Log blank

[Andrew.Petter@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.19045
ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC)
Description
The log window is blank and nothing appears after I try to run a command. (I am new to ChimeraX, but have played around with it for a few days without success. Though I cannot rule out a silly mistake.) I wanted to report it in case more information would be helpful, but do not need a fix.

I stumbled upon this and have tried everything stated in it: https://plato.cgl.ucsf.edu/pipermail/chimerax-users/2023-January/004799.html

I have installed updated drivers, reinstalled chimeraX 1.9, and have access to the User Guide.

I am using the log save function for now, which is more than adequate for my needs. (I discovered this through the following: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/thread/EK34B4NPSMG2CUV6K52JZHJL24BBHE23/)

Log:
> rmsd #1/A: 6-55, 63-138@ca,n to #2/A: 1-50, 67-142@ca,n

RMSD between 252 atom pairs is 1.239  

> log save "C:/Users/Andrew/OneDrive - The University of Texas at
> Dallas/Desktop/test log 2"




OpenGL version: 3.3.0 - Build 26.20.100.7985
OpenGL renderer: Intel(R) UHD Graphics 620
OpenGL vendor: Intel

Python: 3.11.4
Locale: en_US.cp1252
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: windows

Manufacturer: LENOVO
Model: 81N8
OS: Microsoft Windows 10 Home (Build 19045)
Memory: 8,394,625,024
MaxProcessMemory: 137,438,953,344
CPU: 8 Intel(R) Core(TM) i7-8565U CPU @ 1.80GHz
OSLanguage: en-US

Installed Packages:
    alabaster: 1.0.0
    anyio: 4.7.0
    appdirs: 1.4.4
    asttokens: 3.0.0
    auditwheel: 6.1.0
    babel: 2.16.0
    beautifulsoup4: 4.12.3
    blockdiag: 3.0.0
    blosc2: 3.0.0
    build: 1.2.1
    certifi: 2024.8.30
    cftime: 1.6.4.post1
    charset-normalizer: 3.4.0
    ChimeraX-AddCharge: 1.5.18
    ChimeraX-AddH: 2.2.6
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.5
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.16.1
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.58.8
    ChimeraX-AtomicLibrary: 14.1.11
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 3.0.0
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.13.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.4.0
    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: 2.3
    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: 1.9
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.4
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2.6
    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: 1.4.1
    ChimeraX-Hbonds: 2.5
    ChimeraX-Help: 1.3
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.3
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-KVFinder: 1.2.1
    ChimeraX-Label: 1.1.14
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.3
    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: 2.1.6
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.7.2
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.14.2
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.18
    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-MutationScores: 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: 1.14
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.6
    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: 1.1.2
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.6.2
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.3.1
    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: 3.5.6
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.14
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.2.0
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-SimilarStructures: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.18.1
    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: 1.2.3
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.41
    ChimeraX-Umap: 1.0
    ChimeraX-uniprot: 2.3.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.4
    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
    comtypes: 1.4.5
    contourpy: 1.3.1
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.0.10
    debugpy: 1.8.9
    decorator: 5.1.1
    docutils: 0.21.2
    executing: 2.1.0
    filelock: 3.15.4
    fonttools: 4.55.3
    funcparserlib: 2.0.0a0
    glfw: 2.8.0
    grako: 3.16.5
    h11: 0.14.0
    h5py: 3.12.1
    html2text: 2024.2.26
    httpcore: 1.0.7
    httpx: 0.28.1
    idna: 3.10
    ihm: 1.3
    imagecodecs: 2024.6.1
    imagesize: 1.4.1
    ipykernel: 6.29.5
    ipython: 8.26.0
    ipywidgets: 8.1.5
    jedi: 0.19.1
    Jinja2: 3.1.4
    jupyter_client: 8.6.2
    jupyter_core: 5.7.2
    jupyterlab_widgets: 3.0.13
    kiwisolver: 1.4.7
    line_profiler: 4.1.3
    lxml: 5.2.2
    lz4: 4.3.3
    MarkupSafe: 3.0.2
    matplotlib: 3.9.2
    matplotlib-inline: 0.1.7
    msgpack: 1.0.8
    ndindex: 1.9.2
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.10.2
    numpy: 1.26.4
    openvr: 1.26.701
    packaging: 23.2
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pillow: 10.4.0
    pip: 24.2
    pkginfo: 1.11.1
    platformdirs: 4.3.6
    prompt_toolkit: 3.0.48
    psutil: 6.0.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    pyelftools: 0.31
    Pygments: 2.18.0
    pynmrstar: 3.3.4
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.3401
    pyparsing: 3.2.0
    pyproject_hooks: 1.2.0
    PyQt6-commercial: 6.7.1
    PyQt6-Qt6: 6.7.3
    PyQt6-WebEngine-commercial: 6.7.0
    PyQt6-WebEngine-Qt6: 6.7.3
    PyQt6-WebEngineSubwheel-Qt6: 6.7.3
    PyQt6_sip: 13.8.0
    python-dateutil: 2.9.0.post0
    pytz: 2024.2
    pywin32: 306
    pyzmq: 26.2.0
    qtconsole: 5.5.2
    QtPy: 2.4.2
    qtshim: 1.0
    RandomWords: 0.4.0
    requests: 2.32.3
    scipy: 1.14.0
    setuptools: 72.1.0
    sfftk-rw: 0.8.1
    six: 1.16.0
    sniffio: 1.3.1
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.6
    Sphinx: 8.0.2
    sphinx-autodoc-typehints: 2.2.3
    sphinxcontrib-applehelp: 2.0.0
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 2.0.0
    sphinxcontrib-htmlhelp: 2.1.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 2.0.0
    sphinxcontrib-serializinghtml: 2.0.0
    stack-data: 0.6.3
    superqt: 0.6.3
    tables: 3.10.1
    tcia_utils: 1.5.1
    tifffile: 2024.7.24
    tinyarray: 1.2.4
    tornado: 6.4.2
    traitlets: 5.14.3
    typing_extensions: 4.12.2
    tzdata: 2024.2
    urllib3: 2.2.3
    wcwidth: 0.2.13
    webcolors: 24.6.0
    wheel: 0.43.0
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.13
    WMI: 1.5.1
File attachment: bug report - blank log.JPG

bug report - blank log.JPG​

[Andrew.Petter@…]

Added by email2trac

[Tom Goddard]

I sometimes see ChimeraX on Windows show the Log as all black. I suspect that is a bug in the Qt window toolkit. But it could be caused by your Intel graphics driver. ChimeraX shows in this report you are using

OpenGL version: 3.3.0 - Build 26.20.100.7985

That driver version is from 2020 so is quite old. Often laptop vendors don't provide updated graphics drivers but perhaps you can get a newer driver from Intel. The fact that the ChimeraX Help window works and is the same kind of html window as the Log suggests it probably isn't the driver.

When I see the all black Log I think dragging the Log panel title bar out of the application so the Log is a separate floating window fixes it, or resizing the panel by dragging the lower or left edge of the log fixes it. Do either of those solutions make your Log display correctly?

If resizing the Log panel does not make it show the Log text then I think it is likely your old Intel graphics driver is the problem (and somehow the Log is different from the Help window). In that case only updating your Intel graphics driver will fix it.

[Andrew.Petter@…]

I am unable to drag the log panel out (like I would be able to drag the command history or the model panel to get a separate window). The log window itself does not have a title bar to drag (while other tools do), it is just a blank box.

It is also not possible to resize the log window while it is shown. To get the log window to show I have to have it share a window with the command history. The other tools can only be resized when the log panel is hidden.

I will look into getting a newer driver. I will send an update if I have any luck (though, since I can still make use of the program for the little I need it for, it will likely not be a priority on my end).

I appreciate your detailed reply and help!
Andrew

-----Original Message-----
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: Monday, April 21, 2025 3:12 PM
To: goddard@cgl.ucsf.edu; Petter, Andrew Thomas <Andrew.Petter@utdallas.edu>
Cc: gregc@cgl.ucsf.edu
Subject: Re: [ChimeraX] #17429: Log blank

#17429: Log blank
--------------------------------------+-------------------------
          Reporter:  Andrew.Petter@...  |      Owner:  Tom Goddard
              Type:  defect           |     Status:  closed
          Priority:  normal           |  Milestone:
         Component:  UI               |    Version:
        Resolution:  can't reproduce  |   Keywords:
        Blocked By:                   |   Blocking:
Notify when closed:                   |   Platform:  all
           Project:  ChimeraX         |
--------------------------------------+-------------------------
Changes (by Tom Goddard):

 * resolution:   => can't reproduce
 * status:  assigned => closed

Comment:

 I sometimes see ChimeraX on Windows show the Log as all black.  I suspect  that is a bug in the Qt window toolkit.  But it could be caused by your  Intel graphics driver.  ChimeraX shows in this report you are using

     OpenGL version: 3.3.0 - Build 26.20.100.7985

 That driver version is from 2020 so is quite old.  Often laptop vendors  don't provide updated graphics drivers but perhaps you can get a newer  driver from Intel.  The fact that the ChimeraX Help window works and is  the same kind of html window as the Log suggests it probably isn't the  driver.

 When I see the all black Log I think dragging the Log panel title bar out  of the application so the Log is a separate floating window fixes it, or  resizing the panel by dragging the lower or left edge of the log fixes it.
 Do either of those solutions make your Log display correctly?

 If resizing the Log panel does not make it show the Log text then I think  it is likely your old Intel graphics driver is the problem (and somehow  the Log is different from the Help window).  In that case only updating  your Intel graphics driver will fix it.
--
Ticket URL: <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/17429#comment:2>
ChimeraX <https://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker

[Tom Goddard]

It is very strange that the Log does not have a title bar. If you right click on the blank Log does it popup a context menu? If so it will have a menu entry "Dockable Tool" and if you uncheck that it should make the Log panel a separate window which I think must have a title bar and could possibly be resized.

In any case the Log is an HTML window provided by the Qt window toolkit, and Qt implements this in a very flakey way where each HTML window is rendered by a separate process (you might see those processes in Windows TaskManager). Something apparently is going wrong with Qt's HTML rendering. It works on other people's Windows machines, so there is something about your machine, quite possibly the graphics driver that prevents it from working. The ChimeraX Help window is also a Qt HTML window which should be broken in the same way, but the help window appears as a separate window while the Log by default is docked into the ChimeraX main window. That is why I think if you got the Log to be a separate window it is likely to work. Still the underlying problem is something about your Windows system, probably the graphics driver since the HTML is I believe rendered using OpenGL graphics (it uses the Chromium html renderer, a separate project from Qt).

Sorry I don't have better suggestions. The problem is an interaction between your Windows machine configuration and Qt which we don't develop. It is not caused by ChimeraX code. The Qt window toolkit is a massive project, much bigger than the ChimeraX project and we don't have ways to debug Qt.

[Tom Goddard]

By the way, if you are able to unclick "Dockable Tool" that setting is remembered so each time you start ChimeraX the Log will be in a separate window. So if the Log works correctly in a separate window that could be a usable work-around for your problem.

[Andrew.Petter@…]

You were right about the graphics drivers! I downloaded new drivers directly from Intel and everything seems to be working well. I can see outputs in the log and move the log panel around now without issue.

(As for before, a context menu did not appear after right clicking the log panel.)

Thanks again for your help! I'll be sure to remember to manually install driver updates on my old laptops in the future (and not assume they are up to date when device manager says they are).
Andrew

[Tom Goddard]

Excellent! Glad you got it to work. Sadly most laptop vendors update their graphics driver, so the driver just stays at whatever version it had when the computer model was released. If that driver has some bugs then you have to get drivers from the graphics manufacturer (Intel, Nvidia, AMD). Sometimes those graphics drivers don't play entirely nice with the energy saving features of the laptop, but I have not run into that problem so probably it is rare.