Opened 2 years ago

Closed 2 years ago

#10195 closed defect (can't reproduce)

Crash in Qt event loop in _cursor_position possibly adjusting volume levels, also Open dialog shown

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

Description 

The following bug report has been submitted:
Platform:        Windows-10-10.0.22621
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.
Windows fatal exception: code 0x8001010d

Current thread 0x00004808 (most recent call first):
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 1018 in 
  File "C:\Program Files\ChimeraX 1.3\bin\lib\runpy.py", line 87 in _run_code
  File "C:\Program Files\ChimeraX 1.3\bin\lib\runpy.py", line 197 in _run_module_as_main
Windows fatal exception: code 0x8001010e

Thread 0x00004808 (most recent call first):
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 135 in show_open_file_dialog
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 107 in 
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 1018 in 
  File "C:\Program Files\ChimeraX 1.3\bin\lib\runpy.py", line 87 in _run_code
  File "C:\Program Files\ChimeraX 1.3\bin\lib\runpy.py", line 197 in _run_module_as_main
Windows fatal exception: code 0x8001010e

Thread 0x00004808 (most recent call first):
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 135 in show_open_file_dialog
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 107 in 
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 1018 in 
  File "C:\Program Files\ChimeraX 1.3\bin\lib\runpy.py", line 87 in _run_code
  File "C:\Program Files\ChimeraX 1.3\bin\lib\runpy.py", line 197 in _run_module_as_main
Windows fatal exception: code 0x8001010e

Thread 0x00004808 (most recent call first):
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 135 in show_open_file_dialog
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 107 in 
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 1018 in 
  File "C:\Program Files\ChimeraX 1.3\bin\lib\runpy.py", line 87 in _run_code
  File "C:\Program Files\ChimeraX 1.3\bin\lib\runpy.py", line 197 in _run_module_as_main
Windows fatal exception: code 0x8001010e

Thread 0x00004808 (most recent call first):
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 135 in show_open_file_dialog
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 107 in 
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 1018 in 
  File "C:\Program Files\ChimeraX 1.3\bin\lib\runpy.py", line 87 in _run_code
  File "C:\Program Files\ChimeraX 1.3\bin\lib\runpy.py", line 197 in _run_module_as_main
Windows fatal exception: code 0x8001010e

Thread 0x00004808 (most recent call first):
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 135 in show_open_file_dialog
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 107 in 
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 1018 in 
  File "C:\Program Files\ChimeraX 1.3\bin\lib\runpy.py", line 87 in _run_code
  File "C:\Program Files\ChimeraX 1.3\bin\lib\runpy.py", line 197 in _run_module_as_main
Windows fatal exception: code 0x8001010e

Thread 0x00004808 (most recent call first):
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 135 in show_open_file_dialog
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 107 in 
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 1018 in 
  File "C:\Program Files\ChimeraX 1.3\bin\lib\runpy.py", line 87 in _run_code
  File "C:\Program Files\ChimeraX 1.3\bin\lib\runpy.py", line 197 in _run_module_as_main
Windows fatal exception: code 0x8001010e

Thread 0x00004808 (most recent call first):
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 135 in show_open_file_dialog
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 107 in 
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 1018 in 
  File "C:\Program Files\ChimeraX 1.3\bin\lib\runpy.py", line 87 in _run_code
  File "C:\Program Files\ChimeraX 1.3\bin\lib\runpy.py", line 197 in _run_module_as_main
Windows fatal exception: code 0x8001010e

Thread 0x00004808 (most recent call first):
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 135 in show_open_file_dialog
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 107 in 
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 1018 in 
  File "C:\Program Files\ChimeraX 1.3\bin\lib\runpy.py", line 87 in _run_code
  File "C:\Program Files\ChimeraX 1.3\bin\lib\runpy.py", line 197 in _run_module_as_main
Windows fatal exception: code 0x8001010e

Thread 0x00004808 (most recent call first):
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 135 in show_open_file_dialog
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 107 in 
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 1018 in 
  File "C:\Program Files\ChimeraX 1.3\bin\lib\runpy.py", line 87 in _run_code
  File "C:\Program Files\ChimeraX 1.3\bin\lib\runpy.py", line 197 in _run_module_as_main
Windows fatal exception: code 0x8001010e

