ChimeraX bug report submission

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.26200
ChimeraX Version: 1.12rc202606031852 (2026-06-03 18:52:53 UTC)
Description
Replace this text with list of actions that caused this problem to occur

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
You can double click a model's Name or ID in the model panel to edit those
fields  
UCSF ChimeraX version: 1.12rc202606031852 (2026-06-03)  
© 2016-2026 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> help help:quickstart

[Repeated 1 time(s)]

> open C:/Users/iib1m/Downloads/fold_tatd10_401_cepa_dm28_supuestamente.zip

Unrecognized file suffix '.zip'  

> open
> C:/Users/iib1m/Downloads/fold_tatd10_401_cepa_dm28_supuestamente/fold_tatd10_401_cepa_dm28_supuestamente_full_data_0.json

Opening an AlphaFold PAE file requires first opening the predicted atomic
model. Did not find an open atomic model from the same directory. If the
atomic model is already open choose it using menu  
  
Tools / Structure Prediction / AlphaFold Error Plot  
  
or use the open command structure option, for example  
  
open
C:/Users/iib1m/Downloads/fold_tatd10_401_cepa_dm28_supuestamente/fold_tatd10_401_cepa_dm28_supuestamente_full_data_0.json
structure #1  
  
If you are trying to open a JSON file that is not AlphaFold PAE data then you
need to specify the specific JSON format such as  
  
open mole_channels.json format mole  

> open
> C:/Users/iib1m/Downloads/fold_tatd10_401_cepa_dm28_supuestamente/fold_tatd10_401_cepa_dm28_supuestamente_model_0.cif

Chain information for fold_tatd10_401_cepa_dm28_supuestamente_model_0.cif #1  
---  
Chain | Description  
A | .  
  
Computing secondary structure  

> select /A:1-401

3007 atoms, 3075 bonds, 401 residues, 1 model selected  

> select /A:1-401

3007 atoms, 3075 bonds, 401 residues, 1 model selected  

> open
> C:/Users/iib1m/Downloads/fold_tatd10_401_cepa_dm28_supuestamente/fold_tatd10_401_cepa_dm28_supuestamente_model_1.cif

Chain information for fold_tatd10_401_cepa_dm28_supuestamente_model_1.cif #2  
---  
Chain | Description  
A | .  
  
Computing secondary structure  

> hide #1 models

> select add #2

6014 atoms, 6150 bonds, 802 residues, 2 models selected  

> select subtract #2

3007 atoms, 3075 bonds, 401 residues, 1 model selected  

> show target m

[Repeated 1 time(s)]

> hide #1 models

> select subtract #1

Nothing selected  

> open
> C:/Users/iib1m/Downloads/fold_tatd10_401_cepa_dm28_supuestamente/fold_tatd10_401_cepa_dm28_supuestamente_model_3.cif

Chain information for fold_tatd10_401_cepa_dm28_supuestamente_model_3.cif #3  
---  
Chain | Description  
A | .  
  
Computing secondary structure  

> hide #2 models

> show #2 models

> hide #3 models

> open
> C:/Users/iib1m/Downloads/fold_tatd10_cruzi_cepa_cl_brener_401_con_gst_n_terminal/fold_tatd10_cruzi_cepa_cl_brener_401_con_gst_n_terminal_model_0.cif

Chain information for
fold_tatd10_cruzi_cepa_cl_brener_401_con_gst_n_terminal_model_0.cif #4  
---  
Chain | Description  
A | .  
  
Computing secondary structure  

> ui tool show Match→Align

> msa3d #1/A#4/A

Match→Align cutoff: 5.0, in column if within cutoff of: any  
45 residue pairs aligned  
45 fully populated columns  
Pairwise RMSDs across all fully populated columns  
---  
Model | 1 | 4  
1 | 0.000 | 2.924  
4 | 2.924 | 0.000  
  
Overall RMSD: 2.924  
Sequence lengths: 401 631  
SDM (cutoff 5.0): 164.954  
Q-score: 0.004  
Alignment identifier is MA-1  
Showing conservation header ("seq_conservation" residue attribute) for
alignment MA-1  
Chains used in RMSD evaluation for alignment MA-1:
fold_tatd10_401_cepa_dm28_supuestamente_model_0.cif #1/A,
fold_tatd10_cruzi_cepa_cl_brener_401_con_gst_n_terminal_model_0.cif #4/A  
Showing rmsd header ("seq_rmsd" residue attribute) for alignment MA-1  

