Timeline scene instances treated identically

[Elaine Meng]

The following bug report has been submitted:
Platform:        macOS-15.7.4-arm64-arm-64bit
ChimeraX Version: 1.12.dev202603042258 (2026-03-04 22:58:36 UTC)
Description
When you drag two copies of the same scene to the timeline and click on one of them, they both get selected and they both move when you try and move one of them

Log:
UCSF ChimeraX version: 1.12.dev202603042258 (2026-03-04)  
© 2016-2026 Regents of the University of California. All rights reserved.  

> open "/Users/meng/Library/Containers/com.apple.mail/Data/Library/Mail
> Downloads/A943E991-CCCB-4CAB-86A1-5396A9044DF4/anim-sess.cxs"

Log from Tue Mar 3 15:46:15 2026UCSF ChimeraX version: 1.12.dev202603022143
(2026-03-02)  
© 2016-2026 Regents of the University of California. All rights reserved.  

> open /Users/meng/Desktop/morescenes.cxs format session

Log from Tue Feb 24 13:56:47 2026UCSF ChimeraX version: 1.12.dev202602240240
(2026-02-24)  
© 2016-2026 Regents of the University of California. All rights reserved.  

> open /Users/meng/Desktop/scenes3.cxs format session

Log from Thu Nov 20 12:24:37 2025UCSF ChimeraX version: 1.11.dev202511200505
(2025-11-20)  
© 2016-2025 Regents of the University of California. All rights reserved.  

> open /Users/meng/Desktop/scenes3.cxs format session

Log from Thu Nov 20 12:23:34 2025UCSF ChimeraX version: 1.11.dev202511200505
(2025-11-20)  
© 2016-2025 Regents of the University of California. All rights reserved.  

> open /Users/meng/Desktop/scenes2.cxs format session

Log from Thu Sep 25 12:53:25 2025UCSF ChimeraX version: 1.11.dev202509250039
(2025-09-25)  
© 2016-2025 Regents of the University of California. All rights reserved.  

> open /Users/meng/Desktop/scenes2.cxs format session

Log from Thu Sep 25 12:44:00 2025UCSF ChimeraX version: 1.11.dev202509250039
(2025-09-25)  
© 2016-2025 Regents of the University of California. All rights reserved.  

> open scenes2.cxs

Log from Thu Sep 25 12:42:34 2025

> open /Users/meng/Desktop/startup.cxc

> alias reset view orient; view initial

> alias start toolshed show $1

> alias whereprefs info path user unversioned config

> alias previewts toolshed url https://cxtoolshed-
> preview.rbvi.ucsf.edu;toolshed reload available

> alias normalts toolshed url https://cxtoolshed.rbvi.ucsf.edu;toolshed reload
> available

> alias btut open
> http://www.cgl.ucsf.edu/home/meng/chimerax/vdocs/user/tutorials/binding-
> sites.html

> alias segtest open 0557 from emdb; vol threshold #1 min 0; vol scale #2
> value uint8; open 6nzk

executed startup.cxc  
UCSF ChimeraX version: 1.11.dev202509250039 (2025-09-25)  
© 2016-2025 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 1enl

Summary of feedback from opening 1enl fetched from pdb  
---  
warnings | PDB entry 1ENL has been replaced by 2ENL  
Invalid residue range for struct_conf "HELX_P1": residue in non-polymer entity
"1", on line 289  
Invalid residue range for struct_conf "HELX_P2": residue in non-polymer entity
"1", on line 290  
Invalid residue range for struct_conf "HELX_P3": residue in non-polymer entity
"1", on line 291  
Invalid residue range for struct_conf "HELX_P4": residue in non-polymer entity
"1", on line 292  
Invalid residue range for struct_conf "HELX_P5": residue in non-polymer entity
"1", on line 293  
7 messages similar to the above omitted  
Invalid sheet range for struct_sheet_range "MEA 1": residue in non-polymer
entity "1", on line 348  
Invalid sheet range for struct_sheet_range "MEA 2": residue in non-polymer
entity "1", on line 349  
Invalid sheet range for struct_sheet_range "MEA 3": residue in non-polymer
entity "1", on line 350  
Invalid sheet range for struct_sheet_range "BAR 1": residue in non-polymer
entity "1", on line 351  
Invalid sheet range for struct_sheet_range "BAR 2": residue in non-polymer
entity "1", on line 352  
7 messages similar to the above omitted  
note | Fetching compressed mmCIF 1enl from http://files.rcsb.org/download/1enl.cif  
  
1enl title:  
Crystal structure of enolase indicates that enolase and pyruvate kinase
evolved from A common ancestor [more info...]  
  
