Crash at startup showing Rapid Access

[dbratc1@…]

The following bug report has been submitted:
Platform:        Linux-5.15.0-43-generic-x86_64-with-glibc2.35
ChimeraX Version: 1.4 (2022-06-03 23:39:42 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Aborted

Current thread 0x00007efc8dc0ab80 (most recent call first):
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/ui/gui.py", line 838 in rapid_access_shown
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/ui/gui.py", line 860 in showEvent
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/ui/gui.py", line 551 in __init__
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/ui/gui.py", line 237 in build
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/ChimeraX_main.py", line 691 in init
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/ChimeraX_main.py", line 1021 in 
  File "/usr/lib/ucsf-chimerax/lib/python3.9/runpy.py", line 87 in _run_code
  File "/usr/lib/ucsf-chimerax/lib/python3.9/runpy.py", line 197 in _run_module_as_main


Log:
UCSF ChimeraX version: 1.4 (2022-06-03)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 4.6 (Core Profile) Mesa 22.0.1
OpenGL renderer: AMD Radeon Vega 10 Graphics (raven, LLVM 13.0.1, DRM 3.42, 5.15.0-43-generic)
OpenGL vendor: AMD

Python: 3.9.11
Locale: en_US.UTF-8
Qt version: PyQt6 6.3.0, Qt 6.3.0
Qt runtime version: 6.3.0
Qt platform: xcb

XDG_SESSION_TYPE=x11
DESKTOP_SESSION=ubuntu
XDG_SESSION_DESKTOP=ubuntu
XDG_CURRENT_DESKTOP=ubuntu:GNOME
DISPLAY=:1
Manufacturer: ASUSTeK COMPUTER INC.
Model: Zephyrus G GU502DU_GA502DU
OS: Ubuntu 22.04 jammy
Architecture: 64bit ELF
Virtual Machine: none
CPU: 8 AMD Ryzen 7 3750H with Radeon Vega Mobile Gfx
Cache Size: 512 KB
Memory:
	               total        used        free      shared  buff/cache   available
	Mem:            23Gi        18Gi       2.6Gi       431Mi       2.6Gi       4.4Gi
	Swap:          975Mi       974Mi       1.0Mi

Graphics:
	01:00.0 VGA compatible controller [0300]: NVIDIA Corporation TU116M [GeForce GTX 1660 Ti Mobile] [10de:2191] (rev a1)	
	Subsystem: ASUSTeK Computer Inc. TU116M [GeForce GTX 1660 Ti Mobile] [1043:18d1]	
	Kernel driver in use: nvidia

Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.10.1
    backcall: 0.2.0
    blockdiag: 3.0.0
    certifi: 2022.5.18.1
    cftime: 1.6.0
    charset-normalizer: 2.0.12
    ChimeraX-AddCharge: 1.2.3
    ChimeraX-AddH: 2.1.11
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2.1
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.4.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.39.1
    ChimeraX-AtomicLibrary: 7.0
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.1
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.7
    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: 2.2.4
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.1
    ChimeraX-CommandLine: 1.2.3
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.4
    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: 1.1
    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: 1.2
    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: 1.1.1
    ChimeraX-LinuxSupport: 1.0
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    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: 2.0.6
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.7
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.5.5
    ChimeraX-ModelPanel: 1.3.2
    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: 1.9
    ChimeraX-PDB: 2.6.6
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    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: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.6
    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: 1.8
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.0.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.1
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.18.3
    ChimeraX-uniprot: 2.2
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.1.2
    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: 1.1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.4
    cxservices: 1.2
    cycler: 0.11.0
    Cython: 0.29.26
    debugpy: 1.6.0
    decorator: 5.1.1
    distro: 1.6.0
    docutils: 0.17.1
    entrypoints: 0.4
    filelock: 3.4.2
    fonttools: 4.33.3
    funcparserlib: 1.0.0
    grako: 3.16.5
    h5py: 3.7.0
    html2text: 2020.1.16
    idna: 3.3
    ihm: 0.27
    imagecodecs: 2021.11.20
    imagesize: 1.3.0
    ipykernel: 6.6.1
    ipython: 7.31.1
    ipython-genutils: 0.2.0
    jedi: 0.18.1
    Jinja2: 3.0.3
    jupyter-client: 7.1.0
    jupyter-core: 4.10.0
    kiwisolver: 1.4.2
    line-profiler: 3.4.0
    lxml: 4.7.1
    lz4: 3.1.10
    MarkupSafe: 2.1.1
    matplotlib: 3.5.1
    matplotlib-inline: 0.1.3
    msgpack: 1.0.3
    nest-asyncio: 1.5.5
    netCDF4: 1.5.8
    networkx: 2.6.3
    numexpr: 2.8.1
    numpy: 1.22.1
    openvr: 1.16.802
    packaging: 21.3
    ParmEd: 3.4.3
    parso: 0.8.3
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 9.0.1
    pip: 21.3.1
    pkginfo: 1.8.2
    prompt-toolkit: 3.0.29
    psutil: 5.9.0
    ptyprocess: 0.7.0
    pycollada: 0.7.2
    pydicom: 2.2.2
    Pygments: 2.11.2
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    PyQt6-commercial: 6.3.0
    PyQt6-Qt6: 6.3.0
    PyQt6-sip: 13.3.1
    PyQt6-WebEngine-commercial: 6.3.0
    PyQt6-WebEngine-Qt6: 6.3.0
    python-dateutil: 2.8.2
    pytz: 2022.1
    pyzmq: 23.1.0
    qtconsole: 5.3.0
    QtPy: 2.1.0
    RandomWords: 0.3.0
    requests: 2.27.1
    scipy: 1.7.3
    setuptools: 59.8.0
    sfftk-rw: 0.7.2
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 4.3.2
    sphinx-autodoc-typehints: 1.15.2
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 3.0.0
    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-community: 1.0.0
    tables: 3.7.0
    tifffile: 2021.11.2
    tinyarray: 1.2.4
    tornado: 6.1
    traitlets: 5.1.1
    urllib3: 1.26.9
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.1
    wheel-filename: 1.3.0

[Eric Pettersen]

Hi Derek,

Thanks for reporting this problem. So ChimeraX crash at startup but worked the next time you started it? Was there anything different about the time it crashed vs. the time it didn't?

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

[dbratc1@…]

Thanks for getting back to me.
I was attempting to view the files for the conformations of my ligand produced by swissdock. I believe due to the amount of structures it ceased to function. I ended the process with xkill and since it only responds to calls from the terminal despite the icon in my applications tab.

Derek
________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: Friday, August 5, 2022 3:23 PM
Cc: Derek R Bratcher <dbratc1@lsu.edu>; goddard@cgl.ucsf.edu <goddard@cgl.ucsf.edu>; pett@cgl.ucsf.edu <pett@cgl.ucsf.edu>
Subject: Re: [ChimeraX] #7402: Crash at startup showing Rapid Access

[You don't often get email from chimerax-bugs-admin@cgl.ucsf.edu. Learn why this is important at https://aka.ms/LearnAboutSenderIdentification ]

#7402: Crash at startup showing Rapid Access
-------------------------------------+----------------------
          Reporter:  dbratc1@…       |      Owner:  pett
              Type:  defect          |     Status:  feedback
          Priority:  normal          |  Milestone:
         Component:  Window Toolkit  |    Version:
        Resolution:                  |   Keywords:
        Blocked By:                  |   Blocking:
Notify when closed:                  |   Platform:  all
           Project:  ChimeraX        |
-------------------------------------+----------------------
Changes (by pett):

 * status:  accepted => feedback


Comment:

 Hi Derek,
         Thanks for reporting this problem. So ChimeraX crash at startup
 but worked the next time you started it? Was there anything different
 about the time it crashed vs. the time it didn't?

