Intel Mac image save artifacts with silhouette edges

[tommycottle@…]

The following bug report has been submitted:
Platform:        macOS-14.5-x86_64-i386-64bit
ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC)
Description
Whenever I save an image, there image is heavily pixellated and corrupted. I recently updated to Chimera 1.8 for the Alphafold3 compatibility but otherwise have used Chimera with no issues for awhile. I have a 2020 Macbook Pro, so I used the intel version of Chimera 1.8 for MacOS. Any guidance on how I can resolve this would be most appreciated.

Log:
UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open /Users/thomascottle/Downloads/heme_coord_model.cxs format session

Log from Tue Jul 2 13:25:42 2024 Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> /Users/thomascottle/Downloads/fold_alas_pd2_heme/fold_alas_pd2_heme_model_0.cif

Chain information for fold_alas_pd2_heme_model_0.cif #1  
---  
Chain | Description  
A | .  
B | .  
  

> ui tool show "AlphaFold Error Plot"

> alphafold pae #1 file
> /Users/thomascottle/Downloads/fold_alas_pd2_heme/fold_alas_pd2_heme_full_data_0.json

> preset "overall look" "publication 1 (silhouettes)"

Using preset: Overall Look / Publication 1 (Silhouettes)  
Preset expands to these ChimeraX commands:

    
    
    set bg white
    graphics silhouettes t
    lighting depthCue f

  

> select #1/C

43 atoms, 46 bonds, 4 pseudobonds, 1 residue, 2 models selected  

> ui tool show "Color Actions"

> color sel crimson

> color sel fire brick

> color sel sienna

> color sel rosy brown

> select clear

> select /A

4149 atoms, 4247 bonds, 534 residues, 1 model selected  

> select /B

2596 atoms, 2674 bonds, 317 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel wheat

