ArtiaX: wrapped C/C++ object of type QComboBox has been deleted

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        macOS-14.2.1-arm64-arm-64bit
ChimeraX Version: 1.7.1 (2024-01-23 01:58:08 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.7.1 (2024-01-23)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open
> /Users/sergiocruz/Desktop/VisualProteomics/3DTM/HIV/Cage_builder_Chimera/v3_1_Big_Cage_builder_Chimera.cxs

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 60, in
_update_models  
self._populate()  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate  
self.combo.clear()  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
Error processing trigger "add models":  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate  
self.combo.clear()  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 60, in
_update_models  
self._populate()  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate  
self.combo.clear()  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
Error processing trigger "add models":  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate  
self.combo.clear()  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 60, in
_update_models  
self._populate()  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate  
self.combo.clear()  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
Error processing trigger "add models":  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate  
self.combo.clear()  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 60, in
_update_models  
self._populate()  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate  
self.combo.clear()  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
Error processing trigger "add models":  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate  
self.combo.clear()  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 60, in
_update_models  
self._populate()  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate  
self.combo.clear()  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
Error processing trigger "add models":  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate  
self.combo.clear()  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 60, in
_update_models  
self._populate()  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate  
self.combo.clear()  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
Error processing trigger "add models":  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate  
self.combo.clear()  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 60, in
_update_models  
self._populate()  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate  
self.combo.clear()  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
Error processing trigger "add models":  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate  
self.combo.clear()  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 60, in
_update_models  
self._populate()  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate  
self.combo.clear()  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
Error processing trigger "add models":  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate  
self.combo.clear()  
  
See log for complete Python traceback.  
  
Opened 7_hexamers_test.pdb map 3.5 as #4, grid size 255,258,93, pixel 1.17,
shown at level 0.103, step 1, values float32  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 60, in
_update_models  
self._populate()  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate  
self.combo.clear()  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
Error processing trigger "add models":  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate  
self.combo.clear()  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 60, in
_update_models  
self._populate()  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate  
self.combo.clear()  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
Error processing trigger "add models":  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate  
self.combo.clear()  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 60, in
_update_models  
self._populate()  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate  
self.combo.clear()  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
Error processing trigger "add models":  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate  
self.combo.clear()  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 60, in
_update_models  
self._populate()  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate  
self.combo.clear()  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
Error processing trigger "add models":  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate  
self.combo.clear()  
  
See log for complete Python traceback.  
  
Log from Mon Feb 26 23:04:28 2024UCSF ChimeraX version: 1.7.1 (2024-01-23)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open
> /Users/sergiocruz/Desktop/VisualProteomics/3DTM/HIV/Cage_builder_Chimera/v2_Cage_builder_Chimera.cxs

Log from Mon Feb 26 20:45:22 2024 Startup Messages  
---  
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle  
  
Using preset: ArtiaX / Artiax Default  
Preset expands to these ChimeraX commands:

    
    
    set bgColor black
    lighting depthCue false
    camera ortho

  
UCSF ChimeraX version: 1.7.1 (2024-01-23)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/sergiocruz/Downloads/chimera_cage.pyc

Python code was compiled for a different version of Python  

> open /Users/sergiocruz/Downloads/chimera_cage.py

ChimeraX cannot open a regular Chimera session. An exporter from Chimera to  
ChimeraX is available in the latest Chimera release. Use its File->Export
Scene  
menu item, and change the resulting dialog's "File Type" to ChimeraX.  

> ui tool show "Cage Builder"

> view orient

> view

> select clear

Drag select of 138 atoms, 138 bonds  
Drag select of 19 atoms, 14 bonds  
Drag select of 66 atoms, 64 bonds  
Drag select of 1 bonds  
[Repeated 1 time(s)]

> select clear

[Repeated 1 time(s)]Drag select of 1 bonds  
Drag select of 4 atoms, 2 bonds  
Drag select of 6 atoms, 8 bonds  

> select clear

Drag select of 1 bonds  

> select clear

Drag select of 58 atoms, 58 bonds  

> select clear

[Repeated 1 time(s)]Drag select of 3 atoms, 2 bonds  

> select clear

Drag select of 1 bonds  

> select clear

Drag select of 1 bonds  

> select /M:79@M

1 atom, 1 residue, 1 model selected  
Drag select of 1 atoms  

> select clear

Drag select of 1 atoms, 1 bonds  
Drag select of 1 bonds  
Drag select of 1 atoms, 1 bonds  

> select clear

Drag select of 1 atoms  

> undo

Drag select of 5 atoms, 4 bonds  

> select clear

Drag select of 4 atoms, 3 bonds  
Drag select of 1 bonds  

> select clear

[Repeated 1 time(s)]Drag select of 111 atoms, 111 bonds  

> close #2

> select clear

Drag select of 1 bonds  
[Repeated 2 time(s)]

> select clear

Drag select of 1 bonds  
[Repeated 6 time(s)]

> select clear

[Repeated 1 time(s)]Drag select of 2 atoms, 1 bonds  
Drag select of 2 atoms, 2 bonds  
Drag select of 3 atoms, 4 bonds  
Drag select of 1 atoms  
Drag select of 2 atoms, 3 bonds  
Drag select of 1 atoms, 1 bonds  
[Repeated 1 time(s)]

> select clear

Drag select of 3 atoms, 3 bonds  
Drag select of 2 atoms, 4 bonds  
Drag select of 1 atoms, 1 bonds  
Drag select of 1 atoms  
Drag select of 1 atoms, 1 bonds  

> select clear

Drag select of 1 atoms  

> select clear

Drag select of 1 atoms  

> select clear

Drag select of 1 atoms  
Drag select of 1 bonds  
[Repeated 1 time(s)]Drag select of 1 atoms  
Drag select of 1 bonds  

> select clear

Drag select of 1 bonds  
Drag select of 3 atoms, 1 bonds  
Drag select of 1 bonds  
[Repeated 1 time(s)]Drag select of 1 atoms, 1 bonds  
Drag select of 1 bonds  
Drag select of 2 atoms  
Drag select of 2 atoms, 2 bonds  

> select clear

[Repeated 1 time(s)]Drag select of 14 atoms, 13 bonds  
Drag select of 1 bonds  
[Repeated 5 time(s)]Drag select of 1 atoms, 1 bonds  
Drag select of 2 atoms, 1 bonds  
Drag select of 1 bonds  
Drag select of 2 atoms, 3 bonds  

> view

> view orient

Drag select of 1 bonds  

> select clear

Drag select of 1 bonds  

> select clear

Drag select of 1 bonds  
[Repeated 2 time(s)]

> select clear

Drag select of 2 atoms, 2 bonds  

> select clear

[Repeated 2 time(s)]Drag select of 1 bonds  
Drag select of 1 atoms  

> undo

[Repeated 2 time(s)]Drag select of 1 bonds  
[Repeated 5 time(s)]

> select clear

Drag select of 1 bonds  
[Repeated 5 time(s)]

> select clear

Drag select of 1 bonds  
[Repeated 1 time(s)]

> select clear

Drag select of 1 bonds  
Drag select of 1 atoms, 1 bonds  

> select clear

Drag select of 2 atoms, 1 bonds  
Drag select of 1 bonds  
[Repeated 1 time(s)]

> select clear

[Repeated 1 time(s)]Drag select of 1 bonds  
[Repeated 2 time(s)]

> select clear

[Repeated 1 time(s)]Drag select of 1 atoms, 1 bonds  
Drag select of 1 bonds  
[Repeated 1 time(s)]

> select clear

Drag select of 1 bonds  

> select clear

[Repeated 2 time(s)]Drag select of 25 atoms, 16 bonds  
Drag select of 1 bonds  
[Repeated 2 time(s)]

> undo

Drag select of 1 bonds  
[Repeated 2 time(s)]

> select clear

Drag select of 1 bonds  
[Repeated 1 time(s)]

> select clear

[Repeated 1 time(s)]Drag select of 1 bonds  
[Repeated 2 time(s)]Drag select of 4 atoms, 2 bonds  
Drag select of 1 atoms, 2 bonds  

> select clear

[Repeated 1 time(s)]Drag select of 6 atoms, 6 bonds  
Drag select of 7 atoms, 5 bonds  

