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Opened 26 hours ago
#19405 new defect
ChimeraX bug report submission
| Reported by: | Owned by: | ||
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Unassigned | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | ||
| Project: |
Description
The following bug report has been submitted:
Platform: Windows-10-10.0.22621
ChimeraX Version: 1.11.dev202508300055 (2025-08-30 00:55:12 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Windows fatal exception: code 0x8001010d
Current thread 0x00007100 (most recent call first):
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\ui\gui.py", line 368 in event_loop
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\__main__.py", line 1064 in init
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\__main__.py", line 1229 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Windows fatal exception: code 0x8001010e
Thread 0x00007100 (most recent call first):
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 1264 in _browse_parse
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 1406 in parse
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 2800 in _parse_arg
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 2946 in _process_positional_arguments
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 3190 in run
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\run.py", line 49 in run
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\ui\gui.py", line 1224 in
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\ui\gui.py", line 368 in event_loop
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\__main__.py", line 1064 in init
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\__main__.py", line 1229 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Windows fatal exception: code 0x8001010e
Thread 0x00007100 (most recent call first):
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 1264 in _browse_parse
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 1406 in parse
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 2800 in _parse_arg
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 2946 in _process_positional_arguments
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 3190 in run
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\run.py", line 49 in run
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\ui\gui.py", line 1224 in
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\ui\gui.py", line 368 in event_loop
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\__main__.py", line 1064 in init
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\__main__.py", line 1229 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Windows fatal exception: code 0x8001010e
Thread 0x00007100 (most recent call first):
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 1264 in _browse_parse
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 1406 in parse
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 2800 in _parse_arg
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 2946 in _process_positional_arguments
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 3190 in run
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\run.py", line 49 in run
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\ui\gui.py", line 1224 in
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\ui\gui.py", line 368 in event_loop
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\__main__.py", line 1064 in init
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\__main__.py", line 1229 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Windows fatal exception: code 0x8001010e
Thread 0x00007100 (most recent call first):
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 1264 in _browse_parse
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 1406 in parse
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 2800 in _parse_arg
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 2946 in _process_positional_arguments
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 3190 in run
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\run.py", line 49 in run
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\ui\gui.py", line 1224 in
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\ui\gui.py", line 368 in event_loop
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\__main__.py", line 1064 in init
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\__main__.py", line 1229 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Windows fatal exception: code 0x8001010e
Thread 0x00007100 (most recent call first):
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 1264 in _browse_parse
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 1406 in parse
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 2800 in _parse_arg
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 2946 in _process_positional_arguments
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 3190 in run
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\run.py", line 49 in run
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\ui\gui.py", line 1224 in
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\ui\gui.py", line 368 in event_loop
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\__main__.py", line 1064 in init
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\__main__.py", line 1229 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Windows fatal exception: code 0x8001010e
Thread 0x00007100 (most recent call first):
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 1264 in _browse_parse
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 1406 in parse
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 2800 in _parse_arg
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 2946 in _process_positional_arguments
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 3190 in run
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\run.py", line 49 in run
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\ui\gui.py", line 1224 in
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\ui\gui.py", line 368 in event_loop
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\__main__.py", line 1064 in init
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\__main__.py", line 1229 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Windows fatal exception: code 0x8001010e
Thread 0x00007100 (most recent call first):
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 1264 in _browse_parse
File "Windows fatal exception: F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.pycode 0x"8001010e, line
1406 in parse
File Windows fatal exception: "code 0xF:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py8001010e"
, line 2800Windows fatal exception: in code 0x_parse_arg8001010e
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 2946 in _process_positional_arguments
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 3190 in run
File "Windows fatal exception: F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\run.pycode 0x"8001010e, line
49 in Windows fatal exception: runcode 0x
8001010e File
"F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\ui\gui.pyWindows fatal exception: "code 0x, line 8001010e1224
in Windows fatal exception:
code 0x File 8001010e"
F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\ui\gui.py"Windows fatal exception: , line code 0x3688001010e in
event_loop
File Windows fatal exception: "code 0xF:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\__main__.py8001010e"
Windows fatal exception: code 0x, line 8001010e1064
in initWindows fatal exception:
code 0x File 8001010e"
F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\__main__.py", line 1229 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Windows fatal exception: code 0x8001010e
Thread 0x00007100 (most recent call first):
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 1264 in _browse_parse
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 1406 in parse
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 2800 in _parse_arg