> select /A

4149 atoms, 4247 bonds, 534 residues, 1 model selected  

> color sel silver

> color sel dark gray

> color sel light steel blue

> color sel light sky blue

> select clear

> select #1/A 1-100

Expected a keyword  

> select #1/A,1-100

4149 atoms, 4247 bonds, 534 residues, 1 model selected  

> color sel red

> color bfactor #1 palette alphafold

6788 atoms, 852 residues, atom bfactor range 12.4 to 97.9  

> undo

> select #1/A 1:100

Expected a keyword  

> select #1/A:1-100

779 atoms, 797 bonds, 100 residues, 1 model selected  

> color sel cyan

> select #1/A:75-end

3594 atoms, 3680 bonds, 460 residues, 1 model selected  

> hide sel cartoons

> select #1/A:start-50

376 atoms, 383 bonds, 50 residues, 1 model selected  

> select #1/A:start-30

220 atoms, 225 bonds, 30 residues, 1 model selected  

> hide sel cartoons

> undo

> select #1/A:start-10

64 atoms, 64 bonds, 10 residues, 1 model selected  

> hide sel cartoons

> select #1/A:75-50

Nothing selected  

> select #1/A:57-74

139 atoms, 141 bonds, 18 residues, 1 model selected  

> hide sel cartoons

> select #1/A:11-55

346 atoms, 353 bonds, 45 residues, 1 model selected  

> color sel dark gray

> select #1/A:16-17

16 atoms, 16 bonds, 2 residues, 1 model selected  

> select #1/A:17-18

13 atoms, 13 bonds, 2 residues, 1 model selected  

> select #1/A:18-19

18 atoms, 19 bonds, 2 residues, 1 model selected  

> select #1/A:17-18

13 atoms, 13 bonds, 2 residues, 1 model selected  

> color sel byelement

> select /A:19

11 atoms, 11 bonds, 1 residue, 1 model selected  

> color sel byelement

> hide sel cartoons

> show sel cartoons

> hide sel atoms

> select /B

2596 atoms, 2674 bonds, 317 residues, 1 model selected  

> hide sel atoms

> select clear

> select /A

4149 atoms, 4247 bonds, 534 residues, 1 model selected  

> select /B

2596 atoms, 2674 bonds, 317 residues, 1 model selected  

> color sel dark gray

> select /A/B

6745 atoms, 6921 bonds, 851 residues, 1 model selected  

> color sel cornflower blue

> undo

> select clear

> select /A

4149 atoms, 4247 bonds, 534 residues, 1 model selected  

> color sel cornflower blue

> select clear

> select /A:17

6 atoms, 5 bonds, 1 residue, 1 model selected  

> color sel byelement

> select clear

> select /A:17@CB

1 atom, 1 residue, 1 model selected  

> color sel cornflower blue

> select /A:17@CB

1 atom, 1 residue, 1 model selected  

> color sel cornflower blue

> select clear

> select #1/A:17

6 atoms, 5 bonds, 1 residue, 1 model selected  

> color sel cornflower blue

> select #1/A:17@S

Nothing selected  

> select #1/A:17@S*

1 atom, 1 residue, 1 model selected  

> color sel yellow

> select #1/A:17

6 atoms, 5 bonds, 1 residue, 1 model selected  

> color sel cornflower blue

> select #1/A:17@SG

1 atom, 1 residue, 1 model selected  

> select clear

> select #1/A:17@SG

1 atom, 1 residue, 1 model selected  

> color sel yellow

> undo

> select A:17@SG

Expected an objects specifier or a keyword  

> select #1/A:17@SG

1 atom, 1 residue, 1 model selected  

> select clear

> select /A:17@SG

1 atom, 1 residue, 1 model selected  

> select /A:17@SG

1 atom, 1 residue, 1 model selected  

> select /A:17@SG

1 atom, 1 residue, 1 model selected  

> select clear

> select /A:17@SG

1 atom, 1 residue, 1 model selected  

> select S

31 atoms, 31 residues, 1 model selected  

> select clear

> select /A:17

6 atoms, 5 bonds, 1 residue, 1 model selected  

> color sel byelement

> color sel cornflower blue

> ui tool show "Color Actions"

> color sel byelement

> color sel cornflower blue target aspf

> select /A:17

6 atoms, 5 bonds, 1 residue, 1 model selected  

> ui tool show "Color Actions"

> color sel cornflower blue target aspf

> color sel byelement target a

> color sel cornflower blue target a

No target buttons for the coloring action are checked  

> ui tool show "Color Actions"

> color sel byhetero

> select clear

[Repeated 1 time(s)]

> select #1/C

43 atoms, 46 bonds, 4 pseudobonds, 1 residue, 2 models selected  

> color (#!1 & sel) orange red

> ui tool show "Color Actions"

> color sel salmon

> color sel sienna

> color sel orange red

> color sel crimson

> color sel dark red

> color sel maroon

> color sel fire brick

> color sel brown

> color sel chocolate

> select clear

> select #1/C

43 atoms, 46 bonds, 4 pseudobonds, 1 residue, 2 models selected  

> ui tool show "Color Actions"

> color sel indian red

> color sel sienna

> select clear

> color /A:1-4 lime

> color /A:504-534/B:1-15 magenta

> undo

[Repeated 1 time(s)]

> select clear

> select /A/B

6745 atoms, 6921 bonds, 851 residues, 1 model selected  

> select clear

> select /A

4149 atoms, 4247 bonds, 534 residues, 1 model selected  

> color sel blue

> ui tool show "Color Actions"

> color sel royal blue

> select clear

> select /A

4149 atoms, 4247 bonds, 534 residues, 1 model selected  

> select clear

> select /B

2596 atoms, 2674 bonds, 317 residues, 1 model selected  

> color sel dark gray

> select clear

> select #1/C

43 atoms, 46 bonds, 4 pseudobonds, 1 residue, 2 models selected  

> color sel sienna

> select clear

[Repeated 1 time(s)]

> select #1/B:1-105

830 atoms, 850 bonds, 105 residues, 1 model selected  

> color sel dark gray

> select #1/B:105-216

952 atoms, 984 bonds, 112 residues, 1 model selected  

> color sel light gray

> select #1/B:217-end

821 atoms, 845 bonds, 101 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel wheat

> select clear

> select #1/B:1-105

830 atoms, 850 bonds, 105 residues, 1 model selected  

> color sel dark gray

> color sel gray

> select clear

> select #1/B:181-end

1137 atoms, 1172 bonds, 137 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel wheat

> select #1/B:1-149

1194 atoms, 1226 bonds, 149 residues, 1 model selected  

> select clear

> select #1/B:1-149

1194 atoms, 1226 bonds, 149 residues, 1 model selected  

> color sel gray

> select clear

[Repeated 1 time(s)]

> select /A

4149 atoms, 4247 bonds, 534 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel dodger blue

> select clear

> select /A:17

6 atoms, 5 bonds, 1 residue, 1 model selected  

> color sel byhetero

> select up

118 atoms, 121 bonds, 17 residues, 1 model selected  

> select #1/C

43 atoms, 46 bonds, 4 pseudobonds, 1 residue, 2 models selected  

> color (#!1 & sel) byhetero

> select clear

[Repeated 1 time(s)]

> preset "overall look" "publication 2 (depth-cued)"

Using preset: Overall Look / Publication 2 (Depth-Cued)  
Preset expands to these ChimeraX commands:

    
    
    set bg white
    graphics silhouettes f
    lighting depthCue t

  

> preset "molecular surfaces" "atomic coloring (transparent)"

