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#8215 assigned defect

Linux: QAccessibleTree::indexFromLogical: invalid index

Reported by:	20210700031@…	Owned by:	Greg Couch
Priority:	normal	Milestone:
Component:	Window Toolkit	Version:
Keywords:		Cc:	Tom Goddard, Zach Pearson
Blocked By:		Blocking:
Notify when closed:		Platform:	all
Project:	ChimeraX

Description

The following bug report has been submitted:
Platform:        Linux-5.13.0-37-generic-x86_64-with-glibc2.31
ChimeraX Version: 1.3 (2021-12-08 23:08:33 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault

Current thread 0x00007f66621e1740 (most recent call first):
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/save_command/dialog.py", line 39 in display
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/save_command/dialog.py", line 127 in show_save_file_dialog
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/save_command/dialog.py", line 116 in 
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/ui/gui.py", line 301 in event_loop
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/ChimeraX_main.py", line 867 in init
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/ChimeraX_main.py", line 1018 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 before crash start =====
UCSF ChimeraX version: 1.3 (2021-12-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /home/jiangxinyi/minilinker-jxy/minidis-2.cxs format session

opened ChimeraX session  

QSpiApplication::keyEventError "org.freedesktop.DBus.Error.NoReply" "Did not
receive a reply. Possible causes include: the remote application did not send
a reply, the message bus security policy blocked the reply, the reply timeout
expired, or the network connection was broken."  

> save /home/jiangxinyi/minilinker-jxy/mindis-2.tif width 1200 height 1180
> supersample 3

QAccessibleTree::indexFromLogical: invalid index: -1 0 for
QTreeView(0x1155a400, name="treeView")  

Requested invalid tree cell: -1 0  


===== Log before crash end =====

Log:
UCSF ChimeraX version: 1.3 (2021-12-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  

> open minidis-2.cxs

Log from Sat Dec 17 16:45:19 2022UCSF ChimeraX version: 1.3 (2021-12-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  

> open /home/jiangxinyi/minilinker-jxy/minidis-2.cxs format session

Log from Sat Dec 17 16:02:09 2022UCSF ChimeraX version: 1.3 (2021-12-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  

> open /home/jiangxinyi/minilinker-jxy/minidis-2.cxs format session

Log from Sat Dec 17 15:51:55 2022UCSF ChimeraX version: 1.3 (2021-12-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /home/jiangxinyi/minilinker-jxy/one-up/7wz2.pdb

Chain information for 7wz2.pdb #1  
---  
Chain | Description  
A C E | No description available  
  

> set bgColor white

> color #1 #babdb6 transparency 0

[Repeated 1 time(s)]

> show surfaces

WARNING Qt AtSpiAdaptor: Accessible invalid: QAccessibleInterface(0x6673880
invalid) "/org/a11y/atspi/accessible/2147484090"  

[Repeated 5 time(s)]

> color #1.2 #babdb6 transparency 0

[Repeated 1 time(s)]

WARNING QAccessibleTable::indexOfChild invalid child QAccessible::Client ""  

> color #1.3 #babdb6 transparency 0

[Repeated 1 time(s)]

WARNING QAccessibleTable::indexOfChild invalid child QAccessible::Client ""  

> color #1.4 #babdb6 transparency 0

[Repeated 1 time(s)]

WARNING QAccessibleTable::indexOfChild invalid child QAccessible::Client ""  

[Repeated 1 time(s)]

> lighting flat

> lighting soft

> color #1.3 #d3d7cf transparency 0

> color #1.3 #babdb6 transparency 0

WARNING QAccessibleTable::indexOfChild invalid child QAccessible::Client ""  

> color #1.3 #babdb6 transparency 0

> color #1.2 #d3d7cf transparency 0

[Repeated 1 time(s)]

WARNING QAccessibleTable::indexOfChild invalid child QAccessible::Client ""  

[Repeated 1 time(s)]