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 2946 in _process_positional_arguments
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 3190 in run
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\run.py", line 49 in run
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\ui\gui.py", line 1224 in
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\ui\gui.py", line 368 in event_loop
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\__main__.py", line 1064 in init
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\__main__.py", line 1229 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Windows fatal exception: code 0x8001010e
Thread 0x00007100 (most recent call first):
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 1264 in _browse_parse
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 1406 in parse
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 2800 in _parse_arg
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 2946 in _process_positional_arguments
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 3190 in run
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\run.py", line 49 in run
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\ui\gui.py", line 1224 in
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\ui\gui.py", line 368 in event_loop
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\__main__.py", line 1064 in init
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\__main__.py", line 1229 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Windows fatal exception: code 0x8001010e
Thread 0x00007100 (most recent call first):
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 1264 in _browse_parse
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 1406 in parse
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 2800 in _parse_arg
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 2946 in _process_positional_arguments
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 3190 in run
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\run.py", line 49 in run
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\ui\gui.py", line 1224 in
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\ui\gui.py", line 368 in event_loop
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\__main__.py", line 1064 in init
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\__main__.py", line 1229 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Windows fatal exception: code 0x8001010e
Thread 0x00007100 (most recent call first):
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 1264 in _browse_parse
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 1406 in parse
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 2800 in _parse_arg
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 2946 in _process_positional_arguments
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 3190 in run
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\run.py", line 49 in run
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\ui\gui.py", line 1224 in
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\ui\gui.py", line 368 in event_loop
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\__main__.py", line 1064 in init
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\__main__.py", line 1229 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Windows fatal exception: code 0x8001010e
Thread 0x00007100 (most recent call first):
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 1264 in _browse_parse
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 1406 in parse
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 2800 in _parse_arg
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 2946 in _process_positional_arguments
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 3190 in run
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\run.py", line 49 in run
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\ui\gui.py", line 1224 in
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\ui\gui.py", line 368 in event_loop
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\__main__.py", line 1064 in init
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\__main__.py", line 1229 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Windows fatal exception: code 0x8001010e
Thread 0x00007100 (most recent call first):
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 1264 in _browse_parse
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 1406 in parse
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 2800 in _parse_arg
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 2946 in _process_positional_arguments
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 3190 in run
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\run.py", line 49 in run
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\ui\gui.py", line 1224 in
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\ui\gui.py", line 368 in event_loop
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\__main__.py", line 1064 in init
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\__main__.py", line 1229 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Windows fatal exception: code 0x8001010e
Thread 0x00007100 (most recent call first):
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 1264 in _browse_parse
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 1406 in parse
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 2800 in _parse_arg
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 2946 in _process_positional_arguments
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 3190 in run
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\run.py", line 49 in run
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\ui\gui.py", line 1224 in
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\ui\gui.py", line 368 in event_loop
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\__main__.py", line 1064 in init
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\__main__.py", line 1229 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Windows fatal exception: code 0x8001010e
Thread 0x00007100 (most recent call first):
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 1264 in _browse_parse
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 1406 in parse
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 2800 in _parse_arg
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 2946 in _process_positional_arguments
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 3190 in run
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\run.py", line 49 in run
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\ui\gui.py", line 1224 in
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\ui\gui.py", line 368 in event_loop
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\__main__.py", line 1064 in init
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\__main__.py", line 1229 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Windows fatal exception: code 0x8001010e
Thread 0x00007100 (most recent call first):
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 1264 in _browse_parse
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 1406 in parse
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 2800 in _parse_arg
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 2946 in _process_positional_arguments
File Windows fatal exception: "code 0xF:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py8001010e"
, line 3190 in runWindows fatal exception:
code 0x File 8001010e"
F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\run.py"Windows fatal exception: , line code 0x498001010e in
run
Windows fatal exception: File code 0x"8001010eF:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\ui\gui.py
", line Windows fatal exception: 1224 in code 0x8001010e
File "Windows fatal exception: F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\ui\gui.pycode 0x"8001010e, line
368 in Windows fatal exception: event_loopcode 0x
8001010e File
"F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\__main__.pyWindows fatal exception: "code 0x8001010e