> select clear

[Repeated 1 time(s)]Drag select of 4 atoms, 4 bonds  

> select clear

Drag select of 5 atoms, 6 bonds  
Drag select of 13 atoms, 10 bonds  

> select clear

Drag select of 7 atoms, 6 bonds  
Drag select of 12 atoms, 12 bonds  
Drag select of 5 atoms, 4 bonds  

> select clear

Drag select of 13 atoms, 13 bonds  
Drag select of 10 atoms, 12 bonds  

> select clear

Drag select of 11 atoms, 12 bonds  
Drag select of 7 atoms, 5 bonds  
Drag select of 10 atoms, 13 bonds  

> select clear

Drag select of 14 atoms, 15 bonds  
Drag select of 12 atoms, 9 bonds  

> select clear

[Repeated 3 time(s)]Drag select of 1 atoms  
Drag select of 2 atoms  
Drag select of 2 atoms, 5 bonds  

> select clear

Drag select of 5 atoms, 5 bonds  

> select clear

[Repeated 2 time(s)]Drag select of 7 atoms, 7 bonds  

> select clear

Drag select of 1 atoms, 1 bonds  
Drag select of 1 bonds  

> lighting soft

Drag select of 1 bonds  

> select clear

[Repeated 1 time(s)]Drag select of 1 bonds  

> select clear

[Repeated 1 time(s)]Drag select of 1 bonds  
[Repeated 1 time(s)]

> select clear

Drag select of 1 bonds  
Drag select of 1 atoms  
Drag select of 3 atoms, 4 bonds  

> select clear

Drag select of 1 atoms  
[Repeated 1 time(s)]Drag select of 1 bonds  
[Repeated 1 time(s)]Drag select of 2 atoms, 1 bonds  
Drag select of 2 atoms  
Drag select of 1 bonds  
[Repeated 1 time(s)]Drag select of 4 atoms, 2 bonds  
Drag select of 2 atoms  
Drag select of 1 atoms  

> select clear

Drag select of 1 bonds  

> lighting full

> lighting simple

[Repeated 1 time(s)]Drag select of 2 atoms  
[Repeated 1 time(s)]Drag select of 2 atoms, 1 bonds  
Drag select of 7 atoms, 6 bonds  
Drag select of 8 atoms, 5 bonds  

> select clear

Drag select of 2 atoms, 2 bonds  
Drag select of 2 atoms, 1 bonds  
[Repeated 1 time(s)]Drag select of 1 atoms, 1 bonds  
Drag select of 4 atoms, 3 bonds  
Drag select of 2 atoms, 2 bonds  

> select clear

Drag select of 5 atoms, 4 bonds  
Drag select of 5 atoms, 7 bonds  

> select clear

Drag select of 4 atoms, 3 bonds  

> select clear

Drag select of 9 atoms, 9 bonds  
Drag select of 3 atoms, 4 bonds  
Drag select of 2 atoms, 1 bonds  

> select clear

Drag select of 2 atoms, 1 bonds  
Drag select of 4 atoms, 3 bonds  
Drag select of 6 atoms, 5 bonds  
Drag select of 2 atoms  

> select clear

Drag select of 1 bonds  

> select clear

Drag select of 2 atoms  
Drag select of 1 bonds  
[Repeated 1 time(s)]Drag select of 23 atoms, 28 bonds  
Drag select of 2 atoms, 1 bonds  
Drag select of 1 bonds  
Drag select of 2 bonds  
Drag select of 2 atoms, 1 bonds  
Drag select of 5 atoms, 5 bonds  
Drag select of 1 bonds  

> select clear

Drag select of 1 atoms  
Drag select of 2 atoms  
Drag select of 1 bonds  

> select clear

Drag select of 6 atoms, 5 bonds  
Drag select of 8 atoms, 9 bonds  

> select clear

Drag select of 1 bonds  
Drag select of 4 atoms, 4 bonds  
Drag select of 2 atoms, 2 bonds  
Drag select of 4 atoms, 2 bonds  
Drag select of 1 atoms, 2 bonds  
Drag select of 6 atoms, 5 bonds  
Drag select of 7 atoms, 6 bonds  
Drag select of 21 atoms, 18 bonds  
Drag select of 12 atoms, 12 bonds  

> select clear

[Repeated 5 time(s)]Drag select of 1 bonds  

> select clear

Drag select of 1 bonds  
Drag select of 1 atoms  

> select clear

[Repeated 3 time(s)]Drag select of 1 atoms  
[Repeated 1 time(s)]Drag select of 1 bonds  

> select clear

Drag select of 1 bonds  

> select clear

Drag select of 1 bonds  
Drag select of 1 atoms  

> ui mousemode right "move markers"

> marker change #2:1261 position 83.18,262.3,-524.5

Drag select of 1 atoms  

> select clear

Drag select of 1 atoms  

> ui mousemode right "move markers"

[Repeated 1 time(s)]

> undo

Drag select of 1 atoms  

> select clear

[Repeated 1 time(s)]

> color #2 #b900ffff

> save /Users/sergiocruz/Downloads/HIV_capsid_Chimera.cxs includeMaps true

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 273, in discovery  
self.processed[key] = self.process(obj, parents)  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 310, in process  
return copy_state(data, convert=convert)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/state.py", line 232, in copy_state  
return _copy(data)  
^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/state.py", line 217, in _copy  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/state.py", line 217, in <listcomp>  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/state.py", line 217, in _copy  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/state.py", line 217, in <listcomp>  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/state.py", line 230, in _copy  
return convert(data)  
^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 309, in convert  
return add_obj(obj, parents)  
^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 281, in _add_obj  
uid = _UniqueName.from_obj(self.session, obj)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 153, in from_obj  
if obj_cls != bundle_info.get_class(obj_cls.__name__, session.logger):  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/info.py", line 487, in get_class  
return f(class_name)  
^^^^^^^^^^^^^  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-packages/chimerax/artiax/__init__.py",
line 37, in get_class  
raise ValueError("Unknown class name '%s'" % class_name)  
ValueError: Unknown class name 'ArtiaX'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 912, in save  
session.save(output, version=version, include_maps=include_maps)  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 636, in save  
mgr.discovery(self._state_containers)  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 277, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
ValueError: error processing: 'models' -> <chimerax.core.models.Models object
at 0x1028b4610>: Unknown class name 'ArtiaX'  
  
ValueError: error processing: 'models' -> : Unknown class name 'ArtiaX'  
  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 277, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 273, in discovery  
self.processed[key] = self.process(obj, parents)  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 310, in process  
return copy_state(data, convert=convert)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/state.py", line 232, in copy_state  
return _copy(data)  
^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/state.py", line 217, in _copy  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/state.py", line 217, in <listcomp>  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/state.py", line 217, in _copy  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/state.py", line 217, in <listcomp>  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/state.py", line 230, in _copy  
return convert(data)  
^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 309, in convert  
return add_obj(obj, parents)  
^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 281, in _add_obj  
uid = _UniqueName.from_obj(self.session, obj)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 153, in from_obj  
if obj_cls != bundle_info.get_class(obj_cls.__name__, session.logger):  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/info.py", line 487, in get_class  
return f(class_name)  
^^^^^^^^^^^^^  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-packages/chimerax/artiax/__init__.py",
line 37, in get_class  
raise ValueError("Unknown class name '%s'" % class_name)  
ValueError: Unknown class name 'ArtiaX'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/dialog.py", line 127, in <lambda>  
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/dialog.py", line 138, in show_save_file_dialog  
_dlg.display(session, **kw)  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/dialog.py", line 62, in display  
run(session, cmd)  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2908, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/cmd.py", line 86, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2908, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/cmd.py", line 101, in provider_save  
saver_info.save(session, path, **provider_kw)  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core_formats/__init__.py", line 95, in save  
return cxs_save(session, path, **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 912, in save  
session.save(output, version=version, include_maps=include_maps)  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 636, in save  
mgr.discovery(self._state_containers)  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 277, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
ValueError: error processing: 'models' -> <chimerax.core.models.Models object
at 0x1028b4610>: Unknown class name 'ArtiaX'  
  
ValueError: error processing: 'models' -> : Unknown class name 'ArtiaX'  
  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 277, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
  
See log for complete Python traceback.  
  

