ChimeraX bug report submission

[iamkaant@…]

The following bug report has been submitted:
Platform:        macOS-15.6.1-arm64-arm-64bit
ChimeraX Version: 1.11.dev202510230043 (2025-10-23 00:43:15 UTC)
Description
I’ve encountered an issue with ViewDock. After the hit picking and saving the session, all molecules except for those marked as “good” disappeared. If I use “Save” button in the ViewDock window, only good ligands are saved. All ligands are still available in the Models window, but if I save them as a mol2 file, their ranks aren’t saved. 
From some experiments, it seems that the ligands that get shown are the ones visible when the session is saved.

Log:
UCSF ChimeraX version: 1.11.dev202510230043 (2025-10-23)  
© 2016-2025 Regents of the University of California. All rights reserved.  

> open /Users/ak87/ownCloud/owncloud/Calculations/SYNTHON-DOCK/xREAL-
> DOCKING/RETRO/MOR/DOCK-ENUM-DIVERSITY/mor_xreal_diversity_enum_novel_SV.cxs

Updated animation length to 0:05.00  
[Repeated 1 time(s)]

### ViewDock hotkeys on

If clicked into ViewDock dialog or main 3D graphics area, the following keys
are active:

g/m/b/u

    Assign good/maybe/bad/(unrated) rating to chosen compounds
up/down arrow

    Move up/down compound list*
Escape

    Turn hotkeys off (have to use context menu to re-enable)
*Unless in 3D graphics with a selection, in which case normal selection widening/narrowing happens  

### ViewDock hotkeys on

If clicked into ViewDock dialog or main 3D graphics area, the following keys
are active:

g/m/b/u

    Assign good/maybe/bad/(unrated) rating to chosen compounds
up/down arrow

    Move up/down compound list*
Escape

    Turn hotkeys off (have to use context menu to re-enable)
*Unless in 3D graphics with a selection, in which case normal selection widening/narrowing happens  
Log from Fri Oct 24 13:57:46 2025UCSF ChimeraX version: 1.11.dev202510240114
(2025-10-24)  
© 2016-2025 Regents of the University of California. All rights reserved.  

> open /Users/svigneron/Downloads/mor_xreal_diversity_enum_novel.cxs

Updated animation length to 0:05.00  
Log from Thu Oct 23 17:39:24 2025UCSF ChimeraX version: 1.11.dev202510072011
(2025-10-07)  
© 2016-2025 Regents of the University of California. All rights reserved.  

> open /Users/ak87/ownCloud/owncloud/Calculations/SYNTHON-DOCK/xREAL-
> DOCKING/RETRO/MOR/DOCK-ENUM-DIVERSITY/mor_xreal_diversity_enum_novel.cxs

### ViewDock hotkeys on

If clicked into ViewDock dialog or main 3D graphics area, the following keys
are active:

g/m/b/u

    Assign good/maybe/bad/(unrated) rating to chosen compounds
up/down arrow

    Move up/down compound list*
Escape

    Turn hotkeys off (have to use context menu to re-enable)
*Unless in 3D graphics with a selection, in which case normal selection widening/narrowing happens  

### ViewDock hotkeys on

If clicked into ViewDock dialog or main 3D graphics area, the following keys
are active:

g/m/b/u

    Assign good/maybe/bad/(unrated) rating to chosen compounds
up/down arrow

    Move up/down compound list*
Escape

    Turn hotkeys off (have to use context menu to re-enable)
*Unless in 3D graphics with a selection, in which case normal selection widening/narrowing happens  
Log from Wed Oct 22 13:31:03 2025UCSF ChimeraX version: 1.11.dev202510072011
(2025-10-07)  
© 2016-2025 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> /Users/ak87/ownCloud/owncloud/Calculations/JUGGLER/PROSPECTIVE/MOR/SETH/rec.crg.pdb

Chain information for rec.crg.pdb #1  
---  
Chain | Description  
R | No description available  
  
Computing secondary structure  

> open
> /Users/ak87/ownCloud/owncloud/Calculations/JUGGLER/PROSPECTIVE/MOR/SETH/xtal-
> lig.pdb

xtal-lig.pdb title:  
xtal-lig [more info...]  
  
