Model splitting: KeyError: (15, 1)

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Darwin-15.3.0-x86_64-i386-64bit
ChimeraX Version: 0.8 (2018-11-26)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 0.8 (2018-11-26)  
How to cite UCSF ChimeraX  

> open /Users/jliu/Desktop/T7-Ian/ATPase-Jun.cxs format session

opened ChimeraX session  

> lighting soft

> lighting soft

> open /Users/jliu/Desktop/T7-Ian/3-5T4O.pdb

Chain information for 3-5T4O.pdb #14  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D E F | No description available  
G | No description available  
H | No description available  
I J | No description available  
K | No description available  
L | No description available  
M N O P Q R S T U V | No description available  
  

> hide #!14 models

> show #!14 models

> ~select #4

Nothing selected  

> ~select #4

Nothing selected  

> ~select #4

Nothing selected  

> hide #!7 models

> show #!7 models

> hide #!10.1 models

> show #!10.1 models

> hide #!10 models

> show #!10 models

> hide #!12.1 models

> show #!12.1 models

> hide #!7 models

> show #!7 models

> hide #!8 models

> show #!8 models

> fitmap #14 inMap #8

Fit molecule 3-5T4O.pdb (#14) to map ATP-Jun-seg-lp.mrc (#8) using 23568 atoms  
average map value = 0.1036, steps = 84  
shifted from previous position = 30.6  
rotated from previous position = 5.14 degrees  
atoms outside contour = 4925, contour level = 0.02987  
  
Position of 3-5T4O.pdb (#14) relative to ATP-Jun-seg-lp.mrc (#8) coordinates:  
Matrix rotation and translation  
0.96416623 -0.26520078 -0.00721299 -233.73849579  
-0.01509930 -0.02771049 -0.99950195 184.11283621  
0.26486882 0.96379494 -0.03072187 -365.41907382  
Axis 0.98274064 -0.13619226 0.12518987  
Axis point 0.00000000 234.95291471 -98.32900442  
Rotation angle (degrees) 92.70152635  
Shift along axis -300.52582930  
  

> hide #!14 models

> show #!14 models

> split #14

Chain information for 3-5T4O.pdb A #14.1  
---  
Chain | Description  
A | No description available  
  
Chain information for 3-5T4O.pdb B #14.2  
---  
Chain | Description  
B | No description available  
  
Chain information for 3-5T4O.pdb C #14.3  
---  
Chain | Description  
C | No description available  
  
Chain information for 3-5T4O.pdb D #14.4  
---  
Chain | Description  
D | No description available  
  
Chain information for 3-5T4O.pdb E #14.5  
---  
Chain | Description  
E | No description available  
  
Chain information for 3-5T4O.pdb F #14.6  
---  
Chain | Description  
F | No description available  
  
Chain information for 3-5T4O.pdb G #14.7  
---  
Chain | Description  
G | No description available  
  
Chain information for 3-5T4O.pdb H #14.8  
---  
Chain | Description  
H | No description available  
  
Chain information for 3-5T4O.pdb I #14.9  
---  
Chain | Description  
I | No description available  
  
Chain information for 3-5T4O.pdb J #14.10  
---  
Chain | Description  
J | No description available  
  
Chain information for 3-5T4O.pdb K #14.11  
---  
Chain | Description  
K | No description available  
  
Chain information for 3-5T4O.pdb L #14.12  
---  
Chain | Description  
L | No description available  
  
Chain information for 3-5T4O.pdb M #14.13  
---  
Chain | Description  
M | No description available  
  
Chain information for 3-5T4O.pdb N #14.14  
---  
Chain | Description  
N | No description available  
  
Chain information for 3-5T4O.pdb O #14.15  
---  
Chain | Description  
O | No description available  
  
Chain information for 3-5T4O.pdb P #14.16  
---  
Chain | Description  
P | No description available  
  
Chain information for 3-5T4O.pdb Q #14.17  
---  
Chain | Description  
Q | No description available  
  
Chain information for 3-5T4O.pdb R #14.18  
---  
Chain | Description  
R | No description available  
  
Chain information for 3-5T4O.pdb S #14.19  
---  
Chain | Description  
S | No description available  
  