> close #1

> save /Users/sergiocruz/Downloads/ChimeraHIV_models.cxs

> select clear

Drag select of 1 atoms, 1 bonds  
Drag select of 3 atoms, 4 bonds  

> select clear

Drag select of 1 atoms, 1 bonds  
Drag select of 1 bonds  
Drag select of 9 atoms, 9 bonds  

> select subtract /M:286@M

9 atoms, 10 bonds, 9 residues, 1 model selected  
Drag select of 1 atoms, 1 bonds  
Drag select of 2 atoms  

> select clear

[Repeated 1 time(s)]

> hide #2 models

> show #2 models

Drag select of 24 atoms, 26 bonds  

> select clear

Drag select of 1075 atoms, 1075 bonds  

> select clear

[Repeated 1 time(s)]Drag select of 1 bonds  

> select clear

> undo

> select clear

Drag select of 1 bonds  
Drag select of 1 atoms, 2 bonds  
Drag select of 6 atoms, 6 bonds  
Drag select of 50 atoms, 49 bonds  

> select clear

[Repeated 5 time(s)]Drag select of 1 bonds  

> select clear

Drag select of 1 atoms  

> ui mousemode right "move markers"

> marker change #2:1320 position 226,464.8,-518.7

> marker change #2:1320 position 232.8,460.4,-497.8

> marker change #2:1320 position 244.7,452.5,-514.5

Drag select of 1 atoms  
Drag select of 1 bonds  
Drag select of 1 atoms, 1 bonds  
[Repeated 1 time(s)]Drag select of 1 atoms  

> marker change #2:1286 position 245.8,446.1,-519.6

> marker change #2:1286 position 242.7,450.8,-525.9

> marker change #2:1286 position 238.9,454.2,-525.7

Drag select of 1 atoms  
Drag select of 1 bonds  
Drag select of 19 atoms, 19 bonds  

> select clear

Drag select of 14 atoms, 15 bonds  

> select clear

[Repeated 11 time(s)]Drag select of 1 atoms  
[Repeated 1 time(s)]Drag select of 4 atoms, 4 bonds  
Drag select of 9 atoms, 6 bonds  
Drag select of 6 atoms, 3 bonds  
Drag select of 12 atoms, 10 bonds  

> select clear

Drag select of 1 bonds  
Drag select of 5 atoms, 3 bonds  
Drag select of 8 atoms, 7 bonds  
Drag select of 6 atoms, 6 bonds  
Drag select of 16 atoms, 11 bonds  
Drag select of 1 atoms, 2 bonds  
Drag select of 2 atoms, 1 bonds  
Drag select of 5 atoms, 5 bonds  
Drag select of 4 atoms, 4 bonds  
Drag select of 3 atoms, 2 bonds  

> select clear

[Repeated 12 time(s)]Drag select of 30 atoms, 32 bonds  
Drag select of 11 atoms, 11 bonds  
Drag select of 7 atoms, 6 bonds  

> select clear

Drag select of 11 atoms, 11 bonds  

> select clear

[Repeated 1 time(s)]Drag select of 1 atoms  
Drag select of 2 bonds  

> select clear

[Repeated 1 time(s)]Drag select of 2 atoms  

> select clear

Drag select of 1 bonds  

> select clear

Drag select of 1 atoms  
Drag select of 14 atoms, 15 bonds  
Drag select of 28 atoms, 25 bonds  
Drag select of 52 atoms, 55 bonds  

> select clear

[Repeated 5 time(s)]Drag select of 22 atoms, 22 bonds  
Drag select of 24 atoms, 28 bonds  
Drag select of 21 atoms, 18 bonds  

> select clear

[Repeated 1 time(s)]Drag select of 2 atoms  
Drag select of 2 atoms, 1 bonds  

> select clear

Drag select of 1 atoms  
Drag select of 1 bonds  

> select clear

Drag select of 1 atoms, 2 bonds  
Drag select of 4 atoms, 2 bonds  

> select clear

Drag select of 4 atoms, 5 bonds  

> select clear

Drag select of 980 atoms, 980 bonds  

> select clear

[Repeated 6 time(s)]

Window position QRect(1886,1232 674x91) outside any known screen, using
primary screen  

QDockWidget failed to find relevant screen info. screenFrom:
QScreen(0x600003e40d00, name="DELL U2715H") screenTo: QScreen(0x600003e40d00,
name="DELL U2715H") wdgScreen: QScreen(0x600003e40d00, name="DELL U2715H")
orgWdgScreen QScreen(0x0)  

> select clear

[Repeated 16 time(s)]Drag select of 1328 atoms, 1328 bonds  

> save
> /Users/sergiocruz/Desktop/VisualProteomics/3DTM/HIV/Cage_builder_Chimera/v1_Cage_builder_Chimera.cxs

> close

> ui tool show "Cage Builder"

Drag select of 1 bonds  

> select clear

Drag select of 1 bonds  
[Repeated 1 time(s)]Drag select of 2 atoms, 1 bonds  
Drag select of 1 atoms, 1 bonds  
Drag select of 1 bonds  

> select clear

Drag select of 2 atoms, 1 bonds  

> select clear

Drag select of 2 atoms, 1 bonds  
Drag select of 2 atoms  
Drag select of 1 bonds  
[Repeated 1 time(s)]Drag select of 2 atoms, 2 bonds  

> undo

Drag select of 1 bonds  

> select clear

Drag select of 1 bonds  
[Repeated 1 time(s)]

> select clear

[Repeated 1 time(s)]Drag select of 2 atoms, 1 bonds  
Drag select of 1 bonds  

> select clear

[Repeated 1 time(s)]Drag select of 1 bonds  
[Repeated 1 time(s)]Drag select of 9 atoms, 9 bonds  
[Repeated 1 time(s)]

> select clear

Drag select of 1 bonds  
[Repeated 2 time(s)]

> select clear

[Repeated 1 time(s)]Drag select of 1 bonds  

> select clear

Drag select of 1 bonds  
[Repeated 1 time(s)]Drag select of 2 atoms, 1 bonds  
Drag select of 1 bonds  
[Repeated 1 time(s)]Drag select of 1 atoms  

> select clear

Drag select of 1 bonds  
Drag select of 1 atoms, 1 bonds  
Drag select of 2 atoms, 1 bonds  
Drag select of 1 bonds  

> select clear

Drag select of 4 atoms, 5 bonds  
Drag select of 2 atoms, 3 bonds  
Drag select of 1 bonds  
Drag select of 1 atoms, 1 bonds  
Drag select of 9 atoms, 8 bonds  
Drag select of 1 bonds  

> select clear

Drag select of 6 atoms, 6 bonds  
Drag select of 5 atoms, 6 bonds  

> select clear

Drag select of 1 atoms, 2 bonds  

> select clear

Drag select of 1 bonds  

> select clear

[Repeated 1 time(s)]Drag select of 365 atoms, 365 bonds  

> select clear

[Repeated 1 time(s)]Drag select of 1 atoms  

> select clear

[Repeated 1 time(s)]Drag select of 6 atoms, 4 bonds  

> select clear

Drag select of 1 atoms, 1 bonds  
Drag select of 3 atoms, 1 bonds  

> select clear

[Repeated 1 time(s)]Drag select of 1 bonds  

> select clear

Drag select of 4 atoms, 2 bonds  

> select clear

Drag select of 2 atoms, 3 bonds  
Drag select of 7 atoms, 7 bonds  

> select clear

Drag select of 2 atoms, 1 bonds  
Drag select of 1 atoms, 4 bonds  
Drag select of 13 atoms, 11 bonds  

> select clear

Drag select of 6 atoms, 3 bonds  
Drag select of 4 atoms, 5 bonds  
Drag select of 3 atoms, 2 bonds  

> select clear

Drag select of 3 atoms, 2 bonds  
Drag select of 3 atoms, 4 bonds  

> select clear

Drag select of 3 atoms, 1 bonds  
Drag select of 3 atoms, 2 bonds  
Drag select of 2 atoms, 2 bonds  
Drag select of 3 atoms, 1 bonds  
Drag select of 2 atoms, 3 bonds  
Drag select of 3 atoms, 3 bonds  
Drag select of 2 atoms, 2 bonds  
Drag select of 3 atoms, 2 bonds  
Drag select of 1 atoms, 1 bonds  
Drag select of 1 atoms, 2 bonds  
Drag select of 2 atoms, 4 bonds  
Drag select of 2 atoms, 1 bonds  
Drag select of 1 atoms, 1 bonds  
Drag select of 3 atoms, 2 bonds  
Drag select of 1 atoms, 1 bonds  
[Repeated 1 time(s)]Drag select of 3 atoms, 3 bonds  
Drag select of 5 atoms, 3 bonds  
Drag select of 3 atoms, 2 bonds  
Drag select of 1 atoms  
Drag select of 1 bonds  
Drag select of 6 atoms, 5 bonds  