> color #1.4 #d3d7cf transparency 0

[Repeated 1 time(s)]

WARNING QAccessibleTable::indexOfChild invalid child QAccessible::Client ""  

> select #1

25014 atoms, 25602 bonds, 9 pseudobonds, 3228 residues, 2 models selected  

> hide sel cartoons

> transparency (#!1 & sel) 50

> ~select #1

3 models selected  

> transparency 40

> transparency 60

> transparency 50

QSpiApplication::keyEventError "org.freedesktop.DBus.Error.NoReply" "Did not
receive a reply. Possible causes include: the remote application did not send
a reply, the message bus security policy blocked the reply, the reply timeout
expired, or the network connection was broken."  

[Repeated 1 time(s)]

> save /home/jiangxinyi/minilinker-jxy/minidis-2.cxs

> open /home/jiangxinyi/minilinker-jxy/one-up/oneup-nb6-2.pdb

Chain information for oneup-nb6-2.pdb #2  
---  
Chain | Description  
B D F | No description available  
  

WARNING Qt AtSpiAdaptor: Accessible invalid: QAccessibleInterface(0x1d6baa80
invalid) "/org/a11y/atspi/accessible/2147484614"  

[Repeated 5 time(s)]

WARNING QAccessibleTable::indexOfChild invalid child QAccessible::Client ""  

> color #2 plum transparency 0

WARNING QAccessibleTable::indexOfChild invalid child QAccessible::Client ""  

> open /home/jiangxinyi/minilinker-jxy/trimer-up.pdb

Chain information for trimer-up.pdb #3  
---  
Chain | Description  
B D F | No description available  
  

WARNING Qt AtSpiAdaptor: Accessible invalid: QAccessibleInterface(0x119ecb00
invalid) "/org/a11y/atspi/accessible/2147484740"  

[Repeated 5 time(s)]

> color #3 skyblue transparency 0

WARNING QAccessibleTable::indexOfChild invalid child QAccessible::Client ""  

[Repeated 1 time(s)]

> save /home/jiangxinyi/minilinker-jxy/minidis-2.cxs

> help help:contact.html

> select
> ::name="ALA"::name="ARG"::name="ASN"::name="ASP"::name="CYS"::name="GLN"::name="GLU"::name="GLY"::name="HIS"::name="ILE"::name="LEU"::name="LYS"::name="MET"::name="PHE"::name="PRO"::name="SER"::name="THR"::name="TRP"::name="TYR"::name="VAL"

33321 atoms, 34002 bonds, 9 pseudobonds, 3777 residues, 4 models selected  

> ~select #1

8307 atoms, 8400 bonds, 549 residues, 5 models selected  

> ~select #2

3048 atoms, 3090 bonds, 192 residues, 1 model selected  

> ~select #3

Nothing selected  

> select #2/B:1-119

1753 atoms, 1770 bonds, 119 residues, 1 model selected  

> select #2/B:1-119

1753 atoms, 1770 bonds, 119 residues, 1 model selected  

> select #2/B:1-119

1753 atoms, 1770 bonds, 119 residues, 1 model selected  

> select #2/B:1-119

1753 atoms, 1770 bonds, 119 residues, 1 model selected  

> select down

1753 atoms, 1770 bonds, 119 residues, 1 model selected  

QSpiApplication::keyEventError "org.freedesktop.DBus.Error.NoReply" "Did not
receive a reply. Possible causes include: the remote application did not send
a reply, the message bus security policy blocked the reply, the reply timeout
expired, or the network connection was broken."  

[Repeated 16 time(s)]

QSpiApplication::notifyKeyboardListenerCallback with no queued key called  

> select /B D F:1

Expected a keyword  

QSpiApplication::keyEventError "org.freedesktop.DBus.Error.NoReply" "Did not
receive a reply. Possible causes include: the remote application did not send
a reply, the message bus security policy blocked the reply, the reply timeout
expired, or the network connection was broken."  

