Opened 5 years ago

Closed 5 years ago

#3111 closed defect (can't reproduce)

Errors restoring maps produces inconsistent state

Reported by: chimerax-bug-report@… Owned by: Tom Goddard
Priority: normal Milestone:
Component: Sessions Version:
Keywords: Cc: pett
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

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>  
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>  
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>  
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>  
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>  
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>  
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>  
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>  
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>  
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>  
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>  
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.

Change History (2)

comment:1 by pett, 5 years ago

Cc: pett added
Component: Unassigned → Sessions
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Errors restoring maps produces inconsistent state

That error in the model panel seems to indicate that the model hierarchy is "missing a level" (e.g. there is a model #1.3.7 where there is no model #1.3 at all).

Probably will have to be closed as irreproducible.

comment:2 by Tom Goddard, 5 years ago

Resolution: → can't reproduce
Status: assigned → closed

There were many errors restoring this sessions where volume data models were not restored. Testing in current ChimeraX, missing volume data gives the warnings but not tracebacks from model panel. Bug was reported with old ChimeraX 0.91.

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)

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