Opened 2 years ago

Closed 2 years ago

#9751 closed defect (can't reproduce)

Crash in Qt event loop after opening volume series

Reported by: chimerax-bug-report@… Owned by: Tom Goddard
Priority: normal Milestone:
Component: Volume Data Version:
Keywords: Cc: Eric Pettersen, Greg Couch
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Linux-6.2.0-32-generic-x86_64-with-glibc2.35
ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 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 0x00007f62f47d5b80 (most recent call first):
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/ui/gui.py", line 275 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 =====
UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /home/raf58/Downloads/cryosparc_P3_J7_series_0*.mrc

Unknown command: vseries open
/home/raf58/Downloads/cryosparc_P3_J7_series_0*.mrc  

> open /home/raf58/Downloads/cryosparc_P3_J7_series_0/*.mrc

Unknown command: vseries open
/home/raf58/Downloads/cryosparc_P3_J7_series_0/*.mrc  


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

Log:
UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open /home/raf58/Desktop/MRC_2023/individual_modifications/m5C4447.cxs

Opened cryosparc_P28_J25_009_volume_map_sharp (1).mrc z flip as #2, grid size
768,768,768, pixel 0.652, shown at level 0.903, step 1, values float32  
Opened cryosparc_P28_J25_009_volume_map_sharp (1).mrc z flip zone as #6, grid
size 768,768,768, pixel 0.652, shown at level 1.45, step 1, values float32  
Log from Sat Sep 9 14:35:16 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open /home/raf58/Desktop/MRC_2023/individual_modifications/m6A4220.cxs

Opened cryosparc_P28_J25_009_volume_map_sharp (1).mrc z flip as #2, grid size
768,768,768, pixel 0.652, shown at level 0.903, step 1, values float32  
Opened cryosparc_P28_J25_009_volume_map_sharp (1).mrc z flip zone as #6, grid
size 768,768,768, pixel 0.652, shown at level 1.12, step 1, values float32  
Log from Thu Sep 7 17:27:52 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "/home/raf58/Downloads/cryosparc_P28_J25_009_volume_map_sharp (1).mrc"

Opened cryosparc_P28_J25_009_volume_map_sharp (1).mrc as #1, grid size
768,768,768, pixel 0.652, shown at step 1, values float32  

> volume #1 region 0,0,0,767,767,767 step 4

[Repeated 1 time(s)]

> volume #1 change image level -0.1685,0 level 0.8563,0.8 level 5.5,1

> volume #1 level 0.9026

> volume #1 step 1

> vop flip #1

Opened cryosparc_P28_J25_009_volume_map_sharp (1).mrc z flip as #2, grid size
768,768,768, pixel 0.652, shown at step 1, values float32  

> close #1

> open /media/raf58/Data/Desktop/20230719_Lafontaine_HCT116/8g60_1.pdb
> /media/raf58/Data/Desktop/20230719_Lafontaine_HCT116/8g60_2.pdb
> /media/raf58/Data/Desktop/20230719_Lafontaine_HCT116/8g60_3.pdb
> /media/raf58/Data/Desktop/20230719_Lafontaine_HCT116/8g60_4.pdb

Summary of feedback from opening
/media/raf58/Data/Desktop/20230719_Lafontaine_HCT116/8g60_1.pdb  
---  
warning | Ignored bad PDB record found on line 1  
HEADER RIBOSOME 2023-02-14 XXXX  
  
Summary of feedback from opening
/media/raf58/Data/Desktop/20230719_Lafontaine_HCT116/8g60_2.pdb  
---  
warning | Ignored bad PDB record found on line 1  
HEADER RIBOSOME 2023-02-14 XXXX  
  
Summary of feedback from opening
/media/raf58/Data/Desktop/20230719_Lafontaine_HCT116/8g60_3.pdb  
---  
warning | Ignored bad PDB record found on line 1  
HEADER RIBOSOME 2023-02-14 XXXX  
  