> select clear

Drag select of 1 atoms, 1 bonds  
[Repeated 1 time(s)]Drag select of 2 atoms, 1 bonds  
Drag select of 1 bonds  

> select clear

[Repeated 22 time(s)]

> lighting soft

> select clear

[Repeated 4 time(s)]

> ui tool show "Side View"

> view

> select clear

[Repeated 2 time(s)]

> save
> /Users/sergiocruz/Desktop/VisualProteomics/3DTM/HIV/Cage_builder_Chimera/v2_Cage_builder_Chimera.cxs

——— End of log from Mon Feb 26 20:45:22 2024 ———

opened ChimeraX session  

> save
> /Users/sergiocruz/Desktop/VisualProteomics/3DTM/HIV/Cage_builder_Chimera/v2_1_Cage_builder_Chimera.cxs

> open /Users/sergiocruz/Downloads/models_chimera_8ckv/7_hexamers_test.pdb

7_hexamers_test.pdb title:  
Hiv-1 mature capsid hexamer from Ca-IP6 CLPS [more info...]  
  
Chain information for 7_hexamers_test.pdb #2  
---  
Chain | Description  
A B C D E F G H I J K L M N O P Q R S T U V W X Y Z a b c d e f g h i j k l m
n o p | No description available  
  

> lighting soft

> hide atoms

> show atoms

> show cartoons

> hide atoms

> show atoms

> hide #1 models

> hide #!2 atoms

> show #!2 cartoons

> show #1 models

> select add #2

69300 atoms, 70770 bonds, 42 pseudobonds, 8904 residues, 2 models selected  

> ui mousemode right "translate selected atoms"

> select clear

> ui tool show "Cage Builder"

> select clear

> select #2/l:34

7 atoms, 7 bonds, 1 residue, 1 model selected  

> select add #1

1194 atoms, 1194 bonds, 1194 residues, 1 model selected  

> select subtract #1

Nothing selected  

> select add #2

69300 atoms, 70770 bonds, 42 pseudobonds, 8904 residues, 2 models selected  

> ui mousemode right "translate selected atoms"

> ui mousemode right "rotate selected models"

> view matrix models
> #2,0.99851,0.0051069,-0.054275,4.5781,-0.011754,0.99235,-0.12286,18.915,0.053232,0.12332,0.99094,-53.76

> view matrix models
> #2,0.94873,-0.30821,-0.070094,110.77,0.29336,0.94117,-0.16772,-85.039,0.11766,0.13856,0.98334,-82.938

> ui mousemode right "translate selected atoms"

> select clear

[Repeated 1 time(s)]

> select #2/p:151

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select clear

> hide #!2 models

Drag select of 2 atoms, 1 bonds  
Drag select of 68 atoms, 67 bonds  
Drag select of 3 atoms  
Drag select of 335 atoms, 343 bonds  

> select clear

> show #!2 models

> hide cartoons

> show surfaces

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 60, in
_update_models  
self._populate()  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate  
self.combo.clear()  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
Error processing trigger "add models":  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate  
self.combo.clear()  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 60, in
_update_models  
self._populate()  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate  
self.combo.clear()  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
Error processing trigger "add models":  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate  
self.combo.clear()  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 60, in
_update_models  
self._populate()  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate  
self.combo.clear()  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
Error processing trigger "add models":  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate  
self.combo.clear()  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 60, in
_update_models  
self._populate()  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate  
self.combo.clear()  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
Error processing trigger "add models":  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate  
self.combo.clear()  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 60, in
_update_models  
self._populate()  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate  
self.combo.clear()  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
Error processing trigger "add models":  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate  
self.combo.clear()  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 60, in
_update_models  
self._populate()  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate  
self.combo.clear()  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
Error processing trigger "add models":  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate  
self.combo.clear()  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 60, in
_update_models  
self._populate()  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate  
self.combo.clear()  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
Error processing trigger "add models":  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate  
self.combo.clear()  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 60, in
_update_models  
self._populate()  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate  
self.combo.clear()  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
Error processing trigger "add models":  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate  
self.combo.clear()  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 60, in
_update_models  
self._populate()  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate  
self.combo.clear()  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
Error processing trigger "add models":  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate  
self.combo.clear()  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 60, in
_update_models  
self._populate()  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate  
self.combo.clear()  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
Error processing trigger "add models":  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate  
self.combo.clear()  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 60, in
_update_models  
self._populate()  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate  
self.combo.clear()  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
Error processing trigger "add models":  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate  
self.combo.clear()  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 60, in
_update_models  
self._populate()  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate  
self.combo.clear()  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
Error processing trigger "add models":  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate  
self.combo.clear()  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 60, in
_update_models  
self._populate()  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate  
self.combo.clear()  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
Error processing trigger "add models":  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate  
self.combo.clear()  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 60, in
_update_models  
self._populate()  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate  
self.combo.clear()  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
Error processing trigger "add models":  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate  
self.combo.clear()  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 60, in
_update_models  
self._populate()  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate  
self.combo.clear()  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
Error processing trigger "add models":  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate  
self.combo.clear()  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 60, in
_update_models  
self._populate()  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate  
self.combo.clear()  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
Error processing trigger "add models":  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate  
self.combo.clear()  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 60, in
_update_models  
self._populate()  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate  
self.combo.clear()  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
Error processing trigger "add models":  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate  
self.combo.clear()  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 60, in
_update_models  
self._populate()  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate  
self.combo.clear()  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
Error processing trigger "add models":  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate  
self.combo.clear()  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 60, in
_update_models  
self._populate()  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate  
self.combo.clear()  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
Error processing trigger "add models":  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate  
self.combo.clear()  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 60, in
_update_models  
self._populate()  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate  
self.combo.clear()  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
Error processing trigger "add models":  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate  
self.combo.clear()  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 60, in
_update_models  
self._populate()  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate  
self.combo.clear()  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
Error processing trigger "add models":  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate  
self.combo.clear()  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 60, in
_update_models  
self._populate()  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate  
self.combo.clear()  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
Error processing trigger "add models":  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate  
self.combo.clear()  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 60, in
_update_models  
self._populate()  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate  
self.combo.clear()  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
Error processing trigger "add models":  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate  
self.combo.clear()  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 60, in
_update_models  
self._populate()  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate  
self.combo.clear()  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
Error processing trigger "add models":  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate  
self.combo.clear()  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 60, in
_update_models  
self._populate()  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate  
self.combo.clear()  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
Error processing trigger "add models":  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate  
self.combo.clear()  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 60, in
_update_models  
self._populate()  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate  
self.combo.clear()  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
Error processing trigger "add models":  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate  
self.combo.clear()  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 60, in
_update_models  
self._populate()  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate  
self.combo.clear()  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
Error processing trigger "add models":  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate  
self.combo.clear()  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 60, in
_update_models  
self._populate()  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate  
self.combo.clear()  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
Error processing trigger "add models":  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate  
self.combo.clear()  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 60, in
_update_models  
self._populate()  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate  
self.combo.clear()  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
Error processing trigger "add models":  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate  
self.combo.clear()  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 60, in
_update_models  
self._populate()  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate  
self.combo.clear()  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
Error processing trigger "add models":  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate  
self.combo.clear()  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 60, in
_update_models  
self._populate()  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate  
self.combo.clear()  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
Error processing trigger "add models":  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate  
self.combo.clear()  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 60, in
_update_models  
self._populate()  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate  
self.combo.clear()  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
Error processing trigger "add models":  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate  
self.combo.clear()  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 60, in
_update_models  
self._populate()  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate  
self.combo.clear()  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
Error processing trigger "add models":  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate  
self.combo.clear()  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 60, in
_update_models  
self._populate()  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate  
self.combo.clear()  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
Error processing trigger "add models":  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate  
self.combo.clear()  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 60, in
_update_models  
self._populate()  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate  
self.combo.clear()  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
Error processing trigger "add models":  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate  
self.combo.clear()  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 60, in
_update_models  
self._populate()  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate  
self.combo.clear()  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
Error processing trigger "add models":  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate  
self.combo.clear()  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 60, in
_update_models  
self._populate()  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate  
self.combo.clear()  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
Error processing trigger "add models":  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate  
self.combo.clear()  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 60, in
_update_models  
self._populate()  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate  
self.combo.clear()  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
Error processing trigger "add models":  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate  
self.combo.clear()  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 60, in
_update_models  
self._populate()  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate  
self.combo.clear()  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
Error processing trigger "add models":  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate  
self.combo.clear()  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 60, in
_update_models  
self._populate()  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate  
self.combo.clear()  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
Error processing trigger "add models":  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate  
self.combo.clear()  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 60, in
_update_models  
self._populate()  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate  
self.combo.clear()  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
Error processing trigger "add models":  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate  
self.combo.clear()  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 60, in
_update_models  
self._populate()  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate  
self.combo.clear()  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
Error processing trigger "add models":  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate  
self.combo.clear()  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 60, in
_update_models  
self._populate()  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate  
self.combo.clear()  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
Error processing trigger "add models":  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate  
self.combo.clear()  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 60, in
_update_models  
self._populate()  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate  
self.combo.clear()  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
Error processing trigger "add models":  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate  
self.combo.clear()  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 60, in
_update_models  
self._populate()  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate  
self.combo.clear()  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
Error processing trigger "add models":  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate  
self.combo.clear()  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 60, in
_update_models  
self._populate()  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate  
self.combo.clear()  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
Error processing trigger "add models":  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate  
self.combo.clear()  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 60, in
_update_models  
self._populate()  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate  
self.combo.clear()  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
Error processing trigger "add models":  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate  
self.combo.clear()  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 60, in
_update_models  
self._populate()  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate  
self.combo.clear()  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
Error processing trigger "add models":  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate  
self.combo.clear()  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 60, in
_update_models  
self._populate()  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate  
self.combo.clear()  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
Error processing trigger "add models":  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate  
self.combo.clear()  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 60, in
_update_models  
self._populate()  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate  
self.combo.clear()  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
Error processing trigger "add models":  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate  
self.combo.clear()  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 60, in
_update_models  
self._populate()  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate  
self.combo.clear()  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
Error processing trigger "add models":  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate  
self.combo.clear()  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 60, in
_update_models  
self._populate()  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate  
self.combo.clear()  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
Error processing trigger "add models":  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate  
self.combo.clear()  
  

