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Opened 3 years ago
Closed 3 years ago
#7720 closed defect (can't reproduce)
Crash using File→Open on Windows and/or in return statement
| Reported by: | Owned by: | pett | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Platform | Version: | |
| Keywords: | Cc: | Tom Goddard | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Windows-10-10.0.19042
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 0x8001010e
Thread 0x0000312c (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\cli.py", line 1122 in _browse_parse
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\cli.py", line 1210 in parse
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\cli.py", line 2447 in _parse_arg
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\cli.py", line 2588 in _process_positional_arguments
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\cli.py", line 2812 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\run.py", line 36 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 1028 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 0x0000312c (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\cli.py", line 1122 in _browse_parse
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\cli.py", line 1210 in parse
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\cli.py", line 2447 in _parse_arg
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\cli.py", line 2588 in _process_positional_arguments
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\cli.py", line 2812 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\run.py", line 36 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 1028 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 0x0000312c (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\cli.py", line 1122 in _browse_parse
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\cli.py", line 1210 in parse
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\cli.py", line 2447 in _parse_arg
File "C:\Program FiWindows fatal exception: lcode 0xe8001010es
\ChimWindows fatal exception: ecode 0xr8001010ea
X 1.Windows fatal exception: 3code 0x\8001010eb
inWindows fatal exception: \code 0xl8001010ei
b\Windows fatal exception: scode 0xi8001010et
e-Windows fatal exception: pcode 0xa8001010ec
kaWindows fatal exception: gcode 0xe8001010es
\cWindows fatal exception: hcode 0xi8001010em
erWindows fatal exception: acode 0xx8001010e\
coWindows fatal exception: rcode 0xe8001010e\
coWindows fatal exception: mcode 0xm8001010ea
nds\cli.py", line 2588 in _process_positional_arguments
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\cli.py", line 2812 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\run.py", line 36 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 1028 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 0x0000312c (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\cli.py", line 1122 in _browse_parse
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\cli.py", line 1210 in parse
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\cli.py", line 2447 in _parse_arg
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\cli.py", line 2588 in _process_positional_arguments
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\cli.py", line 2812 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\run.py", line 36 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 1028 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 0x0000312c (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\cli.py", line 1122 in _browse_parse
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\cli.py", line 1210 in parse
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\cli.py", line 2447 in _parse_arg
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\cli.py", line 2588 in _process_positional_arguments
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\cli.py", line 2812 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\run.py", line 36 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 1028 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 0x0000312c (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\cli.py", line 1122 in _browse_parse
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\cli.py", line 1210 in parse
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\cli.py", line 2447 in _parse_arg
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\cli.py", line 2588 in _process_positional_arguments
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\cli.py", line 2812 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\run.py", line 36 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 1028 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 0x0000312c (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\cli.py", line 1122 in _browse_parse
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\cli.py", line 1210 in parse
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\cli.py", line 2447 in _parse_arg
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\cli.py", line 2588 in _process_positional_arguments
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\cli.py", line 2812 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\run.py", line 36 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 1028 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 0x0000312c (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\cli.py", line 1122 in _browse_parse
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\cli.py", line 1210 in parse
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\cli.py", line 2447 in _parse_arg
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\cli.py", line 2588 in _process_positional_arguments
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\cli.py", line 2812 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\run.py", line 36 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 1028 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 0x0000312c (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\cli.py", line 1122 in _browse_parse
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\cli.py", line 1210 in parse
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\cli.py", line 2447 in _parse_arg
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\cli.py", line 2588 in _process_positional_arguments
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\cli.py", line 2812 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\run.py", line 36 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 1028 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 0x0000312c (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\cli.py", line 1122 in _browse_parse
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\cli.py", line 1210 in parse
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\cli.py", line 2447 in _parse_arg
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\cli.py", line 2588 in _process_positional_arguments
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\cli.py", line 2812 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\run.py", line 36 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 1028 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 0x0000312c (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\cli.py", line 1122 in _browse_parse
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\cli.py", line 1210 in parse
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\cli.py", line 2447 in _parse_arg
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\cli.py", line 2588 in _process_positional_arguments
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\cli.py", line 2812 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\run.py", line 36 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 1028 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 0x0000312c (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\cli.py", line 1122 in _browse_parse
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\cli.py", line 1210 in parse