 --Eric

         Eric Pettersen
         UCSF Computer Graphics Lab

--
Ticket URL: <https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.rbvi.ucsf.edu%2Ftrac%2FChimeraX%2Fticket%2F7402%23comment%3A2&amp;data=05%7C01%7Cdbratc1%40lsu.edu%7Cd01ca369d6094c11d08308da77206603%7C2d4dad3f50ae47d983a09ae2b1f466f8%7C0%7C0%7C637953278284296111%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&amp;sdata=jA15hrXCT6vGbB%2B%2FAHzs61DTUStBcYQxOUeOxoSktuA%3D&amp;reserved=0>
ChimeraX <https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.rbvi.ucsf.edu%2Fchimerax%2F&amp;data=05%7C01%7Cdbratc1%40lsu.edu%7Cd01ca369d6094c11d08308da77206603%7C2d4dad3f50ae47d983a09ae2b1f466f8%7C0%7C0%7C637953278284296111%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&amp;sdata=KqSIkHLb3K1xIEjYhzOHLrxcucXdvjRXMTQ4Yzdx%2Bx0%3D&amp;reserved=0>
ChimeraX Issue Tracker

[Eric Pettersen]

Ah, I see, so you killed it externally. Do these files freeze ChimeraX every time, or only this once? If they do it every time, then if you send them to me I might be able to do something about it. My direct email is pett@….

--Eric

[dbratc1@…]

I was able to open them using ucfchimera. Thanks for the support.
I also wanted to know how to prepare files for dockx I have looked into the manual and am unable to open
also what is the reason for ucfchimera and chimerax? It seems there are operations like autodock vina that are only available in ucfchimera. chimerax seems to be more viewer oriented.

I come from a very small deptartment, this support i greatly appretiated.

Derek
________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: Friday, August 5, 2022 8:10 PM
Cc: Derek R Bratcher <dbratc1@lsu.edu>; goddard@cgl.ucsf.edu <goddard@cgl.ucsf.edu>; pett@cgl.ucsf.edu <pett@cgl.ucsf.edu>
Subject: Re: [ChimeraX] #7402: Crash at startup showing Rapid Access

[You don't often get email from chimerax-bugs-admin@cgl.ucsf.edu. Learn why this is important at https://aka.ms/LearnAboutSenderIdentification ]

#7402: Crash at startup showing Rapid Access
-------------------------------------+----------------------
          Reporter:  dbratc1@…       |      Owner:  pett
              Type:  defect          |     Status:  feedback
          Priority:  normal          |  Milestone:
         Component:  Window Toolkit  |    Version:
        Resolution:                  |   Keywords:
        Blocked By:                  |   Blocking:
Notify when closed:                  |   Platform:  all
           Project:  ChimeraX        |
-------------------------------------+----------------------

Comment (by pett):

 Ah, I see, so you killed it externally.  Do these files freeze ChimeraX
 every time, or only this once?  If they do it every time, then if you send
 them to me I might be able to do something about it.  My direct email is
 pett@cgl.ucsf.edu.

 --Eric

--
Ticket URL: <https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.rbvi.ucsf.edu%2Ftrac%2FChimeraX%2Fticket%2F7402%23comment%3A4&amp;data=05%7C01%7Cdbratc1%40lsu.edu%7C5d9ba46454d04535c3d408da7748743e%7C2d4dad3f50ae47d983a09ae2b1f466f8%7C0%7C0%7C637953450324381909%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&amp;sdata=fZUGweucUmVk7Er29b5a8Men65QpBijr71Q4ip%2FuIEQ%3D&amp;reserved=0>
ChimeraX <https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.rbvi.ucsf.edu%2Fchimerax%2F&amp;data=05%7C01%7Cdbratc1%40lsu.edu%7C5d9ba46454d04535c3d408da7748743e%7C2d4dad3f50ae47d983a09ae2b1f466f8%7C0%7C0%7C637953450324381909%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&amp;sdata=G7rp4xxt1upMQSPvbCLmFq7R%2BdH%2BU%2B0WBQSChefTlzY%3D&amp;reserved=0>
ChimeraX Issue Tracker

[Eric Pettersen]

The formats that ViewDockX can read are near the top of its Help page: ​https://rbvi.ucsf.edu/chimerax/docs/user/tools/viewdockx.html . It does not read SwissDock format yet, but we have an enhancement-request ticket open for that here: ​https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/4232 . I could add to the recipient list for that ticket if you'd like to be notified when it gets implemented.

Though you have no need for a commercial license, the reasons for the two programs are described succinctly in the "Chimera vs. ChimeraX" section near the top of the commercial licensing page: ​https://rbvi.ucsf.edu/chimera/commercial_license.html

--Eric