> select #1/A:9

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

> select #1/A:5-9

33 atoms, 32 bonds, 5 residues, 1 model selected  

> select #1/A:24

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

> select #1/A:42

11 atoms, 11 bonds, 1 residue, 1 model selected  

> select #1/A:42-46

43 atoms, 44 bonds, 5 residues, 1 model selected  

> hide #4 models

> show #4 models

> ui tool show Match→Align

[Repeated 1 time(s)]

> msa3d #3/A#4/A

Match→Align cutoff: 5.0, in column if within cutoff of: any  
37 residue pairs aligned  
37 fully populated columns  
Pairwise RMSDs across all fully populated columns  
---  
Model | 3 | 4  
3 | 0.000 | 3.034  
4 | 3.034 | 0.000  
  
Overall RMSD: 3.034  
Sequence lengths: 401 631  
SDM (cutoff 5.0): 179.967  
Q-score: 0.003  
Alignment identifier is MA-1  
Showing conservation header ("seq_conservation" residue attribute) for
alignment MA-1  
Chains used in RMSD evaluation for alignment MA-1:
fold_tatd10_401_cepa_dm28_supuestamente_model_3.cif #3/A,
fold_tatd10_cruzi_cepa_cl_brener_401_con_gst_n_terminal_model_0.cif #4/A  
Showing rmsd header ("seq_rmsd" residue attribute) for alignment MA-1  

> ui tool show Match→Align

> msa3d #2/A#4/A columnCriterion all

Match→Align cutoff: 5.0, in column if within cutoff of: all  
30 residue pairs aligned  
30 fully populated columns  
Pairwise RMSDs across all fully populated columns  
---  
Model | 2 | 4  
2 | 0.000 | 2.884  
4 | 2.884 | 0.000  
  
Overall RMSD: 2.884  
Sequence lengths: 401 631  
SDM (cutoff 5.0): 182.272  
Q-score: 0.002  
Alignment identifier is MA-1  
Showing conservation header ("seq_conservation" residue attribute) for
alignment MA-1  
Chains used in RMSD evaluation for alignment MA-1:
fold_tatd10_401_cepa_dm28_supuestamente_model_1.cif #2/A,
fold_tatd10_cruzi_cepa_cl_brener_401_con_gst_n_terminal_model_0.cif #4/A  
Showing rmsd header ("seq_rmsd" residue attribute) for alignment MA-1  

> select #2/A:17

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

> hide #2 models

> show #2 models

> show target m

[Repeated 1 time(s)]

> hide #1 models

> hide #2 models

> sequence chain #2/A

Alignment identifier is 2/A  

> show #2 models

> hide #2 models

> sequence chain #2/A

Destroying pre-existing alignment with identifier 2/A  
Alignment identifier is 2/A  

> show #2 models

> hide #2 models

> select
> #2/A:37-39,60-72,101-103,107-109,139-152,171-187,200-209,228-236,268-270,274-284,330-339,348-362,371-390

1012 atoms, 1018 bonds, 131 residues, 1 model selected  

> rename #3-4 id 5

> rename #5 group

> hide #5.2 models

> hide #!5 models

> hide #5.1 models

> show #5.2 models

> show #5.1 models

> hide #5.2 models

> hide #!5 models

> hide #5.1 models

> show #5.1 models

> hide #!5 models

> show #5.2 models

> hide #5.1 models

> hide #!5 models

> show #5.1 models

> view clip false

[Repeated 1 time(s)]

> ui mousemode right "mark surface"

[Repeated 1 time(s)]