Thread 0x00004808 (most recent call first):
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 135 in show_open_file_dialog
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 107 in 
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 1018 in 
  File "C:\Program Files\ChimeraX 1.3\bin\lib\runpy.py", line 87 in _run_code
  File "C:\Program Files\ChimeraX 1.3\bin\lib\runpy.py", line 197 in _run_module_as_main
Windows fatal exception: code 0x8001010e

Thread 0x00004808 (most recent call first):
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 135 in show_open_file_dialog
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 107 in 
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 1018 in 
  File "C:\Program Files\ChimeraX 1.3\bin\lib\runpy.py", line 87 in _run_code
  File "C:\Program Files\ChimeraX 1.3\bin\lib\runpy.py", line 197 in _run_module_as_main
Windows fatal exception: code 0x8001010e

Thread 0x00004808 (most recent call first):
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 135 in show_open_file_dialog
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 107 in 
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 1018 in 
  File "C:\Program Files\ChimeraX 1.3\bin\lib\runpy.py", line 87 in _run_code
  File "C:\Program Files\ChimeraX 1.3\bin\lib\runpy.py", line 197 in _run_module_as_main
Windows fatal exception: code 0x8001010e

Thread 0x00004808 (most recent call first):
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 135 in show_open_file_dialog
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 107 in 
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 1018 in 
  File "C:\Program Files\ChimeraX 1.3\bin\lib\runpy.py", line 87 in _run_code
  File "C:\Program Files\ChimeraX 1.3\bin\lib\runpy.py", line 197 in _run_module_as_main
Windows fatal exception: code 0x8001010e

Thread 0x00004808 (most recent call first):
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 135 in show_open_file_dialog
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 107 in 
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 1018 in 
  File "C:\Program Files\ChimeraX 1.3\bin\lib\runpy.py", line 87 in _run_code
  File "C:\Program Files\ChimeraX 1.3\bin\lib\runpy.py", line 197 in _run_module_as_main
Windows fatal exception: code 0x8001010e

Thread 0x00004808 (most recent call first):
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\mouse_modes\mousemodes.py", line 515 in _cursor_position
Windows fatal exception: access violation

===== 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
> C:\\\Users\\\nicks\\\OneDrive\\\Downloads\\\cryosparc_P10_J451_013_volume_map_sym_sharp.mrc

Opened cryosparc_P10_J451_013_volume_map_sym_sharp.mrc as #1, grid size
560,560,560, pixel 0.822, shown at level 0.196, step 4, values float32  

> volume #1 step 1

> turn x 90

> ui mousemode right "tape measure"

> marker segment #2 position 203.9,340.9,336.5 toPosition 341,411.6,325 color
> yellow radius 0.2055 label 154.7 labelHeight 15.47 labelColor yellow

> undo

> marker delete #2

> ui mousemode right "mark point"

> marker #2 position 253.2,219.2,136.5 color yellow radius 1

> ui mousemode right "mark surface"

> marker #2 position 229,125.1,139 color yellow radius 1

> marker #2 position 224.3,121.1,141.4 color yellow radius 1

> marker #2 position 224.7,121.9,140.5 color yellow radius 1

> marker change #2:4 radius 50

> marker change #2:4 radius 10

> marker #2 position 294.7,135.6,178.5 color yellow radius 10

> ui mousemode right "link markers"

> marker link #2:5,4 color #659cef radius 0.5

> ui mousemode right "mark point"

> marker #2 position 208,228.6,146.1 color yellow radius 10

> marker #2 position 291.8,235,187.1 color yellow radius 10

> marker #2 position 288.4,234.7,188.4 color yellow radius 10

> marker #2 position 296,235.6,181 color yellow radius 10

> ui mousemode right distance

> distance /M:4@M /M:5@M

Distance between /M mark 4 M and mark 5 M: 80.773Å  

> select clear

> distance /M:4@M /M:5@M

Distance already exists; modify distance properties with 'distance style'  

> ui mousemode right "mark surface"

> marker #2 position 215.3,316.8,155.5 color yellow radius 10

> volume #1 level 0.02691

> volume #1 level 0.08011

> marker #2 position 296.7,131.4,138.8 color yellow radius 10

> marker #2 position 294.2,121.7,139.7 color yellow radius 10

> ui mousemode right "delete markers"

> marker delete #2:12

> marker delete #2:11

> marker delete #2:6

> ui mousemode right "mark plane"

> ui mousemode right "delete markers"

