Alignment observer not in list

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.26100
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:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
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 C:/Users/33766/Downloads/6KSH.cif

Summary of feedback from opening C:/Users/33766/Downloads/6KSH.cif  
---  
notes | Fetching CCD ATP from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/P/ATP/ATP.cif  
Fetching CCD K from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/K/K/K.cif  
Fetching CCD MG from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/G/MG/MG.cif  
Fetching CCD OXL from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/L/OXL/OXL.cif  
  
6KSH.cif title:  
Crystal structure of pyruvate kinase (PYK) from Plasmodium falciparum in
complex with oxalate and ATP [more info...]  
  
Chain information for 6KSH.cif #1  
---  
Chain | Description | UniProt  
A B C D | Pyruvate kinase | C6KTA4_PLAF7 1-511  
  
Non-standard residues in 6KSH.cif #1  
---  
ATP — adenosine-5'-triphosphate  
K — potassium ion  
MG — magnesium ion  
OXL — oxalate ion  
  
53 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  

> select /A/B/C/D

16042 atoms, 15264 bonds, 79 pseudobonds, 2930 residues, 3 models selected  

> ui tool show "Color Actions"

> color sel bychain

> select clear

[Repeated 1 time(s)]

> set bgColor white

> set bgColor black

> select /B

3959 atoms, 3816 bonds, 19 pseudobonds, 681 residues, 3 models selected  

> color (#!1 & sel) byelement

> select clear

> select /A/B/C/D

16042 atoms, 15264 bonds, 79 pseudobonds, 2930 residues, 3 models selected  

> color (#!1 & sel) byelement

> select clear

> set bgColor white

> set bgColor #ffffff00

> view #1 clip false

[Repeated 1 time(s)]

> set bgColor black

> set bgColor transparent

> select #1:.B

Expected an objects specifier or a keyword  

> select #1:B

Nothing selected  

> select #1/B

3959 atoms, 3816 bonds, 19 pseudobonds, 681 residues, 3 models selected  

> hide #1/A

> select clear

> hide #1/A

> select /A

4074 atoms, 3816 bonds, 20 pseudobonds, 796 residues, 3 models selected  

> hide #1/A

> hide #!1 target m

> show #!1 target m

> split chains

Split 6KSH.cif (#1) into 4 models  
Chain information for 6KSH.cif A #1.1  
---  
Chain | Description  
A | No description available  
  
Chain information for 6KSH.cif B #1.2  
---  
Chain | Description  
B | No description available  
  
Chain information for 6KSH.cif C #1.3  
---  
Chain | Description  
C | No description available  
  
Chain information for 6KSH.cif D #1.4  
---  
Chain | Description  
D | No description available  
  

> hide #!1.1 models

> hide #!1.3 models

> hide #!1.4 models

> surface #1.2#!1

> transparency #1.2#!1 50

> transparency #1.2#!1 0

> show #1.2#!1 target ab

> undo

[Repeated 1 time(s)]

> hide #!1.4 models

Drag select of 6KSH.cif B_B SES surface, 2731 of 396022 triangles, 33 atoms,
15 residues, 5 pseudobonds, 34 bonds  

> show (#!1.2 & sel) target ab

> hide #* target a

> show (#!1.2 & sel) target ab

[Repeated 1 time(s)]

> hide (#!1.2 & sel) target a

> show (#!1.2 & sel) target ab

> hbonds sel reveal true

45 hydrogen bonds found  

> color bfactor sel

141 atoms, 22 residues, 1 surfaces, atom bfactor range 38.7 to 107  

> surface hidePatches (#!1.2 & sel)

> mlp sel

Map values for surface "6KSH.cif B_B SES surface": minimum -27.95, mean
-4.932, maximum 26.72  
To also show corresponding color key, enter the above mlp command and add key
true  

> undo

[Repeated 4 time(s)]

> set bgColor white

> set bgColor #ffffff00

Drag select of 6KSH.cif B_B SES surface, 879 of 396022 triangles, 26 atoms, 13
residues, 25 bonds, 8 pseudobonds  

> select clear

> select ::name="ATP"

124 atoms, 132 bonds, 4 residues, 4 models selected  

> style sel & #!1.2 ball

Changed 31 atom styles  

> select
> ::name="ALA"::name="ARG"::name="ASN"::name="ASP"::name="CYS"::name="GLN"::name="GLU"::name="GLY"::name="HIS"::name="ILE"::name="LEU"::name="LYS"::name="MET"::name="PHE"::name="PRO"::name="SER"::name="THR"::name="TYR"::name="VAL"

14932 atoms, 15112 bonds, 31 pseudobonds, 1960 residues, 9 models selected  

> select clear

> set bgColor black

> set bgColor transparent

> select ::name="ATP"

124 atoms, 132 bonds, 4 residues, 4 models selected  

> select sel @< 5

526 atoms, 366 bonds, 84 pseudobonds, 182 residues, 9 models selected  

> style sel & #!1.2 stick

Changed 127 atom styles  

> color (#!1.2 & sel) byelement

> undo

> select clear

> open C:/Users/33766/Downloads/3KHD.cif

3KHD.cif title:  
Crystal Structure of PFF1300w. [more info...]  
  
