Combine into existing model

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        macOS-26.0.1-arm64-arm-64bit
ChimeraX Version: 1.10.1 (2025-07-24 20:15:27 UTC)
Description
Replace this text with list of actions that caused this problem to occur

Log:
UCSF ChimeraX version: 1.10.1 (2025-07-24)  
© 2016-2025 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "/Users/gontzal/Nextcloud/03 Artikuluak Abian/01
> MIP/GSTCTer_af26a/GSTCTer_af26a_unrelaxed_rank_001_alphafold2_ptm_model_2_seed_000.pdb"
> format pdb

Chain information for
GSTCTer_af26a_unrelaxed_rank_001_alphafold2_ptm_model_2_seed_000.pdb #1  
---  
Chain | Description  
A | No description available  
  
Computing secondary structure  

> open "/Users/gontzal/Nextcloud/03 Artikuluak Abian/01
> MIP/Response/Supplemental Figure/CB1 human.pdb"

CB1 human.pdb title:  
Alphafold monomer V2.0 prediction for cannabinoid receptor 1 (P21554) [more
info...]  
  
Chain information for CB1 human.pdb #2  
---  
Chain | Description | UniProt  
A | cannabinoid receptor 1 | CNR1_HUMAN 1-472  
  
Computing secondary structure  

> select clear

> select add #1

2303 atoms, 2358 bonds, 289 residues, 1 model selected  
Drag select of 2 residues  

> select add #1

2303 atoms, 2358 bonds, 289 residues, 1 model selected  

> select add #2

6014 atoms, 6149 bonds, 761 residues, 2 models selected  

> select subtract #1

3711 atoms, 3791 bonds, 472 residues, 1 model selected  

> hide #1 models

> show #1 models

> hide #1 models

> show #1 models

> select subtract #2

Nothing selected  
Drag select of 2 residues  

> select add #2

3711 atoms, 3791 bonds, 472 residues, 1 model selected  

> ui mousemode right "translate selected models"

> ui mousemode right "rotate selected models"

> ui mousemode right "move picked models"

> ui mousemode right zoom

> ui mousemode right translate

> ui mousemode right distance

[Repeated 2 time(s)]

> ui mousemode right pivot

> ui mousemode right "move picked models"

> ui mousemode right select

Drag select of 3 residues  

> ui mousemode right translate

> ui mousemode right "translate selected models"

> view matrix models #1,1,0,0,-9.3603,0,1,0,10.573,0,0,1,-36.637

> view matrix models #1,1,0,0,-15.793,0,1,0,18.224,0,0,1,-47.655

> select add #2

3733 atoms, 3791 bonds, 475 residues, 2 models selected  

> view matrix models
> #1,1,0,0,-6.0199,0,1,0,6.4194,0,0,1,-37.562,#2,1,0,0,9.7727,0,1,0,-11.805,0,0,1,10.093

> view matrix models
> #1,1,0,0,-8.7395,0,1,0,9.8086,0,0,1,-36.546,#2,1,0,0,7.0531,0,1,0,-8.4159,0,0,1,11.109

> view matrix models
> #1,1,0,0,-8.3737,0,1,0,10.263,0,0,1,-28.486,#2,1,0,0,7.419,0,1,0,-7.9617,0,0,1,19.17

> view matrix models
> #1,1,0,0,-9.6231,0,1,0,11.28,0,0,1,-31.094,#2,1,0,0,6.1695,0,1,0,-6.9444,0,0,1,16.561

> ui mousemode right translate

> select add #1

6014 atoms, 6149 bonds, 761 residues, 2 models selected  

> select subtract #2

2303 atoms, 2358 bonds, 289 residues, 1 model selected  

> select subtract #1

Nothing selected  

> ui mousemode right "translate selected models"