Non-standard residues in 1enl #1  
---  
ALA — alanine  
ARG — arginine  
ASN — asparagine  
ASP — aspartic acid  
CYS — cysteine  
GLN — glutamine  
GLU — glutamic acid  
GLY — glycine  
HIS — histidine  
ILE — isoleucine  
LEU — leucine  
LYS — lysine  
MET — methionine  
PHE — phenylalanine  
PRO — proline  
SER — serine  
THR — threonine  
TRP — tryptophan  
TYR — tyrosine  
VAL — valine  
  

> close

> open 4enl

4enl title:  
Crystal structure of holoenzyme refined At 1.9 angstroms resolution: trigonal-
bipyramidal geometry of the cation binding site [more info...]  
  
Chain information for 4enl #1  
---  
Chain | Description | UniProt  
A | ENOLASE | ENO1_YEAST 1-436  
  
Non-standard residues in 4enl #1  
---  
SO4 — sulfate ion  
ZN — zinc ion  
  
4enl mmCIF Assemblies  
---  
1| author_defined_assembly  
  

> scenes save 1

> ui tool show Scenes

> graphics silhouettes true

> set bgColor white

> open 2mnr

2mnr title:  
Mechanism of the reaction catalyzed by mandelate racemase. 2. Crystal
structure of mandelate racemase At 2.5 angstroms resolution: identification of
the active site and possible catalytic residues [more info...]  
  
Chain information for 2mnr #2  
---  
Chain | Description | UniProt  
A | MANDELATE RACEMASE | MANR_PSEPU 3-359  
  
Non-standard residues in 2mnr #2  
---  
MN — manganese (II) ion  
SO4 — sulfate ion  
  
2mnr mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
  

> scenes save ""

> mmaker #2 to #1

Parameters  
---  
Chain pairing | bb  
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 4enl, chain A (#1) with 2mnr, chain A (#2), sequence alignment
score = 219.9  
RMSD between 73 pruned atom pairs is 1.307 angstroms; (across all 312 pairs:
12.638)  
  

> label ligand

> label ligand height 1

> label ligand height 4

> label ligand height 2

> scenes save ""

[Repeated 1 time(s)]

> 2dlabels text "enolase and mandelate racemizing enzyme" color blue xpos .1
> ypos .9

> ui tool show "Side View"

> scenes save ""

> scenes restore 5

> scenes save 5

> save scenes.cxs

> scenes restore 1

> scenes restore 2

> scenes restore 3

> scenes restore 4

> scenes restore 5

> scenes restore 4

> scenes restore 5

> scenes restore 1

> scenes restore 2

> scenes restore 3

> scenes restore 4

> scenes restore 5

> usage scenes restore

scenes restore sceneName  
— Restore the scene named 'scene_name'.  
sceneName: a text string  

> scenes restore 5

> scenes restore 4

> scenes restore 3

> scenes restore 4

> scenes restore 3

> scenes rename 3 scene-three

> scenes rename scene-three three

> scenes rename three matched

> scenes restore 4

> scenes delete 4

> scenes restore 5

> preset cartoons/nucleotides cylinders/stubs

Using preset: Cartoons/Nucleotides / Cylinders/Stubs  
Changed 0 atom styles  
Preset expands to these ChimeraX commands:

    
    
    show nucleic
    hide protein|solvent|H
    surf hide
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    ~worm
    cartoon
    cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    cartoon style ~(nucleic|strand) x round
    cartoon style (nucleic|strand) x rect
    cartoon style protein modeh tube rad 2 sides 24 thick 0.6
    cartoon style nucleic x round width 1.6 thick 1.6
    nucleotides stubs

  

> scenes restore 5

[Repeated 1 time(s)]

> scenes rename 5 title+ribbons

> scenes rename title+ribbons title

> scenes rename title titled

> scenes save ""

> scenes restore 6

> scenes rename 6 titled-tubes

> scenes restore titled-tubes

> save scenes.cxs

> scenes restore matched

> scenes restore 2

> scenes restore 1

> scenes restore 2

> scenes restore matched

> scenes restore titled

> scenes restore titled-tubes

> scenes restore titled

> preset cartoons/nucleotides ribbons/slabs

Using preset: Cartoons/Nucleotides / Ribbons/Slabs  
Changed 0 atom styles  
Preset expands to these ChimeraX commands:

    
    
    show nucleic
    hide protein|solvent|H
    surf hide
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    ~worm
    cartoon
    cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    cartoon style ~(nucleic|strand) x round
    cartoon style (nucleic|strand) x rect
    nucleotides tube/slab shape box