Chain information for 3KHD.cif #2  
---  
Chain | Description | UniProt  
A B C D | Pyruvate kinase | C6KTA4_PLAF7 19-520  
  
3KHD.cif mmCIF Assemblies  
---  
1| software_defined_assembly  
2| software_defined_assembly  
3| software_defined_assembly  
  

> ui tool show Matchmaker

> matchmaker #2/B to #1.2/B pairing ss

Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 6KSH.cif B, chain B (#1.2) with 3KHD.cif, chain B (#2), sequence
alignment score = 2436.8  
RMSD between 361 pruned atom pairs is 0.636 angstroms; (across all 488 pairs:
6.335)  
  

> matchmaker #2/B to #1.2/B pairing ss

Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 6KSH.cif B, chain B (#1.2) with 3KHD.cif, chain B (#2), sequence
alignment score = 2436.8  
RMSD between 361 pruned atom pairs is 0.636 angstroms; (across all 488 pairs:
6.335)  
  

> hide #!1 models

> hide #!1.2 models

> split chains

Did not split 6KSH.cif A, has only one piece  
Did not split 6KSH.cif B, has only one piece  
Did not split 6KSH.cif C, has only one piece  
Did not split 6KSH.cif D, has only one piece  
Split 3KHD.cif (#2) into 4 models  
Chain information for 3KHD.cif A #2.1  
---  
Chain | Description  
A | No description available  
  
Chain information for 3KHD.cif B #2.2  
---  
Chain | Description  
B | No description available  
  
Chain information for 3KHD.cif C #2.3  
---  
Chain | Description  
C | No description available  
  
Chain information for 3KHD.cif D #2.4  
---  
Chain | Description  
D | No description available  
  

> show #!1.2 models

> hide #!2 models

> hide #!2.1 models

> hide #!2.3 models

> hide #!2.4 models

> show #!2 models

Drag select of 6KSH.cif B_B SES surface, 8219 of 396022 triangles, 174 atoms,
990 residues, 61 pseudobonds, 135 bonds  

> surface (#!1.2#!2.2 & sel)

> select clear

[Repeated 1 time(s)]

> transparency #1.2#2.2#!1-2 70

> undo

> transparency #1.2#2.2#!1-2 0

Drag select of 6KSH.cif B_B SES surface, 3KHD.cif B_B SES surface, 174 atoms,
990 residues, 61 pseudobonds, 135 bonds  

> ui tool show "Show Sequence Viewer"

> sequence chain #1.1/A #1.2/B #1.3/C #1.4/D

Alignment identifier is 1  

> sequence chain #2.2/B

Alignment identifier is 2.2/B  

> ui tool show "Modeller Comparative"

> hide #!1.2 models

> show #!1.2 models

> modeller comparative 2.2/B:1 numModels 5 fast false multichain true
> hetPreserve false hydrogens false waterPreserve false

No Modeller license key provided. Get a license key by registering at the
Modeller web site.  

> ui tool show "Show Sequence Viewer"

> sequence chain #2.2/B

Destroying pre-existing alignment with identifier 2.2/B  
Alignment identifier is 2.2/B  

> select add #1.2

7637 atoms, 3816 bonds, 66 pseudobonds, 1181 residues, 8 models selected  

> ui tool show "Blast Protein"

> blastprotein #1.2/B database pdb cutoff 1e-3 matrix BLOSUM62 maxSeqs 100
> version None name bp1

Webservices job id: 0S11O9D2ESJ0U2TR  
Webservices job finished: 0S11O9D2ESJ0U2TR  

QWindowsWindow::setGeometry: Unable to set geometry 1920x1164+0+29 (frame:
1938x1211-9-9) on QWidgetWindow/"MainWindowClassWindow" on "\\\\.\DISPLAY1".
Resulting geometry: 1920x991+0+29 (frame: 1938x1038-9-9) margins: 9, 38, 9, 9
minimum size: 532x931 MINMAXINFO(maxSize=POINT(x=0, y=0), maxpos=POINT(x=0,
y=0), maxtrack=POINT(x=0, y=0), mintrack=POINT(x=683, y=1211)))  

