Log and AlphaFold window are blank, plus various deprecation warnings

[yuliang@…]

The following bug report has been submitted:
Platform:        Linux-5.15.6-200.fc35.x86_64-x86_64-with-glibc2.34
ChimeraX Version: 1.3rc202111292147 (2021-11-29 21:47:39 UTC)
Description
The component in log and AlphaFoldRun window could not show up.

Log:
UCSF ChimeraX version: 1.3rc202111292147 (2021-11-29)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> ui tool show AlphaFold

/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/grako/grammars.py:16:
DeprecationWarning: Using or importing the ABCs from 'collections' instead of
from 'collections.abc' is deprecated since Python 3.3, and in 3.10 it will
stop working  
from collections import defaultdict, Mapping  

> alphafold match p51834

/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/core/fetch.py:336: DeprecationWarning:
distro.linux_distribution() is deprecated. It should only be used as a
compatibility shim with Python's platform.linux_distribution(). Please use
distro.id(), distro.version() and distro.name() instead.  
system = f"{system} {' '.join(distro.linux_distribution())}"  

1 UniProt id does not have an AlphaFold database model: p51834 (UniProt
p51834)  

1 AlphaFold model found using sequence similarity searches: P9WGF3 (UniProt
p51834)  
Sequence Similarity  
---  
AlphaFold Model| Query Sequence| Identity %| Coverage %  
SMC_MYCTU | p51834 | 22.1 | 44.4  
Opened 1 AlphaFold model  
/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/geometry/matrix.py:121: DeprecationWarning: `np.float` is a
deprecated alias for the builtin `float`. To silence this warning, use `float`
by itself. Doing this will not modify any behavior and is safe. If you
specifically wanted the numpy scalar type, use `np.float64` here.  
Deprecated in NumPy 1.20; for more details and guidance:
https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations  
from numpy import array, zeros, float  

> close

/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/core/fetch.py:336: DeprecationWarning:
distro.linux_distribution() is deprecated. It should only be used as a
compatibility shim with Python's platform.linux_distribution(). Please use
distro.id(), distro.version() and distro.name() instead.  
system = f"{system} {' '.join(distro.linux_distribution())}"  
Fetching p51834 UniProt info from https://www.uniprot.org/uniprot/p51834.xml  

> alphafold predict p51834

/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/bug_reporter/bug_reporter_gui.py:718: ResourceWarning:
unclosed file <_io.TextIOWrapper name='/sys/devices/virtual/dmi/id/sys_vendor'
mode='r' encoding='utf-8'>  
vendor = open(dmi_prefix + "sys_vendor", encoding='utf-8').read().strip()  
ResourceWarning: Enable tracemalloc to get the object allocation traceback  
/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/bug_reporter/bug_reporter_gui.py:723: ResourceWarning:
unclosed file <_io.TextIOWrapper
name='/sys/devices/virtual/dmi/id/product_name' mode='r' encoding='utf-8'>  
product = open(dmi_prefix + "product_name", encoding='utf-8').read().strip()  
ResourceWarning: Enable tracemalloc to get the object allocation traceback  
/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/bug_reporter/bug_reporter_gui.py:730: DeprecationWarning:
distro.linux_distribution() is deprecated. It should only be used as a
compatibility shim with Python's platform.linux_distribution(). Please use
distro.id(), distro.version() and distro.name() instead.  
OS: {' '.join(distro.linux_distribution())}  

> alphafold predict p51834

/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/core/fetch.py:336: DeprecationWarning:
distro.linux_distribution() is deprecated. It should only be used as a
compatibility shim with Python's platform.linux_distribution(). Please use
distro.id(), distro.version() and distro.name() instead.  
system = f"{system} {' '.join(distro.linux_distribution())}"  

> open /home/yl2/Downloads/5xg3.pdb

5xg3.pdb title:  
Crystal structure of the atpgs-engaged SMC head domain with an extended coiled
coil bound to the C-terminal domain of SCPA derived from bacillus subtilis
[more info...]  
  
| Chain information for 5xg3.pdb #1  
---  
Chain | Description | UniProt  
A | chromosome partition protein SMC | SMC_BACSU  
B | chromosome partition protein SMC | SMC_BACSU  
C | segregation and condensation protein A |  
D | segregation and condensation protein A |  
  
Non-standard residues in 5xg3.pdb #1  
---  
AGS — phosphothiophosphoric acid-adenylate ester (atp-γ-S; adenosine
5'-(3-thiotriphosphate);adenosine 5'-(γ-thiotriphosphate);
adenosine-5'-diphosphate monothiophosphate)  
CO — cobalt (II) ion  
MG — magnesium ion  
  
/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/geometry/matrix.py:121: DeprecationWarning: `np.float` is a
deprecated alias for the builtin `float`. To silence this warning, use `float`
by itself. Doing this will not modify any behavior and is safe. If you
specifically wanted the numpy scalar type, use `np.float64` here.  
Deprecated in NumPy 1.20; for more details and guidance:
https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations  
from numpy import array, zeros, float  
/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/bug_reporter/bug_reporter_gui.py:718: ResourceWarning:
unclosed file <_io.TextIOWrapper name='/sys/devices/virtual/dmi/id/sys_vendor'
mode='r' encoding='utf-8'>  
vendor = open(dmi_prefix + "sys_vendor", encoding='utf-8').read().strip()  
ResourceWarning: Enable tracemalloc to get the object allocation traceback  
/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/bug_reporter/bug_reporter_gui.py:723: ResourceWarning:
unclosed file <_io.TextIOWrapper
name='/sys/devices/virtual/dmi/id/product_name' mode='r' encoding='utf-8'>  
product = open(dmi_prefix + "product_name", encoding='utf-8').read().strip()  
ResourceWarning: Enable tracemalloc to get the object allocation traceback  
/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/bug_reporter/bug_reporter_gui.py:730: DeprecationWarning:
distro.linux_distribution() is deprecated. It should only be used as a
compatibility shim with Python's platform.linux_distribution(). Please use
distro.id(), distro.version() and distro.name() instead.  
OS: {' '.join(distro.linux_distribution())}  




