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#15953 closed defect (can't reproduce)

Keyboard interrupt during restoration of map data

Reported by:	chimerax-bug-report@…	Owned by:	Tom Goddard
Priority:	normal	Milestone:
Component:	Sessions	Version:
Keywords:		Cc:
Blocked By:		Blocking:
Notify when closed:		Platform:	all
Project:	ChimeraX

Description

The following bug report has been submitted:
Platform:        Linux-5.15.0-121-generic-x86_64-with-glibc2.31
ChimeraX Version: 1.6.dev202301280224 (2023-01-28 02:24:25 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 0x00007f551e965740 (most recent call first):
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-packages/chimerax/ui/gui.py", line 284 in event_loop
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-packages/chimerax/core/__main__.py", line 892 in init
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-packages/chimerax/core/__main__.py", line 1043 in 
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/runpy.py", line 87 in _run_code
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/runpy.py", line 197 in _run_module_as_main
===== Log before crash start =====
UCSF ChimeraX version: 1.6.dev202301280224 (2023-01-28)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> /home/altair/PycharmProjects/UCSF_colab_2024/output/aug/AF_3mc_all_no_mso1/sampcon_filtered_95_100/all_no_mso1.cxs
> format session

Opened LPD_Exo70.mrc as #2, grid size 122,113,111, pixel 5, shown at level
0.00186, step 1, values float32  
Opened LPD_Exo84.mrc as #3, grid size 119,117,121, pixel 5, shown at level
0.00195, step 1, values float32  
Opened LPD_Gyl1_NG_C.mrc as #4, grid size 276,280,262, pixel 5, shown at level
5.8e-07, step 2, values float32  
Opened LPD_Gyp5_NG_C.mrc as #5, grid size 278,267,270, pixel 5, shown at level
6.85e-07, step 2, values float32  
Opened LPD_Myo2_NG_C.mrc as #6, grid size 321,308,323, pixel 5, shown at level
2.69e-07, step 2, values float32  
Opened LPD_Sec2_NG_C.mrc as #7, grid size 298,321,335, pixel 5, shown at level
3.04e-07, step 2, values float32  
Opened LPD_Sec3_C.mrc as #8, grid size 113,111,110, pixel 5, shown at level
0.00197, step 1, values float32  
Opened LPD_Sec3_N.mrc as #9, grid size 185,176,167, pixel 5, shown at level
0.000259, step 1, values float32  
Opened LPD_Sec5.mrc as #10, grid size 116,116,121, pixel 5, shown at level
0.00202, step 1, values float32  
Opened LPD_Sec6.mrc as #11, grid size 109,111,120, pixel 5, shown at level
0.00242, step 1, values float32  
Opened LPD_Sec8.mrc as #12, grid size 114,112,115, pixel 5, shown at level
0.00362, step 1, values float32  
Opened LPD_Sec10.mrc as #13, grid size 117,117,130, pixel 5, shown at level
0.0024, step 1, values float32  
Opened LPD_Sec15.mrc as #14, grid size 126,113,125, pixel 5, shown at level
0.00213, step 1, values float32  
Opened LPD_Smy1_NG_C.mrc as #15, grid size 338,310,357, pixel 5, shown at
level 1.83e-07, step 2, values float32  
opened ChimeraX session  

> select clear

> hide #!15 models

> hide #!4 models

> hide #!5 models

> hide #!6 models

> hide #!7 models

> view

> surface dust #2 size 50

> surface dust #3 size 50

> surface dust #8 size 50

> surface dust #10 size 50

> surface dust #11 size 50

> surface dust #12 size 50

> surface dust #13 size 50

> surface dust #14 size 50

> view

> ui tool show "Map Statistics"