Windows fatal exception: code 0x, line 8001010e1064
in initWindows fatal exception:
code 0x File 8001010e"
F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\__main__.pyWindows fatal exception: "code 0x, line 8001010e1229
in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Windows fatal exception: code 0x8001010e
Thread 0x00007100 (most recent call first):
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 1264 in _browse_parse
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 1406 in parse
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 2800 in _parse_arg
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 2946 in _process_positional_arguments
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 3190 in run
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\run.py", line 49 in run
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\ui\gui.py", line 1224 in
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\ui\gui.py", line 368 in event_loop
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\__main__.py", line 1064 in init
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\__main__.py", line 1229 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Windows fatal exception: code 0x8001010e
Thread 0x00007100 (most recent call first):
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 1264 in _browse_parse
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 1406 in parse
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 2800 in _parse_arg
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 2946 in _process_positional_arguments
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 3190 in run
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\run.py", line 49 in run
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\ui\gui.py", line 1224 in
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\ui\gui.py", line 368 in event_loop
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\__main__.py", line 1064 in init
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\__main__.py", line 1229 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Windows fatal exception: code 0x8001010e
Thread 0x00007100 (most recent call first):
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 1264 in _browse_parse
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 1406 in parse
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 2800 in _parse_arg
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 2946 in _process_positional_arguments
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 3190 in run
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\run.py", line 49 in run
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\ui\gui.py", line 1224 in
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\ui\gui.py", line 368 in event_loop
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\__main__.py", line 1064 in init
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\__main__.py", line 1229 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Windows fatal exception: code 0x8001010e
Thread 0x00007100 (most recent call first):
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 1264 in _browse_parse
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 1406 in parse
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 2800 in _parse_arg
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 2946 in _process_positional_arguments
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 3190 in run
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\run.py", line 49 in run
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\ui\gui.py", line 1224 in
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\ui\gui.py", line 368Windows fatal exception: in code 0xevent_loop8001010e
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\__main__.py", line 1064Windows fatal exception: in code 0xinit8001010e
File "Windows fatal exception: F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\__main__.pycode 0x"8001010e, line 1229
in Windows fatal exception:
code 0x File 8001010e"
", line 88 in _run_code
File "", line 198 in _run_module_as_main
Windows fatal exception: code 0xWindows fatal exception: 8001010ecode 0x
Thread 0x000071008001010e (most recent call first):
File "Windows fatal exception: F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.pycode 0x"8001010e, line
1264Windows fatal exception: in code 0x_browse_parse8001010e
File "Windows fatal exception: F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 1406 in parsecode 0x
8001010e File
"F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 2800 in _parse_argWindows fatal exception:
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py"code 0x, line 8001010e2946
in _process_positional_argumentsWindows fatal exception:
code 0x File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py"8001010e, line 3190 in run
File "
F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\run.py"Windows fatal exception: , line code 0x498001010e in
run
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\ui\gui.py", line 1224 in
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\ui\gui.py", line 368 in event_loop
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\__main__.py", line 1064 in init
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\__main__.py", line 1229 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Windows fatal exception: code 0x8001010e
Thread 0x00007100 (most recent call first):
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 1264 in _browse_parse
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 1406 in parse
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 2800 in _parse_arg
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 2946 in _process_positional_arguments
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 3190 in run
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\run.py", line 49 in run
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\ui\gui.py", line 1224 in
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\ui\gui.py", line 368 in event_loop
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\__main__.py", line 1064 in init
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\__main__.py", line 1229 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Windows fatal exception: code 0x8001010e
Thread 0x00007100 (most recent call first):
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 1264 in _browse_parse
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 1406 in parse
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 2800 in _parse_arg
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 2946 in _process_positional_arguments
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 3190 in run
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\run.py", line 49 in run
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\ui\gui.py", line 1224 in
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\ui\gui.py", line 368 in event_loop
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\__main__.py", line 1064 in init
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\__main__.py", line 1229 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Windows fatal exception: code 0x8001010e
Thread 0x00007100 (most recent call first):
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 1264 in _browse_parse
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 1406 in parse
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 2800 in _parse_arg
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 2946 in _process_positional_arguments
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 3190 in run
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\run.py", line 49 in run
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\ui\gui.py", line 1224 in
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\ui\gui.py", line 368 in event_loop
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\__main__.py", line 1064 in init
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\__main__.py", line 1229 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Windows fatal exception: code 0x8001010e