Drag select of 8 residues  

> view matrix models #1,1,0,0,-13.184,0,1,0,13.507,0,0,1,-32.563

Drag select of 26 residues  

> view matrix models #2,1,0,0,21.029,0,1,0,-11.841,0,0,1,5.1685

> style #1 cartoon

Expected a keyword  

> color deepskyblue #1

Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword  

> style #2 cartoon

Expected a keyword  

> color tan #2

Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword  

> delete :232-end models #1

Expected a keyword  

> delete :232-end model #1

Expected a keyword  

> delete #1:232-end

> delete #2:1-414

Drag select of 5 residues  

> view matrix models #2,1,0,0,-23.087,0,1,0,53.658,0,0,1,-79.667

Drag select of 12 residues  

> select add #1

1889 atoms, 1940 bonds, 231 residues, 1 model selected  

> select add #2

2304 atoms, 2358 bonds, 289 residues, 2 models selected  

> view matrix models
> #1,1,0,0,31.599,0,1,0,-0.84634,0,0,1,-11.403,#2,1,0,0,21.696,0,1,0,39.305,0,0,1,-58.507

> select subtract #1

415 atoms, 418 bonds, 58 residues, 1 model selected  

> select subtract #2

Nothing selected  

> select #2/A:415

6 atoms, 5 bonds, 1 residue, 1 model selected  

> view matrix models #2,1,0,0,22.323,0,1,0,38.807,0,0,1,-58.484

> select add #1

1895 atoms, 1945 bonds, 232 residues, 2 models selected  

> select add #2

2304 atoms, 2358 bonds, 289 residues, 2 models selected  

> bond #1:231@C #2:415@N

Created 0 bonds  

> select subtract #1

415 atoms, 418 bonds, 58 residues, 1 model selected  

> select subtract #2

Nothing selected  
Drag select of 2 residues  
[Repeated 1 time(s)]

> view matrix models #1,1,0,0,30.677,0,1,0,-1.5743,0,0,1,-11.694

> label #1:231@C

> label #2:415@N

> label #1:231@C

> label #2:415@N

> bond #1:231@C #2:415@N

Created 0 bonds  

> combine #1,#2 name GST_CB1 close false

Expected a keyword  

> combine #1,2 modelId 3 name GST_CB1

Remapping chain ID 'A' in CB1 human.pdb #2 to 'B'  

> delete #3:231@OXT

> delete #3:415@H*

> delete #3:231@OXT

> delete #3:415@H*

> bond #3:231@C #3:415@N

Created 0 bonds  

> select add #1

1889 atoms, 1940 bonds, 231 residues, 2 models selected  

> select subtract #1

Nothing selected  

> bond #3:231@C #3:415@N

Created 0 bonds  

> label #3:231@C

> label #3:415@N

> show atoms #3:231

Expected ',' or a keyword  

> show atoms #3:415

Expected ',' or a keyword  

> show #3:231

> show #3:415

> info atoms #3:231

atom id #3/A:231@N idatm_type Npl  
atom id #3/A:231@CA idatm_type C3  
atom id #3/A:231@C idatm_type C2  
atom id #3/A:231@CB idatm_type C3  
atom id #3/A:231@O idatm_type O2  
atom id #3/A:231@OG idatm_type O3  

> info atoms #3:415

atom id #3/B:415@N idatm_type N3+  
atom id #3/B:415@CA idatm_type C3  
atom id #3/B:415@C idatm_type C2  
atom id #3/B:415@CB idatm_type C3  
atom id #3/B:415@O idatm_type O2  
atom id #3/B:415@SG idatm_type S3  

> distance #3/A:231@C #3/B:415@N

Distance between GST_CB1 #3/A SER 231 C and /B CYS 415 N: 3.139Å  
Drag select of 2 residues  

> view matrix models
> #2,1,0,0,21.936,0,1,0,38.832,0,0,1,-58.682,#3,1,0,0,30.289,0,1,0,-1.5497,0,0,1,-11.892

> distance #3/A:231@C #3/B:415@N

Distance already exists; modify distance properties with 'distance style'  

> distance #3/A:231@C #3/B:415@N

Distance already exists; modify distance properties with 'distance style'  

> move #3/B:415-472 z -2

Missing or invalid "axis" argument: Axis argument requires 2 atoms, got 415
atoms  