> measure mapstats #!2-3,8,10-14

Map LPD_Exo70.mrc #2, minimum 0, maximum 0.03642, mean 7.169e-05, SD
0.0006114, RMS 0.0006155  
Map LPD_Exo84.mrc #3, minimum 0, maximum 0.02881, mean 7.977e-05, SD
0.0006179, RMS 0.0006231  
Map LPD_Sec3_C.mrc #8, minimum 0, maximum 0.03742, mean 9.057e-05, SD
0.0007462, RMS 0.0007517  
Map LPD_Sec5.mrc #10, minimum 0, maximum 0.04968, mean 9.549e-05, SD
0.0009196, RMS 0.0009246  
Map LPD_Sec6.mrc #11, minimum 0, maximum 0.05133, mean 9.163e-05, SD
0.0008261, RMS 0.0008311  
Map LPD_Sec8.mrc #12, minimum 0, maximum 0.04208, mean 0.0001486, SD
0.0009685, RMS 0.0009799  
Map LPD_Sec10.mrc #13, minimum 0, maximum 0.02782, mean 9.9e-05, SD 0.0007698,
RMS 0.0007762  
Map LPD_Sec15.mrc #14, minimum 0, maximum 0.0326, mean 8.443e-05, SD
0.0006763, RMS 0.0006816  

> show #!6 models

> show #!7 models

> ui tool show "Map Statistics"

> measure mapstats #!2-3,6-8,10-14

Map LPD_Exo70.mrc #2, minimum 0, maximum 0.03642, mean 7.169e-05, SD
0.0006114, RMS 0.0006155  
Map LPD_Exo84.mrc #3, minimum 0, maximum 0.02881, mean 7.977e-05, SD
0.0006179, RMS 0.0006231  
Map LPD_Myo2_NG_C.mrc #6, step 2, minimum 0, maximum 4.442e-05, mean
2.665e-08, SD 4.141e-07, RMS 4.15e-07  
Map LPD_Sec2_NG_C.mrc #7, step 2, minimum 0, maximum 3.685e-05, mean
2.647e-08, SD 3.932e-07, RMS 3.94e-07  
Map LPD_Sec3_C.mrc #8, minimum 0, maximum 0.03742, mean 9.057e-05, SD
0.0007462, RMS 0.0007517  
Map LPD_Sec5.mrc #10, minimum 0, maximum 0.04968, mean 9.549e-05, SD
0.0009196, RMS 0.0009246  
Map LPD_Sec6.mrc #11, minimum 0, maximum 0.05133, mean 9.163e-05, SD
0.0008261, RMS 0.0008311  
Map LPD_Sec8.mrc #12, minimum 0, maximum 0.04208, mean 0.0001486, SD
0.0009685, RMS 0.0009799  
Map LPD_Sec10.mrc #13, minimum 0, maximum 0.02782, mean 9.9e-05, SD 0.0007698,
RMS 0.0007762  
Map LPD_Sec15.mrc #14, minimum 0, maximum 0.0326, mean 8.443e-05, SD
0.0006763, RMS 0.0006816  

> hide #!1 models

> show #!1 models

> hide #!11 models

> hide #!10 models

> hide #!12 models

> hide #!13 models

> hide #!14 models

> hide #!6 models

> hide #!7 models

> hide #!8 models

> hide #!3 models

> hide #!2 models

> hide #1.1 models

> show #1.1 models

> select clear

> graphics silhouettes false

> graphics silhouettes true

> lighting shadows true

> lighting shadows false

> lighting flat

> lighting full

> lighting shadows false

> lighting flat

> lighting soft

> show #!7 models

> show #7 target s

> show all

> volume zone #7 nearAtoms #1 /L range 510

> volume zone #7 nearAtoms #1 /L range 1000

> transparency #4-7 #15 70 target s

> volume zone #7 nearAtoms #1 /L range 10000

> ui tool show "Measure Volume and Area"

> toolshed show

> ui tool show "Surface Zone"