  

> save scenes.cxs

> scenes restore titled-tubes

> scenes restore titled

> scenes restore titled-tubes

> help 2dl

> 2dlabels #3 visibility false

> scenes save ""

> scenes restore 7

> scenes rename 7 title-hidden

> scenes restore titled-tubes

> scenes restore titled

> scenes restore matched

> scenes restore title-hidden

[Repeated 1 time(s)]

> set bgColor plum

> scenes save title-hidden

> scenes restore titled-tubes

> scenes restore title-hidden

> label delete

> scenes save ""

> scenes restore 8

> scenes rename 8 lab-hidden

> set bgColor cream

Invalid "bgColor" argument: Invalid color name or specifier  

> ui tool show "Color Actions"

> set bgColor linen

> scenes save lab-hidden

> scenes save ""

> scenes restore 9

> scenes rename 9 unclip

> scenes restore titled

> scenes restore titled-tubes

> scenes restore 2

> scenes restore lab-hidden

> scenes restore title-hidden

> scenes restore titled-tubes

> scenes restore matched

> scenes restore 2

> scenes restore 1

> scenes restore titled

> scenes restore titled-tubes

> scenes restore unclip

> scenes restore lab-hidden

> scenes restore title-hidden

> scenes restore lab-hidden

> scenes restore unclip

> hide ligand

> hide solvent

> size ions vdwrad +1

Expected a keyword  

> size ions atomRadius +1

Changed 2 atom radii  

> size ions atomRadius +1

Changed 2 atom radii  

> scenes save ""

> scenes restore 10

> scenes rename 10 bigions

> scenes restore unclip

> scenes restore lab-hidden

> scenes restore title-hidden

> size atomRadius default

Changed 6558 atom radii  

> size stickRadius .5

Changed 6111 bond radii  

> hide solvent

> scenes save ""

> scenes restore 11

> scenes rename 11 fatsticks

> scenes restore unclip

> scenes restore bigions

> scenes restore fatsticks

> save scenes2.cxs

——— End of log from Thu Sep 25 12:42:34 2025 ———

> view name session-start

opened ChimeraX session  

> scenes restore 1

> scenes restore 2

> scenes restore matched

> scenes restore titled

> scenes restore titled-tubes

> scenes restore title-hidden

> scenes restore lab-hidden

> scenes restore unclip

> scenes restore bigions

> scenes restore fatsticks

> size stickRadius .2

Changed 6111 bond radii  

> save scenes2.cxs

——— End of log from Thu Sep 25 12:44:00 2025 ———

> view name session-start

opened ChimeraX session  

> style sphere

Changed 6558 atom styles  

> scenes save spheres

> scenes restore spheres

> scenes restore bigions

> scenes restore fatsticks

> scenes restore bigions

> scenes restore lab-hidden

> scenes restore title-hidden

> style stick

Changed 6558 atom styles  

> color white pseudobonds

> style ions sphere

Changed 2 atom styles  

> save scene whitepbs

Cannot determine format for 'scene'  

> scenes save whitepbs

> scenes restore spheres

> scenes delete spheres

> scenes restore fatsticks

> scenes delete fatsticks

> scenes restore bigions

> scenes delete bigions

> scenes restore unclip

> scenes restore whitepbs

> color lime N atoms

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

> color #1 & C lime atoms

> scenes save greenC

> scenes restore whitepbs

> scenes restore unclip

> scenes restore greenC

> scenes restore lab-hidden

> scenes restore greenC

> hide atoms

> scenes save hideatoms

> scenes restore greenC

> scenes restore hideatoms

> scenes restore greenC

> hide pseudobonds

> scenes save hidepb

> scenes restore whitepbs

> scenes restore hidepb

> save scenes2.cxs

——— End of log from Thu Sep 25 12:53:25 2025 ———

> view name session-start

opened ChimeraX session  

> scenes restore hideatoms

> scenes restore titled-tubes

> 2dlabels add text HELLO! color red

Expected 'all' or a 2d label name or a label models specifier or a keyword  

> 2dlabels text HELLO! color red

> scenes rename titled-tubes hello

> scenes restore hello

> scenes delete hello

> scenes restore titled

> scenes save hello

> 2dlabels text HELLO! color red

> scenes restore hello

> scenes save hello

> 2dlabels text HELLO! color red

> scenes save hello

[Repeated 1 time(s)]

> scenes restore titled

> scenes restore hello

> scenes restore titled

> scenes restore hello

> save scenes3.cxs

——— End of log from Thu Nov 20 12:23:34 2025 ———

> view name session-start

opened ChimeraX session  

> scenes restore titled

> scenes restore hello

> close #3.3

> close #3.2,4

> scenes restore titled

> scenes restore hello

> 2dlabels text HELLO! color red

> scenes save hello

> scenes restore titled

> scenes restore hello

> save scenes3.cxs

——— End of log from Thu Nov 20 12:24:37 2025 ———

> view name session-start

opened ChimeraX session  

> scenes restore 2

> scenes rename 2 apart

> scenes restore title-hidden

> show #3.1 models

> scenes save ""

> scenes restore 18

> scenes rename 18 title-shown

> save morescenes.cxs

[Repeated 1 time(s)]

——— End of log from Tue Feb 24 13:56:47 2026 ———

> view name session-start

opened ChimeraX session  

> ui tool show Animations

Scene 'title-shown' moved from 1.99s to 4.35s  
Scene 'title-hidden' moved from 1.52s to 3.17s  
Scene 'matched' moved from 1.04s to 1.58s  
Scene timeline reset to 0.0s  
Scene 'apart' moved from 0.36s to 1.25s  
Scene 'apart' moved from 1.25s to 0.16s  
Scene timeline reset to 0.0s  
Scene timeline reset to 0.0s  

> scenes restore hideatoms

Scene 'title-hidden' moved from 3.17s to 2.25s  
Scene 'title-shown' moved from 4.35s to 2.40s  

> scenes restore title-shown

Scene 'hideatoms' moved from 3.44s to 4.82s  
Scene timeline reset to 0.0s  
Scene 'hideatoms' moved from 4.82s to 3.43s  
Scene 'hideatoms' moved from 3.43s to 4.68s  
Scene 'hideatoms' moved from 4.68s to 3.24s  

> hide ribbons

> scenes save ""

> scenes restore 19

[Repeated 1 time(s)]

> scenes rename 19 hideribbons

> show ribbons

> hide models

> scenes save ""

> scenes restore 20

> scenes rename 20 hidemodels

Scene 'hideribbons' moved from 4.72s to 4.14s  
Scene timeline reset to 0.0s  
Scene 'apart' moved from 0.16s to 0.13s  
Scene timeline reset to 0.0s  
Scene timeline reset to 0.0s  
Scene timeline reset to 0.0s  
Scene timeline reset to 0.0s  
Scene timeline reset to 0.0s  
Scene timeline reset to 0.0s  
Scene timeline reset to 0.0s  
Scene timeline reset to 0.0s  
Scene timeline reset to 0.0s  
Scene timeline reset to 0.0s  
Scene timeline reset to 0.0s  

> scenes restore title-shown

Scene timeline reset to 0.0s  
Scene timeline reset to 0.0s  

> save anim-sess.cxs

——— End of log from Tue Mar 3 15:46:15 2026 ———

> view name session-start

opened ChimeraX session  
Scene timeline reset to 0.0s  
Scene 'matched' moved from 1.58s to 2.08s  

> scenes restore matched

> scenes restore apart

Scene timeline reset to 0.0s  
Scene timeline reset to 0.0s  
Scene timeline reset to 0.0s  
Scene timeline reset to 0.0s  
Scene timeline reset to 0.0s  
Scene timeline reset to 0.0s  

> scenes restore apart

Scene timeline reset to 0.0s  
Scene timeline reset to 0.0s  
Scene timeline reset to 0.0s  
Scene animation duration set to 10.00s  
Scene 'apart' moved from 0.13s to 0.00s  
Scene 'apart' moved from 0.00s to 6.25s  
Scene 'apart' moved from 6.25s to 0.01s  
Scene 'apart' moved from 0.01s to 6.26s  
Scene 'apart' moved from 6.26s to 6.82s  
Scene 'apart' moved from 0.29s to 0.15s  




OpenGL version: 4.1 Metal - 89.4
OpenGL renderer: Apple M3
OpenGL vendor: Apple

Python: 3.11.9
Locale: en_US.UTF-8
Qt version: PySide6 6.10.1, Qt 6.10.1
Qt runtime version: 6.10.1
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: iMac
      Model Identifier: Mac15,4
      Model Number: Z19700021LL/A
      Chip: Apple M3
      Total Number of Cores: 8 (4 performance and 4 efficiency)
      Memory: 16 GB
      System Firmware Version: 13822.81.10
      OS Loader Version: 11881.140.96

Software:

    System Software Overview:

      System Version: macOS 15.7.4 (24G517)
      Kernel Version: Darwin 24.6.0
      Time since boot: 6 days, 23 hours, 6 minutes

Graphics/Displays:

    Apple M3:

      Chipset Model: Apple M3
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 8
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        iMac:
          Display Type: Built-In Retina LCD
          Resolution: Retina 4.5K (4480 x 2520)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal


Installed Packages:
    accessible-pygments: 0.0.5
    aiohappyeyeballs: 2.6.1
    aiohttp: 3.13.1
    aiosignal: 1.4.0
    alabaster: 1.0.0
    annotated-types: 0.7.0
    anyio: 4.12.1
    appdirs: 1.4.4
    appnope: 0.1.4
    asttokens: 3.0.1
    attrs: 25.4.0
    babel: 2.18.0
    beautifulsoup4: 4.13.5
    blockdiag: 3.0.0
    blosc2: 4.1.2
    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: 3.6.2
    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: 1.64.1
    ChimeraX-AtomicLibrary: 14.2.3
    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: 2.3
    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: 1.12.dev202603042258
    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
    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: 1.3
    ChimeraX-LightingGUI: 1.0
    ChimeraX-ListInfo: 1.3.1
    ChimeraX-Log: 1.2.2
    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: 0.2.0
    ChimeraX-MDcrds: 2.18
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-Minimize: 1.3.6
    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: 2.7.12
    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: 1.5.1
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.8
    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: 2.17.5
    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: 2.5.2
    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: 1.50.3
    ChimeraX-Umap: 1.0
    ChimeraX-uniprot: 2.3.2
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDock: 1.6.1
    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: 8.3.1
    colorama: 0.4.6
    comm: 0.2.3
    contourpy: 1.3.3
    coverage: 7.13.4
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.2.4
    debugpy: 1.8.20
    decorator: 5.2.1
    docutils: 0.21.2
    executing: 2.2.1
    filelock: 3.19.1
    fonttools: 4.61.1
    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: 2.0.0
    iniconfig: 2.3.0
    ipykernel: 7.1.0
    ipython: 9.9.0
    ipython_pygments_lexers: 1.1.1
    ipywidgets: 8.1.8
    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
    jupyterlab_widgets: 3.0.16
    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: 3.10.7
    matplotlib-inline: 0.2.1
    mcp: 1.18.0
    msgpack: 1.1.1
    multidict: 6.7.1
    narwhals: 2.13.0
    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: 2.3.5
    numpy: 1.26.4
    OpenMM: 8.4.0
    openvr: 1.26.701
    packaging: 25.0
    ParmEd: 4.2.2
    parso: 0.8.6
    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: 4.9.2
    plotly: 6.5.0
    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: 2.12.5
    pydantic-settings: 2.13.1
    pydantic_core: 2.41.5
    pydata-sphinx-theme: 0.16.1
    pydicom: 2.4.4
    Pygments: 2.18.0
    pyKVFinder: 0.8.4
    pynmrstar: 3.5.0
    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
    PySide6: 6.10.1
    PySide6_Addons: 6.10.1
    PySide6_Essentials: 6.10.1
    pytest: 9.0.2
    pytest-cov: 7.0.0
    python-dateutil: 2.9.0.post0
    python-dotenv: 1.2.2
    python-multipart: 0.0.22
    pyzmq: 27.1.0
    qtconsole: 5.7.0
    QtPy: 2.4.3
    qtshim: 1.2.1
    RandomWords: 0.4.0
    referencing: 0.37.0
    requests: 2.32.5
    roman-numerals: 4.1.0
    rpds-py: 0.30.0
    scipy: 1.14.0
    setuptools: 80.9.0
    sfftk-rw: 0.8.1
    shiboken6: 6.10.1
    six: 1.17.0
    snowballstemmer: 3.0.1
    sortedcontainers: 2.4.0
    soupsieve: 2.8.3
    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: 3.3.2
    stack-data: 0.6.3
    starlette: 0.52.1
    superqt: 0.7.6
    tables: 3.10.2
    tcia_utils: 1.5.1
    tifffile: 2025.3.13
    tinyarray: 1.2.5
    tomlkit: 0.13.3
    tornado: 6.5.4
    traitlets: 5.14.3
    typing-inspection: 0.4.2
    typing_extensions: 4.15.0
    urllib3: 2.6.3
    uvicorn: 0.41.0
    wcwidth: 0.6.0
    webcolors: 24.11.1
    wheel: 0.45.1
    wheel-filename: 1.4.2
    widgetsnbextension: 4.0.15
    yarl: 1.23.0