> select add #3

2310 atoms, 2358 bonds, 1 pseudobond, 290 residues, 4 models selected  

> select subtract #3

6 atoms, 1 residue, 1 model selected  

> select add #2

415 atoms, 418 bonds, 58 residues, 2 models selected  

> select subtract #2

Nothing selected  

> select #3/B:415-472

415 atoms, 418 bonds, 58 residues, 1 model selected  

> move z -0.5 atoms sel

> move 0,0,-0.5 atoms sel

> move z -0.5 models #3

> distance #3/A:231@C #3/B:415@N

Distance already exists; modify distance properties with 'distance style'  

> distance delete

> distance style hidden

Expected a keyword  

> delete #3/A:231@OXT

> delete #3/B:415@H*

> bond #3/A:231@C #3/B:415@N

Created 0 bonds  

> select add #3

2304 atoms, 2358 bonds, 289 residues, 2 models selected  

> select subtract #3

Nothing selected  

> hide #!3 models

> show #!3 models

> hide #!2 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> show #!2 models

> delete GST_CB1

Missing or invalid "atoms" argument: invalid atoms specifier  

> GST_CB1 delete

Unknown command: GST_CB1 delete  

> close #3

> delete :232-end models #1

Expected a keyword  

> delete :1-414 models #2

Expected a keyword  

> move z -2 models #2 # (ajusta según necesites)

Expected a keyword  

> distance #1:231@C #2:415@N

Distance between
GSTCTer_af26a_unrelaxed_rank_001_alphafold2_ptm_model_2_seed_000.pdb #1/A SER
231 C and CB1 human.pdb #2/A CYS 415 N: 3.234Å  

> combine #1,2 modelId 3 name GST_CB1

Remapping chain ID 'A' in CB1 human.pdb #2 to 'B'  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/cmd_line/tool.py", line 319, in execute  
cmd.run(cmd_text)  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3221, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/cmd.py", line 174, in combine_cmd  
session.models.add([combination])  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 773, in add  
p = self._parent_for_added_model(model, parent, root_model = root_model)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 843, in _parent_for_added_model  
raise ValueError('Tried to add model %s with the same id as another model %s'  
ValueError: Tried to add model GST_CB1 #3 with the same id as another model
distances #3  
  
ValueError: Tried to add model GST_CB1 #3 with the same id as another model
distances #3  
  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 843, in _parent_for_added_model  
raise ValueError('Tried to add model %s with the same id as another model %s'  
  
See log for complete Python traceback.  
  

> Distances delete

Unknown command: Distances delete  

> move z -2 models #2 # (ajusta según necesites)

Expected a keyword  

> distance #1:231@C #2:415@N

Distance already exists; modify distance properties with 'distance style'  

> distance delete

> move z -2 models #2 # (ajusta según necesites)

Expected a keyword  

> distance #1:231@C #2:415@N

Distance between
GSTCTer_af26a_unrelaxed_rank_001_alphafold2_ptm_model_2_seed_000.pdb #1/A SER
231 C and CB1 human.pdb #2/A CYS 415 N: 3.234Å  

> distance #3/A:231@C #3/B:415@N

Expected exactly two atoms and/or measurable objects (e.g. axes, planes), or
one or more measurable objects and one or more atoms, got 0 atoms and 0
measurable objects  

> label #1:231@C

> label #2:415@N

> show atoms #1:231@C

Expected ',' or a keyword  

> show atoms #2:415@N

Expected ',' or a keyword  

> show #1:231@C

> show #2:415@N

> show #1:231

> show #2:415

> label #1:231@C

> label #2:415@N

Drag select of 4 residues, 1 bonds  

> view matrix models
> #1,1,0,0,31.255,0,1,0,-1.4351,0,0,1,-11.443,#2,1,0,0,22.514,0,1,0,38.971,0,0,1,-58.432

Drag select of 2 residues  

> view matrix models
> #1,1,0,0,30.66,0,1,0,-0.95509,0,0,1,-11.291,#2,1,0,0,21.918,0,1,0,39.451,0,0,1,-58.279

> view matrix models
> #1,1,0,0,30.829,0,1,0,-1.0381,0,0,1,-11.268,#2,1,0,0,22.087,0,1,0,39.368,0,0,1,-58.256

