id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 3111 Errors restoring maps produces inconsistent state chimerax-bug-report@… Tom Goddard "{{{ The following bug report has been submitted: Platform: Darwin-18.7.0-x86_64-i386-64bit ChimeraX Version: 0.91 (2019-11-26) Description (Describe the actions that caused this problem to occur here) Log: UCSF ChimeraX version: 0.91 (2019-11-26) © 2016-2019 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /data/disk3/modeling/2020-intact-phage/Intact-20200427.cxs Summary of feedback from opening /data/disk3/modeling/2020-intact- phage/Intact-20200427.cxs --- warnings | restore_snapshot for ""Volume"" returned None restore_snapshot for ""VolumeSurface"" returned None restore_snapshot for ""Volume"" returned None restore_snapshot for ""VolumeSurface"" returned None restore_snapshot for ""Volume"" returned None 37 messages similar to the above omitted notes | Error opening map ""/data/disk3/modeling/2020-intact- phage/Intact-20200427.cxs"": File Intact-20200427.cxs, format mrc MRC data value type (1952539508) is not 8 or 16 bit integers or 32 bit floats Error opening map ""/data/disk3/modeling/2020-intact- phage/fiber-5.4-seg-c6.mrc"": File fiber-5.4-seg-c6.mrc, format mrc File size 23609344 too small for grid size (680,680,680) opened ChimeraX session Traceback (most recent call last): File ""/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/3FED82B3-1CD7-4E14-9F38-0219847341AB/d/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 ""/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/3FED82B3-1CD7-4E14-9F38-0219847341AB/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/model_panel/tool.py"", line 158, in lambda *args, ft=self._fill_tree: ft(always_rebuild=True)) File ""/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/3FED82B3-1CD7-4E14-9F38-0219847341AB/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/model_panel/tool.py"", line 203, in _fill_tree parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1] IndexError: list index out of range Error processing trigger ""new frame"": IndexError: list index out of range File ""/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/3FED82B3-1CD7-4E14-9F38-0219847341AB/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/model_panel/tool.py"", line 203, in _fill_tree parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1] See log for complete Python traceback. Traceback (most recent call last): File ""/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/3FED82B3-1CD7-4E14-9F38-0219847341AB/d/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 ""/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/3FED82B3-1CD7-4E14-9F38-0219847341AB/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/model_panel/tool.py"", line 158, in lambda *args, ft=self._fill_tree: ft(always_rebuild=True)) File ""/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/3FED82B3-1CD7-4E14-9F38-0219847341AB/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/model_panel/tool.py"", line 203, in _fill_tree parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1] IndexError: list index out of range Error processing trigger ""new frame"": IndexError: list index out of range File ""/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/3FED82B3-1CD7-4E14-9F38-0219847341AB/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/model_panel/tool.py"", line 203, in _fill_tree parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1] See log for complete Python traceback. > save /Users/chunyan/Desktop/image1.png supersample 3 > save /Users/chunyan/Desktop/image2.png supersample 3 Traceback (most recent call last): File ""/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/3FED82B3-1CD7-4E14-9F38-0219847341AB/d/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 ""/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/3FED82B3-1CD7-4E14-9F38-0219847341AB/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/model_panel/tool.py"", line 158, in lambda *args, ft=self._fill_tree: ft(always_rebuild=True)) File ""/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/3FED82B3-1CD7-4E14-9F38-0219847341AB/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/model_panel/tool.py"", line 203, in _fill_tree parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1] IndexError: list index out of range Error processing trigger ""new frame"": IndexError: list index out of range File ""/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/3FED82B3-1CD7-4E14-9F38-0219847341AB/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/model_panel/tool.py"", line 203, in _fill_tree parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1] See log for complete Python traceback. Traceback (most recent call last): File ""/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/3FED82B3-1CD7-4E14-9F38-0219847341AB/d/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 ""/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/3FED82B3-1CD7-4E14-9F38-0219847341AB/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/model_panel/tool.py"", line 158, in lambda *args, ft=self._fill_tree: ft(always_rebuild=True)) File ""/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/3FED82B3-1CD7-4E14-9F38-0219847341AB/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/model_panel/tool.py"", line 203, in _fill_tree parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1] IndexError: list index out of range Error processing trigger ""new frame"": IndexError: list index out of range File ""/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/3FED82B3-1CD7-4E14-9F38-0219847341AB/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/model_panel/tool.py"", line 203, in _fill_tree parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1] See log for complete Python traceback. Traceback (most recent call last): File ""/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/3FED82B3-1CD7-4E14-9F38-0219847341AB/d/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 ""/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/3FED82B3-1CD7-4E14-9F38-0219847341AB/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/model_panel/tool.py"", line 158, in lambda *args, ft=self._fill_tree: ft(always_rebuild=True)) File ""/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/3FED82B3-1CD7-4E14-9F38-0219847341AB/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/model_panel/tool.py"", line 203, in _fill_tree parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1] IndexError: list index out of range Error processing trigger ""new frame"": IndexError: list index out of range File ""/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/3FED82B3-1CD7-4E14-9F38-0219847341AB/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/model_panel/tool.py"", line 203, in _fill_tree parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1] See log for complete Python traceback. Traceback (most recent call last): File ""/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/3FED82B3-1CD7-4E14-9F38-0219847341AB/d/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 ""/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/3FED82B3-1CD7-4E14-9F38-0219847341AB/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/model_panel/tool.py"", line 158, in lambda *args, ft=self._fill_tree: ft(always_rebuild=True)) File ""/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/3FED82B3-1CD7-4E14-9F38-0219847341AB/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/model_panel/tool.py"", line 203, in _fill_tree parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1] IndexError: list index out of