> marker delete #2:8

> marker delete #2:7

> marker delete #2:9

> marker delete #2:1

> ui mousemode right "mark surface"

> ui mousemode right "mark center"

Enclosed volume for marked surface: 2.53e+06  

> marker #2 position 230.1,229.8,230 color yellow radius 10

> ui mousemode right "mark surface"

> marker #2 position 293.9,131.3,137.8 color yellow radius 10

> ui mousemode right distance

> distance /M:5@M /M:14@M

Distance between /M mark 5 M and mark 14 M: 40.927Å  

> ui mousemode right "mark surface"

> marker #2 position 193.7,120.9,185.1 color yellow radius 10

> marker #2 position 191.6,134.5,142.1 color yellow radius 10

> ui mousemode right "delete markers"

> marker delete #2:10

> marker delete #2:16

> ui mousemode right "mark surface"

> marker #2 position 189.7,118.5,143.6 color yellow radius 10

> ui mousemode right distance

> distance /M:15@M /M:17@M

Distance between /M mark 15 M and mark 17 M: 41.785Å  

> ui mousemode right "mark center"

Enclosed volume for marked surface: 2.53e+06  

> marker #2 position 230.1,229.8,230 color yellow radius 10

> ui mousemode right "mark surface"

> volume #1 level 0.1056

> volume #1 level 0.131

> marker #2 position 192.8,119.1,234.9 color yellow radius 10

> marker #2 position 226.9,126,235.5 color yellow radius 10

> marker #2 position 269.2,122.5,234 color yellow radius 10

> marker #2 position 291.7,144.6,232.6 color yellow radius 10

> ui mousemode right distance

> distance /M:20@M /M:13@M

Distance between /M mark 20 M and mark 13 M: 104.032Å  

> distance /M:22@M /M:13@M

Distance between /M mark 22 M and mark 13 M: 105.212Å  

> distance /M:22@M /M:20@M

Distance between /M mark 22 M and mark 20 M: 67.576Å  

> select add /M:4@M

2 atoms, 2 residues, 1 model selected  

> color sel orange

> select subtract /M:22@M

1 atom, 1 residue, 1 model selected  

> select add /M:22@M

2 atoms, 2 residues, 1 model selected  

> select subtract /M:4@M

1 atom, 1 residue, 1 model selected  

> color sel yellow

> select clear

> select add /M:5@M

1 atom, 1 residue, 1 model selected  

> color sel orange

> select clear

> ui mousemode right distance

> distance /M:13@M /M:19@M

Distance between /M mark 13 M and mark 19 M: 116.961Å  

> distance /M:19@M /M:20@M

Distance between /M mark 19 M and mark 20 M: 34.775Å  

> select add /M:4@M

1 atom, 1 residue, 1 model selected  

> color sel purple

> ui mousemode right "mark surface"

> marker #2 position 137.8,170,151.1 color yellow radius 10

> marker #2 position 133.5,161.3,139.8 color yellow radius 10

> ui mousemode right distance

> distance /M:23@M /M:24@M

Distance between /M mark 23 M and mark 24 M: 14.894Å  

> ui mousemode right "mark surface"

> marker #2 position 134.2,169.2,230.2 color yellow radius 10

> ui mousemode right distance

> distance /M:13@M /M:25@M

Distance between /M mark 13 M and mark 25 M: 113.438Å  

> distance /M:25@M /M:19@M

Distance between /M mark 25 M and mark 19 M: 77.262Å  

> ui mousemode right "tape measure"

> ui mousemode right distance

> distance /M:25@M /M:20@M

Distance between /M mark 25 M and mark 20 M: 102.395Å  

> preset "overall look" publication

Preset expands to these ChimeraX commands:

    
    
    set bg white
    graphics silhouettes t

  

> ui mousemode right "delete markers"

> marker delete #2:24

> marker delete #2:17

> marker delete #2:15

> marker delete #2:19

> marker delete #2:25

> marker delete #2:13

> marker delete #2:20

> marker delete #2:18

> marker delete #2:21

> marker delete #2:14

> marker delete #2:22

> ui mousemode right "mark surface"

> marker #2 position 200.7,135.9,190.4 color yellow radius 10

> ui mousemode right "delete markers"

> marker delete #2:23

> ui mousemode right "mark surface"

> marker #2 position 138.8,161.1,153.6 color yellow radius 10

> ui mousemode right "delete markers"

> marker delete #2:26

> ui mousemode right "mark surface"