> select add #2

423 atoms, 418 bonds, 59 residues, 3 models selected  

> select add #1

2304 atoms, 2358 bonds, 289 residues, 4 models selected  

> select subtract #1

415 atoms, 418 bonds, 58 residues, 2 models selected  

> select subtract #2

Nothing selected  

> select #2/A:415

6 atoms, 5 bonds, 1 residue, 1 model selected  

> view matrix models #2,1,0,0,21.018,0,1,0,40.493,0,0,1,-59.68

> view matrix models #2,1,0,0,21.666,0,1,0,39.586,0,0,1,-58.037

> view matrix models #2,1,0,0,21.573,0,1,0,40.263,0,0,1,-58.031

> view matrix models #2,1,0,0,21.199,0,1,0,40.266,0,0,1,-57.903

> select #1/A:231

6 atoms, 5 bonds, 1 residue, 1 model selected  

> view matrix models #1,1,0,0,29.881,0,1,0,-0.89521,0,0,1,-10.902

> select clear

[Repeated 1 time(s)]

> view matrix models #2,1,0,0,21.586,0,1,0,40.563,0,0,1,-57.936

> view matrix models #2,1,0,0,21.748,0,1,0,40.346,0,0,1,-57.925

> view matrix models
> #2,0.96252,-0.27096,-0.011142,16.918,0.26016,0.93418,-0.24418,54.351,0.076574,0.23213,0.96967,-51.278

> view matrix models
> #2,0.99879,0.030347,0.038779,20.834,-0.033168,0.99668,0.074315,36.863,-0.036395,-0.075511,0.99648,-59.896

> select add #2

415 atoms, 418 bonds, 58 residues, 2 models selected  

> select subtract #2

Nothing selected  

> select #2/A:415@CA

1 atom, 1 residue, 1 model selected  

> view matrix models
> #2,0.99879,0.030347,0.038779,20.186,-0.033168,0.99668,0.074315,36.825,-0.036395,-0.075511,0.99648,-59.818

> view matrix models
> #2,0.99879,0.030347,0.038779,20.602,-0.033168,0.99668,0.074315,37.33,-0.036395,-0.075511,0.99648,-59.119

> view matrix models
> #2,0.99879,0.030347,0.038779,20.381,-0.033168,0.99668,0.074315,37.705,-0.036395,-0.075511,0.99648,-59.049

> ui mousemode right "rotate selected models"

> view matrix models
> #2,0.99198,0.12297,0.029293,22.013,-0.12249,0.99231,-0.017563,38.656,-0.031228,0.013834,0.99942,-57.609

> select add #2

415 atoms, 418 bonds, 58 residues, 2 models selected  

> select subtract #2

Nothing selected  

> distance #1:231@C #2:415@N

Distance already exists; modify distance properties with 'distance style'  

> distance delete

> distance #1:231@C #2:415@N

Distance between
GSTCTer_af26a_unrelaxed_rank_001_alphafold2_ptm_model_2_seed_000.pdb #1/A SER
231 C and CB1 human.pdb #2/A CYS 415 N: 1.997Å  

> combine #1,2 modelId 3 name GST_CB1

Remapping chain ID 'A' in CB1 human.pdb #2 to 'B'  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/cmd_line/tool.py", line 319, in execute  
cmd.run(cmd_text)  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3221, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/cmd.py", line 174, in combine_cmd  
session.models.add([combination])  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 773, in add  
p = self._parent_for_added_model(model, parent, root_model = root_model)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 843, in _parent_for_added_model  
raise ValueError('Tried to add model %s with the same id as another model %s'  
ValueError: Tried to add model GST_CB1 #3 with the same id as another model
distances #3  
  
ValueError: Tried to add model GST_CB1 #3 with the same id as another model
distances #3  
  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 843, in _parent_for_added_model  
raise ValueError('Tried to add model %s with the same id as another model %s'  
  
See log for complete Python traceback.  
  

