Context Navigation

← Previous Ticket
Next Ticket →

#15794 feedback defect

Crash in event loop

Reported by:	dothideomycetes@…	Owned by:	Eric Pettersen
Priority:	normal	Milestone:
Component:	Core	Version:
Keywords:		Cc:	Tom Goddard
Blocked By:		Blocking:
Notify when closed:		Platform:	all
Project:	ChimeraX

Description

The following bug report has been submitted:
Platform:        Linux-6.5.0-45-generic-x86_64-with-glibc2.35
ChimeraX Version: 1.6 (2023-03-23 07:59:11 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 0x000073601dc47b80 (most recent call first):
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/ui/gui.py", line 284 in event_loop
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/__main__.py", line 892 in init
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/__main__.py", line 1043 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 =====
Startup Messages  
---  
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle  
  
You can double click a model's Name or ID in the model panel to edit those
fields  
UCSF ChimeraX version: 1.6 (2023-03-23)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /home/bacillus/Downloads/cryosparc_P1_J1763_006_volume_map_sharp.mrc
> /home/bacillus/Downloads/cryosparc_P1_J1764_005_volume_map_sharp.mrc

Opened cryosparc_P1_J1763_006_volume_map_sharp.mrc as #1.1, grid size
440,440,440, pixel 0.7, shown at level 0.0148, step 2, values float32  
Opened cryosparc_P1_J1764_005_volume_map_sharp.mrc as #1.2, grid size
440,440,440, pixel 0.7, shown at level 0.0142, step 2, values float32  

> hide #!1 models

> show #!1 models

> hide #!1.1 models

> hide #!1.2 models

> show #!1.2 models

> show #!1.1 models

> hide #!1.1 models

> show #!1.1 models

> hide #!1.1 models

> show #!1.1 models

> surface dust #1.1 size 7

> surface dust #1.2 size 7

> fitmap #1.1 inMap #1.2

Fit map cryosparc_P1_J1763_006_volume_map_sharp.mrc in map
cryosparc_P1_J1764_005_volume_map_sharp.mrc using 106468 points  
correlation = 0.4757, correlation about mean = 0.1358, overlap = 56.01  
steps = 116, shift = 3.44, angle = 5.02 degrees  
  
Position of cryosparc_P1_J1763_006_volume_map_sharp.mrc (#1.1) relative to
cryosparc_P1_J1764_005_volume_map_sharp.mrc (#1.2) coordinates:  
Matrix rotation and translation  
0.99712625 -0.07466305 -0.01283222 13.79020707  
0.07402620 0.99626427 -0.04447043 -3.97593171  
0.01610458 0.04339271 0.99892828 -12.37154649  
Axis 0.50174131 -0.16524317 0.84908795  
Axis point 70.42383224 201.66784458 0.00000000  
Rotation angle (degrees) 5.02314840  
Shift along axis -2.92841900  
  

> fitmap #1.1 inMap #1.2

Fit map cryosparc_P1_J1763_006_volume_map_sharp.mrc in map
cryosparc_P1_J1764_005_volume_map_sharp.mrc using 106468 points  
correlation = 0.4757, correlation about mean = 0.1359, overlap = 56.01  
steps = 36, shift = 0.0125, angle = 0.00494 degrees  
  
Position of cryosparc_P1_J1763_006_volume_map_sharp.mrc (#1.1) relative to
cryosparc_P1_J1764_005_volume_map_sharp.mrc (#1.2) coordinates:  
Matrix rotation and translation  
0.99713226 -0.07458388 -0.01282551 13.78665501  
0.07394688 0.99626874 -0.04450233 -3.95454841  
0.01609681 0.04342630 0.99892695 -12.37091692  
Axis 0.50241378 -0.16525872 0.84868719  
Axis point 70.18463367 201.81149428 0.00000000  
Rotation angle (degrees) 5.02015614  
Shift along axis -2.91890975  
  

> hide #!1.1 models

> show #!1.1 models

> hide #!1.1 models

> fetch 6wvj

Unknown command: fetch 6wvj  

> getpdb 6wvj

Unknown command: getpdb 6wvj  

> getcrd 6wvj

Missing or invalid "atoms" argument: invalid atom specifier  

> pdbimages

pdbimages is provided by the uninstalled bundle PDBImages versions 1.0 – 1.2  

> import 6wvj

Unknown command: import 6wvj  

> help

> open /home/bacillus/Desktop/RNAP_Bsub/6wvj.pdb format pdb

6wvj.pdb title:  
Cryo-em structure of bacillus subtilis RNA polymerase elongation complex [more
info...]  
  
