 PyQt6-WebEngine: 6.10.0 PyQt6-WebEngine-Qt6: 6.10.1 PyQt6_sip: 13.10.3 pytest: 9.0.3 pytest-cov: 7.1.0 python-dateutil: 2.9.0.post0 python-dotenv: 1.2.2 python-multipart: 0.0.28 PyYAML: 6.0.3 pyzmq: 27.1.0 qtconsole: 5.7.0 QtPy: 2.4.3 qtshim: 1.2.2 RandomWords: 0.4.0 referencing: 0.37.0 requests: 2.32.5 rich: 15.0.0 roman-numerals: 4.1.0 rpds-py: 0.30.0 safetensors: 0.7.0 scipy: 1.16.3 scipy: 1.14.0 setuptools: 80.9.0 sfftk-rw: 0.8.1 shellingham: 1.5.4 six: 1.17.0 snowballstemmer: 3.0.1 sortedcontainers: 2.4.0 soupsieve: 2.8.3 Sphinx: 9.0.4 sphinx-autodoc-typehints: 3.6.1 sphinxcontrib-applehelp: 2.0.0 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 2.0.0 sphinxcontrib-htmlhelp: 2.1.0 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 2.0.0 sphinxcontrib-serializinghtml: 2.0.0 sse-starlette: 3.4.4 stack-data: 0.6.3 starfile: 0.5.13 starlette: 1.0.0 superqt: 0.7.6 sympy: 1.14.0 tables: 3.10.2 tcia_utils: 3.2.1 threadpoolctl: 3.6.0 tifffile: 2025.3.13 timm: 1.0.27 tinyarray: 1.2.5 tomli: 2.0.1 torch: 2.9.1 torchvision: 0.24.1 tornado: 6.5.5 tqdm: 4.67.3 traitlets: 5.14.3 triton: 3.5.1 typeguard: 4.3.0 typer: 0.25.1 typing-inspection: 0.4.2 typing_extensions: 4.15.0 typing_extensions: 4.12.2 Unidecode: 1.4.0 urllib3: 2.7.0 uvicorn: 0.47.0 wcwidth: 0.7.0 webcolors: 24.11.1 wheel: 0.45.1 wheel: 0.45.1 wheel-filename: 1.4.2 yarl: 1.23.0 zipp: 3.19.2 }}} " defect new normal Unassigned