> marker #3 position -5.146,14.91,16.58 color yellow radius 1

> marker #3 position -4.311,15.35,16.25 color yellow radius 1

> marker #3 position -3.224,15.73,18.13 color yellow radius 1

> marker #3 position 0.4179,14.45,18.92 color yellow radius 1

> marker #3 position -10.12,2.829,37.71 color yellow radius 1

> marker #3 position 3.168,25.33,-17.46 color yellow radius 1

> marker #3 position 12.71,-0.5708,5.821 color yellow radius 1

> marker #3 position 22.58,-11.83,4.562 color yellow radius 1

> marker #3 position 29.69,-15.12,11.53 color yellow radius 1

> hide #3 models

> ui tool show Match→Align

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.12rc202606031852\bin\Lib\site-
packages\chimerax\ui\options\containers.py", line 467, in _save  
settings.save(settings=save_settings)  
File "C:\Program Files\ChimeraX 1.12rc202606031852\bin\Lib\site-
packages\chimerax\core\settings.py", line 232, in save  
ConfigFile.save(self)  
File "C:\Program Files\ChimeraX 1.12rc202606031852\bin\Lib\site-
packages\chimerax\core\configfile.py", line 335, in save  
with SaveTextFile(self._filename) as f:  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.12rc202606031852\bin\Lib\site-
packages\chimerax\core\safesave.py", line 195, in __init__  
SaveFile.__init__(self, filename, open=open_text, critical=critical)  
File "C:\Program Files\ChimeraX 1.12rc202606031852\bin\Lib\site-
packages\chimerax\core\safesave.py", line 88, in __init__  
self._f = open(self._tmp_filename)  
^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.12rc202606031852\bin\Lib\site-
packages\chimerax\core\safesave.py", line 194, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
OSError: [Errno 22] Invalid argument:
'C:\\\Users\\\iib1m\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\match->align-1.33412.1780667776.79093.tmp'  
  
OSError: [Errno 22] Invalid argument:
'C:\\\Users\\\iib1m\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\match->align-1.33412.1780667776.79093.tmp'  
  
File "C:\Program Files\ChimeraX 1.12rc202606031852\bin\Lib\site-
packages\chimerax\core\safesave.py", line 194, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.12rc202606031852\bin\Lib\site-
packages\chimerax\ui\options\containers.py", line 467, in _save  
settings.save(settings=save_settings)  
File "C:\Program Files\ChimeraX 1.12rc202606031852\bin\Lib\site-
packages\chimerax\core\settings.py", line 232, in save  
ConfigFile.save(self)  
File "C:\Program Files\ChimeraX 1.12rc202606031852\bin\Lib\site-
packages\chimerax\core\configfile.py", line 335, in save  
with SaveTextFile(self._filename) as f:  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.12rc202606031852\bin\Lib\site-
packages\chimerax\core\safesave.py", line 195, in __init__  
SaveFile.__init__(self, filename, open=open_text, critical=critical)  
File "C:\Program Files\ChimeraX 1.12rc202606031852\bin\Lib\site-
packages\chimerax\core\safesave.py", line 88, in __init__  
self._f = open(self._tmp_filename)  
^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.12rc202606031852\bin\Lib\site-
packages\chimerax\core\safesave.py", line 194, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
OSError: [Errno 22] Invalid argument:
'C:\\\Users\\\iib1m\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\match->align-1.33412.1780667776.79093.tmp'  
  
OSError: [Errno 22] Invalid argument:
'C:\\\Users\\\iib1m\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\match->align-1.33412.1780667776.79093.tmp'  
  
File "C:\Program Files\ChimeraX 1.12rc202606031852\bin\Lib\site-
packages\chimerax\core\safesave.py", line 194, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.12rc202606031852\bin\Lib\site-
packages\chimerax\ui\options\containers.py", line 467, in _save  
settings.save(settings=save_settings)  
File "C:\Program Files\ChimeraX 1.12rc202606031852\bin\Lib\site-
packages\chimerax\core\settings.py", line 232, in save  
ConfigFile.save(self)  
File "C:\Program Files\ChimeraX 1.12rc202606031852\bin\Lib\site-
packages\chimerax\core\configfile.py", line 335, in save  
with SaveTextFile(self._filename) as f:  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.12rc202606031852\bin\Lib\site-
packages\chimerax\core\safesave.py", line 195, in __init__  
SaveFile.__init__(self, filename, open=open_text, critical=critical)  
File "C:\Program Files\ChimeraX 1.12rc202606031852\bin\Lib\site-
packages\chimerax\core\safesave.py", line 88, in __init__  
self._f = open(self._tmp_filename)  
^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.12rc202606031852\bin\Lib\site-
packages\chimerax\core\safesave.py", line 194, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
OSError: [Errno 22] Invalid argument:
'C:\\\Users\\\iib1m\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\match->align-1.33412.1780667776.79093.tmp'  
  
OSError: [Errno 22] Invalid argument:
'C:\\\Users\\\iib1m\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\match->align-1.33412.1780667776.79093.tmp'  
  