Summary of feedback from opening
/media/raf58/Data/Desktop/20230719_Lafontaine_HCT116/8g60_4.pdb  
---  
warning | Ignored bad PDB record found on line 1  
HEADER RIBOSOME 2023-02-14 XXXX  
  
Chain information for 8g60_1.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
  
Chain information for 8g60_2.pdb #3  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
F | No description available  
G | No description available  
H | No description available  
I | No description available  
J | No description available  
K | No description available  
L | No description available  
M | No description available  
  
Chain information for 8g60_3.pdb #4  
---  
Chain | Description  
0 | No description available  
1 | No description available  
2 | No description available  
3 | No description available  
4 | No description available  
5 | No description available  
6 | No description available  
7 | No description available  
8 | No description available  
9 | No description available  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
F | No description available  
G | No description available  
H | No description available  
I | No description available  
J | No description available  
K | No description available  
L | No description available  
M | No description available  
N | No description available  
O | No description available  
P | No description available  
Q | No description available  
R | No description available  
S | No description available  
T | No description available  
U | No description available  
V | No description available  
W | No description available  
X | No description available  
Y | No description available  
Z | No description available  
a | No description available  
b | No description available  
c | No description available  
d | No description available  
e | No description available  
f | No description available  
g | No description available  
h | No description available  
i | No description available  
j | No description available  
k | No description available  
l | No description available  
m | No description available  
n | No description available  
o | No description available  
p | No description available  
q | No description available  
r | No description available  
s | No description available  
t | No description available  
u | No description available  
v | No description available  
w | No description available  
x | No description available  
y | No description available  
z | No description available  
  
Chain information for 8g60_4.pdb #5  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
F | No description available  
G | No description available  
H | No description available  
I | No description available  
  

> style stick

Changed 223720 atom styles  

> ui tool show "Fit in Map"

> select add #1

38832 atoms, 43261 bonds, 5 pseudobonds, 1944 residues, 2 models selected  

> select add #3

138459 atoms, 152182 bonds, 20 pseudobonds, 8562 residues, 4 models selected  

> select add #4

214045 atoms, 229058 bonds, 27 pseudobonds, 18007 residues, 6 models selected  

> select add #5

223720 atoms, 239241 bonds, 29 pseudobonds, 18946 residues, 8 models selected  

> fitmap sel inMap #2

Fit molecules 8g60_1.pdb (#1), 8g60_2.pdb (#3), 8g60_3.pdb (#4), 8g60_4.pdb
(#5) to map cryosparc_P28_J25_009_volume_map_sharp (1).mrc z flip (#2) using
223720 atoms  
average map value = 1.014, steps = 48  
shifted from previous position = 0.024  
rotated from previous position = 0.0127 degrees  
atoms outside contour = 117270, contour level = 0.90259  
  
Position of 8g60_1.pdb (#1) relative to cryosparc_P28_J25_009_volume_map_sharp
(1).mrc z flip (#2) coordinates:  
Matrix rotation and translation  
0.99999998 0.00021898 -0.00002446 -0.03829522  
-0.00021898 0.99999998 -0.00002909 0.04789946  
0.00002445 0.00002909 1.00000000 -0.02909931  
Axis 0.13088053 -0.11003561 -0.98527278  
Axis point 227.96113082 185.89852351 0.00000000  
Rotation angle (degrees) 0.01273398  
Shift along axis 0.01838801  
  
Position of 8g60_2.pdb (#3) relative to cryosparc_P28_J25_009_volume_map_sharp
(1).mrc z flip (#2) coordinates:  
Matrix rotation and translation  
0.99999998 0.00021898 -0.00002446 -0.03829522  
-0.00021898 0.99999998 -0.00002909 0.04789946  
0.00002445 0.00002909 1.00000000 -0.02909931  
Axis 0.13088053 -0.11003561 -0.98527278  
Axis point 227.96113082 185.89852351 0.00000000  
Rotation angle (degrees) 0.01273398  
Shift along axis 0.01838801  
  
