Opened 5 years ago

Closed 5 years ago

#3279 closed defect (duplicate)

Prevent bad model hierarchies from being formed

Reported by: chimerax-bug-report@… Owned by: Tom Goddard
Priority: normal Milestone:
Component: Core Version:
Keywords: Cc: Eric Pettersen
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 /Users/chunyan/2020/gp8-asym/gp8-asym-20200507.cxs

opened ChimeraX session  
Traceback (most recent call last):  
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/138DA745-64A9-4F39-90E0-678CBAF89F38/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/138DA745-64A9-4F39-90E0-678CBAF89F38/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/138DA745-64A9-4F39-90E0-678CBAF89F38/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/138DA745-64A9-4F39-90E0-678CBAF89F38/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/138DA745-64A9-4F39-90E0-678CBAF89F38/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/138DA745-64A9-4F39-90E0-678CBAF89F38/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/138DA745-64A9-4F39-90E0-678CBAF89F38/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/138DA745-64A9-4F39-90E0-678CBAF89F38/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/138DA745-64A9-4F39-90E0-678CBAF89F38/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/138DA745-64A9-4F39-90E0-678CBAF89F38/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/138DA745-64A9-4F39-90E0-678CBAF89F38/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/138DA745-64A9-4F39-90E0-678CBAF89F38/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 /Users/chunyan/2020/gp8-asym/gp8-asym-20200507.cxs

opened ChimeraX session  
Traceback (most recent call last):  
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/138DA745-64A9-4F39-90E0-678CBAF89F38/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/138DA745-64A9-4F39-90E0-678CBAF89F38/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/138DA745-64A9-4F39-90E0-678CBAF89F38/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/138DA745-64A9-4F39-90E0-678CBAF89F38/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/138DA745-64A9-4F39-90E0-678CBAF89F38/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/138DA745-64A9-4F39-90E0-678CBAF89F38/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/138DA745-64A9-4F39-90E0-678CBAF89F38/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/138DA745-64A9-4F39-90E0-678CBAF89F38/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/138DA745-64A9-4F39-90E0-678CBAF89F38/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/138DA745-64A9-4F39-90E0-678CBAF89F38/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/138DA745-64A9-4F39-90E0-678CBAF89F38/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/138DA745-64A9-4F39-90E0-678CBAF89F38/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/138DA745-64A9-4F39-90E0-678CBAF89F38/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/138DA745-64A9-4F39-90E0-678CBAF89F38/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/138DA745-64A9-4F39-90E0-678CBAF89F38/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/138DA745-64A9-4F39-90E0-678CBAF89F38/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.  
  

> surface dust #11 size 30

> surface dust #7 size 30

> lighting soft

> toolshed show "Side View"

Traceback (most recent call last):  
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/138DA745-64A9-4F39-90E0-678CBAF89F38/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/138DA745-64A9-4F39-90E0-678CBAF89F38/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/138DA745-64A9-4F39-90E0-678CBAF89F38/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/138DA745-64A9-4F39-90E0-678CBAF89F38/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.  
  

> lighting flat

Traceback (most recent call last):  
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/138DA745-64A9-4F39-90E0-678CBAF89F38/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/138DA745-64A9-4F39-90E0-678CBAF89F38/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/138DA745-64A9-4F39-90E0-678CBAF89F38/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/138DA745-64A9-4F39-90E0-678CBAF89F38/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/138DA745-64A9-4F39-90E0-678CBAF89F38/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/138DA745-64A9-4F39-90E0-678CBAF89F38/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/138DA745-64A9-4F39-90E0-678CBAF89F38/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/138DA745-64A9-4F39-90E0-678CBAF89F38/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/138DA745-64A9-4F39-90E0-678CBAF89F38/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/138DA745-64A9-4F39-90E0-678CBAF89F38/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/138DA745-64A9-4F39-90E0-678CBAF89F38/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/138DA745-64A9-4F39-90E0-678CBAF89F38/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.  
  

> volume #38 level 0.01143

Traceback (most recent call last):  
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/138DA745-64A9-4F39-90E0-678CBAF89F38/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/138DA745-64A9-4F39-90E0-678CBAF89F38/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/138DA745-64A9-4F39-90E0-678CBAF89F38/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/138DA745-64A9-4F39-90E0-678CBAF89F38/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/138DA745-64A9-4F39-90E0-678CBAF89F38/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/138DA745-64A9-4F39-90E0-678CBAF89F38/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/138DA745-64A9-4F39-90E0-678CBAF89F38/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/138DA745-64A9-4F39-90E0-678CBAF89F38/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.  
  