[deleted to fit within ticket size limits]

See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 60, in
_update_models  
self._populate()  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate  
self.combo.clear()  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
Error processing trigger "add models":  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate  
self.combo.clear()  
  
See log for complete Python traceback.  
  

> hide #!3 surfaces

> hide #!3 cartoons

> show #!3 cartoons

> color #!3 bypolymer

> lighting full

> lighting simple

> lighting shadows true

> lighting shadows false

> lighting shadows true

> lighting soft

> hide #10 models

> show #10 models

> set bgColor black

> set bgColor white

> set bgColor black

> set bgColor white

> view

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 60, in
_update_models  
self._populate()  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate  
self.combo.clear()  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
Error processing trigger "remove models":  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate  
self.combo.clear()  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 60, in
_update_models  
self._populate()  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate  
self.combo.clear()  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
Error processing trigger "remove models":  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate  
self.combo.clear()  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 60, in
_update_models  
self._populate()  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate  
self.combo.clear()  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
Error processing trigger "remove models":  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate  
self.combo.clear()  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 60, in
_update_models  
self._populate()  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate  
self.combo.clear()  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
Error processing trigger "remove models":  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate  
self.combo.clear()  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 60, in
_update_models  
self._populate()  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate  
self.combo.clear()  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
Error processing trigger "remove models":  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate  
self.combo.clear()  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 60, in
_update_models  
self._populate()  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate  
self.combo.clear()  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
Error processing trigger "remove models":  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate  
self.combo.clear()  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 60, in
_update_models  
self._populate()  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate  
self.combo.clear()  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
Error processing trigger "remove models":  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate  
self.combo.clear()  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 60, in
_update_models  
self._populate()  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate  
self.combo.clear()  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
Error processing trigger "remove models":  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate  
self.combo.clear()  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 60, in
_update_models  
self._populate()  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate  
self.combo.clear()  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
Error processing trigger "remove models":  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate  
self.combo.clear()  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 60, in
_update_models  
self._populate()  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate  
self.combo.clear()  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
Error processing trigger "remove models":  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate  
self.combo.clear()  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 60, in
_update_models  
self._populate()  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate  
self.combo.clear()  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
Error processing trigger "remove models":  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate  
self.combo.clear()  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 60, in
_update_models  
self._populate()  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate  
self.combo.clear()  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
Error processing trigger "remove models":  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate  
self.combo.clear()  
  
See log for complete Python traceback.  
  

> view orient

> lighting flat

> color #!3 bychain

> show #!3 surfaces

> show #1 models

> hide #!3 models

> graphics quality atomTriangles 300

> graphics quality bondTriangles 60

> graphics quality ribbonDivisions 20

> graphics quality ribbonSides 12

> hide #!4 models

> show #!4 models

Window position QRect(1886,826 674x56) outside any known screen, using primary
screen  

> select add #4

2 models selected  

> view matrix models
> #4,0.53918,-0.74029,0.40157,239.47,-0.053234,-0.50581,-0.861,50.166,0.84051,0.44285,-0.31213,-620.74

> view matrix models
> #4,0.53918,-0.74029,0.40157,381.77,-0.053234,-0.50581,-0.861,129.54,0.84051,0.44285,-0.31213,-518.61

> show #2 models

> hide #1 models

> hide #2 models

> show #1 models

> ui mousemode right "translate selected models"

> view matrix models #1,1,0,0,-94.811,0,1,0,-78.552,0,0,1,7.2141

> view matrix models #1,1,0,0,-133.99,0,1,0,-94.088,0,0,1,-39.432

> ui mousemode right "translate selected models"

> view matrix models #1,1,0,0,-151.27,0,1,0,-240.84,0,0,1,-83.533

Drag select of 4 7_hexamers_test.pdb map 3.5  

> ui mousemode right "translate selected atoms"

> ui mousemode right "rotate selected models"

> view matrix models
> #1,0.9132,0.14632,-0.38033,-338.3,0.089433,0.8386,0.53735,27.053,0.39757,-0.52473,0.75273,-255.03

> select clear

Drag select of 6 atoms, 6 bonds, 4 7_hexamers_test.pdb map 3.5  

> select #4

2 models selected  

> select clear

Drag select of 5 atoms, 6 bonds, 4 7_hexamers_test.pdb map 3.5  

> select clear

Drag select of 5 atoms, 6 bonds  

> ui mousemode right "rotate selected models"

> view matrix models
> #1,0.96845,0.24407,0.050288,-139.53,-0.24895,0.95647,0.15226,-102.56,-0.010936,-0.15998,0.98706,-73.797

> view matrix models
> #1,0.99423,0.057369,0.090688,-108.62,-0.052515,0.9971,-0.055032,-256.71,-0.093582,0.049952,0.99436,-69.392

> ui mousemode right "translate selected atoms"

> save
> /Users/sergiocruz/Desktop/VisualProteomics/3DTM/HIV/Cage_builder_Chimera/v2_2_Cage_builder_Chimera.cxs
> includeMaps true

> select clear

Drag select of 4 7_hexamers_test.pdb map 3.5  

> ui mousemode right "translate selected atoms"

> ui mousemode right rotate

Drag select of 4 7_hexamers_test.pdb map 3.5  

> select clear

Drag select of 4 7_hexamers_test.pdb map 3.5  

> select clear

Drag select of 4 7_hexamers_test.pdb map 3.5  

> ui mousemode right "rotate selected models"

> view matrix models
> #4,-0.1065,-0.9934,0.042645,637.26,0.99398,-0.10748,-0.02134,-269.43,0.025783,0.040115,0.99886,-90.691