> surface zone #7 nearAtoms #1.1 distance 5

> surface zone #7 nearAtoms #1.1 distance 9.51

> surface zone #7 nearAtoms #1.1 distance 18.69

> surface zone #7 nearAtoms #1.1 distance 214.57

> surface unzone #7

> surface zone #7 nearAtoms #1.1 distance 214.57

> select #7

2 models selected  

> select #7

2 models selected  

> select clear

> select /L:1@C

1 atom, 1 residue, 1 model selected  

> surface zone #7 nearAtoms sel distance 481.14

> surface zone #7 nearAtoms sel distance 428.72

> surface unzone #7

> surface zone #7 nearAtoms sel distance 428.72

> help help:user/tools/surfacezone.html

> ui tool show Contacts

> select clear

Drag select of 1 atoms, 7 LPD_Sec2_NG_C.mrc  

> help help:user/tools/measurevolume.html

> select clear

> volume #!7 step 1

> surface dust #7 size 50

> undust

Unknown command: undust  

> select /L:1@C

1 atom, 1 residue, 1 model selected  

> undo

> surface undust

Missing or invalid "surfaces" argument: empty atom specifier  

> surface undust #7

> select /L:1@C

1 atom, 1 residue, 1 model selected  

> surface zone #7 nearAtoms sel distance 6.97

> surface zone #7 nearAtoms sel distance 58.03

> ui tool show "Selection Inspector"

> size sel atomRadius 3

Changed 1 atom radii  

> surface zone #7 nearAtoms sel distance 58.03

> surface zone #7 nearAtoms sel distance 57.63

> surface zone #7 nearAtoms sel distance 57.24

> surface zone #7 nearAtoms sel distance 56.84

> surface zone #7 nearAtoms sel distance 56.45

> surface zone #7 nearAtoms sel distance 56.06

> surface zone #7 nearAtoms sel distance 55.68

> surface zone #7 nearAtoms sel distance 55.29

> surface zone #7 nearAtoms sel distance 54.91

> surface zone #7 nearAtoms sel distance 54.53

> surface zone #7 nearAtoms sel distance 54.16

> surface zone #7 nearAtoms sel distance 53.79

> surface zone #7 nearAtoms sel distance 53.42

> surface zone #7 nearAtoms sel distance 53.05

> surface zone #7 nearAtoms sel distance 52.68

> surface zone #7 nearAtoms sel distance 52.32

> surface zone #7 nearAtoms sel distance 51.96

> surface zone #7 nearAtoms sel distance 377.29

> surface zone #7 nearAtoms sel distance 484.14

> surface zone #7 nearAtoms sel distance 555.87

> surface zone #7 nearAtoms sel distance 56

> surface zone #7 nearAtoms sel distance 569

> surface unzone #7

> surface zone #7 nearAtoms sel distance 569

> show #!4 models

> show #!5 models

> show #!6 models

> show #!15 models

> volume zone #10 nearAtoms #1 /I range 419

> volume zone #4 nearAtoms #1 /I range 419

> volume zone #5 nearAtoms #1 /J range 416

> volume zone #7 nearAtoms #1 /L range 569

> volume zone #6 nearAtoms #1 /M range 547

> volume zone #15 nearAtoms #1 /N range 561

> volume #!4-7,15 step 1

1 atom, 1 residue, 1 model selected  

> ui tool show "Selection Inspector"

> size sel atomRadius 50

Changed 1 atom radii  

> select clear

> show #!2 models

> show #!3 models

> show #!8 models

> show #!9 models

> hide #!9 models

> show #!10 models

> show #!11 models

> show #!12 models

> show #!13 models

> show #!14 models

> view

> movie record

> turn y 2 180

> wait 180

> movie encode /home/altair/Desktop/movie1.mp4

Movie saved to /home/altair/Desktop/movie1.mp4  
  

> hide #!4 models

> hide #!5 models

> hide #!6 models

> hide #!7 models

> hide #!15 models

> view

> movie record

> turn y 2 180

> wait 180

> movie encode /home/altair/Desktop/movie2.mp4

Movie saved to /home/altair/Desktop/movie2.mp4  
  

> view

> movie record

> turn y 2 180

> wait 180

> movie encode /home/altair/Desktop/movie3.mp4

Movie saved to /home/altair/Desktop/movie3.mp4  
  

> show #!4 models

> show #!5 models

> show #!6 models

> show #!7 models

> show #!15 models

> view

> save
> /home/altair/PycharmProjects/UCSF_colab_2024/output/aug/AF_3mc_all_no_mso1/sampcon_filtered_95_100/all_no_mso1.cxs
> includeMaps true