range Error processing trigger ""new frame"": IndexError: list index out of range File ""/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/3FED82B3-1CD7-4E14-9F38-0219847341AB/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/model_panel/tool.py"", line 203, in _fill_tree parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1] See log for complete Python traceback. > open /data/disk3/modeling/2020-intact-phage/Intact-20200427.cxs Summary of feedback from opening /data/disk3/modeling/2020-intact- phage/Intact-20200427.cxs --- warnings | restore_snapshot for ""Volume"" returned None restore_snapshot for ""VolumeSurface"" returned None restore_snapshot for ""Volume"" returned None restore_snapshot for ""VolumeSurface"" returned None restore_snapshot for ""Volume"" returned None 37 messages similar to the above omitted notes | Error opening map ""/data/disk3/modeling/2020-intact- phage/Intact-20200427.cxs"": File Intact-20200427.cxs, format mrc MRC data value type (1952539508) is not 8 or 16 bit integers or 32 bit floats Error opening map ""/data/disk3/modeling/2020-intact- phage/fiber-5.4-seg-c6.mrc"": File fiber-5.4-seg-c6.mrc, format mrc File size 744030208 too small for grid size (680,680,680) opened ChimeraX session Traceback (most recent call last): File ""/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/3FED82B3-1CD7-4E14-9F38-0219847341AB/d/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 ""/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/3FED82B3-1CD7-4E14-9F38-0219847341AB/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/model_panel/tool.py"", line 158, in lambda *args, ft=self._fill_tree: ft(always_rebuild=True)) File ""/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/3FED82B3-1CD7-4E14-9F38-0219847341AB/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/model_panel/tool.py"", line 203, in _fill_tree parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1] IndexError: list index out of range Error processing trigger ""new frame"": IndexError: list index out of range File ""/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/3FED82B3-1CD7-4E14-9F38-0219847341AB/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/model_panel/tool.py"", line 203, in _fill_tree parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1] See log for complete Python traceback. Traceback (most recent call last): File ""/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/3FED82B3-1CD7-4E14-9F38-0219847341AB/d/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 ""/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/3FED82B3-1CD7-4E14-9F38-0219847341AB/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/model_panel/tool.py"", line 158, in lambda *args, ft=self._fill_tree: ft(always_rebuild=True)) File ""/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/3FED82B3-1CD7-4E14-9F38-0219847341AB/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/model_panel/tool.py"", line 203, in _fill_tree parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1] IndexError: list index out of range Error processing trigger ""new frame"": IndexError: list index out of range File ""/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/3FED82B3-1CD7-4E14-9F38-0219847341AB/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/model_panel/tool.py"", line 203, in _fill_tree parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1] See log for complete Python traceback. Traceback (most recent call last): File ""/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/3FED82B3-1CD7-4E14-9F38-0219847341AB/d/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 ""/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/3FED82B3-1CD7-4E14-9F38-0219847341AB/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/model_panel/tool.py"", line 158, in lambda *args, ft=self._fill_tree: ft(always_rebuild=True)) File ""/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/3FED82B3-1CD7-4E14-9F38-0219847341AB/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/model_panel/tool.py"", line 203, in _fill_tree parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1] IndexError: list index out of range Error processing trigger ""new frame"": IndexError: list index out of range File ""/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/3FED82B3-1CD7-4E14-9F38-0219847341AB/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/model_panel/tool.py"", line 203, in _fill_tree parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1] See log for complete Python traceback. > open /data/disk3/modeling/2020-intact-phage/Intact-20200427.cxs Summary of feedback from opening /data/disk3/modeling/2020-intact- phage/Intact-20200427.cxs --- warnings | restore_snapshot for ""Volume"" returned None restore_snapshot for ""VolumeSurface"" returned None restore_snapshot for ""Volume"" returned None restore_snapshot for ""VolumeSurface"" returned None restore_snapshot for ""Volume"" returned None 31 messages similar to the above omitted notes | Error opening map ""/data/disk3/modeling/2020-intact- phage/Intact-20200427.cxs"": File Intact-20200427.cxs, format mrc MRC data value type (1952539508) is not 8 or 16 bit integers or 32 bit floats opened ChimeraX session > lighting soft Traceback (most recent call last): File ""/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/3FED82B3-1CD7-4E14-9F38-0219847341AB/d/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 ""/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/3FED82B3-1CD7-4E14-9F38-0219847341AB/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/model_panel/tool.py"", line 158, in lambda *args, ft=self._fill_tree: ft(always_rebuild=True)) File ""/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/3FED82B3-1CD7-4E14-9F38-0219847341AB/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/model_panel/tool.py"", line 203, in _fill_tree parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1] IndexError: list index out of range Error processing trigger ""new frame"": IndexError: list index out of range File ""/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/3FED82B3-1CD7-4E14-9F38-0219847341AB/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/model_panel/tool.py"", line 203, in _fill_tree parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1] See log for complete Python traceback. Traceback (most recent call last): File ""/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/3FED82B3-1CD7-4E14-9F38-0219847341AB/d/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 ""/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/3FED82B3-1CD7-4E14-9F38-0219847341AB/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/model_panel/tool.py"", line 158, in lambda *args, ft=self._fill_tree: ft(always_rebuild=True)) File ""/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/3FED82B3-1CD7-4E14-9F38-0219847341AB/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/model_panel/tool.py"", line 203, in _fill_tree parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1] IndexError: list index out of range Error processing trigger ""new frame"": IndexError: list index out of range File ""/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/3FED82B3-1CD7-4E14-9F38-0219847341AB/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/model_panel/tool.py"", line 203, in _fill_tree parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1] See log for complete Python traceback. OpenGL version: 4.1 INTEL-12.10.12 OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 655 OpenGL vendor: Intel Inc. }}} " defect closed normal Sessions can't reproduce Eric Pettersen all ChimeraX