silhouettes → tiny boxes

[jeremy@…]

The following bug report has been submitted:
Platform:        macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.6rc202304272016 (2023-04-27 20:16:52 UTC)
Description
Hello, 

I've found since I've gone back to an old INTEL Mac (from a M1 chipped Mac) that chimeraX seems to be having issues correctly rendering maps and models. I've attached a screen shot to show what I mean. It happens both in the program and in saved images. It seems to happen with the 1.6 version below but also with a 1.5 version (and with different models/maps), making me pretty sure it's my computer. 

I'll likey go back to a newer Mac soon so hopefully the problem will sort itself out but I thought I'd flag it up with you either way. 

Cheers, 

Jeremy

Log:
UCSF ChimeraX version: 1.6rc202304272016 (2023-04-27)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open /Users/jeremykeown/Desktop/nuc_density.cxs

Opened cryosparc_P953_J59_011_volume_map_sharp.mrc as #2, grid size
300,300,300, pixel 0.932, shown at level 0.281, step 1, values float32  
Log from Tue May 2 15:41:28 2023UCSF ChimeraX version: 1.5 (2022-11-24)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> /Users/jeremykeown/Library/CloudStorage/Dropbox/Hantaan_Paper/Maps_PDB_refined/P953_RXN_ATP_Final_map_model/Hantaan_core_RNA_RXN_ATP_real_space_refined_009-coot-1_real_space_refined_009.pdb

Chain information for
Hantaan_core_RNA_RXN_ATP_real_space_refined_009-coot-1_real_space_refined_009.pdb
#1  
---  
Chain | Description  
A | No description available  
D | No description available  
  

> open
> /Users/jeremykeown/Library/CloudStorage/Dropbox/Hantaan_Paper/Maps_PDB_refined/P953_RXN_ATP_Final_map_model/cryosparc_P953_J59_011_volume_map_sharp.mrc

Opened cryosparc_P953_J59_011_volume_map_sharp.mrc as #2, grid size
300,300,300, pixel 0.932, shown at level 0.0853, step 2, values float32  

> volume #2 level 0.2255

> volume #2 step 1

> set bgColor white

> ui tool show "Side View"

> select protein

20938 atoms, 21170 bonds, 4 pseudobonds, 1298 residues, 2 models selected  

> hide (#!1 & sel) target a

> select add #1

21148 atoms, 21393 bonds, 4 pseudobonds, 1306 residues, 2 models selected  

> select subtract #1

Nothing selected  

> volume #2 color #b2b2b26a

> volume #2 level 0.2874

> select add #1

21148 atoms, 21393 bonds, 4 pseudobonds, 1306 residues, 2 models selected  

> show sel atoms

> select H

10552 atoms, 1304 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> select /A:892@NH2

1 atom, 1 residue, 1 model selected  

> select up

11 atoms, 10 bonds, 1 residue, 1 model selected  

> select up

52 atoms, 53 bonds, 6 residues, 1 model selected  

> hide sel atoms

> save /Users/jeremykeown/Dropbox/Hantaan_Paper/Figure4/Nuc_Density.png width
> 2048 height 2048 supersample 4 transparentBackground true

> save
> /Users/jeremykeown/Dropbox/Hantaan_Paper/SuppFig4_Active_site_conservation/Nuc_Density.png
> width 2048 height 2048 supersample 4 transparentBackground true

> lighting flat

> lighting shadows true intensity 0.5

> lighting full

> lighting flat

> lighting shadows true intensity 0.5

> lighting shadows false

> lighting full

> lighting soft

> lighting simple

> hide #!2 models

> show #!2 models

> volume style mesh

> volume style surface

> volume step 1

> volume step 2

[Repeated 1 time(s)]

> volume step 1

> volume #2 level 0.2812

> volume style mesh

> save
> /Users/jeremykeown/Dropbox/Hantaan_Paper/SuppFig4_Active_site_conservation/Nuc_Density_mesh.png
> width 2048 height 2048 supersample 4 transparentBackground true

> volume style surface

> volume style mesh

[Repeated 1 time(s)]

> volume style image

> volume style mesh

> volume style surface

> transparency 0

> volume style image

> volume style mesh

> volume style surface

[Repeated 1 time(s)]