> hide #!4 models

> hide #!5 models

> hide #!6 models

> hide #!7 models

> hide #!15 models

> view

> transparency #8-14 50 target s

> transparency #2-3 #8-14 50 target s

> transparency #2-3 #8-14 0 target s

> volume #2 style mesh

> volume #3 style mesh

> volume #4 style mesh

> volume #!2-3,8,10-14 style mesh

> movie record

> turn y 2 180

> wait 180

> movie encode /home/altair/Desktop/movie1.mp4

Movie saved to /home/altair/Desktop/movie1.mp4  
  

> volume #!2-3,8,10-14 style surface

> transparency #2.1#3.1#8.1#10.1#11.1#12.1#13.1#14.1 50

> transparency #2.1#3.1#8.1#10.1#11.1#12.1#13.1#14.1 0

> hide #!8 models

> hide #!10 models

> hide #!11 models

> hide #!12 models

> hide #!13 models

> hide #!14 models

> hide #!3 models

> hide #!2 models

> movie record

> turn y 2 180

> wait 180

> movie encode /home/altair/Desktop/movie1.mp4

Movie saved to /home/altair/Desktop/movie1.mp4  
  

> close

> open
> /home/altair/PycharmProjects/UCSF_colab_2024/output/july/AF_3mc_all/sampcon_filtered_95_100/cluster_center_model_all.rmf3

Opened RMF file produced with IMP 2.18.0, with 1 frame.  

> open
> /home/altair/PycharmProjects/UCSF_colab_2024/output/july/AF_3mc_all/sampcon_filtered_95_100/LPD_Exo70_all.mrc

Opened LPD_Exo70_all.mrc as #2, grid size 100,109,111, pixel 5, shown at level
0.00241, step 1, values float32  

> open
> /home/altair/PycharmProjects/UCSF_colab_2024/output/july/AF_3mc_all/sampcon_filtered_95_100/LPD_Exo84_all.mrc

Opened LPD_Exo84_all.mrc as #3, grid size 121,116,114, pixel 5, shown at level
0.00204, step 1, values float32  

> open
> /home/altair/PycharmProjects/UCSF_colab_2024/output/july/AF_3mc_all/sampcon_filtered_95_100/LPD_Gyl1_NG_C_all.mrc

Opened LPD_Gyl1_NG_C_all.mrc as #4, grid size 307,277,277, pixel 5, shown at
level 4.05e-07, step 2, values float32  

> open
> /home/altair/PycharmProjects/UCSF_colab_2024/output/july/AF_3mc_all/sampcon_filtered_95_100/LPD_Gyp5_NG_C_all.mrc

Opened LPD_Gyp5_NG_C_all.mrc as #5, grid size 333,299,274, pixel 5, shown at
level 3.43e-07, step 2, values float32  

> open
> /home/altair/PycharmProjects/UCSF_colab_2024/output/july/AF_3mc_all/sampcon_filtered_95_100/LPD_Mso1_NG_C_all.mrc

Opened LPD_Mso1_NG_C_all.mrc as #6, grid size 339,355,349, pixel 5, shown at
level 2.16e-09, step 2, values float32  

> open
> /home/altair/PycharmProjects/UCSF_colab_2024/output/july/AF_3mc_all/sampcon_filtered_95_100/LPD_Myo2_NG_C_all.mrc

Opened LPD_Myo2_NG_C_all.mrc as #7, grid size 319,337,342, pixel 5, shown at
level 2.09e-09, step 2, values float32  