Chain information for 6wvj.pdb #2  
---  
Chain | Description | UniProt  
A B | DNA-directed RNA polymerase subunit α | RPOA_BACSU 1-314  
C | DNA-directed RNA polymerase subunit β |  
D | DNA-directed RNA polymerase subunit β' |  
F | DNA-directed RNA polymerase subunit ω |  
N | DNA (5'-D(P*ap*CP*GP*CP*CP*CP*GP*ap*CP*A)-3') |  
R | RNA (5'-R(P*GP*GP*CP*GP*CP*GP*CP*G)-3') |  
T | DNA (5'-
D(*TP*GP*TP*CP*GP*GP*GP*CP*GP*TP*CP*CP*GP*CP*GP*CP*GP*CP*C)-3') |  
  
Non-standard residues in 6wvj.pdb #2  
---  
MG — magnesium ion  
ZN — zinc ion  
  

> fitmap #2 inMap #1.2

Fit molecule 6wvj.pdb (#2) to map cryosparc_P1_J1764_005_volume_map_sharp.mrc
(#1.2) using 22367 atoms  
average map value = 0.005537, steps = 180  
shifted from previous position = 14  
rotated from previous position = 9.45 degrees  
atoms outside contour = 18920, contour level = 0.014188  
  
Position of 6wvj.pdb (#2) relative to
cryosparc_P1_J1764_005_volume_map_sharp.mrc (#1.2) coordinates:  
Matrix rotation and translation  
0.98656211 0.12390826 -0.10649858 4.64854454  
-0.12571528 0.99201186 -0.01039890 26.04036510  
0.10435935 0.02364766 0.99425847 -5.70398997  
Axis 0.10363295 -0.64182191 -0.75981896  
Axis point 148.38995720 -31.37380045 0.00000000  
Rotation angle (degrees) 9.45454778  
Shift along axis -11.89753468  
  

> fitmap #2 inMap #1.2

Fit molecule 6wvj.pdb (#2) to map cryosparc_P1_J1764_005_volume_map_sharp.mrc
(#1.2) using 22367 atoms  
average map value = 0.005537, steps = 44  
shifted from previous position = 0.00114  
rotated from previous position = 0.0027 degrees  
atoms outside contour = 18920, contour level = 0.014188  
  
Position of 6wvj.pdb (#2) relative to
cryosparc_P1_J1764_005_volume_map_sharp.mrc (#1.2) coordinates:  
Matrix rotation and translation  
0.98656036 0.12390431 -0.10651941 4.65153871  
-0.12571625 0.99201129 -0.01044117 26.04523730  
0.10437475 0.02369207 0.99425580 -5.71224259  
Axis 0.10388730 -0.64187361 -0.75974054  
Axis point 148.43985378 -31.41349455 0.00000000  
Rotation angle (degrees) 9.45541864  
Shift along axis -11.89469248  
  

> ui tool show "Fit in Map"

> fitmap #2 inMap #1.2

Fit molecule 6wvj.pdb (#2) to map cryosparc_P1_J1764_005_volume_map_sharp.mrc
(#1.2) using 22367 atoms  
average map value = 0.005537, steps = 44  
shifted from previous position = 0.000317  
rotated from previous position = 0.000463 degrees  
atoms outside contour = 18920, contour level = 0.014188  
  
Position of 6wvj.pdb (#2) relative to
cryosparc_P1_J1764_005_volume_map_sharp.mrc (#1.2) coordinates:  
Matrix rotation and translation  
0.98656069 0.12390765 -0.10651241 4.65038033  
-0.12571916 0.99201095 -0.01043858 26.04554842  
0.10436806 0.02368894 0.99425658 -5.71091904  
Axis 0.10387137 -0.64184098 -0.75977029  
Axis point 148.43942646 -31.40254000 0.00000000  
Rotation angle (degrees) 9.45528384  
Shift along axis -11.89507238  
  