Thread 0x00007100 (most recent call first):
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 1264 in _browse_parse
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 1406 in parse
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 2800 in _parse_arg
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 2946 in _process_positional_arguments
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 3190 in run
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\run.py", line 49 in run
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\ui\gui.py", line 1224 in
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\ui\gui.py", line 368 in event_loop
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\__main__.py", line 1064 in init
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\__main__.py", line 1229 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Windows fatal exception: code 0x8001010e
Thread 0x00007100 (most recent call first):
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 1264 in _browse_parse
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 1406 in parse
File "Windows fatal exception: F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.pycode 0x"8001010e, line
2800 in _parse_arg
Windows fatal exception: File code 0x"8001010eF:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py
", line Windows fatal exception: 2946code 0x in 8001010e_process_positional_arguments
File Windows fatal exception: "code 0xF:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py8001010e"
, line 3190Windows fatal exception: in code 0xrun8001010e
File "Windows fatal exception: F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\run.pycode 0x"8001010e, line
49 in Windows fatal exception: runcode 0x
8001010e File
"F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\ui\gui.pyWindows fatal exception: "code 0x, line 8001010e1224
in Windows fatal exception:
code 0x File 8001010e"
F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\ui\gui.py", line 368 in event_loop
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\__main__.pyWindows fatal exception: "code 0x8001010e
Windows fatal exception: , line code 0x10648001010e in
init
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\__main__.py", line 1229 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Windows fatal exception: code 0x8001010e
Thread 0x00007100 (most recent call first):
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 1264 in _browse_parse
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 1406 in parse
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 2800 in _parse_arg
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 2946 in _process_positional_arguments
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 3190 in run
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\run.py", line 49 in run
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\ui\gui.py", line 1224 in
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\ui\gui.py", line 368 in event_loop
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\__main__.py", line 1064 in init
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\__main__.py", line 1229 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Windows fatal exception: code 0x8001010e
Thread 0x00007100 (most recent call first):
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 1264 in _browse_parse
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 1406 in parse
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 2800 in _parse_arg
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 2946 in _process_positional_arguments
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 3190 in run
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\run.py", line 49 in run
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\ui\gui.py", line 1224 in
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\ui\gui.py", line 368 in event_loop
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\__main__.py", line 1064 in init
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\__main__.py", line 1229 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Windows fatal exception: code 0x8001010e
Thread 0x00007100 (most recent call first):
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 1264 in _browse_parse
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 1406 in parse
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 2800 in _parse_arg
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 2946 in _process_positional_arguments
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 3190 in run
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\run.py", line 49 in run
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\ui\gui.py", line 1224 in
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\ui\gui.py", line 368 in event_loop
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\__main__.py", line 1064 in init
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\__main__.py", line 1229 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Windows fatal exception: code 0x8001010e
Thread 0x00007100 (most recent call first):
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 1264 in _browse_parse
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 1406 in parse
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 2800 in _parse_arg
Windows fatal exception: File code 0x"8001010eF:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py
", line 2946 in Windows fatal exception: _process_positional_argumentscode 0x
8001010e File
"F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.pyWindows fatal exception: "code 0x, line 8001010e3190
in runWindows fatal exception:
code 0x File 8001010e"
F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\run.py"Windows fatal exception: , line code 0x498001010e in
run
Windows fatal exception: File code 0x"8001010eF:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\ui\gui.py
", line Windows fatal exception: 1224code 0x in 8001010e
File Windows fatal exception: "code 0xF:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\ui\gui.py8001010e"
, line 368Windows fatal exception: in code 0xevent_loop8001010e
File "Windows fatal exception: F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\__main__.pycode 0x"8001010e
Windows fatal exception: code 0x, line 8001010e1064
in init
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\__main__.py", line 1229 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Windows fatal exception: code 0x8001010e
Thread 0x00007100 (most recent call first):
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 1264 in _browse_parse
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 1406 in parse
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 2800 in _parse_arg
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 2946 in _process_positional_arguments
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 3190 in run
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\run.py", line 49 in run
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\ui\gui.py", line 1224 in
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\ui\gui.py", line 368 in event_loop
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\__main__.py", line 1064 in init
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\__main__.py", line 1229 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Windows fatal exception: code 0x8001010e
Thread 0x00007100 (most recent call first):
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 1264 in _browse_parse
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 1406 in parse
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 2800 in _parse_arg
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 2946 in _process_positional_arguments
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 3190 in run
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\run.py", line 49 in run
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\ui\gui.py", line 1224 in
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\ui\gui.py", line 368 in event_loop
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\__main__.py", line 1064 in init
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\__main__.py", line 1229 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Windows fatal exception: code 0x8001010e
Thread 0x00007100Windows fatal exception: (most recent call first):
code 0x File 8001010e"
F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py"Windows fatal exception: , line code 0x12648001010e in
_browse_parse
Windows fatal exception: File code 0x"8001010eF:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py
"Windows fatal exception: , line code 0x14068001010e in
parse
Windows fatal exception: File code 0x"8001010eF:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py
"Windows fatal exception: , line code 0x28008001010e in
_parse_arg
Windows fatal exception: File code 0x"8001010eF:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py
"Windows fatal exception: , line code 0x29468001010e in
_process_positional_argumentsWindows fatal exception:
code 0x File 8001010e"
F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py"Windows fatal exception: , line code 0x31908001010e in
run
Windows fatal exception: File code 0x"8001010eF:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\run.py
", line 49 in run
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\ui\gui.py", line 1224 in
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\ui\gui.py", line 368 in event_loop
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\__main__.py", line 1064 in init
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\__main__.py", line 1229 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Windows fatal exception: code 0x8001010e
Thread 0x00007100 (most recent call first):
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 1264 in _browse_parse
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 1406 in parse
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 2800 in _parse_arg
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 2946 in _process_positional_arguments
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 3190 in run
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\run.py", line 49 in run
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\ui\gui.py", line 1224 in
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\ui\gui.py", line 368 in event_loop
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\__main__.py", line 1064 in init
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\__main__.py", line 1229 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Windows fatal exception: code 0x8001010e
Thread 0x00007100 (most recent call first):
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 1264 in _browse_parse
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 1406 in parse
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 2800 in _parse_arg
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 2946 in _process_positional_arguments
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 3190 in run
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\run.py", line 49 in run
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\ui\gui.py", line 1224 in
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\ui\gui.py", line 368 in event_loop
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\__main__.py", line 1064 in init
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\__main__.py", line 1229 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Windows fatal exception: code 0x8001010e
Thread 0x00007100 (most recent call first):
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 1264 in _browse_parse
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 1406 in parse
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 2800 in _parse_arg
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 2946 in _process_positional_arguments
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 3190 in run
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\run.py", line 49 in run
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\ui\gui.py", line 1224 in
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\ui\gui.py", line 368 in event_loop
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\__main__.py", line 1064 in init
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\__main__.py", line 1229 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Windows fatal exception: code 0x8001010e
Thread 0x00007100 (most recent call first):
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 1264 in _browse_parse
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 1406 in parse
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 2800 in _parse_arg
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 2946 in _process_positional_arguments
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 3190 in run
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\run.py", line 49 in run
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\ui\gui.py", line 1224 in
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\ui\gui.py", line 368 in event_loop
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\__main__.py", line 1064 in init
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\__main__.py", line 1229 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Windows fatal exception: code 0x8001010e
Thread 0x00007100 (most recent call first):
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 1264 in _browse_parse
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 1406 in parse
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 2800 in _parse_arg
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 2946 in _process_positional_arguments
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 3190 in run
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\run.py", line 49 in run
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\ui\gui.py", line 1224 in
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\ui\gui.py", line 368 in event_loop
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\__main__.py", line 1064 in init
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\__main__.py", line 1229 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Windows fatal exception: code 0x8001010e
Thread 0x00007100 (most recent call first):
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 1264 in _browse_parse
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 1406 in parse
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 2800 in _parse_arg
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 2946 in _process_positional_arguments
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 3190 in run
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\run.py", line 49 in run
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\ui\gui.py", line 1224 in
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\ui\gui.py", line 368 in event_loop
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\__main__.py", line 1064 in init
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\__main__.py", line 1229 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Windows fatal exception: code 0x8001010e
Thread 0x00007100 (most recent call first):
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 1264 in _browse_parse
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 1406 in parse
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 2800 in _parse_arg
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 2946 in _process_positional_arguments
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 3190 in run
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\run.py", line 49 in run
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\ui\gui.py", line 1224 in
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\ui\gui.py", line 368 in event_loop
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\__main__.py", line 1064 in init
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\__main__.py", line 1229 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Windows fatal exception: code 0x8001010e
Thread 0x00007100 (most recent call first):
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 1264 in _browse_parse
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 1406 in parse
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 2800 in _parse_arg
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 2946 in _process_positional_arguments
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 3190 in run
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\run.py", line 49 in run
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\ui\gui.py", line 1224 in
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\ui\gui.py", line 368 in event_loop
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\__main__.py", line 1064 in init
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\__main__.py", line 1229 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Windows fatal exception: code 0x8001010e
Thread 0x00007100 (most recent call first):
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 1264 in _browse_parse
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 1406 in parse
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 2800 in _parse_arg
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 2946 in _process_positional_arguments
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 3190 in run
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\run.py", line 49 in run
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\ui\gui.py", line 1224 in
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\ui\gui.py", line 368 in event_loop
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\__main__.py", line 1064 in init
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\__main__.py", line 1229 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Windows fatal exception: code 0x8001010e
Thread 0x00007100 (most recent call first):
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 1264 in _browse_parse
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 1406 in parse
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 2800 in _parse_arg
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 2946 in _process_positional_arguments
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 3190 in run
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\run.py", line 49 in run
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\ui\gui.py", line 1224 in
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\ui\gui.py", line 368 in event_loop
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\__main__.py", line 1064 in init
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\__main__.py", line 1229 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Windows fatal exception: code 0x8001010e
Thread 0x00007100 (most recent call first):
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 1264 in _browse_parse
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 1406 in parse
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 2800 in _parse_arg
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 2946 in _process_positional_arguments
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 3190 in run
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\run.py", line 49 in run
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\ui\gui.py", line 1224 in
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\ui\gui.py", line 368 in event_loop
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\__main__.py", line 1064 in init
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\__main__.py", line 1229 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Windows fatal exception: code 0x8001010e
Thread 0x00007100 (most recent call first):
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 1264 in _browse_parse
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 1406 in parse
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 2800 in _parse_arg
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 2946 in _process_positional_arguments
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 3190 in run
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\run.py", line 49 in run
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\ui\gui.py", line 1224 in
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\ui\gui.py", line 368 in event_loop
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\__main__.py", line 1064 in init
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\__main__.py", line 1229 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Windows fatal exception: code 0x8001010e
Thread 0x00007100 (most recent call first):
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 1264 in _browse_parse
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 1406 in parse
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 2800 in _parse_arg
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 2946 in _process_positional_arguments
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 3190 in run
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\run.py", line 49 in run
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\ui\gui.py", line 1224 in
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\ui\gui.py", line 368 in event_loop
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\__main__.py", line 1064 in init
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\__main__.py", line 1229 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Windows fatal exception: code 0x8001010e
Thread 0x00007100 (most recent call first):
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 1264 in _browse_parse
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 1406 in parse
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 2800 in _parse_arg
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 2946 in _process_positional_arguments
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 3190 in run
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\run.py", line 49 in run
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\ui\gui.py", line 1224 in
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\ui\gui.py", line 368 in event_loop
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\__main__.py", line 1064 in init
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\__main__.py", line 1229 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Windows fatal exception: code 0x8001010e
Thread 0x00007100 (most recent call first):
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 1264 in _browse_parse
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 1406 in parse
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 2800 in _parse_arg
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 2946 in _process_positional_arguments
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 3190 in run
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\run.py", line 49 in run
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\ui\gui.py", line 1224 in
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\ui\gui.py", line 368 in event_loop
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\__main__.py", line 1064 in init
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\__main__.py", line 1229 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Windows fatal exception: code 0x8001010e
Thread 0x00007100 (most recent call first):
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 1264 in _browse_parse
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 1406 in parse
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 2800 in _parse_arg
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 2946 in _process_positional_arguments
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 3190 in run
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\run.py", line 49 in run
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\ui\gui.py", line 1224 in
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\ui\gui.py", line 368 in event_loop
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\__main__.py", line 1064 in init
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\__main__.py", line 1229 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Windows fatal exception: code 0x8001010e