Position of 8g60_3.pdb (#4) relative to cryosparc_P28_J25_009_volume_map_sharp
(1).mrc z flip (#2) coordinates:  
Matrix rotation and translation  
0.99999998 0.00021898 -0.00002446 -0.03829522  
-0.00021898 0.99999998 -0.00002909 0.04789946  
0.00002445 0.00002909 1.00000000 -0.02909931  
Axis 0.13088053 -0.11003561 -0.98527278  
Axis point 227.96113082 185.89852351 0.00000000  
Rotation angle (degrees) 0.01273398  
Shift along axis 0.01838801  
  
Position of 8g60_4.pdb (#5) relative to cryosparc_P28_J25_009_volume_map_sharp
(1).mrc z flip (#2) coordinates:  
Matrix rotation and translation  
0.99999998 0.00021898 -0.00002446 -0.03829522  
-0.00021898 0.99999998 -0.00002909 0.04789946  
0.00002445 0.00002909 1.00000000 -0.02909931  
Axis 0.13088053 -0.11003561 -0.98527278  
Axis point 227.96113082 185.89852351 0.00000000  
Rotation angle (degrees) 0.01273398  
Shift along axis 0.01838801  
  

> select clear

> select :3782

21 atoms, 22 bonds, 1 residue, 1 model selected  

> view sel

> select clear

> color #1,3-5 light gray

> color byhetero

> select clear

> select #3/A:3782@CM5

1 atom, 1 residue, 1 model selected  

> select up

21 atoms, 22 bonds, 1 residue, 1 model selected  

> hide #* target a

> show sel target ab

> volume zone #2 nearAtoms sel range 1 newMap true

Opened cryosparc_P28_J25_009_volume_map_sharp (1).mrc z flip zone as #6, grid
size 768,768,768, pixel 0.652, shown at step 1, values float32  

> volume #6 surfaceSmoothing true subdivideSurface true smoothLines true

> volume #6 style mesh

> volume #6 color #c0bfbc

> set bgColor white

> transparency #6 70

> select clear

> hide cartoons

> volume #6 level 1.225

> select #3/A:3782@OP1

1 atom, 1 residue, 1 model selected  

> select up

21 atoms, 22 bonds, 1 residue, 1 model selected  

> fitmap sel inMap #6

Fit molecule 8g60_2.pdb (#3) to map cryosparc_P28_J25_009_volume_map_sharp
(1).mrc z flip zone (#6) using 21 atoms  
average map value = 2.177, steps = 44  
shifted from previous position = 0.113  
rotated from previous position = 0.702 degrees  
atoms outside contour = 0, contour level = 1.2248  
  
Position of 8g60_2.pdb (#3) relative to cryosparc_P28_J25_009_volume_map_sharp
(1).mrc z flip zone (#6) coordinates:  
Matrix rotation and translation  
0.99997258 -0.00670264 0.00314746 0.88593637  
0.00667224 0.99993194 0.00957060 -4.29413943  
-0.00321140 -0.00954933 0.99994925 3.41369858  
Axis -0.79058334 0.26293017 0.55303319  
Axis point 0.00000000 351.69036025 452.78648786  
Rotation angle (degrees) 0.69285419  
Shift along axis 0.05842324  
  

> select clear

> volume #6 level 1.082

> select clear

> save /home/raf58/Desktop/individual_modifications/m5C3782.tif width 1152
> height 804 supersample 3

> save /home/raf58/Desktop/individual_modifications/m5C3782.cxs

> hide atoms

> close #6

> select :4220

23 atoms, 25 bonds, 1 residue, 1 model selected  

> show sel atoms

> view sel

> volume zone #2 nearAtoms sel range 1 newMap true

Opened cryosparc_P28_J25_009_volume_map_sharp (1).mrc z flip zone as #6, grid
size 768,768,768, pixel 0.652, shown at step 1, values float32  