> volume #38 color #ccb2ff

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> volume #38 color #cccac8ab

> volume #38 color #cccac8ad

> volume #38 color #cccac8ae

> hide sel cartoons

> volume #38 color #cc83c8ae

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> volume #38 color #cc852eae

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> volume #38 color #ffca29ae

> volume #38 color #ffcb29ae

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> volume #38 color #ffde29ae

> volume #38 color #ffe129ae

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> volume #38 color #ffe929ae

> volume #38 color #ffec29ae

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> volume #38 color #ffff29ee

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> volume #38 color #ffff29c2

> volume #38 color #ffff29af

> volume #38 color #ffff299c

> volume #38 color #ffff2993

> hide sel cartoons

> volume #38 color #ffd42993

> volume #38 color #d7d42993

> volume #38 color #d7d48793

> volume #38 color #d7d47893

> volume #38 color #d7d47193

> volume #38 color #d7d45193

> volume #38 color #d7d43493

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> volume #38 color #d7d40093

> volume #38 color #d7e60093

> volume #38 color #d7e80093

> volume #38 color #d7ec0093

> volume #38 color #d7ff0093

> volume #38 color #e3ff0093

> volume #38 color #edff0093

> volume #38 color #ffff0093

> surface dust #38 size 30

> volume #38 level 0.008996

> lighting soft

> volume #38 level 0.01065

> graphics silhouettes false

> graphics silhouettes true

> lighting shadows true intensity 0.5

> lighting flat

> lighting full

> lighting soft

> lighting full

> lighting soft

> lighting full

> volume #38 level 0.01065

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> volume #38 level 0.006128

> volume #38 level 0.008301

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> surface dust #41 size 30

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> volume #42.1 step 1

> volume #42.1 level 0.003074

> volume #42.1 level 0.004995

> surface dust #42.1 size 50

> volume #42.1 color #3dc5dbfb

> volume #42.1 color #3dc5dbfc

> volume #42.1 color #3dc5db

> volume #42.1 level 0.0101

> volume #42.1 level 0.009498

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> surface dust #40 size 30

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> lighting flat

> volume #38 level 0.01113

> lighting soft

> volume #11 color #feffffe3

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> volume #11 color #fefffff5

> volume #11 color #fefffffe

> volume #11 color #feffff

> volume #11 color #daffff

> volume #11 color #dae1ff

> volume #11 color #dae1db

> volume #11 color #d9e1db

> lighting flat

> volume #11 color #d9e1dbee

> volume #11 color #d9e1dbed

> volume #11 color #d9e1dbeb

> volume #11 color #d9e1dbde

> volume #11 color #d9e1dbe2

> volume #11 color #d9e1db

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> volume #11 color #d9e2ec

> volume #11 color #d9e6ec

> volume #11 color #d9e9ec

> volume #11 color #d9eaec

> volume #11 color #d9edec

> volume #11 color #d9eeec

> volume #11 color #d9efec

> volume #11 color #d9eeec

> volume #11 color #daeeec

> volume #11 color #dbeeec

> volume #11 color #e4eeec

> volume #11 color #e7eeec

> volume #11 color #eaeeec

> volume #11 color #eceeec

> volume #11 color #efeeec

> volume #11 color #efeeece1

> volume #11 color #efeeecd3

> volume #11 color #efeeeca0

> volume #11 color #efeeec9e

> volume #11 color #efeeec9b

> volume #11 color #efeeec9a

> volume #11 color #efeeec98

> volume #11 color #efeeec95

> volume #11 color #efeeec8f

> volume #11 color #efeeec8a

> volume #11 color #efeeec85

> volume #11 color #efeeec82

> volume #11 color #efeeec7e

> volume #11 color #efeeec7c

> volume #11 color #efeeec7b

> volume #11 color #efeeec7a

> volume #11 color #efeeec7b

> volume #11 color #efeeec80

> volume #11 color #efeeec88

> volume #11 color #efeeec90

> volume #11 color #efeeec98

> volume #11 color #efeeeca6

> volume #11 color #efeeecb8

> volume #11 color #efeeecc6

> volume #11 color #efeeecd2

> volume #11 color #efeeecdf

> volume #11 color #efeeeceb

> volume #11 color #efeeecf4

> volume #11 color #efeeecf6

> volume #11 color #efeeecf8

> volume #11 color #efeeecfb

> volume #11 color #efeeec

> lighting soft

Traceback (most recent call last):  
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/138DA745-64A9-4F39-90E0-678CBAF89F38/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/138DA745-64A9-4F39-90E0-678CBAF89F38/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/138DA745-64A9-4F39-90E0-678CBAF89F38/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/138DA745-64A9-4F39-90E0-678CBAF89F38/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/138DA745-64A9-4F39-90E0-678CBAF89F38/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/138DA745-64A9-4F39-90E0-678CBAF89F38/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/138DA745-64A9-4F39-90E0-678CBAF89F38/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/138DA745-64A9-4F39-90E0-678CBAF89F38/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.  
  