> fitmap #2 inMap #1.2

Fit molecule 6wvj.pdb (#2) to map cryosparc_P1_J1764_005_volume_map_sharp.mrc
(#1.2) using 22367 atoms  
average map value = 0.005537, steps = 44  
shifted from previous position = 0.0007  
rotated from previous position = 0.00135 degrees  
atoms outside contour = 18919, contour level = 0.014188  
  
Position of 6wvj.pdb (#2) relative to
cryosparc_P1_J1764_005_volume_map_sharp.mrc (#1.2) coordinates:  
Matrix rotation and translation  
0.98656142 0.12391880 -0.10649270 4.64667075  
-0.12572909 0.99200978 -0.01043082 26.04647811  
0.10434923 0.02367987 0.99425877 -5.70721140  
Axis 0.10382344 -0.64174414 -0.75985864  
Axis point 148.43722795 -31.36711982 0.00000000  
Rotation angle (degrees) 9.45497994  
Shift along axis -11.89606742  
  

> select add #2

22367 atoms, 22812 bonds, 16 pseudobonds, 2842 residues, 3 models selected  

> ui mousemode right rotate

> ui mousemode right "rotate selected models"

> view matrix models
> #2,-0.054688,-0.31905,-0.94616,292.43,0.76704,-0.62009,0.16476,99.564,-0.63927,-0.71673,0.27863,268

> transparency #1.2.1 50

> view matrix models
> #2,-0.84372,-0.5143,0.15375,282.23,-0.524,0.85126,-0.027975,95.673,-0.11649,-0.10417,-0.98771,278.22

> ui mousemode right "translate selected models"

> view matrix models
> #2,-0.84372,-0.5143,0.15375,283.36,-0.524,0.85126,-0.027975,103.53,-0.11649,-0.10417,-0.98771,305.17

> ui mousemode right "rotate selected models"

> view matrix models
> #2,-0.51291,0.48547,0.70798,47.44,0.51222,0.8349,-0.20142,-2.2454,-0.68888,0.25934,-0.6769,292.3

> view matrix models
> #2,-0.71979,0.22718,-0.65596,271.4,0.044296,-0.92798,-0.37,301.41,-0.69277,-0.29538,0.65789,201.87

> ui mousemode right "move picked models"

> view matrix models
> #2,-0.71979,0.22718,-0.65596,277.75,0.044296,-0.92798,-0.37,301.98,-0.69277,-0.29538,0.65789,201.08

> ui mousemode right "rotate selected models"

> view matrix models
> #2,-0.7409,0.67034,-0.04131,149.33,-0.070465,-0.13876,-0.98782,290.37,-0.66791,-0.72896,0.15004,314.87

> view matrix models
> #2,-0.6518,0.75829,0.012224,120.54,-0.11335,-0.081465,-0.99021,288.68,-0.74987,-0.6468,0.13905,315.91

> view matrix models
> #2,-0.5488,0.81435,-0.18881,124.93,0.17625,-0.10807,-0.97839,254.63,-0.81716,-0.57022,-0.084222,341.55

> view matrix models
> #2,-0.51028,0.85799,-0.058873,98.823,0.12367,0.005462,-0.99231,248.36,-0.85107,-0.51364,-0.1089,341.54

> fitmap #2 inMap #1.2

Fit molecule 6wvj.pdb (#2) to map cryosparc_P1_J1764_005_volume_map_sharp.mrc
(#1.2) using 22367 atoms  
average map value = 0.01178, steps = 320  
shifted from previous position = 11.9  
rotated from previous position = 20.4 degrees  
atoms outside contour = 15576, contour level = 0.014188  
  
Position of 6wvj.pdb (#2) relative to
cryosparc_P1_J1764_005_volume_map_sharp.mrc (#1.2) coordinates:  
Matrix rotation and translation  
-0.47553557 0.78329358 -0.40039619 153.79988628  
0.25886298 -0.31040219 -0.91468052 268.16811977  
-0.84074722 -0.53861087 -0.05515843 334.03764707  
Axis 0.48136390 0.56364318 -0.67126385  
Axis point 237.21534638 251.09446165 0.00000000  
Rotation angle (degrees) 157.00634085  
Shift along axis 0.95744927  
  