Chain information for xtal-lig.pdb #2  
---  
Chain | Description  
P | No description available  
  

> open
> /Users/ak87/ownCloud/owncloud/Calculations/JUGGLER/PROSPECTIVE/MOR/ORBEBB/2024-08-16-NEW-
> GRIDS/0/OG/fentanyl.mol2

Opened fentanyl.mol2 containing 1 structure (54 atoms, 56 bonds)  

### ViewDock hotkeys on

If clicked into ViewDock dialog or main 3D graphics area, the following keys
are active:

g/m/b/u

    Assign good/maybe/bad/(unrated) rating to chosen compounds
up/down arrow

    Move up/down compound list*
Escape

    Turn hotkeys off (have to use context menu to re-enable)
*Unless in 3D graphics with a selection, in which case normal selection widening/narrowing happens  

> close #2

> select add #3

54 atoms, 56 bonds, 1 residue, 1 model selected  

> select sel :< 7

473 atoms, 469 bonds, 44 residues, 2 models selected  

> show sel atoms

> view sel

> select clear

> hide cartoons

Drag select of 473 atoms, 469 bonds  

> ui tool show "Selection Inspector"

> size =sel stickRadius 0.06

Changed 469 bond radii  

> select clear

> select up

2 atoms, 1 bond, 1 residue, 1 model selected  

> select up

54 atoms, 56 bonds, 1 residue, 1 model selected  

> ui tool show H-Bonds

> hbonds sel reveal true

1 hydrogen bonds found  

> save /Users/ak87/ownCloud/owncloud/Calculations/SYNTHON-DOCK/xREAL-
> DOCKING/RETRO/MOR/DOCK-ENUM-DIVERSITY/mor_xreal_diversity_enum_novel.cxs

> open /Users/ak87/ownCloud/owncloud/Calculations/SYNTHON-DOCK/xREAL-
> DOCKING/RETRO/MOR/DOCK-ENUM-DIVERSITY/mor_xreal_diversity_enum_novel.mol2

Opened mor_xreal_diversity_enum_novel.mol2 containing 2575 structures (165458
atoms, 174261 bonds)  

### ViewDock hotkeys on

If clicked into ViewDock dialog or main 3D graphics area, the following keys
are active:

g/m/b/u

    Assign good/maybe/bad/(unrated) rating to chosen compounds
up/down arrow

    Move up/down compound list*
Escape

    Turn hotkeys off (have to use context menu to re-enable)
*Unless in 3D graphics with a selection, in which case normal selection widening/narrowing happens  

> select clear

Drag select of 542 atoms, 543 bonds, 1 pseudobonds  

> label (#1,3#4.1 & sel) text "{0.name} {0.number}{0.insertion_code}"

> select clear

> hbonds #4.2-2575#!4.1 restrict #!1,3 & (main|ligand) reveal true

4182 hydrogen bonds found  

> save /Users/ak87/ownCloud/owncloud/Calculations/SYNTHON-DOCK/xREAL-
> DOCKING/RETRO/MOR/DOCK-ENUM-DIVERSITY/mor_xreal_diversity_enum_novel.cxs

Drag select of 8 atoms, 8 bonds  

> hide sel atoms

> select #1/R:231@OE1

1 atom, 1 residue, 1 model selected  

> select up

10 atoms, 9 bonds, 1 residue, 1 model selected  

> select up

171 atoms, 177 bonds, 16 residues, 1 model selected  

> hide sel atoms

> undo

> select clear

> select up

2 atoms, 1 bond, 1 residue, 1 model selected  

> select up

10 atoms, 9 bonds, 1 residue, 1 model selected  

> hide sel atoms

> save /Users/ak87/ownCloud/owncloud/Calculations/SYNTHON-DOCK/xREAL-
> DOCKING/RETRO/MOR/DOCK-ENUM-DIVERSITY/mor_xreal_diversity_enum_novel.cxs

——— End of log from Wed Oct 22 13:31:03 2025 ———

> view name session-start

opened ChimeraX session  

> ui windowfill toggle

> set bgColor white

> set bgColor #ffffff00

> ui tool show "Color Actions"

> color sel gray target l

> select clear

[Repeated 1 time(s)]Drag select of 9 atoms, 7 bonds  

> ui tool show "Selection Inspector"

