Selection outline invisible on segmentations

[hagelueken@…]

The following bug report has been submitted:
Platform:        Darwin-20.2.0-x86_64-i386-64bit
ChimeraX Version: 1.1.1 (2020-10-07 08:32:49 UTC)
Description
Hi, I have segmented a map with Segger and would like to select the segements to group them. With Chimera, I can see a green outline around the segments. In ChimeraX the green outline is invisible. The selection seems to work though. If do the selection blindly, I can group segements. (Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.1.1 (2020-10-07)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Volumes/isb-
> data/1_lab_members/Hochheiser_Inga/masks_multibody/octamer.mrc

Opened octamer.mrc, grid size 256,256,256, pixel 1.29, shown at level 0.0152,
step 1, values float32  

> volume #1 level 0.01759

> vop gaussian #1 sdev 3.87

> volume #2 level 0.008364

> save
> /Users/gha/Documents/uni/projects/nlrp3_decamer/heidelberg2/octamer_gaussian.mrc
> models #2

> volume #2 level 0.00838

> open
> /Users/gha/Documents/uni/projects/nlrp3_decamer/heidelberg2/MultiBody/run_it008_half1_body001.mrc

Opened run_it008_half1_body001.mrc, grid size 256,256,256, pixel 1.29, shown
at level 0.013, step 1, values float32  

> open
> /Users/gha/Documents/uni/projects/nlrp3_decamer/heidelberg2/MultiBody/run_it008_half1_body002.mrc

Opened run_it008_half1_body002.mrc, grid size 256,256,256, pixel 1.29, shown
at level 0.00465, step 1, values float32  

> open
> /Users/gha/Documents/uni/projects/nlrp3_decamer/heidelberg2/MultiBody/run_it008_half2_body001.mrc

Opened run_it008_half2_body001.mrc, grid size 256,256,256, pixel 1.29, shown
at level 0.013, step 1, values float32  

> open
> /Users/gha/Documents/uni/projects/nlrp3_decamer/heidelberg2/MultiBody/run_it008_half2_body002.mrc

Opened run_it008_half2_body002.mrc, grid size 256,256,256, pixel 1.29, shown
at level 0.00466, step 1, values float32  

> volume #4 level 0.01162

> volume #4 level 0.01192

> hide #!2 models

> volume #4 level 0.01118

> volume #6 level 0.01292

> volume #3 level 0.01173

> open
> /Users/gha/Documents/uni/projects/nlrp3_decamer/heidelberg2/3DRefine/run_class001.mrc

Opened run_class001.mrc, grid size 256,256,256, pixel 1.29, shown at level
0.0134, step 1, values float32  

> volume #7 level 0.008112

> ui tool show "Segment Map"

Segmenting run_class001.mrc, density threshold 0.008112  
Showing run_class001.seg - 0 regions, 0 surfaces  
Only showing 60 of 75 regions.  
Showing 60 of 75 region surfaces  
787 watershed regions, grouped to 75 regions  
Segmenting run_class001.mrc, density threshold 0.008112  
Showing run_class001.seg - 0 regions, 0 surfaces  
Showing 22 region surfaces  
787 watershed regions, grouped to 22 regions  
Segmenting run_class001.mrc, density threshold 0.008112  
Showing run_class001.seg - 0 regions, 0 surfaces  
Only showing 60 of 75 regions.  
Showing 60 of 75 region surfaces  
787 watershed regions, grouped to 75 regions  




OpenGL version: 4.1 ATI-4.2.13
OpenGL renderer: AMD Radeon Pro 5500M OpenGL Engine
OpenGL vendor: ATI Technologies Inc.Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro16,1
      Processor Name: 8-Core Intel Core i9
      Processor Speed: 2,4 GHz
      Number of Processors: 1
      Total Number of Cores: 8
      L2 Cache (per Core): 256 KB
      L3 Cache: 16 MB
      Hyper-Threading Technology: Enabled
      Memory: 16 GB
      System Firmware Version: 1554.60.15.0.0 (iBridge: 18.16.13030.0.0,0)

Software:

    System Software Overview:

      System Version: macOS 11.1 (20C69)
      Kernel Version: Darwin 20.2.0
      Time since boot: 1 day 3:27

Graphics/Displays:

    Intel UHD Graphics 630:

      Chipset Model: Intel UHD Graphics 630
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x3e9b
      Revision ID: 0x0002
      Automatic Graphics Switching: Supported
      gMux Version: 5.0.0
      Metal Family: Supported, Metal GPUFamily macOS 2

    AMD Radeon Pro 5500M:

      Chipset Model: AMD Radeon Pro 5500M
      Type: GPU
      Bus: PCIe
      PCIe Lane Width: x8
      VRAM (Total): 8 GB
      Vendor: AMD (0x1002)
      Device ID: 0x7340
      Revision ID: 0x0040
      ROM Revision: 113-D3220E-190
      VBIOS Version: 113-D32206U1-019
      Option ROM Version: 113-D32206U1-019
      EFI Driver Version: 01.A1.190
      Automatic Graphics Switching: Supported
      gMux Version: 5.0.0
      Metal Family: Supported, Metal GPUFamily macOS 2
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 3072 x 1920 Retina
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal
        DELL U3818DW:
          Resolution: 3840 x 1600 (Ultra-wide 4K)
          UI Looks like: 3840 x 1600 @ 60.00Hz
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Display Serial Number: 5KC038CE0FRL
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Rotation: Supported
          Automatically Adjust Brightness: No
          Connection Type: Thunderbolt/DisplayPort
          Television: Yes

PyQt version: 5.12.3
Compiled Qt version: 5.12.4
Runtime Qt version: 5.12.9
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    appnope: 0.1.0
    Babel: 2.8.0
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2020.6.20
    chardet: 3.0.4
    ChimeraX-AddH: 2.1.3
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.1
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.6.1
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 1.0.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.0
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.0
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.1
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.0
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-CommandLine: 1.1.3
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.1.1
    ChimeraX-CoreFormats: 1.0
    ChimeraX-coulombic: 1.0.1
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-DataFormats: 1.0
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1
    ChimeraX-DistUI: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.1
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.0
    ChimeraX-Hbonds: 2.0
    ChimeraX-Help: 1.0
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.0
    ChimeraX-ImageFormats: 1.0
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0
    ChimeraX-Label: 1.0
    ChimeraX-ListInfo: 1.0
    ChimeraX-Log: 1.1.1
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Map: 1.0.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.0
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 1.1
    ChimeraX-MDcrds: 2.0
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.0
    ChimeraX-mmCIF: 2.2
    ChimeraX-MMTF: 2.0
    ChimeraX-Modeller: 1.0
    ChimeraX-ModelPanel: 1.0
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.0
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0
    ChimeraX-OpenCommand: 1.2.1
    ChimeraX-PDB: 2.1
    ChimeraX-PDBBio: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0
    ChimeraX-PubChem: 2.0
    ChimeraX-Read-Pbonds: 1.0
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.0
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.2
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SeqView: 2.2
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.0
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.0
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.0.4
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.0
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.0
    ChimeraX-ToolshedUtils: 1.0
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.2.3
    ChimeraX-uniprot: 2.0
    ChimeraX-ViewDockX: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.3
    comtypes: 1.1.7
    cxservices: 1.0
    cycler: 0.10.0
    Cython: 0.29.20
    decorator: 4.4.2
    distlib: 0.3.1
    docutils: 0.16
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 2.10.0
    html2text: 2020.1.16
    idna: 2.10
    ihm: 0.16
    imagecodecs: 2020.5.30
    imagecodecs-lite: 2020.1.31
    imagesize: 1.2.0
    ipykernel: 5.3.0
    ipython: 7.15.0
    ipython-genutils: 0.2.0
    jedi: 0.17.2
    Jinja2: 2.11.2
    jupyter-client: 6.1.3
    jupyter-core: 4.6.3
    kiwisolver: 1.2.0
    line-profiler: 2.1.2
    lxml: 4.5.1
    MarkupSafe: 1.1.1
    matplotlib: 3.2.1
    msgpack: 1.0.0
    netifaces: 0.10.9
    networkx: 2.4
    numexpr: 2.7.1
    numpy: 1.18.5
    numpydoc: 1.0.0
    openvr: 1.12.501
    packaging: 20.4
    parso: 0.7.1
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 7.1.2
    pip: 20.2.2
    pkginfo: 1.5.0.1
    prompt-toolkit: 3.0.7
    psutil: 5.7.0
    ptyprocess: 0.6.0
    pycollada: 0.7.1
    pydicom: 2.0.0
    Pygments: 2.6.1
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 2.4.7
    PyQt5-commercial: 5.12.3
    PyQt5-sip: 4.19.19
    PyQtWebEngine-commercial: 5.12.1
    python-dateutil: 2.8.1
    pytz: 2020.1
    pyzmq: 19.0.2
    qtconsole: 4.7.4
    QtPy: 1.9.0
    RandomWords: 0.3.0
    requests: 2.24.0
    scipy: 1.4.1
    setuptools: 49.4.0
    sfftk-rw: 0.6.6.dev0
    six: 1.15.0
    snowballstemmer: 2.0.0
    sortedcontainers: 2.2.2
    Sphinx: 3.1.1
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 1.0.3
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.4
    suds-jurko: 0.6
    tables: 3.6.1
    tifffile: 2020.6.3
    tinyarray: 1.2.2
    tornado: 6.0.4
    traitlets: 5.0.4
    urllib3: 1.25.10
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.34.2