> marker #2 position 199.8,119.8,192.2 color yellow radius 10

> ui mousemode right "delete markers"

> marker delete #2:27

> ui mousemode right "mark surface"

> marker #2 position 133.6,167.2,149.2 color yellow radius 10

> select #1

2 models selected  

> select clear

> hide #!1 models

> marker change #2:4-5 radius 10 markers false

> marker change #2:4-5 radius 8 markers false

> marker change #2:4-5 radius 5 markers false

> marker change #2:4-5 color #ffaa00 markers false

> select clear

> select /M:28@M

1 atom, 1 residue, 1 model selected  

> select add /M:29@M

2 atoms, 2 residues, 1 model selected  

> select subtract /M:28@M

1 atom, 1 residue, 1 model selected  

> marker change #2:29 color red

> select add /M:4@M

2 atoms, 2 residues, 1 model selected  

> ui mousemode right "link markers"

> select clear

> select add /M:29@M

1 atom, 1 residue, 1 model selected  

> select add /M:4@M

2 atoms, 2 residues, 1 model selected  

> ui mousemode right "link markers"

> marker link #2:29,4 color #ffaa00 radius 5

> marker change #2:4,29 color red markers false

> select clear

> ui mousemode right "link markers"

> marker link #2:28,4 color red radius 5

> marker change #2:4,28 color lime markers false

> select add /M:28@M

1 atom, 1 bond, 1 residue, 1 model selected  

> marker change #2:28 color #55ff00

> show #!1 models

> select clear

> color #1 #b25491 models transparency 0

> color #1 #b24124 models transparency 0

> color #1 #b28380 models transparency 0

> ui mousemode right "mark point"

> marker #2 position 237.8,237.7,150.9 color #55ff00 radius 10

> marker #2 position 113.5,246.3,154.2 color #55ff00 radius 10

> marker #2 position -11.44,240.6,162.6 color #55ff00 radius 10

> ui mousemode right "delete markers"

> marker delete #2:32

> marker delete #2:31

> marker delete #2:30

> ui mousemode right "mark point"

> marker #2 position 243.2,231.8,142.4 color #55ff00 radius 10

> marker #2 position 214.9,233.3,195.1 color #55ff00 radius 10

> ui mousemode right "delete markers"

> marker delete #2:34

> marker delete #2:33

> ui mousemode right "mark maximum"

> marker #2 position 225.5,118.1,144.4 color #55ff00 radius 0.822

> marker #2 position 199.8,122.3,192.9 color #55ff00 radius 0.822

> marker #2 position 244.5,118.5,93.96 color #55ff00 radius 0.822

> select clear

> ui mousemode right "delete markers"

> marker delete #2:37

> volume #1 level 0.1865

> save "C:/Users/nicks/OneDrive - Massachusetts Institute of
> Technology/SchwartzLab/Cryo-
> EM/ChimeraX/20231120LabMeeting/20231120-Tino.cxs"

> save "C:/Users/nicks/OneDrive - Massachusetts Institute of
> Technology/SchwartzLab/Cryo-
> EM/ChimeraX/20231120LabMeeting/20231120-Tino.cxs" includeMaps true

> open
> C:/Users/nicks/OneDrive/Downloads/cryosparc_P10_J464_008_volume_map_sym_sharp.mrc

Opened cryosparc_P10_J464_008_volume_map_sym_sharp.mrc as #4, grid size
560,560,560, pixel 0.822, shown at level 0.209, step 4, values float32  

> hide #!1 models

> hide #!3 models

> hide #3.1 models

> hide #2 models

> volume #4 step 1

> preset "overall look" publication

Preset expands to these ChimeraX commands:

    
    
    set bg white
    graphics silhouettes t

  

> preset "molecular surfaces" "ghostly white"

Changed 0 atom styles  
Preset expands to these ChimeraX commands:

    
    
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    surface
    color white targ s trans 80

  

> lighting shadows true

> lighting full

> lighting soft

> lighting simple

> lighting full

> lighting soft

> lighting full

> lighting shadows false

> graphics silhouettes false

> graphics silhouettes true

> lighting shadows true

> lighting full

> volume #4 color #95959533

> volume #4 color #2b2b2b33

> set bgColor gray

> set bgColor white

> lighting soft

> lighting full

> lighting shadows false

> graphics silhouettes false

> lighting shadows true

> preset "overall look" publication

Preset expands to these ChimeraX commands:

    
    
    set bg white
    graphics silhouettes t

  

> lighting soft

> graphics silhouettes false

> graphics silhouettes true

> lighting shadows true intensity 0.5

> lighting flat

> lighting full

> volume #4 color #9f9f9f33

> transparency #4 0

> volume #4 color #75757533

> volume #4 color #e5e5e533

> transparency #4 0

> open
> C:/Users/nicks/OneDrive/Downloads/cryosparc_P10_J464_008_volume_map_sym_sharp.mrc

Opened cryosparc_P10_J464_008_volume_map_sym_sharp.mrc as #5, grid size
560,560,560, pixel 0.822, shown at level 0.209, step 4, values float32  

> hide #!4 models

> volume #5 step 1

> volume #5 color #e5e5e5

> open
> C:/Users/nicks/OneDrive/Downloads/cryosparc_P10_J524_005_volume_map_sharp.mrc

Opened cryosparc_P10_J524_005_volume_map_sharp.mrc as #6, grid size
560,560,560, pixel 0.822, shown at level 0.0526, step 4, values float32  

> hide #!5 models

> volume #6 step 1

> volume #6 level 0.1283

> volume #6 level 0.1499

> volume #6 level 0.09045

> ui tool show "Hide Dust"

> surface dust #6 size 4.93

> volume #6 color #e5e5e5

> open
> C:/Users/nicks/OneDrive/Downloads/cryosparc_P10_J524_005_volume_mask_refine.mrc

Opened cryosparc_P10_J524_005_volume_mask_refine.mrc as #7, grid size
560,560,560, pixel 0.822, shown at level 0.588, step 4, values float32  

> volume #7 level 0.9056

> volume #7 step 1

> volume #7 level 0.9944

> open C:/Users/nicks/OneDrive/Downloads/cryosparc_P10_J521_mask.mrc

Opened cryosparc_P10_J521_mask.mrc as #8, grid size 560,560,560, pixel 0.822,
shown at level 1, step 4, values float32  

> hide #!7 models

> volume #8 level 0.9686

> volume #8 step 1

> open
> C:/Users/nicks/OneDrive/Downloads/cryosparc_P10_J523_006_volume_map_sharp.mrc

Opened cryosparc_P10_J523_006_volume_map_sharp.mrc as #9, grid size
560,560,560, pixel 0.822, shown at level 0.0356, step 4, values float32  

> hide #!8 models

> hide #!5 models

> volume #9 step 1

> surface dust #9 size 4.93

> volume #9 level 0.06085

> volume #9 level 0.09169

> volume #9 color #e5e5e5

> volume #9 level 0.07487

> volume #9 level 0.2235

> volume #9 level 0.26

> volume #9 level 0.2319


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

Log:
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
> C:\\\Users\\\nicks\\\OneDrive\\\Downloads\\\cryosparc_P10_J523_006_volume_map_sharp.mrc

Opened cryosparc_P10_J523_006_volume_map_sharp.mrc as #1, grid size
560,560,560, pixel 0.822, shown at level 0.0356, step 4, values float32  




OpenGL version: 3.3.0 NVIDIA 536.67
OpenGL renderer: NVIDIA GeForce RTX 2080 SUPER/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: HP
Model: OMEN by HP Obelisk Desktop 875-1xxx
OS: Microsoft Windows 11 Home (Build 22621)
Memory: 34,206,101,504
MaxProcessMemory: 137,438,953,344
CPU: 16 Intel(R) Core(TM) i9-9900K CPU @ 3.60GHz
OSLanguage: en-US
Locale: ('en_US', 'cp1252')
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-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
    comtypes: 1.1.10
    cxservices: 1.1
    cycler: 0.11.0
    Cython: 0.29.24
    decorator: 5.1.0
    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
    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
    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
    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
    pywin32: 228
    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
    WMI: 1.5.1

Change History (2)

comment:1 by Eric Pettersen, 2 years ago

Component: Unassigned → General Controls
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Crash in _cursor_position possibly adjusting volume levels

comment:2 by Tom Goddard, 2 years ago

Resolution: → can't reproduce
Status: assigned → closed
Summary: Crash in _cursor_position possibly adjusting volume levels → Crash in Qt event loop in _cursor_position possibly adjusting volume levels, also Open dialog shown

Likely Qt bug in old ChimeraX 1.3.

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