> size =sel stickRadius 0.06

Changed 7 bond radii  

> save /Users/ak87/ownCloud/owncloud/Calculations/SYNTHON-DOCK/xREAL-
> DOCKING/RETRO/MOR/DOCK-ENUM-DIVERSITY/mor_xreal_diversity_enum_novel.cxs

> select clear

[Repeated 2 time(s)]

> ui tool show "Color Actions"

> color dim gray target l

[Repeated 2 time(s)]

> save /Users/ak87/ownCloud/owncloud/Calculations/SYNTHON-DOCK/xREAL-
> DOCKING/RETRO/MOR/DOCK-ENUM-DIVERSITY/mor_xreal_diversity_enum_novel.cxs

Already at top of table  

[Repeated 6 time(s)]

> save /Users/ak87/ownCloud/owncloud/Calculations/SYNTHON-DOCK/xREAL-
> DOCKING/RETRO/MOR/DOCK-ENUM-DIVERSITY/mor_xreal_diversity_enum_novel.cxs

> lighting simple

> lighting soft

> lighting full

> lighting simple

> ui tool show "Side View"

> select #4.1/?:1@C21

1 atom, 1 residue, 1 model selected  

> select add #4

165458 atoms, 174261 bonds, 2575 residues, 2577 models selected  

> select sel :< 5

166406 atoms, 175198 bonds, 4182 pseudobonds, 2668 residues, 2580 models
selected  

> select clear

[Repeated 1 time(s)]

> select add #4

165458 atoms, 174261 bonds, 2575 residues, 2577 models selected  

> select sel :< 5

166406 atoms, 175198 bonds, 4182 pseudobonds, 2668 residues, 2580 models
selected  

> select clear

> select up

2 atoms, 1 bond, 1 residue, 1 model selected  

> select up

54 atoms, 56 bonds, 1 residue, 1 model selected  

> select sel :< 5

165715 atoms, 174512 bonds, 4066 pseudobonds, 2597 residues, 2578 models
selected  

> select ~sel

2608 atoms, 2646 bonds, 270 residues, 5 models selected  

> hide sel atoms

> select clear

> select up

2 atoms, 1 bond, 1 residue, 1 model selected  

> select up

54 atoms, 56 bonds, 1 residue, 1 model selected  

> select sel :< 7

165931 atoms, 174730 bonds, 4179 pseudobonds, 2619 residues, 2578 models
selected  

> show sel & #!1,3#!4.1 atoms

> select clear

Drag select of 536 atoms, 538 bonds, 1 pseudobonds  

> select clear

Drag select of 540 atoms, 542 bonds, 1 pseudobonds  

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

411 atoms, 408 bonds, 41 residues, 1 model selected  

> transparency sel 50

> transparency sel 50 target ab

> transparency sel 70 target ab

> transparency sel 60 target ab

> select clear

> save /Users/ak87/ownCloud/owncloud/Calculations/SYNTHON-DOCK/xREAL-
> DOCKING/RETRO/MOR/DOCK-ENUM-DIVERSITY/mor_xreal_diversity_enum_novel.cxs

> rock x 60 forever cycle 80

> ui windowfill toggle

> rock x 60 forever cycle 60

> stop

> select up

2 atoms, 1 bond, 1 residue, 1 model selected  

> select up

14 atoms, 14 bonds, 1 residue, 1 model selected  

> hide sel atoms

> select up

2 atoms, 1 bond, 1 residue, 1 model selected  

> select up

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

> hide sel atoms

> ui windowfill toggle

Drag select of 519 atoms, 520 bonds, 1 pseudobonds  

> ui tool show "Color Actions"

> color sel light gray target l

> save /Users/ak87/ownCloud/owncloud/Calculations/SYNTHON-DOCK/xREAL-
> DOCKING/RETRO/MOR/DOCK-ENUM-DIVERSITY/mor_xreal_diversity_enum_novel.cxs