File "C:\Program Files\ChimeraX 1.12rc202606031852\bin\Lib\site-
packages\chimerax\core\safesave.py", line 194, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.12rc202606031852\bin\Lib\site-
packages\chimerax\ui\options\containers.py", line 467, in _save  
settings.save(settings=save_settings)  
File "C:\Program Files\ChimeraX 1.12rc202606031852\bin\Lib\site-
packages\chimerax\core\settings.py", line 232, in save  
ConfigFile.save(self)  
File "C:\Program Files\ChimeraX 1.12rc202606031852\bin\Lib\site-
packages\chimerax\core\configfile.py", line 335, in save  
with SaveTextFile(self._filename) as f:  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.12rc202606031852\bin\Lib\site-
packages\chimerax\core\safesave.py", line 195, in __init__  
SaveFile.__init__(self, filename, open=open_text, critical=critical)  
File "C:\Program Files\ChimeraX 1.12rc202606031852\bin\Lib\site-
packages\chimerax\core\safesave.py", line 88, in __init__  
self._f = open(self._tmp_filename)  
^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.12rc202606031852\bin\Lib\site-
packages\chimerax\core\safesave.py", line 194, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
OSError: [Errno 22] Invalid argument:
'C:\\\Users\\\iib1m\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\match->align-1.33412.1780667776.79093.tmp'  
  
OSError: [Errno 22] Invalid argument:
'C:\\\Users\\\iib1m\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\match->align-1.33412.1780667776.79093.tmp'  
  
File "C:\Program Files\ChimeraX 1.12rc202606031852\bin\Lib\site-
packages\chimerax\core\safesave.py", line 194, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  

> open
> C:/Users/iib1m/Downloads/fold_tatd05_de_cruzi_secuencia_de_dm28c/fold_tatd05_de_cruzi_secuencia_de_dm28c_model_0.cif

Chain information for fold_tatd05_de_cruzi_secuencia_de_dm28c_model_0.cif #4  
---  
Chain | Description  
A | .  
  
Computing secondary structure  

> hide #!5 models

> open
> C:/Users/iib1m/Downloads/fold_tatd_de_thermophilus_paper_coincide_con_la_tatd5.zip

Unrecognized file suffix '.zip'  

> open
> C:/Users/iib1m/Downloads/fold_tatd_de_thermophilus_paper_coincide_con_la_tatd5/fold_tatd_de_thermophilus_paper_coincide_con_la_tatd5_model_0.cif

Chain information for
fold_tatd_de_thermophilus_paper_coincide_con_la_tatd5_model_0.cif #6  
---  
Chain | Description  
A | .  
  
Computing secondary structure  

> ui tool show Match→Align

> msa3d #6/A#4/A maxIterations 3 refChain #6/A

Match→Align cutoff: 5.0, in column if within cutoff of: any  
49 residue pairs aligned  
49 fully populated columns  
12 fully populated columns in at least 3 column stetches  
Matching fold_tatd05_de_cruzi_secuencia_de_dm28c_model_0.cif, chain A onto
fold_tatd_de_thermophilus_paper_coincide_con_la_tatd5_model_0.cif, chain A  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.12rc202606031852\bin\Lib\site-
packages\chimerax\match_align\tool.py", line 259, in match_align  
run(self.session, "msa3d " + ' '.join(args))  
File "C:\Program Files\ChimeraX 1.12rc202606031852\bin\Lib\site-
packages\chimerax\core\commands\run.py", line 49, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.12rc202606031852\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3245, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.12rc202606031852\bin\Lib\site-
packages\chimerax\match_align\cmd.py", line 131, in make_alignment  
aligned = [copy(chain) for chain in ordered]  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.12rc202606031852\bin\Lib\site-
packages\chimerax\match_align\cmd.py", line 131, in <listcomp>  
aligned = [copy(chain) for chain in ordered]  
^^^^  
NameError: name 'copy' is not defined  
  
NameError: name 'copy' is not defined  
  
File "C:\Program Files\ChimeraX 1.12rc202606031852\bin\Lib\site-
packages\chimerax\match_align\cmd.py", line 131, in  
aligned = [copy(chain) for chain in ordered]  
^^^^  
  
See log for complete Python traceback.  
  

> hide #5.1 models

> hide #5.2 models

> ui tool show Match→Align

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.12rc202606031852\bin\Lib\site-
packages\chimerax\ui\options\containers.py", line 467, in _save  
settings.save(settings=save_settings)  
File "C:\Program Files\ChimeraX 1.12rc202606031852\bin\Lib\site-
packages\chimerax\core\settings.py", line 232, in save  
ConfigFile.save(self)  
File "C:\Program Files\ChimeraX 1.12rc202606031852\bin\Lib\site-
packages\chimerax\core\configfile.py", line 335, in save  
with SaveTextFile(self._filename) as f:  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.12rc202606031852\bin\Lib\site-
packages\chimerax\core\safesave.py", line 195, in __init__  
SaveFile.__init__(self, filename, open=open_text, critical=critical)  
File "C:\Program Files\ChimeraX 1.12rc202606031852\bin\Lib\site-
packages\chimerax\core\safesave.py", line 88, in __init__  
self._f = open(self._tmp_filename)  
^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.12rc202606031852\bin\Lib\site-
packages\chimerax\core\safesave.py", line 194, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
OSError: [Errno 22] Invalid argument:
'C:\\\Users\\\iib1m\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\match->align-1.33412.1780667776.79093.tmp'  
  