Chain information for 3-5T4O.pdb T #14.20  
---  
Chain | Description  
T | No description available  
  
Chain information for 3-5T4O.pdb U #14.21  
---  
Chain | Description  
U | No description available  
  
Chain information for 3-5T4O.pdb V #14.22  
---  
Chain | Description  
V | No description available  
  
Split 3-5T4O.pdb (#14) into 22 models  

> hide #!14 models

> show #!14 models

> hide #!14 models

> show #!14 models

  
  
  
  
  
  
Chain information for 1-5T4O.pdb #15.1  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D E F | No description available  
G | No description available  
H | No description available  
I J | No description available  
K | No description available  
L | No description available  
M N O P Q R S T U V | No description available  
  
Chain information for 2-5T4O.pdb #15.2  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D E F | No description available  
G | No description available  
H | No description available  
I J | No description available  
K | No description available  
L | No description available  
M N O P Q R S T U V | No description available  
  
Chain information for 3-5T4O.pdb #15.3  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D E F | No description available  
G | No description available  
H | No description available  
I J | No description available  
K | No description available  
L | No description available  
M N O P Q R S T U V | No description available  
  
Chain information for 4-5T4O.pdb #15.4  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D E F | No description available  
G | No description available  
H | No description available  
I J | No description available  
K | No description available  
L | No description available  
M N O P Q R S T U V | No description available  
  
Chain information for 5-5T4O.pdb #15.5  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D E F | No description available  
G | No description available  
H | No description available  
I J | No description available  
K | No description available  
L | No description available  
M N O P Q R S T U V | No description available  
  
Chain information for 6-5T4O.pdb #15.6  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D E F | No description available  
G | No description available  
H | No description available  
I J | No description available  
K | No description available  
L | No description available  
M N O P Q R S T U V | No description available  
  

> close #14

> select #15

141408 atoms, 141318 bonds, 6 pseudobonds, 7 models selected  

> fitmap #15 inMap #6

Fit molecules 1-5T4O.pdb (#15.1), 2-5T4O.pdb (#15.2), 3-5T4O.pdb (#15.3),
4-5T4O.pdb (#15.4), 5-5T4O.pdb (#15.5), 6-5T4O.pdb (#15.6) to map Hole-5.2.mrc
(#6) using 141408 atoms  
average map value = 0.0466, steps = 92  
shifted from previous position = 19  
rotated from previous position = 12.2 degrees  
atoms outside contour = 22656, contour level = 0.013321  
  
Position of 1-5T4O.pdb (#15.1) relative to Hole-5.2.mrc (#6) coordinates:  
Matrix rotation and translation  
-0.92267618 0.37967030 -0.06722437 200.40723181  
0.38484872 0.91753303 -0.10012288 -271.04051928  
0.02366690 -0.11825221 -0.99270150 192.70805635  
Axis -0.19530394 -0.97915488 0.05578612  
Axis point 125.10660435 0.00000000 91.55791034  
Rotation angle (degrees) 177.33976823  
Shift along axis 237.00076172  
  
Position of 2-5T4O.pdb (#15.2) relative to Hole-5.2.mrc (#6) coordinates:  
Matrix rotation and translation  
-0.92267618 0.37967030 -0.06722437 200.40723181  
0.38484872 0.91753303 -0.10012288 -271.04051928  
0.02366690 -0.11825221 -0.99270150 192.70805635  
Axis -0.19530394 -0.97915488 0.05578612  
Axis point 125.10660435 0.00000000 91.55791034  
Rotation angle (degrees) 177.33976823  
Shift along axis 237.00076172  
  
Position of 3-5T4O.pdb (#15.3) relative to Hole-5.2.mrc (#6) coordinates:  
Matrix rotation and translation  
-0.92267618 0.37967030 -0.06722437 200.40723181  
0.38484872 0.91753303 -0.10012288 -271.04051928  
0.02366690 -0.11825221 -0.99270150 192.70805635  
Axis -0.19530394 -0.97915488 0.05578612  
Axis point 125.10660435 0.00000000 91.55791034  
Rotation angle (degrees) 177.33976823  
Shift along axis 237.00076172  
  