Alignment identifier is bp1 [1]  
Associated 6KSH.cif A (1.1) chain A to #1.2/B with 0 mismatches  
Associated 6KSH.cif B (1.2) chain B to #1.2/B with 0 mismatches  
Associated 6KSH.cif C (1.3) chain C to #1.2/B with 0 mismatches  
Associated 6KSH.cif D (1.4) chain D to #1.2/B with 0 mismatches  
Associated 3KHD.cif A (2.1) chain A to #1.2/B with 7 mismatches  
Associated 3KHD.cif B (2.2) chain B to #1.2/B with 8 mismatches  
Associated 3KHD.cif C (2.3) chain C to #1.2/B with 1 mismatch  
Associated 3KHD.cif D (2.4) chain D to #1.2/B with 3 mismatches  

QWindowsWindow::setGeometry: Unable to set geometry 1920x1246+0+29 (frame:
1938x1293-9-9) on QWidgetWindow/"MainWindowClassWindow" on "\\\\.\DISPLAY1".
Resulting geometry: 1920x991+0+29 (frame: 1938x1038-9-9) margins: 9, 38, 9, 9
minimum size: 532x997 MINMAXINFO(maxSize=POINT(x=0, y=0), maxpos=POINT(x=0,
y=0), maxtrack=POINT(x=0, y=0), mintrack=POINT(x=683, y=1293)))  

Alignment identifier is bp1 [2]  
Associated 6KSH.cif A (1.1) chain A to #1.2/B with 0 mismatches  
Associated 6KSH.cif B (1.2) chain B to #1.2/B with 0 mismatches  
Associated 6KSH.cif C (1.3) chain C to #1.2/B with 0 mismatches  
Associated 6KSH.cif D (1.4) chain D to #1.2/B with 0 mismatches  
Associated 3KHD.cif A (2.1) chain A to #1.2/B with 7 mismatches  
Associated 3KHD.cif B (2.2) chain B to #1.2/B with 8 mismatches  
Associated 3KHD.cif C (2.3) chain C to #1.2/B with 1 mismatch  
Associated 3KHD.cif D (2.4) chain D to #1.2/B with 3 mismatches  

QWindowsWindow::setGeometry: Unable to set geometry 1920x1329+0+29 (frame:
1938x1376-9-9) on QWidgetWindow/"MainWindowClassWindow" on "\\\\.\DISPLAY1".
Resulting geometry: 1920x991+0+29 (frame: 1938x1038-9-9) margins: 9, 38, 9, 9
minimum size: 532x1063 MINMAXINFO(maxSize=POINT(x=0, y=0), maxpos=POINT(x=0,
y=0), maxtrack=POINT(x=0, y=0), mintrack=POINT(x=683, y=1376)))  

> select add #1

19720 atoms, 15264 bonds, 126 pseudobonds, 3430 residues, 18 models selected  

> select subtract #1

3678 atoms, 2 pseudobonds, 500 residues, 4 models selected  

> select add #1.2

7637 atoms, 3816 bonds, 66 pseudobonds, 1181 residues, 7 models selected  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\modeller\tool.py", line 347, in _update_sequence_menus  
row_info.fieldItem.widget().destroy()  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\seqalign\widgets.py", line 104, in destroy  
self.alignment.remove_observer(self)  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\seqalign\alignment.py", line 780, in remove_observer  
self.observers.remove(observer)  
ValueError: list.remove(x): x not in list  
  