> volume #2 color #b2b2b2d4

> volume #2 color #b2b2b2

> volume #2 color #b2b2b2fe

> volume #2 color #b2b2b2

> hide #!2 models

> show #!2 models

> volume #2 style mesh

> volume #2 style image

> volume #2 maximumIntensityProjection true

> volume #2 region 0,0,149,299,299,149 step 1 maximumIntensityProjection false
> showOutlineBox true

> volume #2 region 0,0,0,299,299,299 step 1

> volume #2 style surface region 0,0,0,299,299,299 step 1

> volume #2 color #b2b2b21d

> hide #!1 models

> show #!1 models

> volume planes z style image imageMode "full region"

> mousemode rightMode "move planes"

> volume planes z style image imageMode "full region"

> mousemode rightMode "move planes"

> volume #2 color #b2b2b2f9 color white color white

> volume planes z style image imageMode "full region"

> mousemode rightMode "move planes"

> volume #2 color #b2b2b2fe color white color white

> volume #2 style image region all imageMode "tilted slab" tiltedSlabAxis
> 0,0,1 tiltedSlabOffset 139.8 tiltedSlabSpacing 0.932 tiltedSlabPlaneCount 10

> mousemode rightMode "rotate slab"

> volume #2 orthoplanes xyz positionPlanes 150,150,150 style image region all

> mousemode rightMode "move planes"

> volume region all imageMode "full region"

> volume unzone

> mousemode rightMode "crop volume"

> volume style surface

> save /Users/jeremykeown/Desktop/nuc_density.cxs

> save /Users/jeremykeown/Desktop/nuc_density.cxs includeMaps true

——— End of log from Tue May 2 15:41:28 2023 ———

opened ChimeraX session  

> lighting full

[Repeated 1 time(s)]

> lighting soft

[Repeated 4 time(s)]

> select add #1

10596 atoms, 10841 bonds, 4 pseudobonds, 1306 residues, 2 models selected  

> hide sel cartoons

[Repeated 1 time(s)]

> show sel cartoons




OpenGL version: 4.1 INTEL-20.5.7
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics OpenGL Engine
OpenGL vendor: Intel Inc.

Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro16,2
      Processor Name: Quad-Core Intel Core i5
      Processor Speed: 2 GHz
      Number of Processors: 1
      Total Number of Cores: 4
      L2 Cache (per Core): 512 KB
      L3 Cache: 6 MB
      Hyper-Threading Technology: Enabled
      Memory: 16 GB
      System Firmware Version: 1968.100.17.0.0 (iBridge: 20.16.4252.0.0,0)
      OS Loader Version: 577~129

Software:

    System Software Overview:

      System Version: macOS 13.3.1 (22E261)
      Kernel Version: Darwin 22.4.0
      Time since boot: 1 hour, 17 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
        DELL UP2716D:
          Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition)
          UI Looks like: 2560 x 1440 @ 60.00Hz
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Display Serial Number: 533P40BJ126L
          Mirror: Off
          Online: Yes
          Rotation: Supported
          Connection Type: DVI or HDMI
          Adapter Firmware Version: 7.59


