Animation messes up graphics window size

[Elaine Meng]

The following bug report has been submitted:
Platform:        macOS-15.7.3-arm64-arm-64bit
ChimeraX Version: 1.12.dev202602240240 (2026-02-24 02:40:22 UTC)
Description
(1) If you have a session with scenes and windowsize appropriate for those scenes, starting Animations ruins the windowsize since it takes up vertical space and squishes the graphics window.

(2) if you resize to make the graphics window as desired again, then save a session, then restore the session, the graphics window is squished again.  I will attach screenshots before and after saving and restoring.

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

> open /Users/meng/Desktop/morescenes2.cxs format session

Log from Tue Feb 24 14:01:11 2026UCSF ChimeraX version: 1.12.dev202602240240
(2026-02-24)  
© 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

> save morescenes2.cxs

——— End of log from Tue Feb 24 14:01:11 2026 ———

> view name session-start

opened ChimeraX session  




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: PySide6 6.10.1, Qt 6.10.1
Qt runtime version: 6.10.1
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro18,1
      Model Number: MK1F3LL/A
      Chip: Apple M1 Pro
      Total Number of Cores: 10 (8 performance and 2 efficiency)
      Memory: 16 GB
      System Firmware Version: 13822.61.10
      OS Loader Version: 11881.140.96

Software:

    System Software Overview:

      System Version: macOS 15.7.3 (24G419)
      Kernel Version: Darwin 24.6.0
      Time since boot: 5 hours, 50 minutes

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:
        Color LCD:
          Display Type: Built-in Liquid Retina XDR Display
          Resolution: 3456 x 2234 Retina
          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: 4.0.0
    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
    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-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.dev202602240240
    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: 2.17.2
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-Minimize: 1.3.5
    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: 1.15.2
    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-PhenixUI: 1.4.12
    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
    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
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[Elaine Meng]

There is no way to save a session with Animations open and get back the same windowsize you had earlier, short of writing it down and manually using the windowsize command after restoring. Of course I can save a session with scenes and Animations closed, but then I lose the scenes on the timeline (actually I don't know if those are saved, but I imagine that is the eventual goal), not to mention that as soon as I open Animations, the window size gets messed up again.

[Elaine Meng]

Ah yes, as you were probably aware, the scenes on the Animation timeline are not yet saved. The only thing saved is that the Animation tool was open at the time of session-saving.

I thought the windowsize would be saved in a session, but apparently whatever size it is saving is not taking the presence of the Animations tool into account, as per the main point of this ticket.

[Elaine Meng]

session with scenes before I open the Animations tool. graphics windowsize is 624 612.

[Zach Pearson]

When the animations tool is opened instead of shrinking the graphics window it now makes the overall window size grow.

[Zach Pearson]

I noticed the fix I put in wasn't working and was causing the graphics window to expand weirdly, which knocked Qt's hitbox layout out of alignment with the actual buttons being rendered for the whole UI. That's been reverted. But you should be able to save your stuff in sessions now. The best advice I can give is to just resize the window. Qt doesn't play nice with resizing QSurfaces contained by QWindow.

[Elaine Meng]

Most people do not write down the window size at which they saved all their scenes and their session for figures/animations, so it isn't really a solution to say that people should just resize the window.  For reproducibility you need exact dimensions, not whether it looks sorta OK.

[Zach Pearson]

I had a fix that basically worked but it caused the window to flicker when the animations tool opened, because because Qt's dock widget layout has to fully complete before we can resize the window to compensate. If we resize synchronously during the same layout pass, it does what I said and breaks the mapping between UI hitboxes and the UI.

The only way that works without breaking input is to defer the resize to the next event loop iteration, which means the graphics visibly shrinks for one frame before the window grows back.

Are you OK with the flicker? Should I just make the tool undocked by default?

[Elaine Meng]

Do you mean a single flicker or continuous flickering?  If single, my guess without actually seeing that is that it seems tolerable, but something to keep in mind to improve later if other solutions arise.  As the user representative, I'm just saying that the involuntary resizing caused by opening the Animations tools needs to be avoided for its eventual full usability to the community, but you (and possibly other programmers) are the judge of what's feasible and in what time frame, and I respect that.  If you don't think it is reasonably fixable now you could keep the ticket open... I just didn't want for the issue to be lost.  Thanks!

[Eric Pettersen]

My vote would be to start it undocked. I typically start large dialogs undocked. Nonetheless, I recognize some of the convenience of having it docked, but it does compete with the difficulty of maintaining the graphics window size. So my two cents.

[Elaine Meng]

Oooh, I just noticed that in the daily build, restoring a scene after opening the session also restored the window size, which helps a lot.  I didn't notice this behavior before, not sure if it is new or I just failed to notice before.  (Apologies if the latter; however, a user might not know to do that after opening Animations within-session, or after restoring the session that had Animations open.)

[Elaine Meng]

Sorry, me again:  and further, playback restores the scenes so the window size gets corrected at that point. So it's not nearly as bad as I thought, limited to a squashed window when a session (with Animations in it) is first restored or when the Animations tool is first opened.  Adjust response as desired.