ValueError: list.remove(x): x not in list  
  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\seqalign\alignment.py", line 780, in remove_observer  
self.observers.remove(observer)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\modeller\tool.py", line 334, in _list_selection_cb  
mb = self.seq_menu[sel_aln]  
~~~~~~~~~~~~~^^^^^^^^^  
KeyError: <chimerax.seqalign.alignment.Alignment object at 0x000002214422E6D0>  
  
KeyError:  
  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\modeller\tool.py", line 334, in _list_selection_cb  
mb = self.seq_menu[sel_aln]  
~~~~~~~~~~~~~^^^^^^^^^  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\modeller\tool.py", line 334, in _list_selection_cb  
mb = self.seq_menu[sel_aln]  
~~~~~~~~~~~~~^^^^^^^^^  
KeyError: <chimerax.seqalign.alignment.Alignment object at 0x000002214422E6D0>  
  
KeyError:  
  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\modeller\tool.py", line 334, in _list_selection_cb  
mb = self.seq_menu[sel_aln]  
~~~~~~~~~~~~~^^^^^^^^^  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\modeller\tool.py", line 334, in _list_selection_cb  
mb = self.seq_menu[sel_aln]  
~~~~~~~~~~~~~^^^^^^^^^  
KeyError: <chimerax.seqalign.alignment.Alignment object at 0x000002215951BED0>  
  
KeyError:  
  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\modeller\tool.py", line 334, in _list_selection_cb  
mb = self.seq_menu[sel_aln]  
~~~~~~~~~~~~~^^^^^^^^^  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\modeller\tool.py", line 334, in _list_selection_cb  
mb = self.seq_menu[sel_aln]  
~~~~~~~~~~~~~^^^^^^^^^  
KeyError: <chimerax.seqalign.alignment.Alignment object at 0x0000022159751750>  
  
KeyError:  
  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\modeller\tool.py", line 334, in _list_selection_cb  
mb = self.seq_menu[sel_aln]  
~~~~~~~~~~~~~^^^^^^^^^  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\modeller\tool.py", line 264, in launch_modeller  
seq_menu = self.seq_menu[aln]  
~~~~~~~~~~~~~^^^^^  
KeyError: <chimerax.seqalign.alignment.Alignment object at 0x0000022159751750>  
  
KeyError:  
  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\modeller\tool.py", line 264, in launch_modeller  
seq_menu = self.seq_menu[aln]  
~~~~~~~~~~~~~^^^^^  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\modeller\tool.py", line 264, in launch_modeller  
seq_menu = self.seq_menu[aln]  
~~~~~~~~~~~~~^^^^^  
KeyError: <chimerax.seqalign.alignment.Alignment object at 0x0000022159751750>  
  
KeyError:  
  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\modeller\tool.py", line 264, in launch_modeller  
seq_menu = self.seq_menu[aln]  
~~~~~~~~~~~~~^^^^^  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\modeller\tool.py", line 334, in _list_selection_cb  
mb = self.seq_menu[sel_aln]  
~~~~~~~~~~~~~^^^^^^^^^  
KeyError: <chimerax.seqalign.alignment.Alignment object at 0x0000022159751750>  
  
KeyError:  
  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\modeller\tool.py", line 334, in _list_selection_cb  
mb = self.seq_menu[sel_aln]  
~~~~~~~~~~~~~^^^^^^^^^  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\modeller\tool.py", line 334, in _list_selection_cb  
mb = self.seq_menu[sel_aln]  
~~~~~~~~~~~~~^^^^^^^^^  
KeyError: <chimerax.seqalign.alignment.Alignment object at 0x0000022159751750>  
  
KeyError:  
  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\modeller\tool.py", line 334, in _list_selection_cb  
mb = self.seq_menu[sel_aln]  
~~~~~~~~~~~~~^^^^^^^^^  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\modeller\tool.py", line 264, in launch_modeller  
seq_menu = self.seq_menu[aln]  
~~~~~~~~~~~~~^^^^^  
KeyError: <chimerax.seqalign.alignment.Alignment object at 0x0000022159751750>  
  
KeyError:  
  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\modeller\tool.py", line 264, in launch_modeller  
seq_menu = self.seq_menu[aln]  
~~~~~~~~~~~~~^^^^^  
  
See log for complete Python traceback.  
  

> ui tool show "Show Sequence Viewer"

> sequence chain #2.2/B

Destroying pre-existing alignment with identifier 2.2/B  
Alignment identifier is 2.2/B  

> hide #!2 models

> hide #!2.2 models

> select subtract #1.2

3678 atoms, 2 pseudobonds, 500 residues, 4 models selected  

> hide #!1.2 models

> select add #1

19720 atoms, 15264 bonds, 126 pseudobonds, 3430 residues, 17 models selected  

> hide #!1 models

> show #!1 models

> show #!1.1 models

> show #!1.2 models

> show #!1.3 models

> show #!1.4 models

> ui tool show "Show Sequence Viewer"

> sequence chain #1.2/B

Alignment identifier is 1.2/B  

> sequence chain #2.2/B

Destroying pre-existing alignment with identifier 2.2/B  
Alignment identifier is 2.2/B  




OpenGL version: 3.3.14761 Core Profile Forward-Compatible Context 21.30.44.03 30.0.13044.3001
OpenGL renderer: AMD Radeon(TM) Graphics
OpenGL vendor: ATI Technologies Inc.

Python: 3.11.4
Locale: fr_FR.cp1252
Qt version: PyQt6 6.8.1, Qt 6.8.2
Qt runtime version: 6.8.2
Qt platform: windows

Manufacturer: ASUSTeK COMPUTER INC.
Model: VivoBook_ASUSLaptop X513IA_M513IA
OS: Microsoft Windows 11 Famille (Build 26100)
Memory: 7,969,427,456
MaxProcessMemory: 137,438,953,344
CPU: 6 AMD Ryzen 5 4500U with Radeon Graphics         
OSLanguage: fr-FR

Installed Packages:
    alabaster: 1.0.0
    appdirs: 1.4.4
    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: 2025.7.14
    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
    comtypes: 1.4.10
    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
    nvidia-nvjitlink-cu12: 12.9.86
    OpenMM: 8.2.0
    OpenMM-CUDA-12: 8.2.0
    openvr: 1.26.701
    packaging: 24.2
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    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
    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
    pywin32: 310
    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
    WMI: 1.5.1