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Opened 3 years ago
Closed 3 years ago
#8047 closed defect (can't reproduce)
Crash using File→Open dialog on Windows and/or returning from function
| 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 0x00002dfc (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimeWindows fatal exception: code 0x8001010e
raxWindows fatal exception: code 0x8001010e\cor
e\commands\cli.pWindows fatal exception: code 0x8001010ey", line 1122 in _brow
sWindows fatal exception: code 0x8001010e
e_parse
File Windows fatal exception: code 0x8001010e
"C:\ProgrWindows fatal exception: code 0x8001010eam
FWindows fatal exception: code 0xi8001010el
es\CWindows fatal exception: hcode 0xi8001010em
erWindows fatal exception: acode 0xX8001010e
1.Windows fatal exception: 3code 0x\8001010eb
inWindows fatal exception: \code 0xl8001010ei
b\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 0x00002dfc (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 0x00002dfc (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 0x00002dfc (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 0x00002dfc (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 0x00002dfc (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 0x00002dfc (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 0x00002dfc (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 0x00002dfc (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 0x00002dfc (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 0x00002dfc (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 0x00002dfc (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 0x00002dfc (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 0x00002dfc (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 0x00002dfc (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 _procesWindows fatal exception: code 0x8001010es
_posWindows fatal exception: icode 0xt8001010ei
onWindows fatal exception: acode 0xl8001010e_
arWindows fatal exception: gcode 0xu8001010em
eWindows fatal exception: ncode 0xt8001010es
Windows fatal exception: File code 0x"8001010eC
:\Windows fatal exception: Pcode 0xr8001010eo
grWindows fatal exception: acode 0xm8001010e
FWindows fatal exception: icode 0xl8001010ee
sWindows fatal exception: \code 0xC8001010eh
iWindows fatal exception: mcode 0xe8001010er
aX 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 0x00002dfc (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_maWindows fatal exception: code 0x8001010ei
n.pyWindows fatal exception: "code 0x, line 8001010e1018
in
File Windows fatal exception: "code 0xC8001010e:
\Windows fatal exception: Pcode 0xr8001010eo
gWindows fatal exception: rcode 0xa8001010em
Windows fatal exception: Fcode 0xi8001010el
esWindows fatal exception: \code 0xC8001010eh
iWindows fatal exception: mcode 0xe8001010er
aXWindows fatal exception: code 0x18001010e.
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 0x00002dfc (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\Windows fatal exception: code 0x8001010ec
himeWindows fatal exception: rcode 0xa8001010ex
\cWindows fatal exception: ocode 0xr8001010ee
\cWindows fatal exception: ocode 0xm8001010em
aWindows fatal exception: ncode 0xd8001010es
\Windows fatal exception: ccode 0x8001010el
i.Windows fatal exception: pcode 0xy8001010e"
, line 2812Windows fatal exception: in code 0xr8001010eun
File "C:\Program Files\Ch
imWindows fatal exception: ecode 0xr8001010ea
X Windows fatal exception: 1code 0x.8001010e3
\bWindows fatal exception: icode 0xn8001010e\
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:\PWindows fatal exception: code 0xr8001010eo
gram Windows fatal exception: Fcode 0xi8001010el
esWindows fatal exception: \code 0x8001010e
CWindows fatal exception: hcode 0xi8001010em
erWindows fatal exception: acode 0xX8001010e
1.Windows fatal exception: 3code 0x\8001010eb
inWindows fatal exception: \code 0xl8001010ei
b\Windows fatal exception: rcode 0xu8001010en
pyWindows fatal exception: .code 0xp8001010ey
", line Windows fatal exception: 87code 0x in 8001010e_
ruWindows fatal exception: ncode 0x_8001010ec
ode
File "C:\Program Files\ChimeraX 1.3\bin\lib\runpy.py", line 197 in _run_module_as_main
Windows fatal exception: code 0x8001010e
Thread 0x00002dfc (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\Windows fatal exception: code 0xch8001010e
imerax\Windows fatal exception: ccode 0xo8001010er
e\cWindows fatal exception: ocode 0xm8001010em
anWindows fatal exception: dcode 0xs8001010e\
cWindows fatal exception: lcode 0xi8001010e.
pWindows fatal exception: ycode 0x"8001010e, line 2447
in _Windows fatal exception: pcode 0xa8001010er
sWindows fatal exception: ecode 0x_8001010ea
rWindows fatal exception: gcode 0x
8001010e File
"Windows fatal exception: Ccode 0x:8001010e\
PWindows fatal exception: rcode 0xo8001010eg
ram 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 0x00002dfc (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 0x00002dfc (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 0x00002dfc (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 0x00002dfc (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 0x00002dfc (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\ChWindows fatal exception: code 0xime8001010e
raX 1.3\Windows fatal exception: bcode 0xi8001010en\
lib\rWindows fatal exception: code 0xun8001010e
pyWindows fatal exception: .code 0xp8001010ey
"Windows fatal exception: , line code 0x878001010e in
_rWindows fatal exception: ucode 0xn8001010e_c
ode
Windows fatal exception: File code 0x"8001010eC
:\Windows fatal exception: Pcode 0xr8001010eo
grWindows fatal exception: acode 0xm8001010e
FiWindows fatal exception: lcode 0xe8001010es
\CWindows fatal exception: hcode 0xi8001010em
eraX 1.3\bin\lib\runpy.py", line 197 in _run_module_as_main
Windows fatal exception: code 0x8001010e
Thread 0x00002dfc (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 0x00002dfc (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 0x00002dfc (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 0x00002dfc (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 0x00002dfc (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 0x00002dfc (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 0x00002dfc (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 0x00002dfc (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 0x00002dfc (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\cmd_line\tool.py", line 93 in focusOutEvent
Windows fatal exception: access violation
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
Windows fatal exception: code 0x8001010e
===== 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\\\presentations\\\2022_CRBN-
> cluster\\\overview_BRAF_bCAT_HPK1.cxs"
Opened composite_cryosparc_P23_J433_J445_map_zflip.mrc as #1, grid size
360,360,360, pixel 0.745, shown at level 6, step 1, values float32
Opened composite_J523_J527_volume_map.mrc as #2, grid size 350,350,350, pixel
0.86, shown at level 4, step 1, values float32
Opened composite_P29_J482_J497_map.mrc as #5, grid size 480,480,480, pixel
0.745, shown at level 6, step 1, values float32
Log from Tue Oct 11 14:58:37 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\\\presentations\\\2022_CRBN-
> cluster\\\overview_bCAT_HPK1.cxs"
Opened composite_cryosparc_P23_J433_J445_map_zflip.mrc as #1, grid size
360,360,360, pixel 0.745, shown at level 6, step 1, values float32
Opened composite_J523_J527_volume_map.mrc as #2, grid size 350,350,350, pixel
0.86, shown at level 3, step 1, values float32
Log from Tue Oct 11 10:21:47 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\\\presentations\\\2022_CRBN-
> cluster\\\overview_bCAT.cxs"
Opened composite_cryosparc_P23_J433_J445_map_zflip.mrc as #1, grid size
360,360,360, pixel 0.745, shown at level 6, step 1, values float32
Log from Tue Oct 11 09:53:29 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\\\presentations\\\2022_CRBN-cluster\\\overview.cxs"
Opened composite_cryosparc_P23_J433_J445_map_zflip.mrc as #1, grid size
360,360,360, pixel 0.745, shown at level 6, step 1, values float32
Log from Mon Sep 5 13:07:24 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\\\HPK1\\\20220722_grid381_BI03051346_KriosIMP\\\figures\\\overview1.cxs"
Opened composite_cryosparc_P23_J433_J445_map_zflip.mrc as #1, grid size
360,360,360, pixel 0.745, shown at level 6, step 1, values float32
Log from Tue Aug 30 10:43:06 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\\\HPK1\\\20220722_grid381_BI03051346_KriosIMP\\\figures\\\overview1.cxs"
Opened composite_cryosparc_P23_J433_J445_map_zflip.mrc as #1, grid size
360,360,360, pixel 0.745, shown at level 6, step 1, values float32
Log from Tue Aug 30 09:34:18 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\\\HPK1\\\20220722_grid381_BI03051346_KriosIMP\\\figures\\\overview1.cxs"
Opened composite_cryosparc_P23_J433_J445_map_zflip.mrc as #1, grid size
360,360,360, pixel 0.745, shown at level 6, step 1, values float32
Log from Tue Aug 30 09:30:44 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\\\HPK1\\\20220722_grid381_BI03051346_KriosIMP\\\figures\\\overview1.cxs"
Opened composite_cryosparc_P23_J433_J445_map_zflip.mrc as #1, grid size
360,360,360, pixel 0.745, shown at level 6, step 1, values float32
Log from Fri Aug 26 09:39:07 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\\\HPK1\\\20220722_grid381_BI03051346_KriosIMP\\\figures\\\overview1.cxs"
Opened composite_cryosparc_P23_J433_J445_map_zflip.mrc as #1, grid size
360,360,360, pixel 0.745, shown at level 6, step 1, values float32
Log from Fri Aug 26 09:15:30 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\\\HPK1\\\20220722_grid381_BI03051346_KriosIMP\\\figures\\\overview1.cxs"
Opened composite_cryosparc_P23_J433_J445_map_zflip.mrc as #1, grid size
360,360,360, pixel 0.745, shown at level 6, step 1, values float32
Log from Fri Aug 26 09:01:55 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\\\HPK1\\\20220722_grid381_BI03051346_KriosIMP\\\maps\\\composite_cryosparc_P23_J433_J445_map_zflip.mrc"
Opened composite_cryosparc_P23_J433_J445_map_zflip.mrc as #1, grid size
360,360,360, pixel 0.745, shown at level 2.3, step 2, values float32
> volume #1 step 1
> volume #1 level 5.978
> open "C:/Users/petedani/OneDrive - Boehringer
> Ingelheim/Documents/projects/HPK1/20220722_grid381_BI03051346_KriosIMP/coot/CRBN-
> DDB1delta-BI03051346-HPK1_fitJ445-coot-10.pdb"
Chain information for CRBN-DDB1delta-BI03051346-HPK1_fitJ445-coot-10.pdb #2
---
Chain | Description
A | No description available
B | No description available
C | No description available
> color #1 #b2b2b264 models
> color bychain
> ui mousemode right select
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
56 atoms, 64 bonds, 1 residue, 1 model selected
> select #1
2 models selected
> select #1
2 models selected
> select #1
2 models selected
> select down
2 models selected
> ui mousemode right rotate
> ui mousemode right select
> select #1
2 models selected
> select clear
> select #1
2 models selected
> select /B:451@C18
1 atom, 1 residue, 1 model selected
> ui mousemode right select
> select up
56 atoms, 64 bonds, 1 residue, 1 model selected
> color sel byhetero
[Repeated 1 time(s)]
> ui tool show "Color Actions"
> color sel red
> color sel purple
> color sel deep pink
> color sel dark magenta
> color sel dark orchid
> color sel dark red
> color sel dark magenta
> select clear
[Repeated 1 time(s)]
> volume #1 level 6
> select clear
> cd "C:/Users/petedani/OneDrive - Boehringer
> Ingelheim/Documents/projects/HPK1/20220722_grid381_BI03051346_KriosIMP/figures"
Current working directory is: C:\Users\petedani\OneDrive - Boehringer
Ingelheim\Documents\projects\HPK1\20220722_grid381_BI03051346_KriosIMP\figures
> save "C:/Users/petedani/OneDrive - Boehringer
> Ingelheim/Documents/projects/HPK1/20220722_grid381_BI03051346_KriosIMP/figures/overview1.cxs"
> save overview1.png image .png width 600 height 1200 transparentBackground
> true
Expected a keyword
> save overview1.png width 600 height 1200 transparentBackground true
> save overview1.png width 800 height 1200 transparentBackground true
> select clear
> save overview1.png width 800 height 1200 transparentBackground true
[Repeated 2 time(s)]
> save "C:/Users/petedani/OneDrive - Boehringer
> Ingelheim/Documents/projects/HPK1/20220722_grid381_BI03051346_KriosIMP/figures/overview1.cxs"
——— End of log from Fri Aug 26 09:01:55 2022 ———
opened ChimeraX session
> save overview1.png width 800 height 1200 transparentBackground true
> ui mousemode right select
> select /B:451@C17
1 atom, 1 residue, 1 model selected
> select up
56 atoms, 64 bonds, 1 residue, 1 model selected
> ui tool show "Color Actions"
> color sel cyan
> color sel deep sky blue
> color sel dark blue
1 atom, 1 residue, 1 model selected
> ui mousemode right select
> select clear
[Repeated 2 time(s)]
> select #3/B:451@C28
1 atom, 1 residue, 1 model selected
> select up
56 atoms, 64 bonds, 1 residue, 1 model selected
> ui tool show "Color Actions"
> color sel blue
> select clear
> select #3/B:501@ZN
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select clear
> show #!1 models
> color zone #1 near #3 distance 4.47
> select clear
> show #!2 models
> hide #!1 models
> hide #!3 models
> volume #2 color #b2b2b2
> volume #2 level 5
> show #!4 models
> color zone #2 near #4 distance 5.16
> volume #2 level 4.5
> select clear
> save "C:/Users/petedani/OneDrive - Boehringer
> Ingelheim/Documents/presentations/2022_CRBN-cluster/overview_bCAT_HPK1.cxs"
> volume #2 color #b2b2b264
> volume #2 color #b2b2b250
> volume #1 color #b2b2b250
> show #!3 models
> show #!1 models
> hide #!1 models
> hide #!3 models
> volume #2 level 4
> volume #2 level 3
> select clear
> save "C:/Users/petedani/OneDrive - Boehringer
> Ingelheim/Documents/presentations/2022_CRBN-cluster/overview_bCAT_HPK1.cxs"
[Repeated 1 time(s)]
——— End of log from Tue Oct 11 10:21:47 2022 ———
opened ChimeraX session
> hide #!4 models
> show #!4 models
> hide #!2 models
> show #!2 models
> lighting simple
> lighting soft
> volume #!2 style surface
[Repeated 1 time(s)]
> volume #!2 style mesh
> volume #!2 style surface
> show #!1 models
> hide #!2 models
> show #!2 models
> color #2 #7c72b250 models
> color #2 #b2b2b250 models
> hide #!1 models
> save "C:/Users/petedani/OneDrive - Boehringer
> Ingelheim/Documents/presentations/2022_CRBN-cluster/overview_bCAT_HPK1.cxs"
> show #!3 models
> hide #!4 models
> hide #!2 models
> ui mousemode right select
> select #3/C:225
11 atoms, 11 bonds, 1 residue, 1 model selected
> select up
75 atoms, 76 bonds, 9 residues, 1 model selected
> select up
2064 atoms, 2108 bonds, 259 residues, 1 model selected
> ui tool show "Color Actions"
> color sel forest green
> color sel light sea green
> color sel forest green
> select clear
> save "C:/Users/petedani/OneDrive - Boehringer
> Ingelheim/Documents/presentations/2022_CRBN-cluster/overview_bCAT_HPK1.cxs"
> hide #!3 models
> open "C:/Users/petedani/OneDrive - Boehringer
> Ingelheim/Documents/projects/BRAF-CRBN/20220920_grid440_Krios-
> IMP/maps/composite_P29_J482_J497_map.mrc"
Opened composite_P29_J482_J497_map.mrc as #5, grid size 480,480,480, pixel
0.745, shown at level 2.55, step 2, values float32
Drag select of 5 composite_P29_J482_J497_map.mrc
> select clear
> volume #5 step 1
> volume #5 level 6
> select clear
> show #!1 models
> show #!2 models
> select #5
2 models selected
> ui mousemode right "translate selected models"
> view matrix models #5,1,0,0,-54.814,0,1,0,72.703,0,0,1,-30.834
> ui mousemode right "rotate selected models"
> view matrix models
> #5,-0.23616,0.97141,0.024409,41.293,-0.20298,-0.073881,0.97639,130.54,0.95028,0.22563,0.21463,-137.87
> view matrix models
> #5,-0.83141,0.54387,-0.11389,284.43,-0.2289,-0.14846,0.96206,153.22,0.50633,0.82593,0.24792,-155.22
> view matrix models
> #5,-0.80347,-0.24566,-0.5423,509.17,-0.3625,-0.5207,0.77296,290.26,-0.47226,0.81763,0.32932,54.392
> ui mousemode right "translate selected models"
> view matrix models
> #5,-0.80347,-0.24566,-0.5423,495.13,-0.3625,-0.5207,0.77296,198.53,-0.47226,0.81763,0.32932,30.509
> view matrix models
> #5,-0.80347,-0.24566,-0.5423,447.14,-0.3625,-0.5207,0.77296,151.57,-0.47226,0.81763,0.32932,7.5324
> ui mousemode right "rotate selected models"
> view matrix models
> #5,-0.60963,-0.701,-0.37007,454.61,-0.50513,-0.016242,0.86289,72.24,-0.6109,0.71297,-0.3442,189.73
> view matrix models
> #5,-0.92887,-0.366,0.056947,381.92,0.053329,0.019996,0.99838,-88.637,-0.36654,0.9304,0.00094426,26.036
> view matrix models
> #5,-0.83574,-0.48903,-0.24976,443.26,-0.24943,-0.067117,0.96606,3.2233,-0.4892,0.86968,-0.065889,78.458
> view matrix models
> #5,-0.81469,-0.50616,-0.28299,448.11,-0.2853,-0.075005,0.9555,14.959,-0.50486,0.85917,-0.0833,87.392
> ui mousemode right select
> ui mousemode right "translate selected models"
> view matrix models
> #5,-0.81469,-0.50616,-0.28299,439.51,-0.2853,-0.075005,0.9555,17.247,-0.50486,0.85917,-0.0833,78.302
> ui mousemode right "rotate selected models"
> view matrix models
> #5,-0.97938,-0.096816,-0.17733,379.99,-0.18593,0.088514,0.97857,-40.596,-0.079045,0.99136,-0.10469,-39.714
> ui mousemode right select
> select clear
> ui tool show "Fit in Map"
Fit map composite_P29_J482_J497_map.mrc in map
composite_cryosparc_P23_J433_J445_map_zflip.mrc using 319259 points
correlation = 0.8338, correlation about mean = 0.6838, overlap = 3.109e+07
steps = 532, shift = 36.1, angle = 13.6 degrees
Position of composite_P29_J482_J497_map.mrc (#5) relative to
composite_cryosparc_P23_J433_J445_map_zflip.mrc (#1) coordinates:
Matrix rotation and translation
-0.97426897 0.08825764 -0.20739012 331.77511000
-0.18261063 0.23024596 0.95584531 -54.76477731
0.13211139 0.96912200 -0.20820468 -25.85519404
Axis 0.03055487 -0.78132636 -0.62337430
Axis point 163.60764671 0.00000000 32.11333872
Rotation angle (degrees) 167.45186546
Shift along axis 69.04397418
> hide #!2 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> surface dust #5 size 7.45
> cd "C:/Users/petedani/OneDrive - Boehringer
> Ingelheim/Documents/presentations/2022_CRBN-cluster"
Current working directory is: C:\Users\petedani\OneDrive - Boehringer
Ingelheim\Documents\presentations\2022_CRBN-cluster
> save "C:/Users/petedani/OneDrive - Boehringer
> Ingelheim/Documents/presentations/2022_CRBN-
> cluster/overview_BRAF_bCAT_HPK1.cxs"
> open "C:/Users/petedani/OneDrive - Boehringer
> Ingelheim/Documents/projects/BRAF-CRBN/20220920_grid440_Krios-IMP/coot/BRAF-
> CRBN-DDB1delta_fitJ497-coot-1.pdb"
Chain information for BRAF-CRBN-DDB1delta_fitJ497-coot-1.pdb #6
---
Chain | Description
A | No description available
B | No description available
C | No description available
> ui tool show Matchmaker
> matchmaker #!6 to #3/B pairing bs
Parameters
---
Chain pairing | bs
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker CRBN-DDB1delta-BI03051346-HPK1_fitJ445-s2_coot-12.pdb, chain B (#3)
with BRAF-CRBN-DDB1delta_fitJ497-coot-1.pdb, chain B (#6), sequence alignment
score = 1722.1
RMSD between 356 pruned atom pairs is 0.897 angstroms; (across all 381 pairs:
1.211)
> volume #5 color #b2b2b250
> lighting soft
> select #6/A:90
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
80 atoms, 80 bonds, 10 residues, 1 model selected
> select up
6448 atoms, 6565 bonds, 826 residues, 1 model selected
Fit molecule BRAF-CRBN-DDB1delta_fitJ497-coot-1.pdb (#6) to map
composite_P29_J482_J497_map.mrc (#5) using 11647 atoms
average map value = 14.89, steps = 92
shifted from previous position = 0.284
rotated from previous position = 1.75 degrees
atoms outside contour = 1620, contour level = 6
Position of BRAF-CRBN-DDB1delta_fitJ497-coot-1.pdb (#6) relative to
composite_P29_J482_J497_map.mrc (#5) coordinates:
Matrix rotation and translation
0.99999994 0.00018012 -0.00008854 -0.01189073
-0.00018013 0.99999995 0.00003814 0.02093733
0.00008851 -0.00003815 0.99999994 -0.00459851
Axis -0.18672402 -0.43333603 -0.88167682
Axis point 109.50097967 68.92638099 0.00000000
Rotation angle (degrees) 0.01170538
Shift along axis -0.00279821
> ui tool show "Color Actions"
> color sel slate blue
> show #!3 models
> select clear
> hide #!3 models
> show #!3 models
> hide #!3 models
> select #6/B:262
11 atoms, 10 bonds, 1 residue, 1 model selected
> select up
141 atoms, 142 bonds, 16 residues, 1 model selected
> select up
3039 atoms, 3111 bonds, 382 residues, 1 model selected
> color sel salmon
> select clear
> select #6/C:492
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
110 atoms, 111 bonds, 14 residues, 1 model selected
> select up
2160 atoms, 2209 bonds, 270 residues, 1 model selected
> color sel teal
> select clear
> show #!3 models
> show #!4 models
> hide #!4 models
> hide #!3 models
> show #!1 models
> show #!2 models
> show #!3 models
> show #!4 models
> hide #!2 models
> hide #!1 models
> show #!1 models
> hide #!3 models
> hide #!4 models
> hide #!5 models
> hide #!6 models
> show #!4 models
> hide #!4 models
> show #!3 models
> cd "C:/Users/petedani/OneDrive - Boehringer
> Ingelheim/Documents/presentations/2022_CRBN-cluster"
Current working directory is: C:\Users\petedani\OneDrive - Boehringer
Ingelheim\Documents\presentations\2022_CRBN-cluster
> save "C:/Users/petedani/OneDrive - Boehringer
> Ingelheim/Documents/presentations/2022_CRBN-
> cluster/overview_BRAF_bCAT_HPK1.cxs"
> show #!2 models
> show #!4 models
> hide #!3 models
> hide #!1 models
Drag select of 2 composite_J523_J527_volume_map.mrc , 2 residues
Drag select of 2 composite_J523_J527_volume_map.mrc
> select clear
> show #!1 models
> show #!3 models
> hide #!2 models
> hide #!4 models
Drag select of 1 composite_cryosparc_P23_J433_J445_map_zflip.mrc , 3 residues
> select clear
> show #!4 models
> show #!2 models
> hide #!3 models
> hide #!1 models
> show #!3 models
> show #!1 models
> hide #!2 models
> hide #!4 models
> cd "C:/Users/petedani/OneDrive - Boehringer
> Ingelheim/Documents/presentations/2022_CRBN-cluster"
Current working directory is: C:\Users\petedani\OneDrive - Boehringer
Ingelheim\Documents\presentations\2022_CRBN-cluster
> save HPK1-CRBN_overview.png width 600 height 600 transparentBackground true
> save HPK1-CRBN_overview.png width 800 height 400 transparentBackground true
> save HPK1-CRBN_overview.png width 400 height 800 transparentBackground true
[Repeated 3 time(s)]
> save "C:/Users/petedani/OneDrive - Boehringer
> Ingelheim/Documents/presentations/2022_CRBN-
> cluster/overview_BRAF_bCAT_HPK1.cxs"
> show #!2 models
> show #!4 models
> hide #!3 models
> hide #!1 models
> save bCat-CRBN_overview.png width 400 height 800 transparentBackground true
> volume #2 level 4
> save bCat-CRBN_overview.png width 400 height 800 transparentBackground true
> volume #2 level 5
> save bCAT-CRBN_overview.png width 400 height 800 transparentBackground true
[Repeated 1 time(s)]
> volume #2 level 4.5
> volume #2 level 4
> save bCAT-CRBN_overview.png width 400 height 800 transparentBackground true
> show #!5 models
> show #!6 models
> hide #!4 models
> hide #!2 models
> save BRAF-CRBN_overview.png width 400 height 800 transparentBackground true
[Repeated 1 time(s)]
> hide #!5 models
> hide #!6 models
> show #!4 models
> show #!2 models
> save bCAT-CRBN_overview.png width 400 height 800 transparentBackground true
[Repeated 1 time(s)]
> hide #!2 models
> hide #!4 models
> show #!5 models
> show #!6 models
> save BRAF-CRBN_overview.png width 400 height 800 transparentBackground true
> hide #!5 models
> hide #!6 models
> show #!3 models
> show #!1 models
> save HPK1-CRBN_overview.png width 400 height 800 transparentBackground true
> save "C:/Users/petedani/OneDrive - Boehringer
> Ingelheim/Documents/presentations/2022_CRBN-
> cluster/overview_BRAF_bCAT_HPK1.cxs"
——— End of log from Tue Oct 11 14:58:37 2022 ———
opened ChimeraX session
> hide #!1 models
> ui mousemode right select
> select clear
> select #3/A:350
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
54 atoms, 54 bonds, 7 residues, 1 model selected
> select up
6448 atoms, 6565 bonds, 826 residues, 1 model selected
> select down
54 atoms, 54 bonds, 7 residues, 1 model selected
> ui tool show "Color Actions"
> color sel medium slate blue
> color sel slate blue
> select clear
> select #3/A:349
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
54 atoms, 54 bonds, 7 residues, 1 model selected
> color sel medium slate blue
> select clear
> select #3/A:863
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
79 atoms, 78 bonds, 10 residues, 1 model selected
> color sel slate blue
> color sel medium slate blue
> select clear
> select #3/B:316
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
116 atoms, 115 bonds, 14 residues, 1 model selected
> color sel salmon
> color sel dark salmon
> color sel salmon
> select clear
> select #3/B:293
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
73 atoms, 72 bonds, 9 residues, 1 model selected
> color sel salmon
> select #3/B:157
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
40 atoms, 39 bonds, 5 residues, 1 model selected
> color sel dark salmon
> color sel light salmon
> color sel salmon
> select clear
> select #3/B:146
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
46 atoms, 46 bonds, 5 residues, 1 model selected
> color sel coral
> color sel dark salmon
> color sel salmon
Drag select of 4 residues
> select clear
> select #3/B:145
11 atoms, 10 bonds, 1 residue, 1 model selected
> select up
46 atoms, 46 bonds, 5 residues, 1 model selected
> color sel sandy brown
> color sel light coral
> select clear
> select #3/B:156
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
40 atoms, 39 bonds, 5 residues, 1 model selected
> color sel light coral
> select clear
Drag select of 25 residues
===== 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\\\projects\\\KRAS-
> CRBN\\\20221011_grid459_EP-22-57791_BI03790530\\\figures\\\J570-model_overview.cxs"
Opened composite_J561_J570focus.mrc as #1, grid size 360,360,360, pixel 0.749,
shown at level 7, step 1, values float32
Log from Thu Nov 17 13:38:27 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\\\KRAS-
> CRBN\\\20221011_grid459_EP-22-57791_BI03790530\\\figures\\\J570-model_overview.cxs"
Opened composite_J561_J570focus.mrc as #1, grid size 360,360,360, pixel 0.749,
shown at level 5.26, step 1, values float32
Log from Thu Nov 17 11:12:15 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\\\KRAS-
> CRBN\\\20221011_grid459_EP-22-57791_BI03790530\\\maps\\\composite_J561_J570focus.mrc"
Opened composite_J561_J570focus.mrc as #1, grid size 360,360,360, pixel 0.749,
shown at level 1.81, step 2, values float32
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\urllib3\connectionpool.py", line 699, in urlopen
httplib_response = self._make_request(
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\urllib3\connectionpool.py", line 382, in _make_request
self._validate_conn(conn)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\urllib3\connectionpool.py", line 1010, in _validate_conn
conn.connect()
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\urllib3\connection.py", line 416, in connect
self.sock = ssl_wrap_socket(
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\urllib3\util\ssl_.py", line 449, in ssl_wrap_socket
ssl_sock = _ssl_wrap_socket_impl(
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\urllib3\util\ssl_.py", line 493, in _ssl_wrap_socket_impl
return ssl_context.wrap_socket(sock, server_hostname=server_hostname)
File "C:\Program Files\ChimeraX 1.3\bin\lib\ssl.py", line 500, in wrap_socket
return self.sslsocket_class._create(
File "C:\Program Files\ChimeraX 1.3\bin\lib\ssl.py", line 1040, in _create
self.do_handshake()
File "C:\Program Files\ChimeraX 1.3\bin\lib\ssl.py", line 1309, in
do_handshake
self._sslobj.do_handshake()
ssl.SSLCertVerificationError: [SSL: CERTIFICATE_VERIFY_FAILED] certificate
verify failed: unable to get local issuer certificate (_ssl.c:1129)
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py",
line 676, in customEvent
func(*args, **kw)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\toolshed\\__init__.py", line 1502, in on_finish
versions = self.result.get()
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line
771, in get
raise self._value
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line
125, in worker
result = (True, func(*args, **kwds))
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\cxservices\api_client.py", line 148, in __call_api
response_data = self.request(
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\cxservices\api_client.py", line 338, in request
return self.rest_client.GET(url,
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\cxservices\rest.py",
line 233, in GET
return self.request("GET", url,
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\cxservices\rest.py",
line 206, in request
r = self.pool_manager.request(method, url,
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\urllib3\request.py",
line 74, in request
return self.request_encode_url(
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\urllib3\request.py",
line 96, in request_encode_url
return self.urlopen(method, url, **extra_kw)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\urllib3\poolmanager.py", line 417, in urlopen
return self.urlopen(method, redirect_location, **kw)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\urllib3\poolmanager.py", line 375, in urlopen
response = conn.urlopen(method, u.request_uri, **kw)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\urllib3\connectionpool.py", line 783, in urlopen
return self.urlopen(
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\urllib3\connectionpool.py", line 783, in urlopen
return self.urlopen(
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\urllib3\connectionpool.py", line 755, in urlopen
retries = retries.increment(
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\urllib3\util\retry.py", line 574, in increment
raise MaxRetryError(_pool, url, error or ResponseError(cause))
urllib3.exceptions.MaxRetryError:
HTTPSConnectionPool(host='webservices.rbvi.ucsf.edu', port=443): Max retries
exceeded with url:
/cxservices/api/v1/chimerax/newer?uuid=cb868ed8-17ef-5986-b333-a192c9b95fc2&OS=windows&OSVersion=10.0.19042&ChimeraXVersion=1.3
(Caused by SSLError(SSLCertVerificationError(1, '[SSL:
CERTIFICATE_VERIFY_FAILED] certificate verify failed: unable to get local
issuer certificate (_ssl.c:1129)')))
urllib3.exceptions.MaxRetryError:
HTTPSConnectionPool(host='webservices.rbvi.ucsf.edu', port=443): Max retries
exceeded with url:
/cxservices/api/v1/chimerax/newer?uuid=cb868ed8-17ef-5986-b333-a192c9b95fc2&OS=windows&OSVersion=10.0.19042&ChimeraXVersion=1.3
(Caused by SSLError(SSLCertVerificationError(1, '[SSL:
CERTIFICATE_VERIFY_FAILED] certificate verify failed: unable to get local
issuer certificate (_ssl.c:1129)')))
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\urllib3\util\retry.py", line 574, in increment
raise MaxRetryError(_pool, url, error or ResponseError(cause))
See log for complete Python traceback.
\--- Logging error ---
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.3\bin\lib\logging\\__init__.py", line 1086,
in emit
stream.write(msg + self.terminator)
AttributeError: 'NoneType' object has no attribute 'write'
Call stack:
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930, in
_bootstrap
self._bootstrap_inner()
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973, in
_bootstrap_inner
self.run()
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910, in run
self._target(*self._args, **self._kwargs)
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line
125, in worker
result = (True, func(*args, **kwds))
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\cxservices\api_client.py", line 148, in __call_api
response_data = self.request(
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\cxservices\api_client.py", line 338, in request
return self.rest_client.GET(url,
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\cxservices\rest.py",
line 233, in GET
return self.request("GET", url,
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\cxservices\rest.py",
line 206, in request
r = self.pool_manager.request(method, url,
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\urllib3\request.py",
line 74, in request
return self.request_encode_url(
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\urllib3\request.py",
line 96, in request_encode_url
return self.urlopen(method, url, **extra_kw)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\urllib3\poolmanager.py", line 417, in urlopen
return self.urlopen(method, redirect_location, **kw)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\urllib3\poolmanager.py", line 375, in urlopen
response = conn.urlopen(method, u.request_uri, **kw)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\urllib3\connectionpool.py", line 780, in urlopen
log.warning(
Message: "Retrying (%r) after connection broken by '%r': %s"
Arguments: (Retry(total=1, connect=None, read=None, redirect=None,
status=None), SSLError(SSLCertVerificationError(1, '[SSL:
CERTIFICATE_VERIFY_FAILED] certificate verify failed: unable to get local
issuer certificate (_ssl.c:1129)')),
'/cxservices/api/v1/chimerax/newer?uuid=cb868ed8-17ef-5986-b333-a192c9b95fc2&OS=windows&OSVersion=10.0.19042&ChimeraXVersion=1.3')
\--- Logging error ---
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.3\bin\lib\logging\\__init__.py", line 1086,
in emit
stream.write(msg + self.terminator)
AttributeError: 'NoneType' object has no attribute 'write'
Call stack:
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930, in
_bootstrap
self._bootstrap_inner()
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973, in
_bootstrap_inner
self.run()
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910, in run
self._target(*self._args, **self._kwargs)
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line
125, in worker
result = (True, func(*args, **kwds))
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\cxservices\api_client.py", line 148, in __call_api
response_data = self.request(
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\cxservices\api_client.py", line 338, in request
return self.rest_client.GET(url,
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\cxservices\rest.py",
line 233, in GET
return self.request("GET", url,
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\cxservices\rest.py",
line 206, in request
r = self.pool_manager.request(method, url,
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\urllib3\request.py",
line 74, in request
return self.request_encode_url(
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\urllib3\request.py",
line 96, in request_encode_url
return self.urlopen(method, url, **extra_kw)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\urllib3\poolmanager.py", line 417, in urlopen
return self.urlopen(method, redirect_location, **kw)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\urllib3\poolmanager.py", line 375, in urlopen
response = conn.urlopen(method, u.request_uri, **kw)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\urllib3\connectionpool.py", line 783, in urlopen
return self.urlopen(
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\urllib3\connectionpool.py", line 780, in urlopen
log.warning(
Message: "Retrying (%r) after connection broken by '%r': %s"
Arguments: (Retry(total=0, connect=None, read=None, redirect=None,
status=None), SSLError(SSLCertVerificationError(1, '[SSL:
CERTIFICATE_VERIFY_FAILED] certificate verify failed: unable to get local
issuer certificate (_ssl.c:1129)')),
'/cxservices/api/v1/chimerax/newer?uuid=cb868ed8-17ef-5986-b333-a192c9b95fc2&OS=windows&OSVersion=10.0.19042&ChimeraXVersion=1.3')
> volume #1 step 1
> volume #1 level 3.588
> open "C:/Users/petedani/OneDrive - Boehringer
> Ingelheim/Documents/projects/KRAS-
> CRBN/20221011_grid459_EP-22-57791_BI03790530/coot/DDB1delta--CRBN--
> BI03790530--KRAS-G12D_fitJ570-coot-3.pdb"
Chain information for DDB1delta--CRBN--BI03790530--
KRAS-G12D_fitJ570-coot-3.pdb #2
---
Chain | Description
A | No description available
B | No description available
C | No description available
> volume #1 color #b2b2b264
> volume #1 level 5.259
> cd "C:/Users/petedani/OneDrive - Boehringer
> Ingelheim/Documents/projects/KRAS-
> CRBN/20221011_grid459_EP-22-57791_BI03790530/chimera"
Current working directory is: C:\Users\petedani\OneDrive - Boehringer
Ingelheim\Documents\projects\KRAS-
CRBN\20221011_grid459_EP-22-57791_BI03790530\chimera
> save "C:/Users/petedani/OneDrive - Boehringer
> Ingelheim/Documents/projects/KRAS-
> CRBN/20221011_grid459_EP-22-57791_BI03790530/chimera/J570-model_overview.cxs"
> includeMaps true
——— End of log from Thu Nov 17 11:12:15 2022 ———
opened ChimeraX session
> hide #!1 models
> ui mousemode right select
> select /A:860
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
54 atoms, 53 bonds, 7 residues, 1 model selected
> select up
6468 atoms, 6585 bonds, 826 residues, 1 model selected
> ui tool show "Color Actions"
> color sel royal blue
> color sel blue
> color sel royal blue
> color sel slate blue
> select clear
> select /A:262
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
35 atoms, 35 bonds, 4 residues, 1 model selected
> select up
6468 atoms, 6585 bonds, 826 residues, 1 model selected
> color sel medium slate blue
> color sel royal blue
> select clear
[Repeated 1 time(s)]
> select /B:262
11 atoms, 10 bonds, 1 residue, 1 model selected
> select up
133 atoms, 134 bonds, 15 residues, 1 model selected
> select up
3076 atoms, 3148 bonds, 382 residues, 1 model selected
> color sel crimson
> color sel indian red
> color sel fire brick
> color sel indian red
> select clear
> select /C:69
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
79 atoms, 79 bonds, 9 residues, 1 model selected
> select up
1449 atoms, 1481 bonds, 172 residues, 1 model selected
> color sel dark red
> color sel medium purple
> select clear
> show #!1 models
> surface dust #1 size 7.49
> lighting soft
> color #1 #b2b2b250 models
> surface dust #1 size 5
> surface dust #1 size 8
> surface dust #1 size 7.49
> volume #1 level 5.47
> volume #1 level 5
> volume #1 level 5.5
> volume #1 level 8
Drag select of 1 composite_J561_J570focus.mrc , 9 residues
> select clear
> volume #1 level 6
> save "C:/Users/petedani/OneDrive - Boehringer
> Ingelheim/Documents/projects/KRAS-
> CRBN/20221011_grid459_EP-22-57791_BI03790530/figures/J570-model_overview.cxs"
> lighting multiShadow 64
> hide atoms
> show atoms
> select #1
2 models selected
> select clear
> hide #!1 models
> select clear
[Repeated 2 time(s)]
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
71 atoms, 81 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel atoms
> show sel atoms
> hide sel atoms
> show sel atoms
> style sel ball
Changed 71 atom styles
> select clear
> select /C:203@C45
1 atom, 1 residue, 1 model selected
> select up
71 atoms, 81 bonds, 1 residue, 1 model selected
> style sel sphere
Changed 71 atom styles
> style sel ball
Changed 71 atom styles
> select clear
> hide atoms
> select clear
[Repeated 2 time(s)]
> style ball
Changed 10993 atom styles
> show atoms
> select clear
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
71 atoms, 81 bonds, 1 residue, 1 model selected
> select /B:411@N
1 atom, 1 residue, 1 model selected
> select clear
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
72 atoms, 72 bonds, 9 residues, 1 model selected
> select up
3076 atoms, 3148 bonds, 382 residues, 1 model selected
> hide sel atoms
> select clear
[Repeated 1 time(s)]
> select /A:744
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
24 atoms, 23 bonds, 3 residues, 1 model selected
> select up
6468 atoms, 6585 bonds, 826 residues, 1 model selected
> select up
10993 atoms, 11214 bonds, 1380 residues, 1 model selected
> select down
6468 atoms, 6585 bonds, 826 residues, 1 model selected
> hide sel atoms
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
77 atoms, 76 bonds, 10 residues, 1 model selected
> select up
1449 atoms, 1481 bonds, 172 residues, 1 model selected
> select down
77 atoms, 76 bonds, 10 residues, 1 model selected
> select up
1449 atoms, 1481 bonds, 172 residues, 1 model selected
> select down
77 atoms, 76 bonds, 10 residues, 1 model selected
> hide sel atoms
> select clear
[Repeated 1 time(s)]
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
71 atoms, 81 bonds, 1 residue, 1 model selected
> show sel cartoons
> select clear
> select /C:32@CA
1 atom, 1 residue, 1 model selected
> select up
12 atoms, 12 bonds, 1 residue, 1 model selected
> select up
104 atoms, 107 bonds, 12 residues, 1 model selected
> hide sel atoms
> select /C:61@CG
1 atom, 1 residue, 1 model selected
> select up
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
61 atoms, 61 bonds, 8 residues, 1 model selected
> hide sel atoms
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
79 atoms, 79 bonds, 9 residues, 1 model selected
> hide sel atoms
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
11 atoms, 10 bonds, 1 residue, 1 model selected
> select up
89 atoms, 89 bonds, 11 residues, 1 model selected
> hide sel atoms
> select clear
> select /C:121
7 atoms, 7 bonds, 1 residue, 1 model selected
> select up
77 atoms, 77 bonds, 10 residues, 1 model selected
> select up
1449 atoms, 1481 bonds, 172 residues, 1 model selected
> select down
77 atoms, 77 bonds, 10 residues, 1 model selected
> hide sel atoms
> select /C:88@CD
1 atom, 1 residue, 1 model selected
> select up
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
42 atoms, 42 bonds, 5 residues, 1 model selected
> hide sel atoms
> select clear
[Repeated 2 time(s)]
> select /C:168@CG
1 atom, 1 residue, 1 model selected
> select up
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
1449 atoms, 1481 bonds, 172 residues, 1 model selected
> select down
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel atoms
> select /C:2@CG2
1 atom, 1 residue, 1 model selected
> select up
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
19 atoms, 18 bonds, 3 residues, 1 model selected
> hide sel atoms
> select /C:3@CG
1 atom, 1 residue, 1 model selected
> select up
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
63 atoms, 63 bonds, 8 residues, 1 model selected
> hide sel atoms
> select clear
[Repeated 1 time(s)]
> select /C:39
6 atoms, 5 bonds, 1 residue, 1 model selected
> select up
77 atoms, 77 bonds, 9 residues, 1 model selected
> select up
1449 atoms, 1481 bonds, 172 residues, 1 model selected
> select down
77 atoms, 77 bonds, 9 residues, 1 model selected
> hide sel atoms
> select /C:53
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
70 atoms, 69 bonds, 9 residues, 1 model selected
> hide sel atoms
> select /C:153
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
140 atoms, 142 bonds, 16 residues, 1 model selected
> hide sel atoms
> select /C:127
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
89 atoms, 89 bonds, 11 residues, 1 model selected
> select up
1449 atoms, 1481 bonds, 172 residues, 1 model selected
> select down
89 atoms, 89 bonds, 11 residues, 1 model selected
> hide sel atoms
> select clear
> select /C:150@CD
1 atom, 1 residue, 1 model selected
> select up
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
58 atoms, 57 bonds, 8 residues, 1 model selected
> hide sel atoms
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
28 atoms, 30 bonds, 1 residue, 1 model selected
> hide sel atoms
> select /C:12@CA
1 atom, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
28 atoms, 27 bonds, 5 residues, 1 model selected
> hide sel atoms
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
12 atoms, 12 bonds, 1 residue, 1 model selected
> select up
113 atoms, 115 bonds, 12 residues, 1 model selected
> hide sel atoms
> select /C:92@CG
1 atom, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
1449 atoms, 1481 bonds, 172 residues, 1 model selected
> select down
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel atoms
> select /C:110@N
1 atom, 1 residue, 1 model selected
> select up
7 atoms, 7 bonds, 1 residue, 1 model selected
> select up
49 atoms, 49 bonds, 7 residues, 1 model selected
> hide sel atoms
> select /C:105@CB
1 atom, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
38 atoms, 37 bonds, 5 residues, 1 model selected
> hide sel atoms
> select /C:78@CZ
1 atom, 1 residue, 1 model selected
> select up
11 atoms, 11 bonds, 1 residue, 1 model selected
> select up
52 atoms, 53 bonds, 7 residues, 1 model selected
> hide sel atoms
> select /C:76@CB
1 atom, 1 residue, 1 model selected
> select up
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel atoms
> select /C:140@CD
1 atom, 1 residue, 1 model selected
> select up
7 atoms, 7 bonds, 1 residue, 1 model selected
> select up
35 atoms, 36 bonds, 4 residues, 1 model selected
> hide sel atoms
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
12 atoms, 11 bonds, 2 residues, 1 model selected
> hide sel atoms
> select /C:85@CA
1 atom, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
24 atoms, 23 bonds, 3 residues, 1 model selected
> hide sel atoms
> select /C:47@CB
1 atom, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel atoms
> save "C:/Users/petedani/OneDrive - Boehringer
> Ingelheim/Documents/projects/KRAS-
> CRBN/20221011_grid459_EP-22-57791_BI03790530/figures/J570-model_overview.cxs"
> select /C:67
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
79 atoms, 79 bonds, 9 residues, 1 model selected
> select up
1449 atoms, 1481 bonds, 172 residues, 1 model selected
> ui tool show "Color Actions"
> color sel dark cyan
> color sel deep pink
> color sel magenta
> select clear
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
71 atoms, 81 bonds, 1 residue, 1 model selected
> select up
1449 atoms, 1481 bonds, 172 residues, 1 model selected
> color sel dark magenta
> color sel medium violet red
> color sel hot pink
> color sel orchid
> color sel hot pink
> color sel magenta
> select clear
Drag select of 6 residues
> select clear
> select /C:203@C49
1 atom, 1 residue, 1 model selected
> select up
71 atoms, 81 bonds, 1 residue, 1 model selected
> color sel teal
> select clear
[Repeated 1 time(s)]
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
71 atoms, 81 bonds, 1 residue, 1 model selected
> color sel byhetero
> select clear
[Repeated 1 time(s)]
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
71 atoms, 81 bonds, 1 residue, 1 model selected
> color sel teal
> select clear
Drag select of 9 residues
> select clear
> show #!1 models
> lighting soft
> graphics silhouettes true
> hide #!1 models
> show #!1 models
> hide #!2 models
> show #!2 models
> graphics silhouettes false
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting multiShadow 64
> save "C:/Users/petedani/OneDrive - Boehringer
> Ingelheim/Documents/projects/KRAS-
> CRBN/20221011_grid459_EP-22-57791_BI03790530/figures/J570-model_overview.cxs"
> color zone #1 near #2 distance 4.49
> hide #!2 models
> volume #1 level 7.473
> volume #1 level 6.947
> volume #1 level 6.5
> volume #1 level 7
> lighting soft
> cd "C:/Users/petedani/OneDrive - Boehringer
> Ingelheim/Documents/projects/KRAS-
> CRBN/20221011_grid459_EP-22-57791_BI03790530/figures"
Current working directory is: C:\Users\petedani\OneDrive - Boehringer
Ingelheim\Documents\projects\KRAS-
CRBN\20221011_grid459_EP-22-57791_BI03790530\figures
> save overview_volume.png width 800 height 1200 transparentBackground true
> save "C:/Users/petedani/OneDrive - Boehringer
> Ingelheim/Documents/projects/KRAS-
> CRBN/20221011_grid459_EP-22-57791_BI03790530/figures/J570-model_overview.cxs"
> show #!2 models
> hide #!1 models
> graphics silhouettes true
> save "C:/Users/petedani/OneDrive - Boehringer
> Ingelheim/Documents/projects/KRAS-
> CRBN/20221011_grid459_EP-22-57791_BI03790530/figures/J570-model1_overview.cxs"
——— End of log from Thu Nov 17 13:38:27 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 dialog on Windows and/or returning from function |
comment:2 by , 3 years ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | accepted → closed |
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1.3