> combine #1,2 modelId 3 name GST_CB1

Remapping chain ID 'A' in CB1 human.pdb #2 to 'B'  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/cmd_line/tool.py", line 319, in execute  
cmd.run(cmd_text)  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3221, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/cmd.py", line 174, in combine_cmd  
session.models.add([combination])  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 773, in add  
p = self._parent_for_added_model(model, parent, root_model = root_model)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 843, in _parent_for_added_model  
raise ValueError('Tried to add model %s with the same id as another model %s'  
ValueError: Tried to add model GST_CB1 #3 with the same id as another model
distances #3  
  
ValueError: Tried to add model GST_CB1 #3 with the same id as another model
distances #3  
  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 843, in _parent_for_added_model  
raise ValueError('Tried to add model %s with the same id as another model %s'  
  
See log for complete Python traceback.  
  

> combine #1,2 modelId 3 name GST_CB1

Remapping chain ID 'A' in CB1 human.pdb #2 to 'B'  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/cmd_line/tool.py", line 319, in execute  
cmd.run(cmd_text)  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3221, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/cmd.py", line 174, in combine_cmd  
session.models.add([combination])  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 773, in add  
p = self._parent_for_added_model(model, parent, root_model = root_model)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 843, in _parent_for_added_model  
raise ValueError('Tried to add model %s with the same id as another model %s'  
ValueError: Tried to add model GST_CB1 #3 with the same id as another model
distances #3  
  
ValueError: Tried to add model GST_CB1 #3 with the same id as another model
distances #3  
  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 843, in _parent_for_added_model  
raise ValueError('Tried to add model %s with the same id as another model %s'  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 Metal - 90.5
OpenGL renderer: Apple M1
OpenGL vendor: Apple

Python: 3.11.4
Locale: en_US.UTF-8
Qt version: PyQt6 6.8.1, Qt 6.8.2
Qt runtime version: 6.8.2
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro17,1
      Model Number: MYD82Y/A
      Chip: Apple M1
      Total Number of Cores: 8 (4 performance and 4 efficiency)
      Memory: 8 GB
      System Firmware Version: 13822.1.2
      OS Loader Version: 13822.1.2

Software:

    System Software Overview:

      System Version: macOS 26.0.1 (25A362)
      Kernel Version: Darwin 25.0.0
      Time since boot: 3 días, 10 horas y 11 minutos

Graphics/Displays:

    Apple M1:

      Chipset Model: Apple M1
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 8
      Vendor: Apple (0x106b)
      Metal Support: Metal 4
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2560 x 1600 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: No
          Connection Type: Internal


Installed Packages:
    alabaster: 1.0.0
    appdirs: 1.4.4
    appnope: 0.1.4
    asttokens: 3.0.0
    babel: 2.17.0
    beautifulsoup4: 4.13.3
    blockdiag: 3.0.0
    blosc2: 3.6.1
    build: 1.2.2.post1
    certifi: 2023.11.17
    cftime: 1.6.4.post1
    charset-normalizer: 3.4.2
    ChimeraX-AddCharge: 1.5.19
    ChimeraX-AddH: 2.2.7
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.6.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.20.2
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Aniso: 1.1.4
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.60.7
    ChimeraX-AtomicLibrary: 14.1.19
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.3
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 3.0.0
    ChimeraX-Boltz: 1.0
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.2
    ChimeraX-BuildStructure: 2.13.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.5.1
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.5
    ChimeraX-ChemGroup: 2.0.2
    ChimeraX-Clashes: 2.3
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.8
    ChimeraX-CommandLine: 1.3
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.10.1
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.5
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.4
    ChimeraX-Dicom: 1.2.7
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.4
    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: 1.4.1
    ChimeraX-Hbonds: 2.5.1
    ChimeraX-Help: 1.3
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.3
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-KVFinder: 1.6.2
    ChimeraX-Label: 1.1.14
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.3
    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: 2.2.2
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.10.1
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.16
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.19
    ChimeraX-ModelPanel: 1.5.1
    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-MutationScores: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.2
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.2
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.14.1
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.10
    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: 1.1.3
    ChimeraX-ProfileGrids: 1.1.3
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.6.3
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.3.1
    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: 2.0.3
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.5.7
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.17.1
    ChimeraX-Shape: 1.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.2.1
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-SimilarStructures: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.19.1
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.2.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.5.2
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.2.3
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.45.2
    ChimeraX-Umap: 1.0
    ChimeraX-uniprot: 2.3.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.4
    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: 1.1.5
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    contourpy: 1.3.2
    coverage: 7.10.0
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.0.12
    debugpy: 1.8.15
    decorator: 5.2.1
    docutils: 0.21.2
    executing: 2.2.0
    filelock: 3.18.0
    fonttools: 4.59.0
    funcparserlib: 2.0.0a0
    glfw: 2.9.0
    grako: 3.16.5
    h5py: 3.14.0
    html2text: 2024.2.26
    idna: 3.10
    ihm: 2.2
    imagecodecs: 2024.6.1
    imagesize: 1.4.1
    iniconfig: 2.1.0
    ipykernel: 6.29.5
    ipython: 8.26.0
    ipywidgets: 8.1.7
    jedi: 0.19.1
    Jinja2: 3.1.6
    jupyter_client: 8.6.3
    jupyter_core: 5.8.1
    jupyterlab_widgets: 3.0.15
    kiwisolver: 1.4.8
    line_profiler: 4.2.0
    lxml: 5.3.1
    lz4: 4.3.2
    MarkupSafe: 3.0.2
    matplotlib: 3.10.1
    matplotlib-inline: 0.1.7
    msgpack: 1.1.0
    ndindex: 1.10.0
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.11.0
    numpy: 1.26.4
    OpenMM: 8.2.0
    openvr: 1.26.701
    packaging: 24.2
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pexpect: 4.9.0
    pickleshare: 0.7.5
    pillow: 10.4.0
    pip: 25.0.1
    pkginfo: 1.11.1
    platformdirs: 4.3.8
    pluggy: 1.6.0
    prompt_toolkit: 3.0.51
    psutil: 7.0.0
    ptyprocess: 0.7.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    Pygments: 2.18.0
    pynmrstar: 3.3.5
    pynrrd: 1.0.0
    PyOpenGL: 3.1.9
    PyOpenGL-accelerate: 3.1.9
    pyopenxr: 1.1.4501
    pyparsing: 3.2.3
    pyproject_hooks: 1.2.0
    PyQt6-commercial: 6.8.1
    PyQt6-Qt6: 6.8.2
    PyQt6-WebEngine-commercial: 6.8.0
    PyQt6-WebEngine-Qt6: 6.8.2
    PyQt6_sip: 13.10.0
    pytest: 8.4.1
    pytest-cov: 6.2.1
    python-dateutil: 2.9.0.post0
    pytz: 2025.2
    pyzmq: 27.0.0
    qtconsole: 5.5.2
    QtPy: 2.4.3
    qtshim: 1.1
    RandomWords: 0.4.0
    requests: 2.32.3
    roman-numerals-py: 3.1.0
    scipy: 1.14.0
    setuptools: 78.1.0
    sfftk-rw: 0.8.1
    six: 1.16.0
    snowballstemmer: 3.0.1
    sortedcontainers: 2.4.0
    soupsieve: 2.7
    Sphinx: 8.2.3
    sphinx-autodoc-typehints: 3.1.0
    sphinxcontrib-applehelp: 2.0.0
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 2.0.0
    sphinxcontrib-htmlhelp: 2.1.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 2.0.0
    sphinxcontrib-serializinghtml: 2.0.0
    stack-data: 0.6.3
    superqt: 0.7.1
    tables: 3.10.2
    tcia_utils: 1.5.1
    tifffile: 2025.3.13
    tinyarray: 1.2.4
    tornado: 6.5.1
    traitlets: 5.14.3
    typing_extensions: 4.14.1
    tzdata: 2025.2
    urllib3: 2.5.0
    wcwidth: 0.2.13
    webcolors: 24.11.1
    wheel: 0.45.1
    wheel-filename: 1.4.2
    widgetsnbextension: 4.0.14

[Eric Pettersen]

This no longer raises a traceback.