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\cli.py", line 2447 in _parse_arg
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\cli.py", line 2588 in _process_positional_arguments
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\cli.py", line 2812 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\run.py", line 36 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 1028 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 0x0000312c (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\cli.py", line 1122 in _browse_parse
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\cli.py", line 1210 in parse
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\cli.py", line 2447 in _parse_arg
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\cli.py", line 2588 in _process_positional_arguments
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\cli.py", line 2812 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\run.py", line 36 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 1028 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 0x0000312c (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\cli.py", line 1122 in _browse_parse
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\cli.py", line 1210 in parse
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\cli.py", line 2447 in _parse_arg
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\cli.py", line 2588 in _process_positional_arguments
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\cli.py", line 2812 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\run.py", line 36 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 1028 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-paWindows fatal exception: code 0x8001010e
ckaWindows fatal exception: gcode 0xe8001010es
\CWindows fatal exception: hcode 0xi8001010em
erWindows fatal exception: acode 0xX8001010e_
mWindows fatal exception: acode 0xi8001010en
.pWindows fatal exception: ycode 0x"8001010e, line
867 in iWindows fatal exception: ncode 0xi8001010et
Windows fatal exception: File code 0x"8001010eC
:Windows fatal exception: \code 0xP8001010er
oWindows fatal exception: gcode 0xr8001010ea
mWindows fatal exception: code 0xF8001010ei
les\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 0x0000312c (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\cli.py", line 1122 in _browse_parse
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\cli.py", line 1210 in parse
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\cli.py", line 2447 in _parse_arg
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\cli.py", line 2588 in _process_positional_arguments
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\cli.py", line 2812 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\run.py", line 36 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 1028 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 0x0000312c (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\cli.py", line 1122 in _browse_parse
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\cli.py", line 1210 in parse
File "C:\Program Files\ChimeraX 1.3\bin\lib\siWindows fatal exception: code 0x8001010et
e-paWindows fatal exception: ccode 0xk8001010ea
geWindows fatal exception: scode 0x\8001010ec
hiWindows fatal exception: mcode 0xe8001010er
aWindows fatal exception: xcode 0x\8001010ec
orWindows fatal exception: ecode 0x\8001010ec
omWindows fatal exception: mcode 0xa8001010en
dsWindows fatal exception: \code 0xc8001010el
iWindows fatal exception: .code 0xp8001010ey
"Windows fatal exception: , line code 0x24478001010e in
_Windows fatal exception: pcode 0xa8001010er
se_arg
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\cli.py", line 2588 in _process_positional_arguments
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\cli.py", line 2812 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\run.py", line 36 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 1028 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\Windows fatal exception: code 0x8001010e
sitWindows fatal exception: ecode 0x-8001010ep
acWindows fatal exception: kcode 0xa8001010eg
esWindows fatal exception: \code 0xC8001010eh
iWindows fatal exception: mcode 0xe8001010er
aXWindows fatal exception: _code 0xm8001010ea
iWindows fatal exception: ncode 0x.8001010ep
y"Windows fatal exception: , line code 0x10188001010e in
Windows fatal exception: File code 0x"8001010eC
:\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 0x0000312c (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\cli.py", line 1122 in _browse_parse
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimeraxWindows fatal exception: code 0x\8001010ec
ore\Windows fatal exception: ccode 0xo8001010em
manWindows fatal exception: dcode 0xs8001010e\
cliWindows fatal exception: .code 0xp8001010ey
"Windows fatal exception: , line code 0x12108001010e in
pWindows fatal exception: acode 0xr8001010es
e
Windows fatal exception: File code 0x"8001010eC
:Windows fatal exception: \code 0xP8001010er
ogWindows fatal exception: rcode 0xa8001010em
FiWindows fatal exception: lcode 0xe8001010es
\ChWindows fatal exception: icode 0xme8001010er
aX 1.3\bin\lib\site-packages\chimerax\core\commands\cli.py", line 2447 in _parse_arg
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\cli.py", line 2588 in _process_positional_arguments
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\cli.py", line 2812 in run
File "C:\Program Files\Windows fatal exception: code 0x8001010eC
himWindows fatal exception: ecode 0xr8001010ea
X Windows fatal exception: 1code 0x.8001010e3
\bWindows fatal exception: icode 0xn8001010e\
lWindows fatal exception: icode 0xb8001010e\
sWindows fatal exception: icode 0xt8001010ee
-pWindows fatal exception: acode 0xc8001010ek
aWindows fatal exception: gcode 0xe8001010es
\chWindows fatal exception: icode 0xm8001010ee
raWindows fatal exception: xcode 0x\8001010ec
orWindows fatal exception: ecode 0x\8001010ec
ommands\run.py", line 36 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 1028 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 0x0000312c (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\cli.py", line 1122 in _browse_parse
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\cli.py", line 1210 in parse
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\cli.py", line 2447 in _parse_arg
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\cli.py", line 2588 in _process_positional_arguments
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\cli.py", line 2812 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\run.py", line 36 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 1028 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 0x0000312c (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\cli.py", line 1122 in _browse_parse
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\cli.py", line 1210 in parse
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\cli.py", line 2447 in _parse_arg
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\cli.py", line 2588 in _process_positional_arguments
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\cli.py", line 2812 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\run.py", line 36 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 1028 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 0x0000312c (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\cli.py", line 1122 in _browse_parse
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\cli.py", line 1210 in parse
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\cli.py", line 2447 in _parse_arg
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\cli.py", line 2588 in _process_positional_arguments
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\cli.py", line 2812 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\run.py", line 36 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 1028 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 0x0000312c (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\atomic\molc.py", line 323 in pointer
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.