OpenGL version: 4.6 (Core Profile) Mesa 21.2.5
OpenGL renderer: Mesa Intel(R) HD Graphics 5500 (BDW GT2)
OpenGL vendor: Intel
Manufacturer: LENOVO
Model: 20BSCTO1WW
OS: Fedora Linux 35 
Architecture: 64bit ELF
Virutal Machine: none
CPU: 4 Intel(R) Core(TM) i5-5300U CPU @ 2.30GHz
Cache Size: 3072 KB
Memory:
	               total        used        free      shared  buff/cache   available
	Mem:           7.6Gi       2.7Gi       1.0Gi       1.5Gi       3.9Gi       3.2Gi
	Swap:           14Gi          0B        14Gi

Graphics:
	00:02.0 VGA compatible controller [0300]: Intel Corporation HD Graphics 5500 [8086:1616] (rev 09)	
	Subsystem: Lenovo Device [17aa:2227]	
	Kernel driver in use: i915
Locale: ('en_US', 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2021.10.8
    cftime: 1.5.1.1
    charset-normalizer: 2.0.8
    ChimeraX-AddCharge: 1.2.2
    ChimeraX-AddH: 2.1.3
    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: 4.2
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.0
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.6.1
    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: 2.2.2
    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: 1.3rc202111292147
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    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-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: 1.1
    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-LinuxSupport: 1.0
    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: 2.0.4
    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: 1.2.6
    ChimeraX-ModelPanel: 1.2.1
    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: 2.6.5
    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: 1.0.1
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0.1
    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: 2.4.6
    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: 1.6.1
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 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: 1.2.1
    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: 0.11.0
    Cython: 0.29.24
    decorator: 5.1.0
    distro: 1.6.0
    docutils: 0.17.1
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 3.6.0
    html2text: 2020.1.16
    idna: 3.3
    ihm: 0.21
    imagecodecs: 2021.4.28
    imagesize: 1.3.0
    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: 4.9.1
    kiwisolver: 1.3.2
    line-profiler: 3.3.0
    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: 21.3
    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: 3.0.23
    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: 3.0.6
    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: 2.2.0
    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
    tables: 3.6.1
    tifffile: 2021.4.8
    tinyarray: 1.2.3
    tornado: 6.1
    traitlets: 5.1.1
    urllib3: 1.26.7
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.0
    wheel-filename: 1.3.0
File attachment: Screenshot from 2021-12-06 00-03-55.png

Screenshot from 2021-12-06 00-03-55.png​

[yuliang@…]

Added by email2trac

[pett]

Reported by Yuliang Zhang

[Tom Goddard]

The Log panel and AlphaFold panels are Qt html widgets and it sounds like those are not working on your Linux system. That is probably because some necessary library is missing on your Linux system that Qt QWebEngine view needs. Did you install the generic ChimeraX Linux version? That is especially prone to missing libraries.

Reassigning to Greg Couch our Linux person to advise more on how to find what library is missing.

There are also several deprecation warnings, but none are about this html widget problem. But we should fix those too. Here is a summary

1) import of collections by grako/grammars.py (third party package)
2) distro.linux_distribution() used by user agent code in core/fetch.py.
3) numpy.float used in geometry/matrix.py
4) unclosed file and distro.linux_distribution() used in linux distribution info in bug_reporter_gui.py

[Tom Goddard]

I fixed the numpy.float deprecation warning. Now using float64.

[Greg Couch]

Just checking, which ChimeraX Linux release are you using? The CentOS 8 rpm?

[yuliang@…]

Hi, Greg

Thanks for your reply. My system is Fedora 35. I installed chimeraX from rpm file.

Sent from my iPhone

[yuliang@…]

The UCSF ChimeraX version is 1.3rc202111292147 (2021-11-29). The rpm is
chimerax-rc.rpm. Probably it is from CentOS 8 version.

On Mon, Dec 6, 2021 at 5:33 PM ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
wrote:

[Greg Couch]

So I was able to duplicate this running Fedora 35 in a virtual machine. Changing the display manager from using wayland to using Xorg did not help. And switching to the latest PyQt5 (5.15.6) did not help. This is probably a Qt bug, and would be fixed with the latest commercial version of Qt 5. Non-commercial licensees, like us, need to switch to Qt 6 to get bug fixes.

And this bug is fixed by switching to PyQt6 (and Qt 6), but that isn't in any current ChimeraX release. There is super preliminary support for PyQt6 in the daily builds. If you install the chimerax-daily rpm, you can then run, as root, "chimerax-daily -m pip install PyQt6 PyQt6-WebEngine" to get PyQt6. "Soon" after the ChimeraX 1.3 release is out, we will be switching the daily build to come with Qt 6, so that step will not be necessary.

[yuliang@…]

Great! I appreciate your help. The information is really helpful. I will install PyQt6 as you suggested. Hopefully, the new version will be released soon.

Sent from my iPhone

[Greg Couch]

The Qt 6 support has only been lightly tested. The basic stuff works, but there are probably bugs that won't be found without more testing. So please be a tester and report those bugs. And please note that you are using PyQt6. It should be obvious from the Python tracebacks, but it will help remind whoever deals with the ticket.