> select clear

> rock x 60 forever cycle 60

> ui windowfill toggle

> rock x 60 forever cycle 50

> stop

> select clear

Already at top of table  

Drag select of 2 atoms, 1 bonds  

> select up

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

> hide sel atoms

> select clear

Drag select of 1 atoms, 1 bonds  

> select up

2 atoms, 1 bond, 1 residue, 1 model selected  

> select up

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

> hide sel atoms

Drag select of 2 atoms, 1 bonds  

> select up

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

> hide sel atoms

Drag select of 1 atoms, 1 bonds  

> select up

2 atoms, 1 bond, 1 residue, 1 model selected  

> select up

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

> hide sel atoms

> rock x 60 forever cycle 60

> stop

> rock x 60 forever cycle 50

> set bgColor gray

> set bgColor #80808000

> set bgColor black

> set bgColor transparent

> set bgColor white

> set bgColor #ffffff00

> stop

Drag select of 484 atoms, 483 bonds, 1 pseudobonds  

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

355 atoms, 349 bonds, 35 residues, 1 model selected  

> transparency sel 30 target ab

> select clear

> rock x 60 forever cycle 50

> stop

> save /Users/ak87/ownCloud/owncloud/Calculations/SYNTHON-DOCK/xREAL-
> DOCKING/RETRO/MOR/DOCK-ENUM-DIVERSITY/mor_xreal_diversity_enum_novel.cxs

> rock x 80 forever cycle 60

> stop

> rock x 80 forever cycle 50

> stop

> rock x 80 forever cycle 50

> stop

> rock x 80 forever cycle 50

> ui windowfill toggle

> hide #!3 models

> ui windowfill toggle

> stop

> save /Users/ak87/ownCloud/owncloud/Calculations/SYNTHON-DOCK/xREAL-
> DOCKING/RETRO/MOR/DOCK-ENUM-DIVERSITY/mor_xreal_diversity_enum_novel.cxs

Desktop color scheme is dark  

> rock x 80 forever cycle 50

> stop

> save /Users/ak87/ownCloud/owncloud/Calculations/SYNTHON-DOCK/xREAL-
> DOCKING/RETRO/MOR/DOCK-ENUM-DIVERSITY/mor_xreal_diversity_enum_novel.cxs

> rock x 80 forever cycle 50

> stop

> save /Users/ak87/ownCloud/owncloud/Calculations/SYNTHON-DOCK/xREAL-
> DOCKING/RETRO/MOR/DOCK-ENUM-DIVERSITY/mor_xreal_diversity_enum_novel.cxs

> rock x 80 forever cycle 50

> stop

> save /Users/ak87/ownCloud/owncloud/Calculations/SYNTHON-DOCK/xREAL-
> DOCKING/RETRO/MOR/DOCK-ENUM-DIVERSITY/mor_xreal_diversity_enum_novel.cxs

Desktop color scheme is light  

> rock x 80 forever cycle 50

> select ~sel & ##selected

Nothing selected  

> stop

> save /Users/ak87/ownCloud/owncloud/Calculations/SYNTHON-DOCK/xREAL-
> DOCKING/RETRO/MOR/DOCK-ENUM-DIVERSITY/mor_xreal_diversity_enum_novel.cxs

> rock x 80 forever cycle 50

> stop

> rock x 80 forever cycle 50

> stop

> save /Users/ak87/ownCloud/owncloud/Calculations/SYNTHON-DOCK/xREAL-
> DOCKING/RETRO/MOR/DOCK-ENUM-DIVERSITY/mor_xreal_diversity_enum_novel.cxs

> rock x 80 forever cycle 50

Already at bottom of table  

[Repeated 2 time(s)]

> stop

> save /Users/ak87/ownCloud/owncloud/Calculations/SYNTHON-DOCK/xREAL-
> DOCKING/RETRO/MOR/DOCK-ENUM-DIVERSITY/mor_xreal_diversity_enum_novel.cxs

> rock x 80 forever cycle 50

Already at bottom of table  

[Repeated 2 time(s)]

> stop

> save /Users/ak87/ownCloud/owncloud/Calculations/SYNTHON-DOCK/xREAL-
> DOCKING/RETRO/MOR/DOCK-ENUM-DIVERSITY/mor_xreal_diversity_enum_novel.cxs

Already at bottom of table  

[Repeated 1 time(s)]

> save /Users/ak87/ownCloud/owncloud/Calculations/SYNTHON-DOCK/xREAL-
> DOCKING/RETRO/MOR/DOCK-ENUM-DIVERSITY/mor_xreal_diversity_enum_novel.cxs