> select #4

2 models selected  
Drag select of 6 atoms, 6 bonds, 4 7_hexamers_test.pdb map 3.5  
Drag select of 4 7_hexamers_test.pdb map 3.5  

> ui mousemode right "translate selected atoms"

> ui mousemode right "translate selected models"

> view matrix models
> #4,-0.1065,-0.9934,0.042645,650.67,0.99398,-0.10748,-0.02134,-283.07,0.025783,0.040115,0.99886,-37.51

> ui mousemode right "rotate selected models"

> view matrix models
> #4,0.35133,-0.93548,0.03796,457.91,0.93581,0.34963,-0.04493,-273.55,0.028759,0.051309,0.99827,-39.113

> ui mousemode right "translate selected models"

> view matrix models
> #4,0.35133,-0.93548,0.03796,462.96,0.93581,0.34963,-0.04493,-274.4,0.028759,0.051309,0.99827,-39.084

> view matrix models
> #4,0.35133,-0.93548,0.03796,461.25,0.93581,0.34963,-0.04493,-276.71,0.028759,0.051309,0.99827,-39.042

> ui mousemode right "rotate selected models"

> view matrix models
> #4,0.3423,-0.93312,-0.11004,456.29,0.93797,0.34623,-0.018251,-275.96,0.055131,-0.09697,0.99376,-45.966

> view matrix models
> #4,0.46066,-0.885,0.067678,415.95,0.88493,0.46383,0.041894,-253.77,-0.068467,0.040592,0.99683,1.7049

> select clear

> select #4

2 models selected  
Drag select of 4 7_hexamers_test.pdb map 3.5  

> ui mousemode right "rotate selected models"

> view matrix models
> #4,0.34778,-0.93506,0.068689,464.51,0.9355,0.35095,0.04098,-271.6,-0.062426,0.050006,0.9968,-1.0895

> select clear

[Repeated 7 time(s)]Drag select of 2 bonds, 4 7_hexamers_test.pdb map 3.5  

> select clear

> set bgColor black

> ui tool show "Side View"

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 60, in
_update_models  
self._populate()  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate  
self.combo.clear()  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
Error processing trigger "add models":  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate  
self.combo.clear()  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 60, in
_update_models  
self._populate()  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate  
self.combo.clear()  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
Error processing trigger "add models":  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate  
self.combo.clear()  
  
See log for complete Python traceback.  
  
Drag select of 4 7_hexamers_test.pdb map 3.5  

> ui mousemode right "rotate selected models"

> view matrix models
> #4,0.30636,-0.94979,0.063499,481.9,0.95017,0.30916,0.040017,-276.55,-0.057639,0.048075,0.99718,-3.0054

> ui mousemode right "translate selected atoms"

[Repeated 1 time(s)]

> ui mousemode right "translate selected models"

> view matrix models
> #4,0.30636,-0.94979,0.063499,485.07,0.95017,0.30916,0.040017,-275.78,-0.057639,0.048075,0.99718,-3.2256

> select clear

> view

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 60, in
_update_models  
self._populate()  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate  
self.combo.clear()  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
Error processing trigger "remove models":  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate  
self.combo.clear()  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 60, in
_update_models  
self._populate()  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate  
self.combo.clear()  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
Error processing trigger "remove models":  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate  
self.combo.clear()  
  
See log for complete Python traceback.  
  

> lighting soft

> hide #!4 models

> show #2 models

> hide #2 models

> show #!4 models

Drag select of 74 atoms, 74 bonds, 4 7_hexamers_test.pdb map 3.5  

> hide #!4 models

> show #!3 models

> hide #!3 models

> close #3

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 60, in
_update_models  
self._populate()  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate  
self.combo.clear()  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
Error processing trigger "remove models":  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate  
self.combo.clear()  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 60, in
_update_models  
self._populate()  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate  
self.combo.clear()  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
Error processing trigger "remove models":  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate  
self.combo.clear()  
  
See log for complete Python traceback.  
  

> ui mousemode right "translate selected models"

> view matrix models
> #1,0.99423,0.057369,0.090688,-59.224,-0.052515,0.9971,-0.055032,-203.04,-0.093582,0.049952,0.99436,-53.132

> ui mousemode right "translate selected atoms"

> select clear

[Repeated 4 time(s)]Drag select of 87 atoms, 84 bonds  

> select clear

Drag select of 82 atoms, 82 bonds  

> ui mousemode right "translate selected atoms"

> select clear

[Repeated 2 time(s)]Drag select of 1 bonds  

> select clear

[Repeated 8 time(s)]Drag select of 1 atoms  

> select clear

[Repeated 5 time(s)]Drag select of 1 atoms  
Drag select of 2 atoms, 2 bonds  
[Repeated 1 time(s)]Drag select of 5 atoms, 2 bonds  
Drag select of 3 atoms, 2 bonds  

> select clear

Drag select of 2 atoms, 2 bonds  
Drag select of 4 atoms, 2 bonds  
Drag select of 4 atoms, 3 bonds  
[Repeated 1 time(s)]Drag select of 3 atoms, 2 bonds  
Drag select of 6 atoms, 6 bonds  
Drag select of 6 atoms, 4 bonds  
Drag select of 15 atoms, 15 bonds  
Drag select of 2 atoms, 4 bonds  
Drag select of 14 atoms, 15 bonds  
Drag select of 13 atoms, 9 bonds  
Drag select of 10 atoms, 8 bonds  
Drag select of 12 atoms, 14 bonds  
Drag select of 27 atoms, 26 bonds  

> select clear

Drag select of 3 atoms, 2 bonds  
Drag select of 594 atoms, 594 bonds  

> ui mousemode right "translate selected models"

> view matrix models
> #1,0.99423,0.057369,0.090688,-286.67,-0.052515,0.9971,-0.055032,-314.44,-0.093582,0.049952,0.99436,-42.823

> ui mousemode right "translate selected atoms"

> select clear

[Repeated 2 time(s)]Drag select of 1 bonds  
Drag select of 3 atoms, 3 bonds  

> select clear

Drag select of 11 atoms, 8 bonds  

> select clear

Drag select of 11 atoms, 9 bonds  
Drag select of 71 atoms, 74 bonds  

> select clear

Drag select of 8 atoms, 9 bonds  

> select clear

Drag select of 4 atoms, 2 bonds  
Drag select of 6 atoms, 5 bonds  
Drag select of 5 atoms, 5 bonds  
Drag select of 9 atoms, 6 bonds  

> select clear

[Repeated 3 time(s)]Drag select of 1 bonds  

> select clear

[Repeated 1 time(s)]Drag select of 1 atoms  
[Repeated 1 time(s)]Drag select of 4 atoms, 3 bonds  
Drag select of 2 atoms, 3 bonds  
Drag select of 4 atoms, 4 bonds  
Drag select of 12 atoms, 10 bonds  
Drag select of 31 atoms, 31 bonds  

> select clear

Drag select of 1 atoms, 2 bonds  
Drag select of 3 atoms, 1 bonds  
Drag select of 2 atoms, 2 bonds  
Drag select of 474 atoms, 473 bonds  
Drag select of 54 atoms, 51 bonds  

> select clear

[Repeated 1 time(s)]Drag select of 37 atoms, 32 bonds  
Drag select of 33 atoms, 28 bonds  
Drag select of 34 atoms, 37 bonds  
Drag select of 38 atoms, 39 bonds  
Drag select of 64 atoms, 62 bonds  

> select clear

Drag select of 71 atoms, 65 bonds  

> select clear

Drag select of 43 atoms, 43 bonds  

> select clear

Drag select of 13 atoms, 12 bonds  
Drag select of 26 atoms, 26 bonds  
Drag select of 1 atoms, 2 bonds  
Drag select of 12 atoms, 11 bonds  

> select clear

Drag select of 12 atoms, 12 bonds  
Drag select of 17 atoms, 15 bonds  

> select clear

Drag select of 44 atoms, 41 bonds  

> select clear

Drag select of 14 atoms, 16 bonds  
Drag select of 89 atoms, 88 bonds  

> select clear

Drag select of 90 atoms, 96 bonds  
Drag select of 4 atoms, 5 bonds  
Drag select of 10 atoms, 11 bonds  
Drag select of 1 bonds  
Drag select of 27 atoms, 22 bonds  
Drag select of 27 atoms, 25 bonds  
Drag select of 65 atoms, 66 bonds  