Installed Packages:
    alabaster: 0.7.13
    appdirs: 1.4.4
    appnope: 0.1.3
    asttokens: 2.2.1
    Babel: 2.12.1
    backcall: 0.2.0
    beautifulsoup4: 4.11.2
    blockdiag: 3.0.0
    build: 0.10.0
    certifi: 2021.10.8
    cftime: 1.6.2
    charset-normalizer: 3.1.0
    ChimeraX-AddCharge: 1.5.9.1
    ChimeraX-AddH: 2.2.4
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.3.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.9.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.3
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.43.10
    ChimeraX-AtomicLibrary: 10.0.6
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3.2
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.1
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.8
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.2
    ChimeraX-ChangeChains: 1.0.2
    ChimeraX-CheckWaters: 1.3.1
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.3
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.6rc202304272016
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.4.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2
    ChimeraX-DistMonitor: 1.4
    ChimeraX-DockPrep: 1.1.1
    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: 1.2.1
    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-Label: 1.1.7
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.2
    ChimeraX-Map: 1.1.4
    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: 2.0.12
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.12
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.9
    ChimeraX-ModelPanel: 1.3.7
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.0
    ChimeraX-NRRD: 1.0
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.10.1
    ChimeraX-PDB: 2.7.2
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 3.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.1
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.8.3
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.1
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.10.3
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1.2
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Topography: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.28.4
    ChimeraX-uniprot: 2.2.2
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.1
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.1.3
    contourpy: 1.0.7
    cxservices: 1.2.2
    cycler: 0.11.0
    Cython: 0.29.33
    debugpy: 1.6.7
    decorator: 5.1.1
    docutils: 0.19
    executing: 1.2.0
    filelock: 3.9.0
    fonttools: 4.39.3
    funcparserlib: 1.0.1
    grako: 3.16.5
    h5py: 3.8.0
    html2text: 2020.1.16
    idna: 3.4
    ihm: 0.35
    imagecodecs: 2022.9.26
    imagesize: 1.4.1
    importlib-metadata: 6.6.0
    ipykernel: 6.21.1
    ipython: 8.10.0
    ipython-genutils: 0.2.0
    ipywidgets: 8.0.6
    jedi: 0.18.2
    Jinja2: 3.1.2
    jupyter-client: 8.0.2
    jupyter-core: 5.3.0
    jupyterlab-widgets: 3.0.7
    kiwisolver: 1.4.4
    line-profiler: 4.0.2
    lxml: 4.9.2
    lz4: 4.3.2
    MarkupSafe: 2.1.2
    matplotlib: 3.6.3
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.6
    netCDF4: 1.6.2
    networkx: 2.8.8
    nibabel: 5.0.1
    nptyping: 2.5.0
    numexpr: 2.8.4
    numpy: 1.23.5
    openvr: 1.23.701
    packaging: 21.3
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 9.3.0
    pip: 23.0
    pkginfo: 1.9.6
    platformdirs: 3.5.0
    prompt-toolkit: 3.0.38
    psutil: 5.9.4
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.14.0
    pynrrd: 1.0.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    pyproject-hooks: 1.0.0
    PyQt6-commercial: 6.4.2
    PyQt6-Qt6: 6.4.3
    PyQt6-sip: 13.4.1
    PyQt6-WebEngine-commercial: 6.4.0
    PyQt6-WebEngine-Qt6: 6.4.3
    python-dateutil: 2.8.2
    pytz: 2023.3
    pyzmq: 25.0.2
    qtconsole: 5.4.0
    QtPy: 2.3.1
    RandomWords: 0.4.0
    requests: 2.28.2
    scipy: 1.9.3
    setuptools: 67.4.0
    setuptools-scm: 7.0.5
    sfftk-rw: 0.7.3
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.4.1
    sphinx: 6.1.3
    sphinx-autodoc-typehints: 1.22
    sphinxcontrib-applehelp: 1.0.4
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.1
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    stack-data: 0.6.2
    tables: 3.7.0
    tcia-utils: 1.2.0
    tifffile: 2022.10.10
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.3.1
    traitlets: 5.9.0
    typing-extensions: 4.5.0
    tzdata: 2023.3
    urllib3: 1.26.15
    wcwidth: 0.2.6
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.7
    zipp: 3.15.0
File attachment: Screenshot 2023-05-02 at 15.37.07.png

Screenshot 2023-05-02 at 15.37.07.png​

[jeremy@…]

Added by email2trac

[Eric Pettersen]

Hi Jeremy,

Thanks for reporting this problem. It is a known problem with the graphics of that particular Mac model. The only "solutions" are to not use silhouettes or use another Mac. Sorry!

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

info from previous tickets:

The incorrect silhouette edge display in ChimeraX is caused by defective Apple Intel graphics driver in your specific laptop model MacBookPro16,2. It has been reported many times. Only Apple could fix that. They won't fix it because they've replaced Intel graphics with their Apple Silicon chips. Sorry I have no solution, other than use a different computer, or just don't use silhouette edges.

Here are details from the previous report ticket #5129:

Several people have reported this bug, tickets #4768, #4628, #4541, #4273. All reports are on the exact same MacBookPro16,2 model with Intel graphics. It appears to be a bug in the Mac OpenGL graphics driver that effects only this one model of Mac. Unfortunately Apple has no interest in improving their graphics drivers for the community standard OpenGL library, they deprecated OpenGL a few years ago when Mac switched to their proprietary Metal graphics. Only Apple can fix this. In working many hours with previous reporters we did not find any way to work around the graphics driver bug. Sorry to say but the only solution to get functioning ChimeraX graphics is to use a different computer. Another option is to use our older Chimera program which uses a much older generation OpenGL and does not seem to have this problem.

I believe this problem was only observed in past reports when silhouette edges were being used. If that is the case for you the best solution is to not use silhouettes.