glClear: invalid framebuffer operation

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.3.dev202110221141 (2021-10-22 11:41:52 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.3.dev202110221141 (2021-10-22)  
© 2016-2021 Regents of the University of California. All rights reserved.  

> open "/Users/popwongpalee/Downloads/best_VgrG5 CT.cxs"

Log from Sun Oct 24 17:37:30 2021UCSF ChimeraX version: 1.3.dev202110221141
(2021-10-22)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> ui tool show AlphaFold

> alphafold predict
> NDSASTLLQTLHKQSATGAIRLSAGQDASALLQKQLDKLKGTVRKFMIVSGLANAGSAAAAAGLIKGGGKLADLPWAGFGISAAQFAGATGVSTALMATSRTLLANVAKLQEALPLVADLSLGKQGIALAAKNLTHATRMSLTVDGVSWSTHAKGPGAAGAAMSVGKGRWGVEAAKHAHVHASDTLLFAVPADPTTQFDLKDLIGLRRDLDECMKDIADLEADISENEVLSTDQNTFGVSALIPTPPSPAGALAAVAIKVKQAKLVELKAKQKLVALKVDNLQQKFAKHVQHLSAVRMSASDAQLGFKGNRLVATADGVTLAHAQGKAKLDVREAKIGVTAGKSSVELDEGKIAAGCGSASLKLGSDGAIDVSATDVKLNGTNVKLNGSASLKFDGQLIQLG

Running AlphaFold prediction  
Chain information for best_model.pdb #1  
---  
Chain | Description  
A | No description available  
  
AlphaFold prediction finished  
Results in /Users/Pop/Downloads/ChimeraX/AlphaFold/prediction_1  

> select clear

> hbonds reveal true

237 hydrogen bonds found  

> coulombic

Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for best_model.pdb_A SES surface #1.2: minimum, -13.99, mean
1.01, maximum 19.76  
To also show corresponding color key, enter the above coulombic command and
add key true  

> hide #1.1 models

> hide #1.2 models

> show #1.1 models

> mlp

Map values for surface "best_model.pdb_A SES surface": minimum -28.34, mean
-2.766, maximum 24.63  
To also show corresponding color key, enter the above mlp command and add key
true  

> mlp

Map values for surface "best_model.pdb_A SES surface": minimum -28.34, mean
-2.766, maximum 24.63  
To also show corresponding color key, enter the above mlp command and add key
true  

> hide #1.2 models

> show #1.2 models

> hide #1.2 models

> show #1.2 models

> hide #1.2 models

> show #1.2 models

> hide #1.2 models

> save /Users/Pop/Downloads/ChimeraX/AlphaFold/prediction_1/best_model.cxs

——— End of log from Sun Oct 24 17:37:30 2021 ———

opened ChimeraX session  

> open "/Users/popwongpalee/Downloads/ChimeraX/AlphaFold/VgrG5 CT-
> PAAR5/best_model.pdb"

Chain information for best_model.pdb #2  
---  
Chain | Description  
A | No description available  
  

> ui tool show Matchmaker

> matchmaker #2 to #1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker best_model.pdb, chain A (#1) with best_model.pdb, chain A (#2),
sequence alignment score = 1685.4  
RMSD between 37 pruned atom pairs is 1.323 angstroms; (across all 402 pairs:
17.098)  
  

> select #1

5879 atoms, 5911 bonds, 237 pseudobonds, 402 residues, 2 models selected  

> ~select #1

1 model selected  

> select #1

5879 atoms, 5911 bonds, 237 pseudobonds, 402 residues, 2 models selected  

> hide #1.1 models

> select clear

Alignment identifier is 1/A  
Alignment identifier is 2/A  

> select
> #2/A:2-16,28-53,58-63,77-79,83-86,91-120,194-234,249-292,477-479,550-552

2680 atoms, 2682 bonds, 175 residues, 1 model selected  

> select #1/A:2-16,28-49,58-64,77-82,84-86,94-119,126-133,196-231,249-291

2565 atoms, 2565 bonds, 139 pseudobonds, 166 residues, 2 models selected  

> select clear

> select
> #2/A:2-16,28-53,58-63,77-79,83-86,91-120,194-234,249-292,477-479,550-552

2680 atoms, 2682 bonds, 175 residues, 1 model selected  

> select
> #2/A:185-190,294-299,304-307,310-315,318-322,328-333,336-341,344-349,352-357,360-364,370-373,450-453,456-462,465-471,473-475,546-549,554-560

1366 atoms, 1358 bonds, 92 residues, 1 model selected  

> select clear

> ui mousemode right translate

> hide #!1 models

> show #!1 models

> hide #2 models

> select
> #1/A:140-144,147-153,159-165,311-315,318-322,361-364,370-373,377-379,382-384

640 atoms, 634 bonds, 25 pseudobonds, 43 residues, 2 models selected  

> show #2 models

> select
> #2/A:185-190,294-299,304-307,310-315,318-322,328-333,336-341,344-349,352-357,360-364,370-373,450-453,456-462,465-471,473-475,546-549,554-560

1366 atoms, 1358 bonds, 92 residues, 1 model selected  

> help help:user/tools/modelpanel.html

> rename #2 VgrG5 CT-PAAR

Expected a keyword  

> rename #2 VgrG5CT-PAAR

> rename #1 VgrG5CT

> select clear

> save "/Users/popwongpalee/Downloads/ChimeraX/AlphaFold/VgrG5 CT-
> PAAR5/best_VgrG5CT-PAAR5.cxs"

> rename #2 VgrG5CT-PAAR5

> save "/Users/popwongpalee/Downloads/ChimeraX/AlphaFold/VgrG5 CT-
> PAAR5/best_VgrG5CT-PAAR5.cxs"

> hide #!1 models

> mlp #2

Map values for surface "VgrG5CT-PAAR5_A SES surface": minimum -27.41, mean
-3.5, maximum 25.47  
To also show corresponding color key, enter the above mlp command and add key
true  

> select
> #2/A:185-190,294-299,304-307,310-315,318-322,328-333,336-341,344-349,352-357,360-364,370-373,450-453,456-462,465-471,473-475,546-549,554-560

1366 atoms, 1358 bonds, 92 residues, 1 model selected  

> hide #2.1 models

> show #2.1 models

> hide #2.1 models

> select clear

> select #2/A:182

10 atoms, 9 bonds, 1 residue, 1 model selected  

> select #2/A:182-184

33 atoms, 32 bonds, 3 residues, 1 model selected  

> select #2/A:177

17 atoms, 17 bonds, 1 residue, 1 model selected  

> select #2/A:177-184

110 atoms, 112 bonds, 8 residues, 1 model selected  

> show #2.1 models

> hide #2.1 models

> select
> #2/A:185-190,294-299,304-307,310-315,318-322,328-333,336-341,344-349,352-357,360-364,370-373,450-453,456-462,465-471,473-475,546-549,554-560

1366 atoms, 1358 bonds, 92 residues, 1 model selected  

> select
> #2/A:2-16,28-53,58-63,77-79,83-86,91-120,194-234,249-292,477-479,550-552

2680 atoms, 2682 bonds, 175 residues, 1 model selected  

> select
> #2/A:185-190,294-299,304-307,310-315,318-322,328-333,336-341,344-349,352-357,360-364,370-373,450-453,456-462,465-471,473-475,546-549,554-560

1366 atoms, 1358 bonds, 92 residues, 1 model selected  

> select #2/A:290

16 atoms, 15 bonds, 1 residue, 1 model selected  

> select #2/A:290-293

69 atoms, 69 bonds, 4 residues, 1 model selected  

> select #2/A:289

17 atoms, 17 bonds, 1 residue, 1 model selected  

> select #2/A:289-293

86 atoms, 87 bonds, 5 residues, 1 model selected  

> open /Users/popwongpalee/Downloads/NP_414878.1.fa

Summary of feedback from opening /Users/popwongpalee/Downloads/NP_414878.1.fa  
---  
note | Alignment identifier is NP_414878.1.fa  
  
Opened 1 sequences from NP_414878.1.fa  
Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/statusbar.py", line 84, in _expose_event  
self.status(self._last_message, self._last_color)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/statusbar.py", line 150, in status  
r.draw_background()  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/graphics/opengl.py", line 1166, in draw_background  
GL.glClear(flags)  
File "src/errorchecker.pyx", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError  
OpenGL.error.GLError: GLError(  
err = 1286,  
description = b'invalid framebuffer operation',  
baseOperation = glClear,  
cArguments = (16640,)  
)  
  
OpenGL.error.GLError: GLError(  
err = 1286,  
description = b'invalid framebuffer operation',  
baseOperation = glClear,  
cArguments = (16640,)  
)  
  
File "src/errorchecker.pyx", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError  
  
See log for complete Python traceback.  
  

Back buffer dpr of 1 doesn't match <_NSViewBackingLayer: 0x6000029178d0>
contents scale of 2 - updating layer to match.  

Back buffer dpr of 2 doesn't match <_NSViewBackingLayer: 0x6000029178d0>
contents scale of 1 - updating layer to match.  




OpenGL version: 4.1 INTEL-16.1.12
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics OpenGL Engine
OpenGL vendor: Intel Inc.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: 1554.80.3.0.0 (iBridge: 18.16.14347.0.0,0)

Software:

    System Software Overview:

      System Version: macOS 11.2.3 (20D91)
      Kernel Version: Darwin 20.3.0
      Time since boot: 54 days 23:41

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 Family: Supported, Metal GPUFamily macOS 2
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2560 x 1600 Retina
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal
        BenQ EW277HDR:
          Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
          UI Looks like: 1920 x 1080 @ 60.00Hz
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Display Serial Number: S7J01523SL0 
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Rotation: Supported
          Adapter Type: DVI or HDMI
          Automatically Adjust Brightness: Yes

Locale: (None, 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    appnope: 0.1.2
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2021.5.30
    cftime: 1.5.1
    charset-normalizer: 2.0.7
    ChimeraX-AddCharge: 1.1.4
    ChimeraX-AddH: 2.1.10
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.2.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.31
    ChimeraX-AtomicLibrary: 4.1.5
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.1
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.0
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.6
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.2
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.1
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5
    ChimeraX-CommandLine: 1.1.5
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.3.dev202110221141
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.1
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.5
    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: 1.1
    ChimeraX-Hbonds: 2.1.2
    ChimeraX-Help: 1.2
    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
    ChimeraX-Label: 1.1
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.4
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 2.0.3
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.4
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.2.3
    ChimeraX-ModelPanel: 1.2
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.2
    ChimeraX-OpenCommand: 1.7
    ChimeraX-PDB: 2.6.4
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.4.5
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.1
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.6
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1
    ChimeraX-ToolshedUtils: 1.2
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.13.6
    ChimeraX-uniprot: 2.2
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.0.1
    ChimeraX-VIPERdb: 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: 0.4.4
    cxservices: 1.1
    cycler: 0.10.0
    Cython: 0.29.24
    decorator: 5.1.0
    docutils: 0.17.1
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 3.5.0
    html2text: 2020.1.16
    idna: 3.3
    ihm: 0.21
    imagecodecs: 2021.4.28
    imagesize: 1.2.0
    ipykernel: 5.5.5
    ipython: 7.23.1
    ipython-genutils: 0.2.0
    jedi: 0.18.0
    Jinja2: 3.0.1
    jupyter-client: 6.1.12
    jupyter-core: 4.8.1
    kiwisolver: 1.3.2
    lxml: 4.6.3
    lz4: 3.1.3
    MarkupSafe: 2.0.1
    matplotlib: 3.4.3
    matplotlib-inline: 0.1.3
    msgpack: 1.0.2
    netCDF4: 1.5.7
    networkx: 2.6.3
    numexpr: 2.7.3
    numpy: 1.21.2
    openvr: 1.16.801
    packaging: 21.0
    ParmEd: 3.2.0
    parso: 0.8.2
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 8.3.2
    pip: 21.2.4
    pkginfo: 1.7.1
    prompt-toolkit: 3.0.21
    psutil: 5.8.0
    ptyprocess: 0.7.0
    pycollada: 0.7.1
    pydicom: 2.1.2
    Pygments: 2.10.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 2.4.7
    PyQt5-commercial: 5.15.2
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.2
    python-dateutil: 2.8.2
    pytz: 2021.3
    pyzmq: 22.3.0
    qtconsole: 5.1.1
    QtPy: 1.11.2
    RandomWords: 0.3.0
    requests: 2.26.0
    scipy: 1.7.1
    setuptools: 57.5.0
    sfftk-rw: 0.7.1
    six: 1.16.0
    snowballstemmer: 2.1.0
    sortedcontainers: 2.4.0
    Sphinx: 4.2.0
    sphinx-autodoc-typehints: 1.12.0
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    suds-jurko: 0.6
    tifffile: 2021.4.8
    tinyarray: 1.2.3
    tornado: 6.1
    traitlets: 5.1.0
    urllib3: 1.26.7
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.0
    wheel-filename: 1.3.0

[Tom Goddard]

Drawing a status line message fails. The OpenGL make_current() does not return any error but the first OpenGL call glClear() to draw the background fails with invalid framebuffer operation. I suspect this OpenGL error has something to do with two displays, one a retina display the other not. Immediately following the OpenGL error are messages

Back buffer dpr of 1 doesn't match <_NSViewBackingLayer: 0x6000029178d0>
contents scale of 2 - updating layer to match.

Back buffer dpr of 2 doesn't match <_NSViewBackingLayer: 0x6000029178d0>
contents scale of 1 - updating layer to match.