> hide sel surfaces

> hide sel cartoons

> hide sel atoms

> show sel cartoons

> view matrix models
> #2,0.67669,-0.1839,0.71293,-0.95308,-0.1887,0.89264,0.40936,10.459,-0.71168,-0.41154,0.56934,226.27

> view matrix models
> #2,0.33098,0.33549,0.88199,-44.562,-0.7828,0.61955,0.058093,161.46,-0.52695,-0.70965,0.46768,253.56

> view matrix models
> #2,0.63507,0.07508,0.76879,-35.49,-0.70322,0.46803,0.5352,113.12,-0.31963,-0.88052,0.35003,263.8

> fitmap #2 inMap #1.2

Fit molecule 6wvj.pdb (#2) to map cryosparc_P1_J1764_005_volume_map_sharp.mrc
(#1.2) using 22367 atoms  
average map value = 0.01286, steps = 192  
shifted from previous position = 6.14  
rotated from previous position = 14.9 degrees  
atoms outside contour = 14657, contour level = 0.014188  
  
Position of 6wvj.pdb (#2) relative to
cryosparc_P1_J1764_005_volume_map_sharp.mrc (#1.2) coordinates:  
Matrix rotation and translation  
0.65928265 0.29117335 0.69322759 -52.81692947  
-0.74738453 0.35461508 0.56184030 132.62875268  
-0.08223603 -0.88851913 0.45141002 220.03154454  
Axis -0.74564038 0.39867151 -0.53393019  
Axis point 0.00000000 227.75221993 7.65895087  
Rotation angle (degrees) 76.54663303  
Shift along axis -25.22374436  
  

> select subtract #2

Nothing selected  

> hide #!2 models

> ui mousemode right "contour level"

> volume #1.2 level 0.007204

> volume #1.2 level 0.05131

> volume #1.2 level 0.06492

> ui mousemode right zoom

> volume #1.2 level 0.003867

> volume #1.2 step 1

> volume #1.2 level 0.01122

> ui mousemode right "contour level"

> volume #1.2 level 0.01008

> volume #1.2 level 0.009703

> surface dust #1.2 size 7

> volume #1.2 level 0.01572

> surface dust #1.2 size 7

> hide #!1.2 models

> show #!1.1 models

> volume #1.1 level 0.01402

> volume #1.1 level 0.01321

> volume #1.1 level 0.012

> surface dust #1.1 size 7

> show #!1.2 models

> hide #!1.2 models

> show #!1.2 models

> hide #!1.1 models

> volume #1.2 level -0.06142

> volume #1.2 level -0.05915

> undo

> ui mousemode right "contour level"

> ui mousemode right "pick blobs"

> volume showOutlineBox true

> volume showOutlineBox false

> volume showOutlineBox true

> volume showOutlineBox false

Volume zone shortcut requires 1 displayed atomic model and 1 map, got 0 atomic
models, 2 maps.  

> volume region all imageMode "full region"

> volume unzone

> mousemode rightMode "crop volume"

> volume region all imageMode "full region"

> volume unzone

> mousemode rightMode "crop volume"

> volume step 1

> volume step 2

> volume hide

> volume show

> transparency 0

> transparency 50

> transparency 0

> transparency 50

> volume showOutlineBox true

> volume showOutlineBox false

> volume planes z style image imageMode "full region"

> mousemode rightMode "move planes"

> volume planes z style image imageMode "full region"

> mousemode rightMode "move planes"

> volume #1.1 style image region all imageMode "tilted slab" tiltedSlabAxis
> 0,0,1 tiltedSlabOffset 154.1 tiltedSlabSpacing 0.7004 tiltedSlabPlaneCount
> 10

> mousemode rightMode "rotate slab"

> volume #1.2 style image region all imageMode "tilted slab" tiltedSlabAxis
> 0,0,1 tiltedSlabOffset 154.1 tiltedSlabSpacing 0.7004 tiltedSlabPlaneCount
> 10