[Repeated 46 time(s)]

QSpiApplication::notifyKeyboardListenerCallback with no queued key called  

[Repeated 4 time(s)]

> select #3/B:1-64

1016 atoms, 1030 bonds, 64 residues, 1 model selected  

> select #3/B:1-64

1016 atoms, 1030 bonds, 64 residues, 1 model selected  

> select #3/B:1-64

1016 atoms, 1030 bonds, 64 residues, 1 model selected  

> select #3/B:1-64

1016 atoms, 1030 bonds, 64 residues, 1 model selected  

> select #3/B:1-64

1016 atoms, 1030 bonds, 64 residues, 1 model selected  

> save /home/jiangxinyi/minilinker-jxy/minidis-2.cxs

——— End of log from Sat Dec 17 15:51:55 2022 ———

opened ChimeraX session  

> ui tool show "Show Sequence Viewer"

> sequence chain #2/B #2/D #2/F

Alignment identifier is 1  

> select #3

3048 atoms, 3090 bonds, 192 residues, 1 model selected  

> ~select #3

Nothing selected  

> select #2/B-F:119

33 atoms, 30 bonds, 3 residues, 1 model selected  

> select #2/B-F:119

33 atoms, 30 bonds, 3 residues, 1 model selected  

> hide (sel-residues & (protein|nucleic)) target a

> cartoon hide sel-residues

> show (sel-residues & ((protein&@ca)|(nucleic&@p))) target ab

> hide sel cartoons

> hide sel atoms

> hide (sel-residues & (protein|nucleic)) target a

> cartoon hide sel-residues

> show (sel-residues & backbone) target ab

> hide (sel-residues & (protein|nucleic)) target a

> cartoon hide sel-residues

> show (sel-residues & ((protein&@ca)|(nucleic&@p))) target ab

> hide (sel-residues & (protein|nucleic)) target a

> cartoon hide sel-residues

> show (sel-residues & ((protein&@ca)|(nucleic&@p))) target ab

> style sel sphere

Changed 33 atom styles  

> ui tool show "Color Actions"

> color sel #ef2929ff

> select clear

QSpiApplication::keyEventError "org.freedesktop.DBus.Error.NoReply" "Did not
receive a reply. Possible causes include: the remote application did not send
a reply, the message bus security policy blocked the reply, the reply timeout
expired, or the network connection was broken."  

> select #3/B:1-64

1016 atoms, 1030 bonds, 64 residues, 1 model selected  

> select #3/B:1-64

1016 atoms, 1030 bonds, 64 residues, 1 model selected  

WARNING QAccessibleTable::indexOfChild invalid child QAccessible::Client ""  

> show #3 target m

> select #3

3048 atoms, 3090 bonds, 192 residues, 1 model selected  

> ~select #3

Nothing selected  

> ui tool show "Show Sequence Viewer"

> sequence chain #3/B #3/D #3/F

Alignment identifier is 2  

> select #3/B-F:1

54 atoms, 51 bonds, 3 residues, 1 model selected  

> select #3/B-F:1

54 atoms, 51 bonds, 3 residues, 1 model selected  

> style sel sphere

Changed 54 atom styles  

> show sel atoms

> hide (sel-residues & (protein|nucleic)) target a

> cartoon hide sel-residues

> show (sel-residues & ((protein&@ca)|(nucleic&@p))) target ab

> color sel red

> select clear

QSpiApplication::keyEventError "org.freedesktop.DBus.Error.NoReply" "Did not
receive a reply. Possible causes include: the remote application did not send
a reply, the message bus security policy blocked the reply, the reply timeout
expired, or the network connection was broken."  