Position of 4-5T4O.pdb (#15.4) relative to Hole-5.2.mrc (#6) coordinates:  
Matrix rotation and translation  
-0.92267618 0.37967030 -0.06722437 200.40723181  
0.38484872 0.91753303 -0.10012288 -271.04051928  
0.02366690 -0.11825221 -0.99270150 192.70805635  
Axis -0.19530394 -0.97915488 0.05578612  
Axis point 125.10660435 0.00000000 91.55791034  
Rotation angle (degrees) 177.33976823  
Shift along axis 237.00076172  
  
Position of 5-5T4O.pdb (#15.5) relative to Hole-5.2.mrc (#6) coordinates:  
Matrix rotation and translation  
-0.92267618 0.37967030 -0.06722437 200.40723181  
0.38484872 0.91753303 -0.10012288 -271.04051928  
0.02366690 -0.11825221 -0.99270150 192.70805635  
Axis -0.19530394 -0.97915488 0.05578612  
Axis point 125.10660435 0.00000000 91.55791034  
Rotation angle (degrees) 177.33976823  
Shift along axis 237.00076172  
  
Position of 6-5T4O.pdb (#15.6) relative to Hole-5.2.mrc (#6) coordinates:  
Matrix rotation and translation  
-0.92267618 0.37967030 -0.06722437 200.40723181  
0.38484872 0.91753303 -0.10012288 -271.04051928  
0.02366690 -0.11825221 -0.99270150 192.70805635  
Axis -0.19530394 -0.97915488 0.05578612  
Axis point 125.10660435 0.00000000 91.55791034  
Rotation angle (degrees) 177.33976823  
Shift along axis 237.00076172  
  

> surface #15

> lighting flat

> split #15.1 chains

Chain information for 1-5T4O.pdb A #15.1.1  
---  
Chain | Description  
A | No description available  
  
Chain information for 1-5T4O.pdb B #15.1.2  
---  
Chain | Description  
B | No description available  
  
Chain information for 1-5T4O.pdb C #15.1.3  
---  
Chain | Description  
C | No description available  
  
Chain information for 1-5T4O.pdb D #15.1.4  
---  
Chain | Description  
D | No description available  
  
Chain information for 1-5T4O.pdb E #15.1.5  
---  
Chain | Description  
E | No description available  
  
Chain information for 1-5T4O.pdb F #15.1.6  
---  
Chain | Description  
F | No description available  
  
Chain information for 1-5T4O.pdb G #15.1.7  
---  
Chain | Description  
G | No description available  
  
Chain information for 1-5T4O.pdb H #15.1.8  
---  
Chain | Description  
H | No description available  
  
Chain information for 1-5T4O.pdb I #15.1.9  
---  
Chain | Description  
I | No description available  
  
Chain information for 1-5T4O.pdb J #15.1.10  
---  
Chain | Description  
J | No description available  
  
Chain information for 1-5T4O.pdb K #15.1.11  
---  
Chain | Description  
K | No description available  
  
Chain information for 1-5T4O.pdb L #15.1.12  
---  
Chain | Description  
L | No description available  
  
Chain information for 1-5T4O.pdb M #15.1.13  
---  
Chain | Description  
M | No description available  
  
Chain information for 1-5T4O.pdb N #15.1.14  
---  
Chain | Description  
N | No description available  
  
Chain information for 1-5T4O.pdb O #15.1.15  
---  
Chain | Description  
O | No description available  
  
Chain information for 1-5T4O.pdb P #15.1.16  
---  
Chain | Description  
P | No description available  
  
Chain information for 1-5T4O.pdb Q #15.1.17  
---  
Chain | Description  
Q | No description available  
  
Chain information for 1-5T4O.pdb R #15.1.18  
---  
Chain | Description  
R | No description available  
  
Chain information for 1-5T4O.pdb S #15.1.19  
---  
Chain | Description  
S | No description available  
  
Chain information for 1-5T4O.pdb T #15.1.20  
---  
Chain | Description  
T | No description available  
  
Chain information for 1-5T4O.pdb U #15.1.21  
---  
Chain | Description  
U | No description available  
  
Chain information for 1-5T4O.pdb V #15.1.22  
---  
Chain | Description  
V | No description available  
  