——— End of log from Thu Oct 23 17:39:24 2025 ———

> view name session-start

opened ChimeraX session  

> hide #3.1 models

> show #3.1 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> hide #1.1 models

> lighting simple

> lighting soft

[Repeated 1 time(s)]

> lighting full

> lighting simple

> cn

Unknown command: cn  

> save /Users/svigneron/Downloads/mor_xreal_diversity_enum_novel_SV.cxs

——— End of log from Fri Oct 24 13:57:46 2025 ———

> view name session-start

opened ChimeraX session  

Cell requested for row 0 is out of bounds for table with 2579 rows! Resizing
table model.  




OpenGL version: 4.1 Metal - 89.4
OpenGL renderer: Apple M1 Pro
OpenGL vendor: Apple

Python: 3.11.9
Locale: en_US.UTF-8
Qt version: PyQt6 6.9.1, Qt 6.9.0
Qt runtime version: 6.9.2
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro18,1
      Model Number: MK193LL/A
      Chip: Apple M1 Pro
      Total Number of Cores: 10 (8 performance and 2 efficiency)
      Memory: 16 GB
      System Firmware Version: 11881.140.96
      OS Loader Version: 11881.140.96

Software:

    System Software Overview:

      System Version: macOS 15.6.1 (24G90)
      Kernel Version: Darwin 24.6.0
      Time since boot: 53 дні, 1 година і 23 хвилини

Graphics/Displays:

    Apple M1 Pro:

      Chipset Model: Apple M1 Pro
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 16
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        LG HDR 4K:
          Resolution: 5120 x 2880 (5K/UHD+ - Ultra High Definition Plus)
          UI Looks like: 2560 x 1440 @ 60.00Hz
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Rotation: Supported
        Color LCD:
          Display Type: Built-in Liquid Retina XDR Display
          Resolution: 3456 x 2234 Retina
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal


Installed Packages:
    aiohappyeyeballs: 2.6.1
    aiohttp: 3.13.1
    aiosignal: 1.4.0
    alabaster: 1.0.0
    annotated-types: 0.7.0
    anyio: 4.11.0
    appdirs: 1.4.4
    appnope: 0.1.4
    asttokens: 3.0.0
    attrs: 25.4.0
    babel: 2.17.0
    beautifulsoup4: 4.13.5
    blockdiag: 3.0.0
    blosc2: 3.10.2
    build: 1.3.0
    certifi: 2025.7.14
    cftime: 1.6.5
    charset-normalizer: 3.4.4
    ChimeraX-AddCharge: 1.5.20
    ChimeraX-AddH: 2.2.8
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.6.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 3.0.2
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Animations: 1.0
    ChimeraX-Aniso: 1.3.2
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.60.18
    ChimeraX-AtomicLibrary: 14.2.1
    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
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.5
    ChimeraX-ChemGroup: 2.0.2
    ChimeraX-Clashes: 2.3
    ChimeraX-clix: 0.2.4
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.8
    ChimeraX-CommandLine: 1.3.0
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.11.dev202510230043
    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: 2.5.3
    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: 1.7.2
    ChimeraX-Label: 1.2
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.2.1
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.2
    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-MCPServer: 0.1.0
    ChimeraX-MDcrds: 2.17.1
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-Minimize: 1.3.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.16
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.22
    ChimeraX-ModelPanel: 1.6
    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: 1.15.1
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.11
    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: 1.4
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.6.5
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.3.2
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.2
    ChimeraX-Scenes: 0.2.5
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.3
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.5.10
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.17.2
    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: 1.48.4
    ChimeraX-Umap: 1.0
    ChimeraX-uniprot: 2.3.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDock: 1.5.1
    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: 8.3.0
    colorama: 0.4.6
    comm: 0.2.3
    contourpy: 1.3.3
    coverage: 7.11.0
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.1.4
    debugpy: 1.8.17
    decorator: 5.2.1
    docutils: 0.21.2
    executing: 2.2.1
    filelock: 3.19.1
    fonttools: 4.60.1
    frozenlist: 1.8.0
    funcparserlib: 2.0.0a0
    glfw: 2.10.0
    grako: 3.16.5
    h11: 0.16.0
    h5py: 3.15.1
    html2text: 2025.4.15
    httpcore: 1.0.9
    httpx: 0.28.1
    httpx-sse: 0.4.3
    idna: 3.11
    ihm: 2.2
    imagecodecs: 2024.6.1
    imagesize: 1.4.1
    iniconfig: 2.3.0
    ipykernel: 6.30.1
    ipython: 9.5.0
    ipython_pygments_lexers: 1.1.1
    ipywidgets: 8.1.7
    jedi: 0.19.2
    Jinja2: 3.1.6
    jsonschema: 4.25.1
    jsonschema-specifications: 2025.9.1
    jupyter_client: 8.6.3
    jupyter_core: 5.9.1
    jupyterlab_widgets: 3.0.15
    kiwisolver: 1.4.9
    line_profiler: 5.0.0
    lxml: 6.0.2
    lz4: 4.3.2
    Markdown: 3.8.2
    MarkupSafe: 3.0.3
    matplotlib: 3.10.5
    matplotlib-inline: 0.1.7
    mcp: 1.18.0
    msgpack: 1.1.1
    multidict: 6.7.0
    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: 2.14.1
    numpy: 1.26.4
    OpenMM: 8.2.0
    openvr: 1.26.701
    packaging: 25.0
    ParmEd: 4.2.2
    parso: 0.8.5
    pep517: 0.13.1
    pexpect: 4.9.0
    pickleshare: 0.7.5
    pillow: 11.3.0
    pip: 25.2
    pkginfo: 1.12.1.2
    platformdirs: 4.5.0
    pluggy: 1.6.0
    prompt_toolkit: 3.0.52
    propcache: 0.4.1
    psutil: 7.0.0
    ptyprocess: 0.7.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pybind11: 3.0.1
    pycollada: 0.8
    pydantic: 2.12.3
    pydantic-settings: 2.11.0
    pydantic_core: 2.41.4
    pydicom: 2.4.4
    Pygments: 2.18.0
    pynmrstar: 3.3.6
    pynrrd: 1.0.0
    PyOpenGL: 3.1.10
    PyOpenGL-accelerate: 3.1.10
    pyopenxr: 1.1.4501
    pyparsing: 3.2.5
    pyproject_hooks: 1.2.0
    PyQt6-commercial: 6.9.1
    PyQt6-Qt6: 6.9.2
    PyQt6-WebEngine-commercial: 6.9.0
    PyQt6-WebEngine-Qt6: 6.9.2
    PyQt6_sip: 13.10.2
    pytest: 8.4.2
    pytest-cov: 7.0.0
    python-dateutil: 2.9.0.post0
    python-dotenv: 1.1.1
    python-multipart: 0.0.20
    pytz: 2025.2
    pyzmq: 27.1.0
    qtconsole: 5.7.0
    QtPy: 2.4.3
    qtshim: 1.2
    RandomWords: 0.4.0
    referencing: 0.37.0
    requests: 2.32.5
    roman-numerals-py: 3.1.0
    rpds-py: 0.28.0
    scipy: 1.14.0
    Send2Trash: 1.8.3
    SEQCROW: 1.9.4
    setuptools: 80.9.0
    sfftk-rw: 0.8.1
    six: 1.17.0
    sniffio: 1.3.1
    snowballstemmer: 3.0.1
    sortedcontainers: 2.4.0
    soupsieve: 2.8
    Sphinx: 8.2.3
    sphinx-autodoc-typehints: 3.2.0
    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
    sse-starlette: 3.0.2
    stack-data: 0.6.3
    starlette: 0.48.0
    superqt: 0.7.6
    tables: 3.10.2
    tcia_utils: 1.5.1
    tifffile: 2025.3.13
    tinyarray: 1.2.5
    tornado: 6.5.2
    traitlets: 5.14.3
    typing-inspection: 0.4.2
    typing_extensions: 4.15.0
    tzdata: 2025.2
    urllib3: 2.5.0
    uvicorn: 0.38.0
    wcwidth: 0.2.14
    webcolors: 24.11.1
    wheel: 0.45.1
    wheel-filename: 1.4.2
    widgetsnbextension: 4.0.14
    yarl: 1.22.0