> mousemode rightMode "rotate slab"

> volume #1.1 orthoplanes xyz positionPlanes 220,220,220 style image region
> all

> mousemode rightMode "move planes"

> volume #1.2 orthoplanes xyz positionPlanes 220,220,220 style image region
> all

> mousemode rightMode "move planes"

> volume #1.1 orthoplanes xyz positionPlanes 220,220,220 style image region
> all

> mousemode rightMode "move planes"

> volume #1.2 orthoplanes xyz positionPlanes 220,220,220 style image region
> all

> mousemode rightMode "move planes"

> volume region all imageMode "full region"

> volume unzone

> mousemode rightMode "crop volume"

> volume style surface

> transparency 0

> volume showOutlineBox false

> volume showOutlineBox true

> volume showOutlineBox false

> volume style surface

> volume style mesh

> volume style image

> hide #!1.1 models

> show #!1.1 models

> hide #!1.1 models

> show #!1.1 models

> hide #!1.2 models

> show #!1.2 models

> hide #!1.2 models

> show #!1.2 models

> volume show

> reset

Unknown command: reset  

> restart

Unknown command: restart  

> volume #1.1 color #ff7800 color white color white

> volume #1.2 color #2ec27e color white color white

> volume #1.1 level -0.003977,0 level 0.02495,0.8 level 0.1514,1

> volume #1.1 style surface

> volume #1.2 style surface

> volume #1.2 level 0.01464

> volume #1.1 level 0.01411

> surface dust #1.1 size 7

> surface dust #1.2 size 7

> hide #!1.1 models

> show #!1.1 models

> hide #!1.1 models

> hide #!1.2 models

> show #!1.1 models

> show #!1.2 models

> hide #!1.1 models


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

Log:
Startup Messages  
---  
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle  
  
UCSF ChimeraX version: 1.6 (2023-03-23)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 4.6 (Core Profile) Mesa 23.2.1-1ubuntu3.1~22.04.2
OpenGL renderer: Mesa Intel(R) UHD Graphics (CML GT2)
OpenGL vendor: Intel

Python: 3.9.11
Locale: en_US.UTF-8
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: xcb

XDG_SESSION_TYPE=x11
DESKTOP_SESSION=ubuntu
XDG_SESSION_DESKTOP=ubuntu
XDG_CURRENT_DESKTOP=ubuntu:GNOME
DISPLAY=:1
Manufacturer: Dell Inc.
Model: G5 5500
OS: Ubuntu 22.04 Jammy Jellyfish
Architecture: 64bit ELF
Virtual Machine: none
CPU: 12 Intel(R) Core(TM) i7-10750H CPU @ 2.60GHz
Cache Size: 12288 KB
Memory:
	               total        used        free      shared  buff/cache   available
	Mem:            15Gi       2.3Gi       2.6Gi       616Mi        10Gi        12Gi
	Swap:          2.0Gi       0.0Ki       2.0Gi

Graphics:
	00:02.0 VGA compatible controller [0300]: Intel Corporation CometLake-H GT2 [UHD Graphics] [8086:9bc4] (rev 05)	
	DeviceName: Onboard - Video	
	Subsystem: Dell CometLake-H GT2 [UHD Graphics] [1028:09e2]