Split 1-5T4O.pdb (#15.1) into 22 models  
Traceback (most recent call last):  
File
"/Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/cmd_line/tool.py", line 229, in execute  
cmd.run(cmd_text)  
File
"/Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/commands/cli.py", line 2581, in run  
result = ci.function(session, **kw_args)  
File
"/Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/std_commands/split.py", line 67, in split  
models.add(olist)  
File
"/Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/models.py", line 436, in add  
del self._models[model.id]  
KeyError: (15, 1)  
  
KeyError: (15, 1)  
  
File
"/Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/models.py", line 436, in add  
del self._models[model.id]  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/triggerset.py", line 126, in invoke  
return self._func(self._name, data)  
File
"/Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/model_panel/tool.py", line 123, in <lambda>  
lambda *args, ft=self._fill_tree, ar=always_rebuild: ft(always_rebuild=ar))  
File
"/Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/model_panel/tool.py", line 160, 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 "frame drawn": list index out of range:  
IndexError: list index out of range  
  
File
"/Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/model_panel/tool.py", line 160, in _fill_tree  
parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1]  
  
See log for complete Python traceback.  
  

> hide #!15 models

> show #!15 models

> ~select #15

1 model selected  

> hide #!15 models

> show #!15 models

> hide #!15 models

> show #!15 models

> hide #!15 models

> show #!15 models

> hide #!12.1 models

> hide #!8.1 models

> hide #!9 models

> hide #!9.1 models

> hide #!10 models

> hide #!10.1 models

> hide #!11 models

> hide #!11.1 models

> hide #!12 models

> hide #!8 models

> hide #!7.1 models

> hide #!7 models

> hide #!13 models

> show #!13 models

> select #15

117840 atoms, 117765 bonds, 6 pseudobonds, 7 models selected  

> close #15

Traceback (most recent call last):  
File
"/Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/model_panel/tool.py", line 69, in <lambda>  
for i in self.tree.selectedItems()]] or self.models, ses))  
File
"/Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/model_panel/tool.py", line 268, in close  
concise_model_spec(session, [m for m in models if isinstance(m, Model)]))  
File
"/Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/commands/run.py", line 31, in run  
results = command.run(text, log=log)  
File
"/Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/commands/cli.py", line 2581, in run  
result = ci.function(session, **kw_args)  
File
"/Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/std_commands/close.py", line 32, in close  
m.close(cmodels)  
File
"/Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/models.py", line 559, in close  
mremoved = self.remove(models)  
File
"/Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/models.py", line 547, in remove  
parent = self._models[model_id[:-1]]  
KeyError: (15, 1, 11)  
  
KeyError: (15, 1, 11)  
  
File
"/Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/models.py", line 547, in remove  
parent = self._models[model_id[:-1]]  
  
See log for complete Python traceback.  
  

> hide #!15 models

> ~select #15

1 model selected  

> ~select #15

1 model selected  

> close #15

Traceback (most recent call last):  
File
"/Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/model_panel/tool.py", line 69, in <lambda>  
for i in self.tree.selectedItems()]] or self.models, ses))  
File
"/Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/model_panel/tool.py", line 268, in close  
concise_model_spec(session, [m for m in models if isinstance(m, Model)]))  
File
"/Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/commands/run.py", line 31, in run  
results = command.run(text, log=log)  
File
"/Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/commands/cli.py", line 2581, in run  
result = ci.function(session, **kw_args)  
File
"/Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/std_commands/close.py", line 32, in close  
m.close(cmodels)  
File
"/Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/models.py", line 559, in close  
mremoved = self.remove(models)  
File
"/Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/models.py", line 538, in remove  
m.removed_from_session(session)  
File
"/Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/atomic/structure.py", line 135, in removed_from_session  
self._graphics_updater.remove_structure(self)  
File
"/Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/atomic/structure.py", line 2459, in remove_structure  
self._structures.remove(s)  
KeyError: <chimerax.atomic.structure.AtomicStructure object at 0x16b7e0080>  
  
KeyError:  
  
File
"/Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/atomic/structure.py", line 2459, in remove_structure  
self._structures.remove(s)  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 INTEL-10.12.13
OpenGL renderer: Intel(R) HD Graphics 6000
OpenGL vendor: Intel Inc.

[Tom Goddard]

Fixed.

Splitting an atomic model that was not at the top level of the model hierarchy had a bug.