id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 2279 Apparent race condition in remove-model trigger handling chimerax-bug-report@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: Darwin-18.6.0-x86_64-i386-64bit ChimeraX Version: 0.91 (2019-07-10) Description (Describe the actions that caused this problem to occur here) Log: Startup Messages --- warning | 'clip' is a prefix of an existing command 'clipper' UCSF ChimeraX version: 0.91 (2019-07-10) © 2016-2019 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /Users/nadiariera/Downloads/cryosparc_P11_J33_004_volume_map.mrc Opened cryosparc_P11_J33_004_volume_map.mrc, grid size 400,400,400, pixel 0.834, shown at level 0.106, step 2, values float32 > set bgColor white > lighting full > toolshed show ""Segment Map"" Segmenting cryosparc_P11_J33_004_volume_map.mrc, density threshold 0.120577 Showing cryosparc_P11_J33_004_volume_map.seg - 0 regions, 0 surfaces Showing 23 region surfaces 30 watershed regions, grouped to 23 regions > select 3 models selected Segmenting cryosparc_P11_J33_004_volume_map.mrc, density threshold 0.119804 Showing cryosparc_P11_J33_004_volume_map.seg - 0 regions, 0 surfaces Showing 23 region surfaces 30 watershed regions, grouped to 23 regions > select clear Segmenting cryosparc_P11_J33_004_volume_map.mrc, density threshold 0.119804 Showing cryosparc_P11_J33_004_volume_map.seg - 0 regions, 0 surfaces Only showing 20 of 23 regions. Showing 20 of 23 region surfaces 30 watershed regions, grouped to 23 regions Segmenting cryosparc_P11_J33_004_volume_map.mrc, density threshold 0.119804 Showing cryosparc_P11_J33_004_volume_map.seg - 0 regions, 0 surfaces Showing 2 region surfaces 30 watershed regions, grouped to 2 regions Segmenting cryosparc_P11_J33_004_volume_map.mrc, density threshold 0.119804 Showing cryosparc_P11_J33_004_volume_map.seg - 0 regions, 0 surfaces Only showing 10 of 23 regions. Showing 10 of 23 region surfaces 30 watershed regions, grouped to 23 regions > lighting simple Smoothing and grouping, standard deviation 5 voxels Only showing 10 of 21 regions. Showing 10 of 21 region surfaces Got 21 regions after smoothing 5 voxels. > select ~sel 2 models selected > hide #!1 models > select ~sel Nothing selected > save ""/Users/nadiariera/Desktop/S2C2 Project submission/Segmented_nanodisc_from_P11_J33_004.mrc"" models #1 > hide #!2 models Traceback (most recent call last): File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/segger/segment_dialog.py"", line 1178, in model_closed_cb if self.chosen_map in mlist: File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/segger/segment_dialog.py"", line 420, in _get_chosen_map return self._map_menu.value File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 255, in value return self.item_map[text] KeyError: 'cryosparc_P11_J33_004_volume_map.mrc #1' Error processing trigger ""remove models"": 'cryosparc_P11_J33_004_volume_map.mrc #1': KeyError: 'cryosparc_P11_J33_004_volume_map.mrc #1' File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 255, in value return self.item_map[text] See log for complete Python traceback. Traceback (most recent call last): File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 287, in _items_change prev_value = self.value File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 255, in value return self.item_map[text] KeyError: 'cryosparc_P11_J33_004_volume_map.mrc #1' Error processing trigger ""remove models"": 'cryosparc_P11_J33_004_volume_map.mrc #1': KeyError: 'cryosparc_P11_J33_004_volume_map.mrc #1' File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 255, in value return self.item_map[text] See log for complete Python traceback. Traceback (most recent call last): File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/segger/segment_dialog.py"", line 1178, in model_closed_cb if self.chosen_map in mlist: File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/segger/segment_dialog.py"", line 420, in _get_chosen_map return self._map_menu.value File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 255, in value return self.item_map[text] KeyError: 'cryosparc_P11_J33_004_volume_map.mrc #1' Error processing trigger ""remove models"": 'cryosparc_P11_J33_004_volume_map.mrc #1': KeyError: 'cryosparc_P11_J33_004_volume_map.mrc #1' [removed a bunch of these] File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 255, in value return self.item_map[text] See log for complete Python traceback. Traceback (most recent call last): File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 287, in _items_change prev_value = self.value File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 255, in value return self.item_map[text] KeyError: 'cryosparc_P11_J33_004_volume_map.mrc #1' Error processing trigger ""remove models"": 'cryosparc_P11_J33_004_volume_map.mrc #1': KeyError: 'cryosparc_P11_J33_004_volume_map.mrc #1' File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 255, in value return self.item_map[text] See log for complete Python traceback. Traceback (most recent call last): File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/segger/segment_dialog.py"", line 1178, in model_closed_cb if self.chosen_map in mlist: File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/segger/segment_dialog.py"", line 420, in _get_chosen_map return self._map_menu.value File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 255, in value return self.item_map[text] KeyError: 'cryosparc_P11_J33_004_volume_map.mrc #1' Error processing trigger ""remove models"": 'cryosparc_P11_J33_004_volume_map.mrc #1': KeyError: 'cryosparc_P11_J33_004_volume_map.mrc #1' File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 255, in value return self.item_map[text] See log for complete Python traceback. Traceback (most recent call last): File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 287, in _items_change prev_value = self.value File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 255, in value return self.item_map[text] KeyError: 'cryosparc_P11_J33_004_volume_map.mrc #1' Error processing trigger ""remove models"": 'cryosparc_P11_J33_004_volume_map.mrc #1': KeyError: 'cryosparc_P11_J33_004_volume_map.mrc #1' File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 255, in value return self.item_map[text] See log for complete Python traceback. Traceback (most recent call last): File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/segger/segment_dialog.py"", line 1178, in model_closed_cb if self.chosen_map in mlist: File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/segger/segment_dialog.py"", line 420, in _get_chosen_map return self._map_menu.value File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 255, in value return self.item_map[text] KeyError: 'cryosparc_P11_J33_004_volume_map.mrc #1' Error processing trigger ""remove models"": 'cryosparc_P11_J33_004_volume_map.mrc #1': KeyError: 'cryosparc_P11_J33_004_volume_map.mrc #1' File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 255, in value return self.item_map[text] See log for complete Python traceback. Traceback (most recent call last): File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 287, in _items_change prev_value = self.value File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 255, in value return self.item_map[text] KeyError: 'cryosparc_P11_J33_004_volume_map.mrc #1' Error processing trigger ""remove models"": 'cryosparc_P11_J33_004_volume_map.mrc #1': KeyError: 'cryosparc_P11_J33_004_volume_map.mrc #1' File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py"", line 255, in value return self.item_map[text] See log for complete Python traceback. OpenGL version: 4.1 INTEL-12.9.22 OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 650 OpenGL vendor: Intel Inc. }}} " defect accepted minor General Controls Tom Goddard all ChimeraX