> fitmap sel inMap #2

Fit molecule 8g60_2.pdb (#3) to map cryosparc_P28_J25_009_volume_map_sharp
(1).mrc z flip (#2) using 23 atoms  
average map value = 2.269, steps = 52  
shifted from previous position = 0.89  
rotated from previous position = 2.44 degrees  
atoms outside contour = 0, contour level = 0.90259  
  
Position of 8g60_2.pdb (#3) relative to cryosparc_P28_J25_009_volume_map_sharp
(1).mrc z flip (#2) coordinates:  
Matrix rotation and translation  
0.99921845 -0.00523544 -0.03918000 10.12772351  
0.00579259 0.99988352 0.01412032 -4.24568024  
0.03910151 -0.01433624 0.99913240 -5.59179812  
Axis -0.33868724 -0.93169910 0.13125453  
Axis point 147.93783720 0.00000000 253.73984028  
Rotation angle (degrees) 2.40770885  
Shift along axis -0.20838310  
  

> close #6

> volume zone #2 nearAtoms sel range 1 newMap true

Opened cryosparc_P28_J25_009_volume_map_sharp (1).mrc z flip zone as #6, grid
size 768,768,768, pixel 0.652, shown at step 1, values float32  

> fitmap sel inMap #6

Fit molecule 8g60_2.pdb (#3) to map cryosparc_P28_J25_009_volume_map_sharp
(1).mrc z flip zone (#6) using 23 atoms  
average map value = 2.27, steps = 40  
shifted from previous position = 0.0174  
rotated from previous position = 0.24 degrees  
atoms outside contour = 0, contour level = 0.90259  
  
Position of 8g60_2.pdb (#3) relative to cryosparc_P28_J25_009_volume_map_sharp
(1).mrc z flip zone (#6) coordinates:  
Matrix rotation and translation  
0.99926339 -0.00546957 -0.03798378 9.92587004  
0.00616134 0.99981685 0.01811907 -5.18227264  
0.03787772 -0.01833975 0.99911407 -4.19878388  
Axis -0.42909092 -0.89282871 0.13688638  
Axis point 116.10770300 0.00000000 256.72887842  
Rotation angle (degrees) 2.43487464  
Shift along axis -0.20697520  
  

> volume #6 style mesh

> volume #6 surfaceSmoothing true subdivideSurface true smoothLines true

> volume #6 color #c0bfbc

> transparency #6 70

> select clear

> volume #6 level 1.117

> save /home/raf58/Desktop/individual_modifications/m6A4220.tif width 1152
> height 804 supersample 3

> save /home/raf58/Desktop/individual_modifications/m6A4220.cxs

——— End of log from Thu Sep 7 17:27:52 2023 ———

opened ChimeraX session  

> hide atoms

> close #6

> select #3:4447

21 atoms, 22 bonds, 1 residue, 1 model selected  

> view sel

> show sel atoms

> ui tool show "Fit in Map"

> fitmap sel inMap #2

Fit molecule 8g60_2.pdb (#3) to map cryosparc_P28_J25_009_volume_map_sharp
(1).mrc z flip (#2) using 21 atoms  
average map value = 2.453, steps = 52  
shifted from previous position = 1.07  
rotated from previous position = 2.66 degrees  
atoms outside contour = 0, contour level = 0.90259  
  
Position of 8g60_2.pdb (#3) relative to cryosparc_P28_J25_009_volume_map_sharp
(1).mrc z flip (#2) coordinates:  
Matrix rotation and translation  
0.99943813 -0.00440471 -0.03322697 8.75622564  
0.00347476 0.99960206 -0.02799377 5.59947926  
0.03333705 0.02786259 0.99905571 -15.31677427  
Axis 0.64017805 -0.76290010 0.09030781  
Axis point 466.58590223 0.00000000 256.59178347  
Rotation angle (degrees) 2.50035898  
Shift along axis -0.04952422  
  