> select clear

Drag select of 39 atoms, 32 bonds  
Drag select of 23 atoms, 27 bonds  

> select clear

[Repeated 1 time(s)]Drag select of 23 atoms, 21 bonds  

> select clear

Drag select of 162 atoms, 159 bonds  

> select clear

Drag select of 477 atoms, 475 bonds  

> select clear

Drag select of 1533 atoms, 1536 bonds  

> select clear

[Repeated 49 time(s)]Drag select of 1 bonds  

> select clear

[Repeated 1 time(s)]Drag select of 1 atoms  

> select clear

[Repeated 2 time(s)]Drag select of 1 bonds  
[Repeated 1 time(s)]

> select clear

[Repeated 3 time(s)]Drag select of 1 bonds  
[Repeated 1 time(s)]Drag select of 1 atoms  

> select clear

Drag select of 1 atoms  

> select clear

Drag select of 1 bonds  
Drag select of 1 atoms  

> select clear

[Repeated 10 time(s)]Drag select of 1 atoms  
Drag select of 1 bonds  

> select clear

[Repeated 1 time(s)]Drag select of 1 bonds  
[Repeated 2 time(s)]

> select clear

Drag select of 1 bonds  
Drag select of 1 atoms  
Drag select of 1 bonds  
Drag select of 1 atoms  
Drag select of 1 bonds  
Drag select of 1 atoms, 1 bonds  
Drag select of 1 bonds  

> select clear

Drag select of 1 bonds  
[Repeated 1 time(s)]

> select clear

Drag select of 2 atoms, 1 bonds  
Drag select of 1 atoms, 1 bonds  

> select clear

Drag select of 1 bonds  
[Repeated 1 time(s)]Drag select of 4 atoms, 3 bonds  
Drag select of 6 atoms, 5 bonds  

> view

> select clear

Drag select of 1 atoms, 1 bonds  
Drag select of 2 atoms, 1 bonds  
Drag select of 4 atoms, 1 bonds  
Drag select of 6 atoms, 5 bonds  

> select clear

Drag select of 3 atoms, 2 bonds  
Drag select of 1 atoms, 1 bonds  

> select clear

Drag select of 4 atoms, 2 bonds  
Drag select of 1 atoms, 1 bonds  
Drag select of 1 bonds  
Drag select of 2 atoms, 1 bonds  
Drag select of 9 atoms, 6 bonds  
Drag select of 2 atoms, 2 bonds  
Drag select of 1 bonds  
[Repeated 3 time(s)]Drag select of 2 atoms, 1 bonds  

> select clear

[Repeated 1 time(s)]Drag select of 2 atoms, 3 bonds  

> select clear

Drag select of 1 bonds  
Drag select of 8 atoms, 5 bonds  
Drag select of 1 atoms, 1 bonds  

> select clear

Drag select of 1 atoms, 2 bonds  
Drag select of 4 atoms, 3 bonds  
Drag select of 6 atoms, 3 bonds  
Drag select of 8 atoms, 4 bonds  
Drag select of 8 atoms, 5 bonds  
Drag select of 14 atoms, 16 bonds  
Drag select of 6 atoms, 8 bonds  
Drag select of 5 atoms, 6 bonds  
Drag select of 45 atoms, 42 bonds  

> select clear

Drag select of 10 atoms, 13 bonds  

> select clear

[Repeated 1 time(s)]Drag select of 26 atoms, 27 bonds  
Drag select of 3 atoms, 2 bonds  

> select clear

[Repeated 6 time(s)]Drag select of 1 bonds  

> select clear

[Repeated 9 time(s)]Drag select of 29 atoms, 32 bonds  

> select clear

Drag select of 74 atoms, 72 bonds  

> select clear

[Repeated 1 time(s)]Drag select of 39 atoms, 42 bonds  
Drag select of 9 atoms, 10 bonds  
Drag select of 4 atoms, 4 bonds  
Drag select of 8 atoms, 10 bonds  

> select clear

Drag select of 28 atoms, 24 bonds  
Drag select of 20 atoms, 19 bonds  

> select clear

[Repeated 1 time(s)]Drag select of 1 bonds  

> select clear

[Repeated 7 time(s)]Drag select of 9 atoms, 10 bonds  

> select clear

[Repeated 17 time(s)]

> save
> /Users/sergiocruz/Desktop/VisualProteomics/3DTM/HIV/Cage_builder_Chimera/v3_Big_Cage_builder_Chimera.cxs

> select clear

> ui mousemode right "tape measure"

> scalebar 500

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 60, in
_update_models  
self._populate()  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate  
self.combo.clear()  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
Error processing trigger "add models":  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate  
self.combo.clear()  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 60, in
_update_models  
self._populate()  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate  
self.combo.clear()  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
Error processing trigger "add models":  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate  
self.combo.clear()  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 60, in
_update_models  
self._populate()  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate  
self.combo.clear()  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
Error processing trigger "add models":  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate  
self.combo.clear()  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 60, in
_update_models  
self._populate()  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate  
self.combo.clear()  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
Error processing trigger "add models":  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate  
self.combo.clear()  
  
See log for complete Python traceback.  
  
Drag select of 1158 atoms, 1158 bonds  

> view

> view orient

> show #2 models

> hide #2 models

> open
> /Users/sergiocruz/Downloads/Swiss_model/Rot_Swiss_modeLhexamer_Template7t12.pdb

Rot_Swiss_modeLhexamer_Template7t12.pdb title:  
SWISS-MODEL SERVER (https://swissmodel.expasy.org) Untitled Project [more
info...]  
  
Chain information for Rot_Swiss_modeLhexamer_Template7t12.pdb #5  
---  
Chain | Description  
A B C D E F | No description available  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 60, in
_update_models  
self._populate()  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate  
self.combo.clear()  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
Error processing trigger "add models":  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate  
self.combo.clear()  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 60, in
_update_models  
self._populate()  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate  
self.combo.clear()  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
Error processing trigger "add models":  
RuntimeError: wrapped C/C++ object of type QComboBox has been deleted  
  
File "/Users/sergiocruz/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/widgets/ModelChooserWidget.py", line 63, in _populate  
self.combo.clear()  
  
See log for complete Python traceback.  
  
Drag select of 10290 atoms  

> ui mousemode right "translate selected models"

> ui mousemode right "translate selected atoms"

> ui mousemode right "rotate selected models"

> view matrix models
> #5,0.29547,0.71395,0.6348,984.9,0.43051,0.49367,-0.75561,-812.2,-0.85285,0.49655,-0.1615,88.107

> view matrix models
> #5,0.21365,0.76225,0.61101,1050.6,0.50562,0.44888,-0.73679,-874.35,-0.83588,0.46636,-0.2895,-3.8948

> ui mousemode right "translate selected atoms"

> hide sel atoms

> show sel cartoons

> ui mousemode right "rotate selected models"

> view matrix models
> #5,0.1255,0.78199,0.61053,1151.7,0.44145,0.5071,-0.74025,-823.3,-0.88847,0.36241,-0.28157,115.91

> ui mousemode right "translate selected atoms"

> ui mousemode right "rotate selected models"

> view matrix models
> #5,0.60214,0.55101,0.57777,636.98,0.58135,0.19341,-0.79033,-889.52,-0.54723,0.81178,-0.20387,-464.78

> view matrix models
> #5,0.72649,0.23406,0.64609,677.74,0.67495,-0.066501,-0.73486,-846,-0.12903,0.96995,-0.20629,-1064.9

> save
> /Users/sergiocruz/Desktop/VisualProteomics/3DTM/HIV/Cage_builder_Chimera/v3_1_Big_Cage_builder_Chimera.cxs

> sym #3 #1,p6

No structures specified.  