> volume #40 level 0.003183

> surface dust #42.1 size 10

> surface dust #11 size 10

> surface dust #11 size 30

> surface dust #11 size 40

> surface dust #11 size 50

> volume #11 level 0.002434

> view

Traceback (most recent call last):  
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/138DA745-64A9-4F39-90E0-678CBAF89F38/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/138DA745-64A9-4F39-90E0-678CBAF89F38/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/138DA745-64A9-4F39-90E0-678CBAF89F38/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/138DA745-64A9-4F39-90E0-678CBAF89F38/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/138DA745-64A9-4F39-90E0-678CBAF89F38/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/138DA745-64A9-4F39-90E0-678CBAF89F38/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/138DA745-64A9-4F39-90E0-678CBAF89F38/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/138DA745-64A9-4F39-90E0-678CBAF89F38/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.  
  

> volume #11 level 0.003434

> surface dust #11 size 50

> volume #11 level 0.003719

> volume #11 level 0.004148

> volume #11 level 0.004005

> volume #11 level 0.003577

> toolshed show "Side View"

> view

> view orient

Traceback (most recent call last):  
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/138DA745-64A9-4F39-90E0-678CBAF89F38/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/138DA745-64A9-4F39-90E0-678CBAF89F38/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/138DA745-64A9-4F39-90E0-678CBAF89F38/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/138DA745-64A9-4F39-90E0-678CBAF89F38/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.  
  

> volume #11 color #efeec8

> volume #11 color #efeed4

> volume #11 color #efeeb0

> volume #11 color #efb2b0

> volume #11 color #c1b2b0

> volume #11 color #c1e8b0

> volume #11 color #c1e888

> volume #11 color #c1e887

> volume #11 color #c1e856

> volume #11 color #c1e83a

> volume #11 color #c1d83a

> volume #11 color #e3d83a

> volume #11 color #f7d83a

> volume #11 color #f7ef3a

> volume #11 color #f7fb3a

> volume #11 color #f7fb39

> volume #11 color #f7fb32

> volume #11 color #f7fb00

> volume #11 color #f7ce00

> volume #11 color #f7e400

> volume #11 color #f7f800

> volume #11 color #e8f800

> volume #11 color #e4f800

> volume #11 color #e3f800

> volume #11 color #e8f800

> volume #11 color #eff800

> volume #11 color #fff800

> volume #11 color #ffe200

> volume #11 color #ffe300

> volume #11 color #ffe700

> volume #11 color #ffee00

> volume #11 color #fff100

> volume #11 color #fff600

> volume #11 color #fff700

> volume #11 color #fff900

> volume #11 color #fffa00

> volume #11 color #fffb00

> volume #11 color #fffc00

> volume #11 color #fffd00

> volume #11 color yellow

> volume #11 color #ffff0c

> volume #11 color #ffff12

> volume #11 color #ffff14

> volume #11 color #ffff15

> volume #11 color #ffff16

> volume #11 color #ffff18

> volume #11 color #ffff1f

> volume #11 color #ffff21

> volume #11 color #ffff23

> volume #11 level 0.004005

> volume #11 level 0.004

> volume #11 level 0.003

> volume #11 level 0.003571

> volume #11 color #ffff23a2

> volume #11 color #ffff2371

> volume #11 level 0.004

> volume #11 level 0.004714

> volume #11 level 0.004571

> volume #11 level 0.004

> volume #11 level 0.003714

> volume #11 level 0.003571

> volume #11 color #bdff2371

> volume #11 color #bdbc2371

> volume #11 color #bdbcc071

> volume #11 color #bdbcc0c5

> volume #11 color #e4bcc0c5

> volume #11 color #e4e5c0c5

> volume #11 color #e4e5e3c5

> volume #11 color #e4e5e2c5

> volume #11 color #e4e5dcc5

> volume #11 color #e4dcdcc5

> volume #11 color #dcdcdcc5

> volume #11 color #dcdcdc99

Traceback (most recent call last):  
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/138DA745-64A9-4F39-90E0-678CBAF89F38/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/138DA745-64A9-4F39-90E0-678CBAF89F38/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/138DA745-64A9-4F39-90E0-678CBAF89F38/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/138DA745-64A9-4F39-90E0-678CBAF89F38/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.  
  

> volume #11 color #dcdcdc97

> volume #11 color #dcdcdc7c

> volume #11 color #dcdcdc76

> volume #11 color #dcdcdc74

> volume #11 color #dcdcdc73

> volume #11 color #dcdcdc71

> volume #11 color #dcdcdc70

> volume #11 color #dcdcdc6f

> volume #11 color #dcdcdc6e

> volume #11 color #dcdcdc6d

> volume #11 color #dcdcdc6c

> volume #11 color #dcdcdc6a

> volume #11 color #dcdcdc69

> volume #11 color #dcdcdc68

> volume #11 color #dcdcdc66

> volume #11 color #dcdcdc65

Traceback (most recent call last):  
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/138DA745-64A9-4F39-90E0-678CBAF89F38/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/138DA745-64A9-4F39-90E0-678CBAF89F38/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/138DA745-64A9-4F39-90E0-678CBAF89F38/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/138DA745-64A9-4F39-90E0-678CBAF89F38/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.  
  

> volume #10 level 0.018

Traceback (most recent call last):  
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/138DA745-64A9-4F39-90E0-678CBAF89F38/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/138DA745-64A9-4F39-90E0-678CBAF89F38/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/138DA745-64A9-4F39-90E0-678CBAF89F38/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/138DA745-64A9-4F39-90E0-678CBAF89F38/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.  
  

> volume #11 level 0.006714

> volume #11 color #dcdcaf65

> volume #11 color #dcdc9365

> volume #11 color #dc909365

> volume #11 color #90909365

> volume #11 color #90909367

> volume #11 color #90909371

> volume #11 color #909093bc

> volume #11 color #909093d7

> volume #11 color #909093ee

> volume #11 color #909093fd

> volume #11 color #909093

> volume #11 color #919093

> volume #11 color #949093

> volume #11 color #ae9093

> volume #11 color #b89093

> volume #11 color #be9093

> volume #11 color #c09093

> volume #11 color #c39093

> volume #11 color #c89093

> volume #11 color #cc9093

> volume #11 color #d09093

> volume #11 color #d29093

> volume #11 color #d39093

> volume #11 color #d49093

> volume #11 color #d69093

> volume #11 color #da9093

> volume #11 color #dc9093

> volume #11 color #e79093

> volume #11 color #ed9093

> volume #11 color #f19093

> volume #11 color #f49093

> volume #11 color #f79093

> volume #11 color #ff9093

> volume #11 color #ffa093

> volume #11 color #ffa293

> volume #11 color #ffbc93

> volume #11 color #ffbf93

> volume #11 color #ffc893

> volume #11 color #ffce93

> volume #11 color #ffd393

> volume #11 color #ffd793

> volume #11 color #ffd893

> volume #11 color #ffda93

> volume #11 color #ffdb93

> volume #11 color #ffdb92

> volume #11 color #ffdb8d

> volume #11 color #ffdb54

> volume #11 color #ffdb47

> volume #11 color #ffdb44

> volume #11 color #ffdb40

> volume #11 color #ffdb3c

> volume #11 color #ffdb39

> volume #11 color #ffdb36

> volume #11 color #ffdb33

> volume #11 color #ffdb32

> volume #11 color #ffdb31

> volume #11 color #ffdb2b

> volume #11 color #ffdb26

> volume #11 color #ffdb24

> volume #11 color #ffdb2e

> volume #11 color #ffdb31

> volume #11 color #ffdb36

> volume #11 color #ffdb3b

> volume #11 color #ffdb3f

> volume #11 color #ffdb43

> volume #11 color #ffdb45

> volume #11 color #ffdb48

> volume #11 color #ffdb4a

> volume #11 color #ffdb4b

> volume #11 color #ffdb4c

> volume #11 color #ffdb4e

> volume #11 color #ffdb4f

> volume #11 color #ffdb54

> volume #11 color #ffdb5b

> volume #11 color #ffdb5c

> volume #11 color #ffdb5d

> volume #11 color #ffdb5e

> volume #11 color #ffdb5f

> volume #11 color #ffdb60

> volume #11 color #ffdb61

> volume #11 color #ffdb63

> volume #11 color #ffdb67

> volume #11 color #ffdb68

> volume #11 color #ffdb69

> volume #11 color #ffdb6a

> volume #11 color #ffdc6a

> volume #11 color #ffe36a

> volume #11 color #ffe96a

> volume #11 color #ffec6a

> volume #11 color #ffed6a

> volume #11 color #ffee6a

> volume #11 level 0.003714

Traceback (most recent call last):  
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/138DA745-64A9-4F39-90E0-678CBAF89F38/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/138DA745-64A9-4F39-90E0-678CBAF89F38/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/138DA745-64A9-4F39-90E0-678CBAF89F38/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/138DA745-64A9-4F39-90E0-678CBAF89F38/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.  
  

> view name p1

> roll y

Unknown command: movie stip  

> movie stop

No movie being recorded.  

> stop

> view p1

> view p1

> roll z

> stop

> movie reset

No movie being recorded.  

> open /Users/chunyan/2020/gp8-c12/gp8-mono_real_space_refined-small-c12.pdb

Chain information for gp8-mono_real_space_refined-small-c12.pdb #44  
---  
Chain | Description  
A B C D E F G H I J K L | No description available  
  
Traceback (most recent call last):  
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/138DA745-64A9-4F39-90E0-678CBAF89F38/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/138DA745-64A9-4F39-90E0-678CBAF89F38/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/138DA745-64A9-4F39-90E0-678CBAF89F38/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/138DA745-64A9-4F39-90E0-678CBAF89F38/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.  
  

> view

> hide sel cartoons

> hide sel atoms

> open /Users/chunyan/2020/gp8-c12/gp8-WCY-C12-coot-basedon-newdata-
> mono-C12.pdb

Chain information for gp8-WCY-C12-coot-basedon-newdata-mono-C12.pdb #46  
---  
Chain | Description  
A B C D E F G H I J K L | No description available  
  
Traceback (most recent call last):  
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/138DA745-64A9-4F39-90E0-678CBAF89F38/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/138DA745-64A9-4F39-90E0-678CBAF89F38/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/138DA745-64A9-4F39-90E0-678CBAF89F38/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/138DA745-64A9-4F39-90E0-678CBAF89F38/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.  
  

> ui mousemode rightMode "translate selected models"

> ui mousemode rightMode "rotate selected models"

> lighting flat

> hide sel atoms

> show sel cartoons

> show sel cartoons

> ui mousemode rightMode "translate selected models"

> ui mousemode rightMode "rotate selected models"

> fitmap #46 inMap #11

Fit molecule gp8-WCY-C12-coot-basedon-newdata-mono-C12.pdb (#46) to map
gp8-basen-new.mrc (#11) using 49008 atoms  
average map value = 0.01412, steps = 144  
shifted from previous position = 10.1  
rotated from previous position = 15.3 degrees  
atoms outside contour = 7777, contour level = 0.0037143  
  
Position of gp8-WCY-C12-coot-basedon-newdata-mono-C12.pdb (#46) relative to
gp8-basen-new.mrc (#11) coordinates:  
Matrix rotation and translation  
0.59665156 0.80250003 -0.00078510 -83.56315012  
0.80250041 -0.59665117 0.00068583 166.64122190  
0.00008194 -0.00103925 -0.99999945 421.53198690  
Axis -0.89349136 -0.44908033 0.00019668  
Axis point 0.00000000 104.43443074 210.71179598  
Rotation angle (degrees) 179.94468917  
Shift along axis -0.08943471  
  

> volume #11 color #ffee8f

> volume #11 color #ffb18f

> volume #11 color #b4b18f

> volume #11 color #b4b1b3

> volume #11 color #b4b1b3fe

> volume #11 color #b4b1b3f2

> volume #11 color #b4b1b3e4

> volume #11 color #b4b1b3d5

> volume #11 color #b4b1b3c6

> volume #11 color #b4b1b3ba

> volume #11 color #b4b1b3b0

> volume #11 color #b4b1b3a6

> volume #11 color #b4b1b39e

> volume #11 color #b4b1b397

> volume #11 color #b4b1b390

> volume #11 color #b4b1b38c

> volume #11 color #b4b1b389

> volume #11 color #b4b1b384

> volume #11 color #b4b1b380

> volume #11 color #b4b1b370

> volume #11 color #b4b1b361

> volume #11 color #b4b1b393

> volume #11 color #b4b1b3b6

> volume #11 color #b4b1b3b8

> volume #11 color #b4b1b3b9

> volume #11 color #b4b1b3c4

> volume #11 color #b4b1e5c4

> volume #11 color #b4dfe5c4

> volume #11 color #d5dfe5c4

> volume #11 color #d5dfe577

> volume #11 color #d5dfe55b

> volume #11 color #d5dfe553

> volume #11 color #d5dfe551

> volume #11 color #d5dfe550

> volume #11 color #d5dfe562

> volume #11 color #d5dfe580

> volume #11 color #d5dfe592

> volume #11 color #d5dfe59b

> volume #11 color #d5dfe59c

> volume #11 color #d5dfe59d

> volume #11 color #d5dfe59e

> volume #11 color #d5dfe59f

> volume #11 color #d5dfe5a0

> volume #11 color #d5dfe5a1

> volume #11 color #e2dfe5a1

> volume #11 color #e2dee5a1

> volume #11 color #e2dce5a1

> volume #11 color #e1dce5a1

> volume #11 color #dcdce5a1

> volume #11 color #dcdce4a1

> volume #11 color #dcdcdca1

> select #46

49008 atoms, 49740 bonds, 1 model selected  

> hide sel cartoons

Traceback (most recent call last):  
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/138DA745-64A9-4F39-90E0-678CBAF89F38/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/138DA745-64A9-4F39-90E0-678CBAF89F38/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/138DA745-64A9-4F39-90E0-678CBAF89F38/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/138DA745-64A9-4F39-90E0-678CBAF89F38/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.  
  

> volume #11 color gainsboro

> volume #11 color #dcdc5b

> volume #11 color #dcdc13

> show sel atoms

> hide sel atoms

> lighting soft

> lighting soft

> lighting simple

> lighting full

> lighting soft

> lighting full

> volume #40 level 0.003297

> volume #11 level 0.003

> volume #11 level 0.004

> volume #11 level 0.0035

> volume #11 level 0.006071

> volume #11 level 0.007

> volume #11 level 0.005

> volume #11 level 0.006

> volume #11 color #dcdc13ac

> volume #11 color #dcdc138b

> show sel cartoons

> show sel cartoons

> color #46: yellow

> select #46

49008 atoms, 49740 bonds, 1 model selected  

> color #46 yellow

> volume #11 color #dcdcdb8b

> volume #11 color #dcdcdb8c

> volume #11 color #dcdcdb8d

> volume #11 color #dcdcdb9e

> volume #11 color #dcdcdba5

> volume #11 color #dcdcdba6

> volume #11 color #dcdcdba8

> volume #11 color #dcdcdba9

> volume #11 color #dcdcdbaa

> volume #11 color #dcdcdbac

> volume #11 color #dcdcdbad

> volume #11 color #dcdcdbae

> volume #11 color #dcdcdbaf

> volume #11 color #dcdcdbb0

> volume #11 color #dcdcdbb1

> volume #11 color #dcdcdbb0

> volume #11 color #dcdc46b0

> volume #11 color #dcdcd9b0

> volume #11 color #dcdcdcb0

> volume #11 color #dcdcdc99

> volume #11 color #dcebdc99

> volume #11 color #dcffdc99

> volume #11 color #ecffdc99

> volume #11 color #f0ffdc99

> volume #11 color #ffffdc99

> volume #11 color #ffffe899

> volume #11 color #ffffec99

> volume #11 color #ffffff99

> select clear

> volume #11 level 0.005

> volume #11 level 0.007

> volume #11 level 0.0054

> surface dust #11 size 11

> surface dust #11 size 20

> surface dust #11 size 10

> volume #11 level 0.005

> surface dust #11 size 20

> surface dust #11 size 10

> volume #11 level 0.004

> volume #11 level 0.006

> volume #11 level 0.0055




OpenGL version: 4.1 INTEL-12.10.12
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 655
OpenGL vendor: Intel Inc.

Change History (3)

comment:1 by Tom Goddard, 5 years ago

Component: Unassigned → General Controls
Owner: set to Eric Pettersen
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Model panel, list index out of range, restoring session

comment:2 by Eric Pettersen, 5 years ago

Cc: Eric Pettersen added
Component: General Controls → Core
Owner: changed from Eric Pettersen to Tom Goddard
Summary: Model panel, list index out of range, restoring session → Prevent bad model hierarchies from being formed

comment:3 by Eric Pettersen, 5 years ago

Resolution: → duplicate
Status: assigned → closed
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