> open
> /home/altair/PycharmProjects/UCSF_colab_2024/output/july/AF_3mc_all/sampcon_filtered_95_100/LPD_Sec2_NG_C_all.mrc

Opened LPD_Sec2_NG_C_all.mrc as #8, grid size 296,290,313, pixel 5, shown at
level 3.91e-07, step 2, values float32  

> open
> /home/altair/PycharmProjects/UCSF_colab_2024/output/july/AF_3mc_all/sampcon_filtered_95_100/LPD_Sec3_C_all.mrc

Opened LPD_Sec3_C_all.mrc as #9, grid size 106,101,115, pixel 5, shown at
level 0.00236, step 1, values float32  

> open
> /home/altair/PycharmProjects/UCSF_colab_2024/output/july/AF_3mc_all/sampcon_filtered_95_100/LPD_Sec3_N_all.mrc

Opened LPD_Sec3_N_all.mrc as #10, grid size 167,161,155, pixel 5, shown at
level 0.000355, step 1, values float32  

> open
> /home/altair/PycharmProjects/UCSF_colab_2024/output/july/AF_3mc_all/sampcon_filtered_95_100/LPD_Sec5_all.mrc

Opened LPD_Sec5_all.mrc as #11, grid size 115,118,120, pixel 5, shown at level
0.0021, step 1, values float32  

> open
> /home/altair/PycharmProjects/UCSF_colab_2024/output/july/AF_3mc_all/sampcon_filtered_95_100/LPD_Sec6_all.mrc

Opened LPD_Sec6_all.mrc as #12, grid size 107,99,95, pixel 5, shown at level
0.00363, step 1, values float32  

> open
> /home/altair/PycharmProjects/UCSF_colab_2024/output/july/AF_3mc_all/sampcon_filtered_95_100/LPD_Sec8_all.mrc

Opened LPD_Sec8_all.mrc as #13, grid size 101,109,106, pixel 5, shown at level
0.0051, step 1, values float32  

> open
> /home/altair/PycharmProjects/UCSF_colab_2024/output/july/AF_3mc_all/sampcon_filtered_95_100/LPD_Sec10_all.mrc

Opened LPD_Sec10_all.mrc as #14, grid size 123,125,133, pixel 5, shown at
level 0.00167, step 1, values float32  

> open
> /home/altair/PycharmProjects/UCSF_colab_2024/output/july/AF_3mc_all/sampcon_filtered_95_100/LPD_Sec15_all.mrc

Opened LPD_Sec15_all.mrc as #15, grid size 112,114,111, pixel 5, shown at
level 0.00313, step 1, values float32  

> open
> /home/altair/PycharmProjects/UCSF_colab_2024/output/july/AF_3mc_all/sampcon_filtered_95_100/LPD_Smy1_NG_C_all.mrc

Opened LPD_Smy1_NG_C_all.mrc as #16, grid size 346,337,344, pixel 5, shown at
level 2.08e-09, step 2, values float32  

> close

> open
> /home/altair/PycharmProjects/UCSF_colab_2024/output/july/AF_3mc_all/sampcon_filtered_95_100/all_95_100.cxs

Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/core/session.py", line 734, in restore  
obj = sm.restore_snapshot(self, data)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/map/session.py", line 219, in restore_snapshot  
grids = grid_data_from_state(data, gdcache, session, rfp)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/map/session.py", line 392, in grid_data_from_state  
path = absolute_path(s['path'], file_paths, ask = ask,  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/map/session.py", line 136, in absolute_path  
apath = file_paths.find(fpath,ask)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/map/session.py", line 261, in find  
while dnew and basename(dnew) == basename(dorig):  
File "/usr/bin/../../usr/lib/ucsf-chimerax-daily/lib/python3.9/posixpath.py",
line 143, in basename  
sep = _get_sep(p)  
File "/usr/bin/../../usr/lib/ucsf-chimerax-daily/lib/python3.9/posixpath.py",
line 41, in _get_sep  
def _get_sep(path):  
KeyboardInterrupt  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 138, in invoke  
return self._func(self._name, data)  
File "/home/altair/.local/share/ChimeraX/1.6/site-
packages/chimerax/rmf/io.py", line 175, in   
_restore_chimera_obj(session, model))  
File "/home/altair/.local/share/ChimeraX/1.6/site-
packages/chimerax/rmf/io.py", line 366, in _restore_chimera_obj  
_restore_nodes_chimera_obj(session, [model.rmf_hierarchy], model_by_id)  
File "/home/altair/.local/share/ChimeraX/1.6/site-
packages/chimerax/rmf/io.py", line 354, in _restore_nodes_chimera_obj  
_restore_nodes_chimera_obj(session, n.children, model_by_id)  
File "/home/altair/.local/share/ChimeraX/1.6/site-
packages/chimerax/rmf/io.py", line 354, in _restore_nodes_chimera_obj  
_restore_nodes_chimera_obj(session, n.children, model_by_id)  
File "/home/altair/.local/share/ChimeraX/1.6/site-
packages/chimerax/rmf/io.py", line 354, in _restore_nodes_chimera_obj  
_restore_nodes_chimera_obj(session, n.children, model_by_id)  
[Previous line repeated 3 more times]  
File "/home/altair/.local/share/ChimeraX/1.6/site-
packages/chimerax/rmf/io.py", line 352, in _restore_nodes_chimera_obj  
n.chimera_obj = _load_snapshot_chimera_obj(session, n.chimera_obj,  
File "/home/altair/.local/share/ChimeraX/1.6/site-
packages/chimerax/rmf/io.py", line 338, in _load_snapshot_chimera_obj  
return model_by_id[data['structure']].atoms[data['index']]  
KeyError: (1, 1)  
  
Error processing trigger "end restore session":  
KeyError: (1, 1)  
  
File "/home/altair/.local/share/ChimeraX/1.6/site-
packages/chimerax/rmf/io.py", line 338, in _load_snapshot_chimera_obj  
return model_by_id[data['structure']].atoms[data['index']]  
  
See log for complete Python traceback.  
  


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

Log:
UCSF ChimeraX version: 1.6.dev202301280224 (2023-01-28)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 4.6 (Core Profile) Mesa 21.2.6
OpenGL renderer: Mesa Intel(R) UHD Graphics 620 (WHL GT2)
OpenGL vendor: Intel

Python: 3.9.11
Locale: en_GB.UTF-8
Qt version: PyQt6 6.4.0, Qt 6.4.0
Qt runtime version: 6.4.2
Qt platform: xcb

XDG_SESSION_TYPE=x11
DESKTOP_SESSION=ubuntu
XDG_SESSION_DESKTOP=ubuntu
XDG_CURRENT_DESKTOP=ubuntu:GNOME
DISPLAY=:0
Manufacturer: HP
Model: HP ProBook 430 G6
OS: Ubuntu 20.04 Focal Fossa
Architecture: 64bit ELF
Virtual Machine: none
CPU: 8 Intel(R) Core(TM) i7-8565U CPU @ 1.80GHz
Cache Size: 8192 KB
Memory:
	              total        used        free      shared  buff/cache   available
	Mem:           15Gi        10Gi       749Mi       1.0Gi       4.5Gi       3.9Gi
	Swap:         2.0Gi       2.0Gi        46Mi

Graphics:
	00:02.0 VGA compatible controller [0300]: Intel Corporation UHD Graphics 620 (Whiskey Lake) [8086:3ea0] (rev 02)	
	DeviceName: Onboard IGD	
	Subsystem: Hewlett-Packard Company UHD Graphics 620 (Whiskey Lake) [103c:8536]