> sym #5 #1,p6

Made 197 graphical clones for Rot_Swiss_modeLhexamer_Template7t12.pdb symmetry
#1,p6  

> view

> sym clear

> select add #5

10290 atoms, 10524 bonds, 1314 residues, 1 model selected  

> select subtract #5

Nothing selected  

> select add #5

10290 atoms, 10524 bonds, 1314 residues, 1 model selected  

> ui mousemode right "translate selected models"

> select clear

> ui mousemode right "translate selected atoms"

> select add #5

10290 atoms, 10525 bonds, 1314 residues, 2 models selected  

> ui mousemode right "translate selected atoms"

> view sel

> ui mousemode right "rotate selected models"

> view matrix models
> #1,0.99096,0.050165,0.12442,-261.55,-0.049855,0.99874,-0.0056093,-295.7,-0.12455,-0.00064439,0.99221,31.231,#5,0.35763,0.50828,-0.78343,-387.14,-0.1454,-0.79837,-0.58435,1167.9,-0.92247,0.32289,-0.21162,699.38

> ui mousemode right "translate selected models"

> ui mousemode right "translate selected atoms"

> select clear

[Repeated 1 time(s)]

> select add #5

10290 atoms, 10524 bonds, 1314 residues, 1 model selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #5,-0.27135,0.95833,-0.089275,-285.4,-0.84607,-0.28172,-0.45254,1393,-0.45884,-0.047263,0.88726,343.85

> view matrix models
> #5,-0.28103,0.95895,-0.037994,-284.73,-0.90246,-0.27753,-0.32946,1431.6,-0.32648,-0.058301,0.9434,185.08

> ui mousemode right "translate selected atoms"

> ui mousemode right "rotate selected models"

> view matrix models
> #5,-0.51997,0.85398,0.018646,117.08,-0.84992,-0.51942,0.088532,1567.7,0.08529,0.030186,0.9959,-429.1

> view matrix models
> #5,-0.25543,0.94515,0.20357,-344.81,-0.93937,-0.29244,0.17908,1399.8,0.22879,-0.14548,0.96254,-396.66

> view matrix models
> #5,0.83174,0.54543,0.10356,-1195.6,-0.54159,0.83815,-0.064628,-338.26,-0.12205,-0.0023359,0.99252,-137.91

> ui mousemode right "translate selected models"

> view matrix models
> #5,0.83174,0.54543,0.10356,-1197.2,-0.54159,0.83815,-0.064628,-333.2,-0.12205,-0.0023359,0.99252,-141.48

> view matrix models
> #5,0.83174,0.54543,0.10356,-1197.7,-0.54159,0.83815,-0.064628,-331.96,-0.12205,-0.0023359,0.99252,-142.77

> ui mousemode right "rotate selected models"

> view matrix models
> #5,0.69197,0.71749,0.079948,-1220,-0.71564,0.69631,-0.054916,41.592,-0.09507,-0.019213,0.99529,-156.87

> ui mousemode right "translate selected models"

> view matrix models
> #5,0.69197,0.71749,0.079948,-1219.2,-0.71564,0.69631,-0.054916,40.994,-0.09507,-0.019213,0.99529,-157.96

> view sel

> select clear

> save
> /Users/sergiocruz/Desktop/VisualProteomics/3DTM/HIV/Cage_builder_Chimera/v3_1_Big_Cage_builder_Chimera.cxs

——— End of log from Mon Feb 26 23:04:28 2024 ———

opened ChimeraX session  




OpenGL version: 4.1 Metal - 88
OpenGL renderer: Apple M1 Max
OpenGL vendor: Apple

Python: 3.11.2
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro18,4
      Model Number: Z15G002NZD/A
      Chip: Apple M1 Max
      Total Number of Cores: 10 (8 performance and 2 efficiency)
      Memory: 32 GB
      System Firmware Version: 10151.61.4
      OS Loader Version: 10151.61.4

Software:

    System Software Overview:

      System Version: macOS 14.2.1 (23C71)
      Kernel Version: Darwin 23.2.0
      Time since boot: 4 days, 8 hours, 24 minutes

Graphics/Displays:

    Apple M1 Max:

      Chipset Model: Apple M1 Max
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 24
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-in Liquid Retina XDR Display
          Resolution: 3024 x 1964 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: No
          Connection Type: Internal
        DELL U2715H:
          Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition)
          UI Looks like: 2560 x 1440 @ 60.00Hz
          Mirror: Off
          Online: Yes
          Rotation: Supported


Installed Packages:
    alabaster: 0.7.16
    appdirs: 1.4.4
    appnope: 0.1.3
    asttokens: 2.4.1
    Babel: 2.14.0
    backcall: 0.2.0
    beautifulsoup4: 4.11.2
    blockdiag: 3.0.0
    blosc2: 2.0.0
    build: 0.10.0
    certifi: 2022.12.7
    cftime: 1.6.3
    charset-normalizer: 3.3.2
    ChimeraX-AddCharge: 1.5.13
    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.4.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.12.2
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-ArtiaX: 0.3
    ChimeraX-Atomic: 1.49.1
    ChimeraX-AtomicLibrary: 12.1.5
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3.2
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.10.5
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.2
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.3.2
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.5
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.7.1
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2
    ChimeraX-DistMonitor: 1.4
    ChimeraX-DockPrep: 1.1.3
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-Label: 1.1.8
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.1.6
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.1.4
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.1.2
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.6.1
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.12.1
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.14
    ChimeraX-ModelPanel: 1.4
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.1
    ChimeraX-NRRD: 1.1
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.13.1
    ChimeraX-PDB: 2.7.3
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.4
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.2
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.2
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.11
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.2
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.12.4
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1.2
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.2.2
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.33.3
    ChimeraX-uniprot: 2.3
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.3.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.3
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.1
    contourpy: 1.2.0
    cxservices: 1.2.2
    cycler: 0.12.1
    Cython: 0.29.33
    debugpy: 1.8.0
    decorator: 5.1.1
    docutils: 0.19
    executing: 2.0.1
    filelock: 3.9.0
    fonttools: 4.47.2
    funcparserlib: 2.0.0a0
    geomdl: 5.3.1
    glfw: 2.6.4
    grako: 3.16.5
    h5py: 3.10.0
    html2text: 2020.1.16
    idna: 3.6
    ihm: 0.38
    imagecodecs: 2023.9.18
    imagesize: 1.4.1
    ipykernel: 6.23.2
    ipython: 8.14.0
    ipython-genutils: 0.2.0
    ipywidgets: 8.1.1
    jedi: 0.18.2
    Jinja2: 3.1.2
    jupyter-client: 8.2.0
    jupyter-core: 5.7.1
    jupyterlab-widgets: 3.0.9
    kiwisolver: 1.4.5
    line-profiler: 4.0.2
    lxml: 4.9.2
    lz4: 4.3.2
    MarkupSafe: 2.1.4
    matplotlib: 3.7.2
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.6.0
    netCDF4: 1.6.2
    networkx: 3.1
    nibabel: 5.0.1
    nptyping: 2.5.0
    numexpr: 2.8.8
    numpy: 1.25.1
    openvr: 1.23.701
    packaging: 21.3
    pandas: 2.2.0
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pexpect: 4.9.0
    pickleshare: 0.7.5
    pillow: 10.2.0
    pip: 23.0
    pkginfo: 1.9.6
    platformdirs: 4.1.0
    prompt-toolkit: 3.0.43
    psutil: 5.9.5
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    py-cpuinfo: 9.0.0
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.16.1
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.2801
    pyparsing: 3.0.9
    pyproject-hooks: 1.0.0
    PyQt6-commercial: 6.3.1
    PyQt6-Qt6: 6.3.2
    PyQt6-sip: 13.4.0
    PyQt6-WebEngine-commercial: 6.3.1
    PyQt6-WebEngine-Qt6: 6.3.2
    python-dateutil: 2.8.2
    pytz: 2023.3.post1
    pyzmq: 25.1.2
    qtconsole: 5.4.3
    QtPy: 2.4.1
    RandomWords: 0.4.0
    requests: 2.31.0
    scipy: 1.11.1
    setuptools: 67.4.0
    setuptools-scm: 7.0.5
    sfftk-rw: 0.7.3
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.5
    sphinx: 6.1.3
    sphinx-autodoc-typehints: 1.22
    sphinxcontrib-applehelp: 1.0.8
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.6
    sphinxcontrib-htmlhelp: 2.0.5
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.7
    sphinxcontrib-serializinghtml: 1.1.10
    stack-data: 0.6.3
    starfile: 0.5.4
    superqt: 0.5.0
    tables: 3.8.0
    tcia-utils: 1.5.1
    tifffile: 2023.7.18
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.4
    traitlets: 5.9.0
    typing-extensions: 4.9.0
    tzdata: 2023.4
    urllib3: 2.1.0
    wcwidth: 0.2.13
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.9