Opened 16 months ago
Closed 16 months ago
#15543 closed defect (nonchimerax)
Intel Mac image save artifacts with silhouette edges
Reported by: | Owned by: | Tom Goddard | |
---|---|---|---|
Priority: | normal | Milestone: | |
Component: | Input/Output | Version: | |
Keywords: | Cc: | ||
Blocked By: | Blocking: | ||
Notify when closed: | Platform: | all | |
Project: | ChimeraX |
Description
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: alabaster: 0.7.16 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 webcolors: 1.13 wheel: 0.43.0 wheel-filename: 1.4.1 widgetsnbextension: 4.0.11 File attachment: heme_coord_model.png
Attachments (1)
Change History (3)
by , 16 months ago
Attachment: | heme_coord_model.png added |
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comment:1 by , 16 months ago
Component: | Unassigned → Input/Output |
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Owner: | set to |
Platform: | → all |
Project: | → ChimeraX |
Status: | new → assigned |
Summary: | ChimeraX bug report submission → Bad image save |
Reported by Thomas Cottle
comment:2 by , 16 months ago
Resolution: | → nonchimerax |
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Status: | assigned → closed |
Summary: | Bad image save → Intel Mac image save artifacts with silhouette edges |
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.
Added by email2trac