> open "C:\\\Users\\\petedani\\\OneDrive - Boehringer
> Ingelheim\\\Documents\\\projects\\\Periostin\\\complex1\\\2022-04-14_grid248_EP-22-57369_Krios-
> IMP\\\chimera\\\J300map_coot4model-top.cxs"
Opened cryosparc_P33_J300_009_volume_map.mrc as #1, grid size 400,400,400,
pixel 0.745, shown at level 0.0884, step 1, values float32
Log from Mon May 9 15:03:13 2022UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "C:\\\Users\\\petedani\\\OneDrive - Boehringer
> Ingelheim\\\Documents\\\projects\\\Periostin\\\complex1\\\2022-04-14_grid248_EP-22-57369_Krios-
> IMP\\\cryosparc\\\cryosparc_P33_J300_009_volume_map.mrc"
Opened cryosparc_P33_J300_009_volume_map.mrc as #1, grid size 400,400,400,
pixel 0.745, shown at level 0.0185, step 2, values float32
> volume #1 step 1
> volume #1 level 0.1192
> volume #1 level 0.1034
> volume #1 level 0.09187
> open "C:/Users/petedani/OneDrive - Boehringer
> Ingelheim/Documents/projects/Periostin/complex1/2022-04-14_grid248_EP-22-57369_Krios-
> IMP/coot/complex1-coot-4.pdb"
Chain information for complex1-coot-4.pdb #2
---
Chain | Description
A B | No description available
H S | No description available
L V | No description available
> style ball
Changed 15620 atom styles
> style stick
Changed 15620 atom styles
> show cartoons
[Repeated 3 time(s)]
> hide atoms
> color #1 #b2b2b2f9 models
> color #1 #b2b2b20a models
> color #1 #b2b2b264 models
> color #1 #b2b2b296 models
> show cartoons
> show atoms
[Repeated 1 time(s)]
> hide atoms
> show surfaces
> hide surfaces
> volume #1 level 0.07172
> color bychain
> color bfactor
15620 atoms, 2052 residues, 6 surfaces, atom bfactor range 61.5 to 379
> color bychain
> color zone #1 near #2 distance 4.47
> ui tool show "Color Actions"
> color bychain
[Repeated 3 time(s)]
> select chain A
Expected an objects specifier or a keyword
> select chainA
Expected an objects specifier or a keyword
> select chains A
Expected an objects specifier or a keyword
> select chains A
Expected an objects specifier or a keyword
> select chains A
Expected an objects specifier or a keyword
> hide #!1 models
> ui mousemode right select
> select /A:426
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:427
8 atoms, 7 bonds, 1 residue, 1 model selected
> select clear
> color tomato
> color bychain
> select /A:238
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
58 atoms, 58 bonds, 7 residues, 2 models selected
> select up
4600 atoms, 4676 bonds, 594 residues, 2 models selected
> select up
15620 atoms, 15930 bonds, 2052 residues, 2 models selected
> select down
4600 atoms, 4676 bonds, 594 residues, 7 models selected
> color sel cornflower blue
> select /B:119
5 atoms, 4 bonds, 1 residue, 1 model selected
> select /B:119
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
4600 atoms, 4676 bonds, 594 residues, 2 models selected
> color sel royal blue
> select clear
[Repeated 1 time(s)]
> select /B:150
11 atoms, 10 bonds, 1 residue, 1 model selected
> select up
4600 atoms, 4676 bonds, 594 residues, 2 models selected
> color sel medium blue
> select clear
[Repeated 3 time(s)]
> select /S:85
6 atoms, 5 bonds, 1 residue, 1 model selected
> select up
1641 atoms, 1682 bonds, 219 residues, 2 models selected
> color sel fire brick
> select clear
[Repeated 5 time(s)]
> select /H:155
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
1641 atoms, 1682 bonds, 219 residues, 2 models selected
> color sel sea green
> select clear
> select /L:16
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
1569 atoms, 1607 bonds, 213 residues, 2 models selected
> color sel chartreuse
> select clear
[Repeated 4 time(s)]
> select /V:174
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /V:174
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
1569 atoms, 1607 bonds, 213 residues, 2 models selected
> color sel coral
> select clear
Drag select of 9 residues
> select clear
> show #!1 models
> color zone #1 near #2 distance 4.47
> set bgColor white
> lighting soft
> volume #1 level 0.1118
> volume #1 level 0.04352
> volume #1 level 0.05836
> color #1 #ff634796 models
> color zone #1 near #2 distance 4.47
> color #1 #ff634797 models
> color #1 #ff634796 models
> color #1 #f3fdff96 models
> color #1 #fcfffe96 models
> color #1 #f5ffd096 models
> color #1 #9effda96 models
> color #1 #ffece696 models
> color #1 #746b6996 models
Drag select of 1 cryosparc_P33_J300_009_volume_map.mrc , 30 residues
> select clear
> volume #1 level 0.1385
> select clear
> show atoms
Drag select of 1 cryosparc_P33_J300_009_volume_map.mrc
> select clear
> hide atoms
> select /A:284
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> select /A:283
7 atoms, 7 bonds, 1 residue, 1 model selected
> select down
7 atoms, 7 bonds, 1 residue, 2 models selected
> select up
30 atoms, 30 bonds, 4 residues, 2 models selected
> select up
4600 atoms, 4676 bonds, 594 residues, 2 models selected
> select down
30 atoms, 30 bonds, 4 residues, 2 models selected
> show sel atoms
> select /A:286
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
55 atoms, 54 bonds, 7 residues, 2 models selected
> show sel atoms
> select /A:293
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
4600 atoms, 4676 bonds, 594 residues, 2 models selected
> select down
8 atoms, 7 bonds, 1 residue, 2 models selected
> select #1
2 models selected
> select /A:292
4 atoms, 3 bonds, 1 residue, 1 model selected
> select up
55 atoms, 54 bonds, 7 residues, 2 models selected
> show sel atoms
> style sel stick
Changed 55 atom styles
> style sel stick
Changed 55 atom styles
Drag select of 1 cryosparc_P33_J300_009_volume_map.mrc , 9 residues
Drag select of 2 residues
> close #2
> open "C:/Users/petedani/OneDrive - Boehringer
> Ingelheim/Documents/projects/Periostin/complex1/2022-04-14_grid248_EP-22-57369_Krios-
> IMP/coot/complex1-coot-4_real_space_refined_007mod.pdb"
Chain information for complex1-coot-4_real_space_refined_007mod.pdb #2
---
Chain | Description
A B | No description available
H S | No description available
L V | No description available
> hide atoms
> show cartoons
Drag select of 1 cryosparc_P33_J300_009_volume_map.mrc , 23 residues
> select clear
> hide #!1 models
> select /A:166
10 atoms, 10 bonds, 1 residue, 1 model selected
> select up
84 atoms, 84 bonds, 11 residues, 1 model selected
> select up
4600 atoms, 4676 bonds, 594 residues, 1 model selected
> select up
15620 atoms, 15930 bonds, 2052 residues, 1 model selected
> select down
4600 atoms, 4676 bonds, 594 residues, 1 model selected
> color sel cornflower blue
> select clear
> select /B:243
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
58 atoms, 58 bonds, 7 residues, 1 model selected
> select up
4600 atoms, 4676 bonds, 594 residues, 1 model selected
> color sel cornflower blue
> select clear
> show #!1 models
> hide #!1 models
> show #!1 models
> volume #1 level 0.07172
> volume #1 level 0.07
> volume #1 level 0.0702
> volume #1 level 0.072
> volume #1 level 0.075
> save "C:/Users/petedani/OneDrive - Boehringer
> Ingelheim/Documents/projects/Periostin/complex1/2022-04-14_grid248_EP-22-57369_Krios-
> IMP/chimera/J300map_coot4model.cxs"
> color zone #1 near #2 distance 4.47
> hide #2 models
> save "C:/Users/petedani/OneDrive - Boehringer
> Ingelheim/Documents/projects/Periostin/complex1/2022-04-14_grid248_EP-22-57369_Krios-
> IMP/chimera/J300map_coot4model.cxs"
> save "C:/Users/petedani/OneDrive - Boehringer
> Ingelheim/Documents/projects/Periostin/complex1/2022-04-14_grid248_EP-22-57369_Krios-
> IMP/chimera/J300map_coot4model-top.cxs"
> show #2 models
> hide #2 models
> save "C:/Users/petedani/OneDrive - Boehringer
> Ingelheim/Documents/projects/Periostin/complex1/2022-04-14_grid248_EP-22-57369_Krios-
> IMP/chimera/J300map_coot4model-top.cxs"
> save C:\Users\petedani\Desktop\image1.png supersample 3
> save C:\Users\petedani\Desktop\image2.png supersample 3
> save C:\Users\petedani\Desktop\image3.png supersample 3
> save C:\Users\petedani\Desktop\image4.png supersample 3
> save C:\Users\petedani\Desktop\image5.png supersample 3
> save C:\Users\petedani\Desktop\image6.png supersample 3
> save C:\Users\petedani\Desktop\image7.png supersample 3
> save C:\Users\petedani\Desktop\image8.png supersample 3
> save C:\Users\petedani\Desktop\image9.png supersample 3
> save C:\Users\petedani\Desktop\image10.png supersample 3
> save C:\Users\petedani\Desktop\image11.png supersample 3
> save C:\Users\petedani\Desktop\image12.png supersample 3
> save C:\Users\petedani\Desktop\image13.png supersample 3
> save "C:/Users/petedani/OneDrive - Boehringer
> Ingelheim/Documents/projects/Periostin/complex1/2022-04-14_grid248_EP-22-57369_Krios-
> IMP/chimera/J300map_coot4model-top.cxs"
> lighting soft
> lighting full
> lighting soft
> save C:\Users\petedani\Desktop\image14.png supersample 3
> select clear
[Repeated 1 time(s)]
> save C:\Users\petedani\Desktop\image15.png supersample 3
> save C:\Users\petedani\Desktop\image16.png supersample 3
> save C:\Users\petedani\Desktop\image17.png supersample 3
> save C:\Users\petedani\Desktop\image18.png supersample 3
> save C:\Users\petedani\Desktop\image19.png supersample 3
> save C:\Users\petedani\Desktop\image20.png supersample 3
> save C:\Users\petedani\Desktop\image21.png supersample 3
> volume #1 level 0.08836
> select #1
2 models selected
> save test.png
Permission denied writing file test.png
> select clear
> save test.png
Permission denied writing file test.png
> save /Documents/test.png
Directory "/Documents" does not exist
> cd "C:/Users/petedani/OneDrive - Boehringer
> Ingelheim/Documents/projects/Periostin/complex1/2022-04-14_grid248_EP-22-57369_Krios-
> IMP/chimera"
Current working directory is: C:\Users\petedani\OneDrive - Boehringer
Ingelheim\Documents\projects\Periostin\complex1\2022-04-14_grid248_EP-22-57369_Krios-
IMP\chimera
> save C:\Users\petedani\Desktop\image22.png supersample 3
> save test.png
[Repeated 1 time(s)]
> save C:\Users\petedani\Desktop\image23.png supersample 3
> show #2 models
> hide #!1 models
> show #!1 models
> hide #2 models
> save J300map-top.png
> show #2 models
> hide #!1 models
> save coot4model-top.png
> save "C:/Users/petedani/OneDrive - Boehringer
> Ingelheim/Documents/projects/Periostin/complex1/2022-04-14_grid248_EP-22-57369_Krios-
> IMP/chimera/J300map_coot4model-top.cxs"
——— End of log from Mon May 9 15:03:13 2022 ———
opened ChimeraX session
> show #!1 models
> hide #2 models
> volume #1 level 0.07685
> volume #1 level 0.075
> save "C:/Users/petedani/OneDrive - Boehringer
> Ingelheim/Documents/presentations/2022_annual-report/Periostin-Fab.cxs"
> volume #1 level 0.08
> volume #1 level 0.07
> volume #1 level 0.075
> volume #1 level 0.078
> save "C:/Users/petedani/OneDrive - Boehringer
> Ingelheim/Documents/presentations/2022_annual-report/Periostin-Fab.cxs"
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
> open "C:\\\Users\\\petedani\\\OneDrive - Boehringer
> Ingelheim\\\Documents\\\presentations\\\2022_annual-report\\\Periostin-
> Fab.cxs"
Opened cryosparc_P33_J300_009_volume_map.mrc as #1, grid size 400,400,400,
pixel 0.745, shown at level 0.078, step 1, values float32
Log from Tue Oct 4 10:56:30 2022UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
> open "C:\\\Users\\\petedani\\\OneDrive - Boehringer
> Ingelheim\\\Documents\\\projects\\\Periostin\\\complex1\\\2022-04-14_grid248_EP-22-57369_Krios-
> IMP\\\chimera\\\J300map_coot4model-top.cxs"
Opened cryosparc_P33_J300_009_volume_map.mrc as #1, grid size 400,400,400,
pixel 0.745, shown at level 0.0884, step 1, values float32
Log from Mon May 9 15:03:13 2022UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "C:\\\Users\\\petedani\\\OneDrive - Boehringer
> Ingelheim\\\Documents\\\projects\\\Periostin\\\complex1\\\2022-04-14_grid248_EP-22-57369_Krios-
> IMP\\\cryosparc\\\cryosparc_P33_J300_009_volume_map.mrc"
Opened cryosparc_P33_J300_009_volume_map.mrc as #1, grid size 400,400,400,
pixel 0.745, shown at level 0.0185, step 2, values float32
> volume #1 step 1
> volume #1 level 0.1192
> volume #1 level 0.1034
> volume #1 level 0.09187
> open "C:/Users/petedani/OneDrive - Boehringer
> Ingelheim/Documents/projects/Periostin/complex1/2022-04-14_grid248_EP-22-57369_Krios-
> IMP/coot/complex1-coot-4.pdb"
Chain information for complex1-coot-4.pdb #2
---
Chain | Description
A B | No description available
H S | No description available
L V | No description available
> style ball
Changed 15620 atom styles
> style stick
Changed 15620 atom styles
> show cartoons
[Repeated 3 time(s)]
> hide atoms
> color #1 #b2b2b2f9 models
> color #1 #b2b2b20a models
> color #1 #b2b2b264 models
> color #1 #b2b2b296 models
> show cartoons
> show atoms
[Repeated 1 time(s)]
> hide atoms
> show surfaces
> hide surfaces
> volume #1 level 0.07172
> color bychain
> color bfactor
15620 atoms, 2052 residues, 6 surfaces, atom bfactor range 61.5 to 379
> color bychain
> color zone #1 near #2 distance 4.47
> ui tool show "Color Actions"
> color bychain
[Repeated 3 time(s)]
> select chain A
Expected an objects specifier or a keyword
> select chainA
Expected an objects specifier or a keyword
> select chains A
Expected an objects specifier or a keyword
> select chains A
Expected an objects specifier or a keyword
> select chains A
Expected an objects specifier or a keyword
> hide #!1 models
> ui mousemode right select
> select /A:426
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:427
8 atoms, 7 bonds, 1 residue, 1 model selected
> select clear
> color tomato
> color bychain
> select /A:238
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
58 atoms, 58 bonds, 7 residues, 2 models selected
> select up
4600 atoms, 4676 bonds, 594 residues, 2 models selected
> select up
15620 atoms, 15930 bonds, 2052 residues, 2 models selected
> select down
4600 atoms, 4676 bonds, 594 residues, 7 models selected
> color sel cornflower blue
> select /B:119
5 atoms, 4 bonds, 1 residue, 1 model selected
> select /B:119
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
4600 atoms, 4676 bonds, 594 residues, 2 models selected
> color sel royal blue
> select clear
[Repeated 1 time(s)]
> select /B:150
11 atoms, 10 bonds, 1 residue, 1 model selected
> select up
4600 atoms, 4676 bonds, 594 residues, 2 models selected
> color sel medium blue
> select clear
[Repeated 3 time(s)]
> select /S:85
6 atoms, 5 bonds, 1 residue, 1 model selected
> select up
1641 atoms, 1682 bonds, 219 residues, 2 models selected
> color sel fire brick
> select clear
[Repeated 5 time(s)]
> select /H:155
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
1641 atoms, 1682 bonds, 219 residues, 2 models selected
> color sel sea green
> select clear
> select /L:16
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
1569 atoms, 1607 bonds, 213 residues, 2 models selected
> color sel chartreuse
> select clear
[Repeated 4 time(s)]
> select /V:174
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /V:174
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
1569 atoms, 1607 bonds, 213 residues, 2 models selected
> color sel coral
> select clear
Drag select of 9 residues
> select clear
> show #!1 models
> color zone #1 near #2 distance 4.47
> set bgColor white
> lighting soft
> volume #1 level 0.1118
> volume #1 level 0.04352
> volume #1 level 0.05836
> color #1 #ff634796 models
> color zone #1 near #2 distance 4.47
> color #1 #ff634797 models
> color #1 #ff634796 models
> color #1 #f3fdff96 models
> color #1 #fcfffe96 models
> color #1 #f5ffd096 models
> color #1 #9effda96 models
> color #1 #ffece696 models
> color #1 #746b6996 models
Drag select of 1 cryosparc_P33_J300_009_volume_map.mrc , 30 residues
> select clear
> volume #1 level 0.1385
> select clear
> show atoms
Drag select of 1 cryosparc_P33_J300_009_volume_map.mrc
> select clear
> hide atoms
> select /A:284
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> select /A:283
7 atoms, 7 bonds, 1 residue, 1 model selected
> select down
7 atoms, 7 bonds, 1 residue, 2 models selected
> select up
30 atoms, 30 bonds, 4 residues, 2 models selected
> select up
4600 atoms, 4676 bonds, 594 residues, 2 models selected
> select down
30 atoms, 30 bonds, 4 residues, 2 models selected
> show sel atoms
> select /A:286
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
55 atoms, 54 bonds, 7 residues, 2 models selected
> show sel atoms
> select /A:293
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
4600 atoms, 4676 bonds, 594 residues, 2 models selected
> select down
8 atoms, 7 bonds, 1 residue, 2 models selected
> select #1
2 models selected
> select /A:292
4 atoms, 3 bonds, 1 residue, 1 model selected
> select up
55 atoms, 54 bonds, 7 residues, 2 models selected
> show sel atoms
> style sel stick
Changed 55 atom styles
> style sel stick
Changed 55 atom styles
Drag select of 1 cryosparc_P33_J300_009_volume_map.mrc , 9 residues
Drag select of 2 residues
> close #2
> open "C:/Users/petedani/OneDrive - Boehringer
> Ingelheim/Documents/projects/Periostin/complex1/2022-04-14_grid248_EP-22-57369_Krios-
> IMP/coot/complex1-coot-4_real_space_refined_007mod.pdb"
Chain information for complex1-coot-4_real_space_refined_007mod.pdb #2
---
Chain | Description
A B | No description available
H S | No description available
L V | No description available
> hide atoms
> show cartoons
Drag select of 1 cryosparc_P33_J300_009_volume_map.mrc , 23 residues
> select clear
> hide #!1 models
> select /A:166
10 atoms, 10 bonds, 1 residue, 1 model selected
> select up
84 atoms, 84 bonds, 11 residues, 1 model selected
> select up
4600 atoms, 4676 bonds, 594 residues, 1 model selected
> select up
15620 atoms, 15930 bonds, 2052 residues, 1 model selected
> select down
4600 atoms, 4676 bonds, 594 residues, 1 model selected
> color sel cornflower blue
> select clear
> select /B:243
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
58 atoms, 58 bonds, 7 residues, 1 model selected
> select up
4600 atoms, 4676 bonds, 594 residues, 1 model selected
> color sel cornflower blue
> select clear
> show #!1 models
> hide #!1 models
> show #!1 models
> volume #1 level 0.07172
> volume #1 level 0.07
> volume #1 level 0.0702
> volume #1 level 0.072
> volume #1 level 0.075
> save "C:/Users/petedani/OneDrive - Boehringer
> Ingelheim/Documents/projects/Periostin/complex1/2022-04-14_grid248_EP-22-57369_Krios-
> IMP/chimera/J300map_coot4model.cxs"
> color zone #1 near #2 distance 4.47
> hide #2 models
> save "C:/Users/petedani/OneDrive - Boehringer
> Ingelheim/Documents/projects/Periostin/complex1/2022-04-14_grid248_EP-22-57369_Krios-
> IMP/chimera/J300map_coot4model.cxs"
> save "C:/Users/petedani/OneDrive - Boehringer
> Ingelheim/Documents/projects/Periostin/complex1/2022-04-14_grid248_EP-22-57369_Krios-
> IMP/chimera/J300map_coot4model-top.cxs"
> show #2 models
> hide #2 models
> save "C:/Users/petedani/OneDrive - Boehringer
> Ingelheim/Documents/projects/Periostin/complex1/2022-04-14_grid248_EP-22-57369_Krios-
> IMP/chimera/J300map_coot4model-top.cxs"
> save C:\Users\petedani\Desktop\image1.png supersample 3
> save C:\Users\petedani\Desktop\image2.png supersample 3
> save C:\Users\petedani\Desktop\image3.png supersample 3
> save C:\Users\petedani\Desktop\image4.png supersample 3
> save C:\Users\petedani\Desktop\image5.png supersample 3
> save C:\Users\petedani\Desktop\image6.png supersample 3
> save C:\Users\petedani\Desktop\image7.png supersample 3
> save C:\Users\petedani\Desktop\image8.png supersample 3
> save C:\Users\petedani\Desktop\image9.png supersample 3
> save C:\Users\petedani\Desktop\image10.png supersample 3
> save C:\Users\petedani\Desktop\image11.png supersample 3
> save C:\Users\petedani\Desktop\image12.png supersample 3
> save C:\Users\petedani\Desktop\image13.png supersample 3
> save "C:/Users/petedani/OneDrive - Boehringer
> Ingelheim/Documents/projects/Periostin/complex1/2022-04-14_grid248_EP-22-57369_Krios-
> IMP/chimera/J300map_coot4model-top.cxs"
> lighting soft
> lighting full
> lighting soft
> save C:\Users\petedani\Desktop\image14.png supersample 3
> select clear
[Repeated 1 time(s)]
> save C:\Users\petedani\Desktop\image15.png supersample 3
> save C:\Users\petedani\Desktop\image16.png supersample 3
> save C:\Users\petedani\Desktop\image17.png supersample 3
> save C:\Users\petedani\Desktop\image18.png supersample 3
> save C:\Users\petedani\Desktop\image19.png supersample 3
> save C:\Users\petedani\Desktop\image20.png supersample 3
> save C:\Users\petedani\Desktop\image21.png supersample 3
> volume #1 level 0.08836
> select #1
2 models selected
> save test.png
Permission denied writing file test.png
> select clear
> save test.png
Permission denied writing file test.png
> save /Documents/test.png
Directory "/Documents" does not exist
> cd "C:/Users/petedani/OneDrive - Boehringer
> Ingelheim/Documents/projects/Periostin/complex1/2022-04-14_grid248_EP-22-57369_Krios-
> IMP/chimera"
Current working directory is: C:\Users\petedani\OneDrive - Boehringer
Ingelheim\Documents\projects\Periostin\complex1\2022-04-14_grid248_EP-22-57369_Krios-
IMP\chimera
> save C:\Users\petedani\Desktop\image22.png supersample 3
> save test.png
[Repeated 1 time(s)]
> save C:\Users\petedani\Desktop\image23.png supersample 3
> show #2 models
> hide #!1 models
> show #!1 models
> hide #2 models
> save J300map-top.png
> show #2 models
> hide #!1 models
> save coot4model-top.png
> save "C:/Users/petedani/OneDrive - Boehringer
> Ingelheim/Documents/projects/Periostin/complex1/2022-04-14_grid248_EP-22-57369_Krios-
> IMP/chimera/J300map_coot4model-top.cxs"
——— End of log from Mon May 9 15:03:13 2022 ———
opened ChimeraX session
> show #!1 models
> hide #2 models
> volume #1 level 0.07685
> volume #1 level 0.075
> save "C:/Users/petedani/OneDrive - Boehringer
> Ingelheim/Documents/presentations/2022_annual-report/Periostin-Fab.cxs"
> volume #1 level 0.08
> volume #1 level 0.07
> volume #1 level 0.075
> volume #1 level 0.078
> save "C:/Users/petedani/OneDrive - Boehringer
> Ingelheim/Documents/presentations/2022_annual-report/Periostin-Fab.cxs"
——— End of log from Tue Oct 4 10:56:30 2022 ———
opened ChimeraX session
OpenGL version: 3.3.0 - Build 27.20.100.9749
OpenGL renderer: Intel(R) UHD Graphics
OpenGL vendor: Intel
Manufacturer: LENOVO
Model: 20S1S1J52S
OS: Microsoft Windows 10 Enterprise (Build 19042)
Memory: 16,885,047,296
MaxProcessMemory: 137,438,953,344
CPU: 8 Intel(R) Core(TM) i5-10310U CPU @ 1.70GHz
OSLanguage: en-US
Locale: ('de_AT', '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 , 3 years ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Platform |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Crash using File→Open on Windows and/or in return statement |
comment:2 by , 3 years ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | accepted → closed |
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1.3