[pett]

Reported by Gregor Hagelueken

[Tom Goddard]

This sounds like a macOS graphics driver bug. If that is the problem I would expect no objects show a green selection outline. Is the green outline shown if you you select your MRC map surface?

You can see in the Log panel when you select a volume it shows the equivalent command, e.g. "select #1". It does not show a command for selecting a segmentation segment I guess because there is no command that does that (no way to name the segment).

I tried selecting a segmentation surface (open 1547 from emdb, segment, ctrl-click segment) with the same version of ChimeraX (1.1.1) on macOS 11.2 and the green outline is shown. My machine had different graphics AMD Radeon Pro 580.

[Tom Goddard]

I see you have two displays. Does the green outline appear if you run ChimeraX without a second display? Maybe the graphics driver has trouble with the external display. Not likely, but worth trying.

[hagelueken@…]

Hi,

Thanks for your help!
Here is an example when I select a molecule. It also looks weird and the green boxes change all the time when I rotate the view.

Cheers,
Gregor

-----
PD Dr. Gregor Hagelueken
Institute of Structural Biology

Biomedical Center (BMZ)
Building 13, Rm 2G 022/023
University of Bonn
Venusberg Campus 1
53127 Bonn, Germany

Phone: +49 228 287-51200

WWW:  http://www.isb.uni-bonn.de/
-----
On 11. Feb 2021, 23:59 +0100, ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>, wrote:

[hagelueken@…]

Added by email2trac

[Tom Goddard]

So selection outlines are messed up. This is probably because the Apple graphics driver is doing something very unusual, giving incompatible offscreen and onscreen framebuffers. The green outline is rendered offscreen and then copied to the screen. It might have to do with differences in multisampling. You can make ChimeraX render everything (models and outlines) offscreen and then copy to the screen with this ChimeraX command

graphics quality colorDepth 16

If you use that command and then select do the outlines appear correct?

[hagelueken@…]

Hi Tom,

Cool, that works!

Thanks and have a nice WE,
Gregor

-----
PD Dr. Gregor Hagelueken
Institute of Structural Biology

Biomedical Center (BMZ)
Building 13, Rm 2G 022/023
University of Bonn
Venusberg Campus 1
53127 Bonn, Germany

Phone: +49 228 287-51200

WWW:  http://www.isb.uni-bonn.de/
-----
On 12. Feb 2021, 20:14 +0100, ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>, wrote:

[goddard@…]

Ok, I have put a fix in so ChimeraX will automatically use the offscreen mode when drawing selection outlines for macOS with AMD Radeon Pro 5500M graphics.  So if you use tonight's ChimeraX daily build or newer you will not have to use the colorDepth trick to fix the outlines, they will just work.