ViewDock: saving ligands

[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

[Eric Pettersen]

Reported by Andrii

[Eric Pettersen]

Hi Andrii,

Currently, the "Save" button saves the compounds you have displayed in the table. If you frequently want to save the hidden compounds also, I could add an option for that. Let me know. Until then, you would have to unhide compounds you want saved.

--Eric

[iamkaant@…]

Hi Eric,

Thank you for looking into the issue. I saved the sessions as the CXS 
files. I think the issue appeared in Oct 23 daily build. I installed 
previous daily builds, but I could not open the sessions that I've saved 
with the newer versions because of the outdated Animations bundle. I 
think the compound ratings are present in the session files, but I have 
no way of recovering them now. Could you advise on how to do it?

  -- Andrii

On 10/27/25 1:57 PM, ChimeraX wrote:
>
>
>
>

[Eric Pettersen]

Hi Andrii,

Are you saying that you can't open your session file in the latest daily build? Or can't open it only in earlier daily builds?

--Eric

[iamkaant@…]

When I open the session file in the Oct 23 daily build, it only displays 
a portion of ligands in the ViewDock window that were visible on saving. 
Unhiding the other raitings doesn\u2019t display them in the ViewDock table. 
Essentially, the data on all other ligands is lost, although the ligands 
are still visible in the Models window. Since my session contains ~2000 
ligands that I\u2019ve rated manually, I would very much like to recover that 
information.

If I install an earlier build, I cannot open the session file because of 
the error |install Animations bundle version 1.0 or newer|.

Sincerely,
Andrii

On 10/27/25 2:10 PM, ChimeraX wrote:

>
>

​

[Eric Pettersen]

Hi Andrii,

I see the problem in the code, it's forgetting about the undisplayed ligands during the session save. I will fix that. In your session, are all the undisplayed ligands the same rating (e.g. "bad")? If so, I could fix up your session if I had access to your original file of ligands and the session file. Do you have an account on plato or Wynton? Or if the files themselves weren't crazy large (< 250MB say), you could mail them to me directly at pett@… .

--Eric

[Eric Pettersen]

Fixed in tomorrow's build.

Fix: ​https://github.com/RBVI/ChimeraX/commit/2b9e6ed8aa579f0883d72fdb6c1b5a2d4d729fd7