id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
8933	silhouettes → tiny boxes	jeremy@…	Tom Goddard	"{{{
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

}}}

[attachment:""Screenshot 2023-05-02 at 15.37.07.png""]
"	defect	closed	normal		Graphics		nonchimerax		Eric Pettersen				all	ChimeraX