> volume zone #2 nearAtoms sel range 1 newMap true

Opened cryosparc_P28_J25_009_volume_map_sharp (1).mrc z flip zone as #6, grid
size 768,768,768, pixel 0.652, shown at step 1, values float32  

> volume #6 surfaceSmoothing true subdivideSurface true smoothLines true

> volume #6 color #c0bfbc

> volume #6 style mesh

> transparency #6 70

> select clear

[Repeated 1 time(s)]

> volume #6 level 1.451

> save /home/raf58/Desktop/MRC_2023/individual_modifications/m5C4447.tif width
> 1188 height 804 supersample 3

> save /home/raf58/Desktop/MRC_2023/individual_modifications/m5C4447.cxs

——— End of log from Sat Sep 9 14:35:16 2023 ———

opened ChimeraX session  




OpenGL version: 4.6 (Core Profile) Mesa 23.0.4-0ubuntu1~22.04.1
OpenGL renderer: Mesa Intel(R) UHD Graphics 630 (CFL GT2)
OpenGL vendor: Intel

Python: 3.9.11
Locale: en_GB.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: Micro-Star International Co., Ltd.
Model: GL65 9SD
OS: Ubuntu 22.04 Jammy Jellyfish
Architecture: 64bit ELF
Virtual Machine: none
CPU: 12 Intel(R) Core(TM) i7-9750H CPU @ 2.60GHz
Cache Size: 12288 KB
Memory:
	               total        used        free      shared  buff/cache   available
	Mem:            62Gi       5.7Gi        52Gi       428Mi       4.2Gi        55Gi
	Swap:          2.0Gi          0B       2.0Gi

Graphics:
	00:02.0 VGA compatible controller [0300]: Intel Corporation CoffeeLake-H GT2 [UHD Graphics 630] [8086:3e9b]	
	DeviceName: Onboard - Video	
	Subsystem: Micro-Star International Co., Ltd. [MSI] CoffeeLake-H GT2 [UHD Graphics 630] [1462:129b]

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: 1.5.9.1
    ChimeraX-AddH: 2.2.5
    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: 1.6.1
    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: 1.4
    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: 2.7.2
    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: 1.10.3
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1.2
    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-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 (6)

comment:1 by Eric Pettersen, 2 years ago

Component: Unassigned → Volume Data
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Crash working with volume series

comment:2 by Tom Goddard, 2 years ago

Summary: Crash working with volume series → Crash in Qt event loop after opening volume series

I wonder if the user killed ChimeraX from the shell (on Linux). It looks like all they did is open a series of MRC files (open /path/*.mrc) two times. Oddly the log shows unknown command vseries open messages even though the log does not indicate they typed such a command. Is that message coming from the open command?

comment:3 by Tom Goddard, 2 years ago

Aha. Typing the command "vseries open /path/*.mrc" logs the command name as "open". I guess it is an alias. But then the error "Uknown command: vseries open /path/*.mrc" seems odd.

So the user actually did not open any data before the crash happened.

comment:4 by Eric Pettersen, 2 years ago

Cc: Eric Pettersen Greg Couch added

The logging is some kind of interaction between the fact that map_series declares a "vseries" command but only registers subcommands with however the command-processing system handles that. For instance, running the command "vseries xyzzy" logs:

xyzzy
Unknown command: vseries xyzzy

comment:5 by Tom Goddard, 2 years ago

Yep. I have submitted another bug report that command logging is broken in this situation, bug #9759.

comment:6 by Tom Goddard, 2 years ago

Resolution: → can't reproduce
Status: assigned → closed

From the Log, the user did not open any data or run any commands when the Qt crash (segmentation fault) happened in the Qt event loop. No telling what happened.

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