OSError: [Errno 22] Invalid argument:
'C:\\\Users\\\iib1m\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\match->align-1.33412.1780667776.79093.tmp'  
  
File "C:\Program Files\ChimeraX 1.12rc202606031852\bin\Lib\site-
packages\chimerax\core\safesave.py", line 194, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 - Build 32.0.101.7080
OpenGL renderer: Intel(R) Iris(R) Xe Graphics
OpenGL vendor: Intel

Python: 3.11.9
Locale: es_AR.cp1252
Qt version: PyQt6 6.10.2, Qt 6.10.0
Qt runtime version: 6.10.2
Qt platform: windows

Manufacturer: Dell Inc.
Model: Inspiron 15 3511
OS: Microsoft Windows 11 Home Single Language (Build 26200.8457)
Memory: 8,311,836,672
MaxProcessMemory: 137,438,953,344
CPU: 8 11th Gen Intel(R) Core(TM) i5-1135G7 @ 2.40GHz
OSLanguage: es-ES

Installed Packages:
    accessible-pygments: 0.0.5
    aiohappyeyeballs: 2.6.2
    aiohttp: 3.13.4
    aiosignal: 1.4.0
    alabaster: 1.0.0
    annotated-types: 0.7.0
    anyio: 4.13.0
    appdirs: 1.4.4
    asttokens: 3.0.1
    attrs: 26.1.0
    babel: 2.18.0
    beautifulsoup4: 4.13.5
    blockdiag: 3.0.0
    blosc2: 4.4.2
    bs4: 0.0.2
    build: 1.3.0
    certifi: 2026.5.20
    cftime: 1.6.5
    charset-normalizer: 3.4.7
    ChimeraX-AddCharge: 1.5.20
    ChimeraX-AddH: 2.2.8
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.6.2
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 3.2
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Animations: 1.0
    ChimeraX-Aniso: 1.3.2
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.67.1
    ChimeraX-AtomicLibrary: 14.4
    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: 1.1
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.2
    ChimeraX-BuildStructure: 2.13.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.6.0
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4.1
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.5
    ChimeraX-ChemGroup: 2.0.2
    ChimeraX-Clashes: 2.4
    ChimeraX-Cluster: 1.0
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.8
    ChimeraX-CommandLine: 1.3.1
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.12rc202606031852
    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: 1.2.2
    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: 2.5.3
    ChimeraX-Help: 1.3
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.4
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-KVFinder: 1.8.2
    ChimeraX-Label: 1.5
    ChimeraX-LightingGUI: 1.0
    ChimeraX-ListInfo: 1.3.1
    ChimeraX-Log: 1.2.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.3
    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-MatchAlign: 1.2
    ChimeraX-MatchMaker: 2.4.1
    ChimeraX-MCopy: 1.0
    ChimeraX-MCPServer: 0.2.0
    ChimeraX-MDcrds: 2.19
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-Minimize: 1.3.9
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.16
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.23
    ChimeraX-ModelPanel: 1.6.1
    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: 1.0.1
    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: 1.15.4
    ChimeraX-OpenFold: 1.0
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.13
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.5
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1.4
    ChimeraX-ProfileGrids: 1.6
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.8.2
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.3.3
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.2
    ChimeraX-Scenes: 0.3.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.3
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.5.12
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.18
    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-SNFG: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.19.3
    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: 2.5.3
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.2.4
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.50.8
    ChimeraX-Umap: 1.0
    ChimeraX-uniprot: 2.3.2
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDock: 1.6.2
    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: 1.1.5
    ChimeraX-Zone: 1.0.1
    click: 8.4.1
    colorama: 0.4.6
    comm: 0.2.3
    comtypes: 1.4.11
    contourpy: 1.3.3
    coverage: 7.14.1
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.2.4
    debugpy: 1.8.21
    decorator: 5.3.1
    docutils: 0.21.2
    executing: 2.2.1
    filelock: 3.19.1
    fonttools: 4.63.0
    frozenlist: 1.8.0
    funcparserlib: 2.0.0a0
    glfw: 2.10.0
    grako: 3.16.5
    h11: 0.16.0
    h5py: 3.16.0
    html2text: 2025.4.15
    httpcore: 1.0.9
    httpx: 0.28.1
    httpx-sse: 0.4.3
    idna: 3.18
    ihm: 2.2
    imagecodecs: 2024.6.1
    imagesize: 2.0.0
    iniconfig: 2.3.0
    ipykernel: 7.1.0
    ipython: 9.9.0
    ipython_pygments_lexers: 1.1.1
    jedi: 0.19.2
    Jinja2: 3.1.6
    jsonschema: 4.26.0
    jsonschema-specifications: 2025.9.1
    jupyter_client: 8.8.0
    jupyter_core: 5.9.1
    kiwisolver: 1.5.0
    line_profiler: 5.0.0
    lxml: 6.0.2
    lz4: 4.3.2
    Markdown: 3.8.2
    MarkupSafe: 3.0.3
    matplotlib: 3.10.7
    matplotlib-inline: 0.2.2
    mcp: 1.18.0
    msgpack: 1.1.1
    multidict: 6.7.1
    narwhals: 2.22.0
    ndindex: 1.10.1
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.14.1
    numpy: 1.26.4
    nvidia-nvjitlink-cu12: 12.9.86
    OpenMM: 8.4.0
    OpenMM-CUDA-12: 8.4.0
    openvr: 1.26.701
    packaging: 25.0
    ParmEd: 4.2.2
    parso: 0.8.7
    pep517: 0.13.1
    pickleshare: 0.7.5
    pillow: 11.3.0
    pip: 25.2
    pkginfo: 1.12.1.2
    platformdirs: 4.10.0
    plotly: 6.8.0
    pluggy: 1.6.0
    prompt_toolkit: 3.0.52
    propcache: 0.5.2
    psutil: 7.0.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pybind11: 3.0.1
    pycollada: 0.8
    pydantic: 2.13.4
    pydantic-settings: 2.14.1
    pydantic_core: 2.46.4
    pydata-sphinx-theme: 0.18.0
    pydicom: 2.4.4
    Pygments: 2.18.0
    pynmrstar: 3.5.1
    pynrrd: 1.0.0
    PyOpenGL: 3.1.10
    PyOpenGL-accelerate: 3.1.10
    pyopenxr: 1.1.4501
    pyparsing: 3.3.2
    pyproject_hooks: 1.2.0
    PyQt6-commercial: 6.10.2
    PyQt6-Qt6: 6.10.2
    PyQt6-WebEngine-commercial: 6.10.0
    PyQt6-WebEngine-Qt6: 6.10.2
    PyQt6_sip: 13.10.3
    pytest: 9.0.3
    pytest-cov: 7.1.0
    python-dateutil: 2.9.0.post0
    python-dotenv: 1.2.2
    python-multipart: 0.0.32
    pywin32: 311
    pyzmq: 27.1.0
    qtconsole: 5.7.0
    QtPy: 2.4.3
    qtshim: 1.2.2
    RandomWords: 0.4.0
    referencing: 0.37.0
    requests: 2.32.5
    roman-numerals: 4.1.0
    rpds-py: 2026.5.1
    scipy: 1.14.0
    setuptools: 80.9.0
    sfftk-rw: 0.8.1
    six: 1.17.0
    snowballstemmer: 3.1.1
    sortedcontainers: 2.4.0
    soupsieve: 2.8.4
    Sphinx: 9.0.4
    sphinx-autodoc-typehints: 3.6.1
    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
    sse-starlette: 3.4.4
    stack-data: 0.6.3
    starlette: 1.2.1
    superqt: 0.7.6
    tables: 3.10.2
    tcia_utils: 3.2.1
    threadpoolctl: 3.6.0
    tifffile: 2025.3.13
    tinyarray: 1.2.5
    tornado: 6.5.6
    tqdm: 4.67.3
    traitlets: 5.14.3
    typing-inspection: 0.4.2
    typing_extensions: 4.15.0
    tzdata: 2026.2
    Unidecode: 1.4.0
    urllib3: 2.7.0
    uvicorn: 0.49.0
    wcwidth: 0.7.0
    webcolors: 24.11.1
    wheel: 0.45.1
    wheel-filename: 1.4.2
    WMI: 1.5.1
    yarl: 1.24.2