Installed Packages:
    alabaster: 0.7.13
    appdirs: 1.4.4
    asttokens: 2.2.1
    Babel: 2.11.0
    backcall: 0.2.0
    blockdiag: 3.0.0
    build: 0.8.0
    certifi: 2022.12.7
    cftime: 1.6.2
    charset-normalizer: 2.1.1
    ChimeraX-AddCharge: 1.5.8
    ChimeraX-AddH: 2.2.3
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.3.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.8
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.3
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.43.7
    ChimeraX-AtomicLibrary: 10.0.3
    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: 2.7.2
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.1
    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.dev202301280224
    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: 1.1
    ChimeraX-DistMonitor: 1.3.3
    ChimeraX-DockPrep: 1.1
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.2.1
    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: 2.0.11
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.11
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.8
    ChimeraX-ModelPanel: 1.3.6
    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-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.10
    ChimeraX-PDB: 2.6.13
    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: 1.0
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.1
    ChimeraX-RMF: 0.14
    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: 2.8.1
    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: 1.10.1
    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-Tug: 1.0.1
    ChimeraX-UI: 1.26
    ChimeraX-uniprot: 2.2.2
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.1.6
    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: 0.4.5
    comm: 0.1.2
    contourpy: 1.0.7
    cxservices: 1.2.2
    cycler: 0.11.0
    Cython: 0.29.32
    debugpy: 1.6.6
    decorator: 5.1.1
    distro: 1.7.0
    docutils: 0.19
    entrypoints: 0.4
    executing: 1.2.0
    filelock: 3.7.1
    fonttools: 4.38.0
    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: 6.0.0
    ipykernel: 6.19.2
    ipython: 8.7.0
    ipython-genutils: 0.2.0
    jedi: 0.18.2
    Jinja2: 3.1.2
    jupyter-client: 7.4.8
    jupyter-core: 5.1.5
    kiwisolver: 1.4.4
    line-profiler: 3.5.1
    lxml: 4.9.1
    lz4: 4.0.2
    MarkupSafe: 2.1.2
    matplotlib: 3.6.2
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.6
    netCDF4: 1.6.0
    networkx: 2.8.8
    numexpr: 2.8.4
    numpy: 1.23.5
    openvr: 1.23.701
    packaging: 23.0
    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: 22.2.2
    pkginfo: 1.8.3
    platformdirs: 2.6.2
    prompt-toolkit: 3.0.36
    psutil: 5.9.4
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.12.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    PyQt6-commercial: 6.4.0
    PyQt6-Qt6: 6.4.2
    PyQt6-sip: 13.4.0
    PyQt6-WebEngine-commercial: 6.4.0
    PyQt6-WebEngine-Qt6: 6.4.2
    python-dateutil: 2.8.2
    pytz: 2022.7.1
    pyzmq: 25.0.0
    qtconsole: 5.4.0
    QtPy: 2.3.0
    RandomWords: 0.4.0
    requests: 2.28.1
    scipy: 1.9.3
    setuptools: 65.1.1
    sfftk-rw: 0.7.3
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 5.1.1
    sphinx-autodoc-typehints: 1.19.1
    sphinxcontrib-applehelp: 1.0.4
    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
    stack-data: 0.6.2
    tables: 3.7.0
    tifffile: 2022.10.10
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.2
    traitlets: 5.8.0
    urllib3: 1.26.14
    wcwidth: 0.2.6
    webcolors: 1.12
    wheel: 0.37.1
    wheel-filename: 1.4.1
    zipp: 3.12.0

Change History (2)

comment:1 by pett, 13 months ago

Component:	Unassigned → Sessions
Owner:	set to Tom Goddard
Platform:	→ all
Project:	→ ChimeraX
Status:	new → assigned
Summary:	ChimeraX bug report submission → Keyboard interrupt during restoration of map data

comment:2 by Tom Goddard, 13 months ago

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

User typed ctrl-C at shell where ChimeraX was run on Linux during a session restore. No indication why. It then crashed with a seg fault in the Qt event loop. No indication of what caused the seg fault.

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