> view orient

[Repeated 2 time(s)]

> save /home/jiangxinyi/minilinker-jxy/minidis-2.cxs

——— End of log from Sat Dec 17 16:02:09 2022 ———

opened ChimeraX session  

> open /home/jiangxinyi/minilinker-jxy/trimer-up.pdb

Chain information for trimer-up.pdb #4  
---  
Chain | Description  
B D F | No description available  
  

> close #3

WARNING Qt AtSpiAdaptor: Accessible invalid: QAccessibleInterface(0x691db20
invalid) "/org/a11y/atspi/accessible/2147484032"  

[Repeated 5 time(s)]

> color #4 skyblue transparency 0

WARNING QAccessibleTable::indexOfChild invalid child QAccessible::Client ""  

> select #4/B:1-64

1016 atoms, 1030 bonds, 64 residues, 1 model selected  

> select #4/B:1-64

1016 atoms, 1030 bonds, 64 residues, 1 model selected  

> select #4/B:1-64

1016 atoms, 1030 bonds, 64 residues, 1 model selected  

> ui tool show "Show Sequence Viewer"

> sequence chain #4/B #4/D #4/F

Alignment identifier is 2  

> select #4/B-F:1

54 atoms, 51 bonds, 3 residues, 1 model selected  

> select #4/B-F:1

54 atoms, 51 bonds, 3 residues, 1 model selected  

> style sel sphere

Changed 54 atom styles  

> show sel atoms

> hide (sel-residues & (protein|nucleic)) target a

> cartoon hide sel-residues

> show (sel-residues & ((protein&@ca)|(nucleic&@p))) target ab

> color sel red

> select clear

QSpiApplication::keyEventError "org.freedesktop.DBus.Error.NoReply" "Did not
receive a reply. Possible causes include: the remote application did not send
a reply, the message bus security policy blocked the reply, the reply timeout
expired, or the network connection was broken."  

> view orient

> save /home/jiangxinyi/minilinker-jxy/minidis-2.cxs

——— End of log from Sat Dec 17 16:45:19 2022 ———

opened ChimeraX session  

> ui tool show Registration




OpenGL version: 3.3.0 NVIDIA 390.144
OpenGL renderer: NVS 310/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Dell Inc.
Model: Precision T5600
OS: Ubuntu 20.04 focal
Architecture: 64bit ELF
Virutal Machine: none
CPU: 8 Intel(R) Xeon(R) CPU E5-2609 0 @ 2.40GHz
Cache Size: 10240 KB
Memory:
	              total        used        free      shared  buff/cache   available
	Mem:           31Gi       1.9Gi        22Gi       6.0Mi       6.5Gi        29Gi
	Swap:         2.0Gi          0B       2.0Gi

Graphics:
	03:00.0 VGA compatible controller [0300]: NVIDIA Corporation GF119 [NVS 310] [10de:107d] (rev a1)	
	Subsystem: NVIDIA Corporation GF119 [NVS 310] [10de:094e]	
	Kernel driver in use: nvidia
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: 2.0.9
    ChimeraX-AddCharge: 1.2.2
    ChimeraX-AddH: 2.1.11
    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: 1.3
    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: 1.13.7
    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: 2.8.0
    numpy: 1.21.2
    openvr: 1.16.801
    packaging: 21.3
    ParmEd: 3.2.0
    parso: 0.8.3
    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: 1.11.3
    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

Change History (2)

comment:1 by Eric Pettersen, 3 years ago

Cc:	Tom Goddard Zach Pearson added
Component:	Unassigned → Window Toolkit
Owner:	set to Greg Couch
Platform:	→ all
Project:	→ ChimeraX
Status:	new → assigned
Summary:	ChimeraX bug report submission → Linux: QAccessibleTree::indexFromLogical: invalid index

Reported by Xinyi Jiang

comment:2 by Greg Couch, 3 years ago

Can you share the session that causes the problems? If you need to keep the data it is private, please email it to me at gregc@…. Or you can attach it in your response to the ticket.

It would also be nice to know if the problem persists with ChimeraX 1.5, which has a much newer version of Qt in it. If you send the session to me, I can test it. Or you can test it, and let me know.

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