Using preset: Molecular Surfaces / Atomic Coloring (Transparent)  
Changed 0 atom styles  
Preset expands to these ChimeraX commands:

    
    
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    surface
    color fromatoms targ s trans 70

  

> undo

[Repeated 2 time(s)]

> preset "overall look" "publication 1 (silhouettes)"

Using preset: Overall Look / Publication 1 (Silhouettes)  
Preset expands to these ChimeraX commands:

    
    
    set bg white
    graphics silhouettes t
    lighting depthCue f

  

> surface hidePatches

> preset "overall look" "publication 1 (silhouettes)"

Using preset: Overall Look / Publication 1 (Silhouettes)  
Preset expands to these ChimeraX commands:

    
    
    set bg white
    graphics silhouettes t
    lighting depthCue f

  

> save heme_coord_model.png 4000 2000 transparentBackground true

Expected a keyword  

> save /Users/thomascottle/Downloads/heme_coord_model.png width 4000 height
> 3037 supersample 3 transparentBackground true

> preset "overall look" "publication 1 (silhouettes)"

Using preset: Overall Look / Publication 1 (Silhouettes)  
Preset expands to these ChimeraX commands:

    
    
    set bg white
    graphics silhouettes t
    lighting depthCue f

  

> save /Users/thomascottle/Downloads/heme_coord_model.png width 860 height 653
> supersample 3

> preset "overall look" "publication 1 (silhouettes)"

Using preset: Overall Look / Publication 1 (Silhouettes)  
Preset expands to these ChimeraX commands:

    
    
    set bg white
    graphics silhouettes t
    lighting depthCue f

  

> save /Users/thomascottle/Downloads/heme_coord_model.png width 860 height 653
> supersample 3

> preset "overall look" "publication 1 (silhouettes)"

Using preset: Overall Look / Publication 1 (Silhouettes)  
Preset expands to these ChimeraX commands:

    
    
    set bg white
    graphics silhouettes t
    lighting depthCue f

  

> save /Users/thomascottle/Downloads/heme_coord_model.tif width 860 height 653
> supersample 3

> preset "overall look" "publication 1 (silhouettes)"

Using preset: Overall Look / Publication 1 (Silhouettes)  
Preset expands to these ChimeraX commands:

    
    
    set bg white
    graphics silhouettes t
    lighting depthCue f

  

> save /Users/thomascottle/Downloads/heme_coord_model.cxs

——— End of log from Tue Jul 2 13:25:42 2024 ———

opened ChimeraX session  

> preset "overall look" "publication 1 (silhouettes)"

Using preset: Overall Look / Publication 1 (Silhouettes)  
Preset expands to these ChimeraX commands:

    
    
    set bg white
    graphics silhouettes t
    lighting depthCue f

  

> save "/Users/thomascottle/Desktop/Kardon Lab/Manuscript
> Drafts/heme_coord_model.png" width 1000 height 756 supersample 3

> preset "overall look" "publication 1 (silhouettes)"

Using preset: Overall Look / Publication 1 (Silhouettes)  
Preset expands to these ChimeraX commands:

    
    
    set bg white
    graphics silhouettes t
    lighting depthCue f

  




OpenGL version: 4.1 INTEL-22.5.11
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics OpenGL Engine
OpenGL vendor: Intel Inc.

Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro16,2
      Processor Name: Quad-Core Intel Core i7
      Processor Speed: 2.3 GHz
      Number of Processors: 1
      Total Number of Cores: 4
      L2 Cache (per Core): 512 KB
      L3 Cache: 8 MB
      Hyper-Threading Technology: Enabled
      Memory: 32 GB
      System Firmware Version: 2022.100.22.0.0 (iBridge: 21.16.5077.0.0,0)
      OS Loader Version: 580~2215

Software:

    System Software Overview:

      System Version: macOS 14.5 (23F79)
      Kernel Version: Darwin 23.5.0
      Time since boot: 4 days, 13 hours, 52 minutes

Graphics/Displays:

    Intel Iris Plus Graphics:

      Chipset Model: Intel Iris Plus Graphics
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x8a53
      Revision ID: 0x0007
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2560 x 1600 Retina
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal


Installed Packages:
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    appdirs: 1.4.4
    appnope: 0.1.4
    asttokens: 2.4.1
    Babel: 2.15.0
    beautifulsoup4: 4.12.3
    blockdiag: 3.0.0
    blosc2: 2.0.0
    build: 1.2.1
    certifi: 2023.11.17
    cftime: 1.6.4
    charset-normalizer: 3.3.2
    ChimeraX-AddCharge: 1.5.17
    ChimeraX-AddH: 2.2.6
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.5
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.12.7
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.57.1
    ChimeraX-AtomicLibrary: 14.0.6
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.4.6
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.12.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.7
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.4
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.6
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.8
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.3
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2.4
    ChimeraX-DiffPlot: 1.0
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.3
    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: 1.1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-Label: 1.1.10
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.1.6
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.2
    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: 2.1.3
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.7.1
    ChimeraX-MedicalToolbar: 1.0.3
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.14.1
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.17
    ChimeraX-ModelPanel: 1.5
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.2
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.2
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.13.5
    ChimeraX-PDB: 2.7.5
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.4
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1.1
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.4.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.2
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.2
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.0.15
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.11.2
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.16.5
    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
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.39.1
    ChimeraX-uniprot: 2.3
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.3
    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: 1.1.4
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    contourpy: 1.2.1
    cxservices: 1.2.2
    cycler: 0.12.1
    Cython: 3.0.10
    debugpy: 1.8.1
    decorator: 5.1.1
    docutils: 0.20.1
    executing: 2.0.1
    filelock: 3.13.4
    fonttools: 4.53.0
    funcparserlib: 2.0.0a0
    glfw: 2.7.0
    grako: 3.16.5
    h5py: 3.11.0
    html2text: 2024.2.26
    idna: 3.7
    ihm: 1.0
    imagecodecs: 2024.1.1
    imagesize: 1.4.1
    ipykernel: 6.29.2
    ipython: 8.21.0
    ipywidgets: 8.1.3
    jedi: 0.19.1
    jinja2: 3.1.4
    jupyter-client: 8.6.0
    jupyter-core: 5.7.2
    jupyterlab-widgets: 3.0.11
    kiwisolver: 1.4.5
    line-profiler: 4.1.2
    lxml: 5.2.1
    lz4: 4.3.3
    MarkupSafe: 2.1.5
    matplotlib: 3.8.4
    matplotlib-inline: 0.1.7
    msgpack: 1.0.8
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.10.0
    numpy: 1.26.4
    openvr: 1.26.701
    packaging: 23.2
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pexpect: 4.9.0
    pillow: 10.3.0
    pip: 24.0
    pkginfo: 1.10.0
    platformdirs: 4.2.2
    prompt-toolkit: 3.0.47
    psutil: 5.9.8
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    pygments: 2.17.2
    pynmrstar: 3.3.4
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.3401
    pyparsing: 3.1.2
    pyproject-hooks: 1.1.0
    PyQt6-commercial: 6.6.1
    PyQt6-Qt6: 6.6.3
    PyQt6-sip: 13.6.0
    PyQt6-WebEngine-commercial: 6.6.0
    PyQt6-WebEngine-Qt6: 6.6.3
    python-dateutil: 2.9.0.post0
    pytz: 2024.1
    pyzmq: 26.0.3
    qtconsole: 5.5.1
    QtPy: 2.4.1
    RandomWords: 0.4.0
    requests: 2.31.0
    scipy: 1.13.0
    setuptools: 69.5.1
    setuptools-scm: 8.0.4
    sfftk-rw: 0.8.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.5
    sphinx: 7.2.6
    sphinx-autodoc-typehints: 2.0.1
    sphinxcontrib-applehelp: 1.0.8
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.6
    sphinxcontrib-htmlhelp: 2.0.5
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.7
    sphinxcontrib-serializinghtml: 1.1.10
    stack-data: 0.6.3
    superqt: 0.6.3
    tables: 3.8.0
    tcia-utils: 1.5.1
    tifffile: 2024.1.30
    tinyarray: 1.2.4
    tornado: 6.4.1
    traitlets: 5.14.2
    typing-extensions: 4.12.2
    tzdata: 2024.1
    urllib3: 2.2.1
    wcwidth: 0.2.13
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    wheel: 0.43.0
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.11
File attachment: heme_coord_model.png

heme_coord_model.png​

[tommycottle@…]

Added by email2trac

[Eric Pettersen]

Reported by Thomas Cottle

[Tom Goddard]

Those artifacts are a defect in Apple's Intel graphics driver. It is specific to your specific MacBook Pro model (16,2). I believe it only happens when using silhouette edges. The only remedy is to turn of silhouette edges (command "graphics silhouette false" or use the Graphics Toolbar tab and click the silhouettes icon to turn them off). Only Apple could fix this and they certainly won't because it is an Intel Mac. The problem does not happen on M1/M2/M3 Macs, nor does it happen on other Intel Mac models. If you need to save an image with silhouettes the only option is to save a ChimeraX session (.cxs file suffix) and copy it to another computer that has a working graphics driver to save the image. Old Chimera silhouette edges I think work because it uses very old (and limited) graphics that Apple's graphics driver can handle.