Installed Packages:
    alabaster: 0.7.13
    appdirs: 1.4.4
    asttokens: 2.2.1
    Babel: 2.12.1
    backcall: 0.2.0
    beautifulsoup4: 4.11.2
    blockdiag: 3.0.0
    build: 0.10.0
    certifi: 2023.5.7
    cftime: 1.6.2
    charset-normalizer: 3.1.0
    ChimeraX-AddCharge: 1.5.9
    ChimeraX-AddH: 2.2.3
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.3.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.9.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.3
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.43.10
    ChimeraX-AtomicLibrary: 10.0.6
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3.2
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.1
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.8
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.2
    ChimeraX-ChangeChains: 1.0.2
    ChimeraX-CheckWaters: 1.3.1
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.3
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.6
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.4.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2
    ChimeraX-DistMonitor: 1.3.3
    ChimeraX-DockPrep: 1.1.1
    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: 1.1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-Label: 1.1.7
    ChimeraX-LinuxSupport: 1.0.1
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.2
    ChimeraX-Map: 1.1.4
    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: 2.0.12
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.12
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.9
    ChimeraX-ModelPanel: 1.3.7
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.0
    ChimeraX-NRRD: 1.0
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.10.1
    ChimeraX-PDB: 2.7
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 3.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.1
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.8.3
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.1
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.10.2
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.28.4
    ChimeraX-uniprot: 2.2.2
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.1
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.1.3
    contourpy: 1.0.7
    cxservices: 1.2.2
    cycler: 0.11.0
    Cython: 0.29.33
    debugpy: 1.6.7
    decorator: 5.1.1
    distro: 1.7.0
    docutils: 0.19
    executing: 1.2.0
    filelock: 3.9.0
    fonttools: 4.39.3
    funcparserlib: 1.0.1
    grako: 3.16.5
    h5py: 3.8.0
    html2text: 2020.1.16
    idna: 3.4
    ihm: 0.35
    imagecodecs: 2022.9.26
    imagesize: 1.4.1
    importlib-metadata: 6.6.0
    ipykernel: 6.21.1
    ipython: 8.10.0
    ipython-genutils: 0.2.0
    ipywidgets: 8.0.6
    jedi: 0.18.2
    Jinja2: 3.1.2
    jupyter-client: 8.0.2
    jupyter-core: 5.3.0
    jupyterlab-widgets: 3.0.7
    kiwisolver: 1.4.4
    line-profiler: 4.0.2
    lxml: 4.9.2
    lz4: 4.3.2
    MarkupSafe: 2.1.2
    matplotlib: 3.6.3
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.6
    netCDF4: 1.6.2
    networkx: 2.8.8
    nibabel: 5.0.1
    nptyping: 2.5.0
    numexpr: 2.8.4
    numpy: 1.23.5
    openvr: 1.23.701
    packaging: 23.1
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 9.3.0
    pip: 23.0
    pkginfo: 1.9.6
    platformdirs: 3.5.0
    prompt-toolkit: 3.0.38
    psutil: 5.9.4
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.14.0
    pynrrd: 1.0.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    pyproject-hooks: 1.0.0
    PyQt6-commercial: 6.4.2
    PyQt6-Qt6: 6.4.3
    PyQt6-sip: 13.4.1
    PyQt6-WebEngine-commercial: 6.4.0
    PyQt6-WebEngine-Qt6: 6.4.3
    python-dateutil: 2.8.2
    pytz: 2023.3
    pyzmq: 25.0.2
    qtconsole: 5.4.0
    QtPy: 2.3.1
    RandomWords: 0.4.0
    requests: 2.28.2
    scipy: 1.9.3
    setuptools: 67.4.0
    sfftk-rw: 0.7.3
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.4.1
    sphinx: 6.1.3
    sphinx-autodoc-typehints: 1.22
    sphinxcontrib-applehelp: 1.0.4
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.1
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    stack-data: 0.6.2
    tables: 3.7.0
    tcia-utils: 1.2.0
    tifffile: 2022.10.10
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.3.1
    traitlets: 5.9.0
    typing-extensions: 4.5.0
    tzdata: 2023.3
    urllib3: 1.26.15
    wcwidth: 0.2.6
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.7
    zipp: 3.15.0

Change History (2)

comment:1 by Eric Pettersen, 15 months ago

Cc:	Tom Goddard added
Component:	Unassigned → Core
Owner:	set to Eric Pettersen
Platform:	→ all
Project:	→ ChimeraX
Status:	new → accepted
Summary:	ChimeraX bug report submission → Crash in event loop

Hi Martin,

Thanks for reporting this problem. The information in the report doesn't give a really clear indication of what went wrong. Do you remember what you were doing when the crash occurred?
Also, you could consider upgrading to ChimeraX 1.8. You're currently running 1.6.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

comment:2 by Eric Pettersen, 15 months ago

Status:	accepted → feedback

Note: See TracTickets for help on using tickets.

Download in other formats: