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#3301 closed defect (duplicate)

Model panel, list index out of range, restoring session

Reported by:	chimerax-bug-report@…	Owned by:	Eric Pettersen
Priority:	normal	Milestone:
Component:	General Controls	Version:
Keywords:		Cc:	Tom Goddard
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-20200521-with-movie.cxs

opened ChimeraX session  
Traceback (most recent call last):  
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/DAE93E9E-A35E-408E-8D05-D79BAD7AD232/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/DAE93E9E-A35E-408E-8D05-D79BAD7AD232/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/DAE93E9E-A35E-408E-8D05-D79BAD7AD232/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/DAE93E9E-A35E-408E-8D05-D79BAD7AD232/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/DAE93E9E-A35E-408E-8D05-D79BAD7AD232/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/DAE93E9E-A35E-408E-8D05-D79BAD7AD232/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/DAE93E9E-A35E-408E-8D05-D79BAD7AD232/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/DAE93E9E-A35E-408E-8D05-D79BAD7AD232/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.  
  

> select #43

4 models selected  

> hide #43

> preset cartoons/nucleotides cylinders/stubs

Changed 0 atom styles  
Preset expands to these ChimeraX commands:

    
    
    show nucleic
    hide protein|solvent|H
    surf hide
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    cartoon
    cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    cartoon style ~(nucleic|strand) x round
    cartoon style (nucleic|strand) x rect
    cartoon style protein modeh tube rad 2 sides 24 thick 0.6
    cartoon style nucleic x round width 1.6 thick 1.6
    nucleotides stubs

  

> hide #44

> select #44

49008 atoms, 49740 bonds, 1 model selected  

> hide sel cartoons

> select #37

49008 atoms, 49740 bonds, 1 model selected  

> hide sel cartoons

> select #37:300-400

9360 atoms, 9480 bonds, 1 model selected  

> show sel cartoons

> lighting soft

> select clear

> open /Users/chunyan/2020/gp8-asym/part/channel-genome-interaction/gp8-new-
> assembled-300-400-0524-refined.pdb

Chain information for gp8-new-assembled-300-400-0524-refined.pdb #27  
---  
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/DAE93E9E-A35E-408E-8D05-D79BAD7AD232/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/DAE93E9E-A35E-408E-8D05-D79BAD7AD232/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/DAE93E9E-A35E-408E-8D05-D79BAD7AD232/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/DAE93E9E-A35E-408E-8D05-D79BAD7AD232/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.  
  

> matchmaker #27 to #37

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker gp8-new-assembled.pdb, chain F (#37) with gp8-new-
assembled-300-400-0524-refined.pdb, chain F (#27), sequence alignment score =
461.5  
RMSD between 96 pruned atom pairs is 0.739 angstroms; (across all 101 pairs:
1.001)  
  

> select #27

9360 atoms, 9480 bonds, 1 model selected  

> hide sel atoms

> show sel cartoons

> select #37

49008 atoms, 49740 bonds, 1 model selected  

> hide sel cartoons

> select #27

9360 atoms, 9480 bonds, 1 model selected  

> volume #25 color #ffffad

> volume #25 color #ffa9ad

> volume #25 color #a6a9ad

> volume #25 color #a6a9adfe

> volume #25 color #a6a9adf8

> volume #25 color #a6a9ad93

> volume #25 color #a6a9ad8f

> volume #25 color #a6a9ad80

> volume #25 color #a6a9ad75

> volume #25 color #a6a9ad6d

> volume #25 color #a6a9ad68

> volume #25 color #a6a9ad67

> volume #25 color #a6a9ad68

> volume #25 color #a6a9ad6c

> volume #25 color #a6a9ad71

> volume #25 color #a6a9ad73

> volume #25 color #a6a9ad75

> volume #25 color #a6a9ad79

> volume #25 color #a6a9ad7e

> volume #25 color #a6a9ad84

> volume #25 color #a6a9ad88

> volume #25 color #a6a9ad89

> volume #25 color #a6a9ad8a

> volume #25 color #a6a9ad8b

> volume #25 color #a6a9ad8e

> volume #25 color #a6a9ad8f

> volume #25 color #a6a9ad90

> volume #25 color #a6a9ad92

> volume #25 color #a6a9ad94

> volume #25 level 0.00397

> toolshed show "Side View"

Traceback (most recent call last):  
File
"/private/var/folders/_7/78g_4hlj7_72zms4nq9fj3ph0000gn/T/AppTranslocation/DAE93E9E-A35E-408E-8D05-D79BAD7AD232/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/DAE93E9E-A35E-408E-8D05-D79BAD7AD232/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/DAE93E9E-A35E-408E-8D05-D79BAD7AD232/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/DAE93E9E-A35E-408E-8D05-D79BAD7AD232/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 Eric Pettersen, 5 years ago

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

comment:2 by Eric Pettersen, 5 years ago

Resolution:	→ duplicate
Status:	accepted → closed

Similar to #3279 -- same user, related session. Would be nice if these weren't anonymous and a session were provided.

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