Thread 0x00007100 (most recent call first):
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 1264 in _browse_parse
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 1406 in parse
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 2800 in _parse_arg
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 2946 in _process_positional_arguments
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 3190 in run
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\run.py", line 49 in run
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\ui\gui.py", line 1224 in
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\ui\gui.py", line 368 in event_loop
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\__main__.py", line 1064 in init
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\__main__.py", line 1229 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Windows fatal exception: code 0x8001010e
Thread 0x00007100 (most recent call first):
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 1264 in _browse_parse
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 1406 in parse
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 2800 in _parse_arg
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 2946 in _process_positional_arguments
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 3190 in run
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\run.py", line 49 in run
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\ui\gui.py", line 1224 in
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\ui\gui.py", line 368 in event_loop
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\__main__.py", line 1064 in init
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\__main__.py", line 1229 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Windows fatal exception: code 0x8001010e
Thread 0x00007100 (most recent call first):
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 1264 in _browse_parse
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 1406 in parse
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 2800 in _parse_arg
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 2946 in _process_positional_arguments
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 3190 in run
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\run.py", line 49 in run
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\ui\gui.py", line 1224 in
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\ui\gui.py", line 368 in event_loop
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\__main__.py", line 1064 in init
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\__main__.py", line 1229 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Windows fatal exception: code 0x8001010e
Thread 0x00007100 (most recent call first):
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 1264 in _browse_parse
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 1406 in parse
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 2800 in _parse_arg
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 2946 in _process_positional_arguments
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 3190 in run
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\run.py", line 49 in run
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\ui\gui.py", line 1224 in
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\ui\gui.py", line 368 in event_loop
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\__main__.py", line 1064 in init
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\__main__.py", line 1229 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Windows fatal exception: code 0x8001010e
Thread 0x00007100 (most recent call first):
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 1264 in _browse_parse
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 1406 in parse
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 2800 in _parse_arg
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 2946 in _process_positional_arguments
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 3190 in run
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\run.py", line 49 in run
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\ui\gui.py", line 1224 in
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\ui\gui.py", line 368 in event_loop
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\__main__.py", line 1064 in init
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\__main__.py", line 1229 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Windows fatal exception: code 0x8001010e
Thread 0x00007100 (most recent call first):
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 1264 in _browse_parse
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 1406 in parse
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 2800 in _parse_arg
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 2946 in _process_positional_arguments
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 3190 in run
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\commands\run.py", line 49 in run
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\ui\gui.py", line 1224 in
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\ui\gui.py", line 368 in event_loop
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\__main__.py", line 1064 in init
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\__main__.py", line 1229 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Windows fatal exception: access violation
Thread 0x00008034 (most recent call first):
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\threading.py", line 331 in wait
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\threading.py", line 629 in wait
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\threading.py", line 1399 in run
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\threading.py", line 1045 in _bootstrap_inner
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\threading.py", line 1002 in _bootstrap
Current thread 0x00007100 (most recent call first):
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\ui\gui.py", line 368 in event_loop
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\__main__.py", line 1064 in init
File "F:\ChimeraX 1.11.dev202508300055\bin\Lib\site-packages\chimerax\core\__main__.py", line 1229 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
===== Log before crash start =====
> open E:/xwechat_files/wxid_idejr78pt1sr22_f116/msg/file/2025-10/BL4R.pdb
BL4R.pdb title:
\--- [more info...]
Chain information for BL4R.pdb #1
---
Chain | Description
A | No description available
B | No description available
C | No description available
Non-standard residues in BL4R.pdb #1
---
GOL — (GOL)
Computing secondary structure
> open "D:/桌面/BLB4 and BLB21/BLB21_ABC.cif"
Summary of feedback from opening D:/桌面/BLB4 and BLB21/BLB21_ABC.cif
---
warnings | Missing entity information. Treating each chain as a separate entity.
Missing or incorrect sequence information. Inferred polymer connectivity.
Chain information for BLB21_ABC.cif #2
---
Chain | Description
A | No description available
B | No description available
C | No description available
Computing secondary structure
> mmaker #2/B to #1/B showAlignment true
Parameters
---
Chain pairing | bb
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 BL4R.pdb, chain B (#1) with BLB21_ABC.cif, chain B (#2), sequence
alignment score = 863.7
Alignment identifier is 1
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1
Hiding conservation header for alignment 1
Chains used in RMSD evaluation for alignment 1: BL4R.pdb #1/B, BLB21_ABC.cif
#2/B
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1
RMSD between 176 pruned atom pairs is 0.815 angstroms; (across all 179 pairs:
0.876)
> mmaker #2 to #1
Parameters
---
Chain pairing | bb
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 BL4R.pdb, chain A (#1) with BLB21_ABC.cif, chain A (#2), sequence
alignment score = 954.1
RMSD between 182 pruned atom pairs is 0.547 angstroms; (across all 182 pairs:
0.547)
> select #1/B:2-165,167-188 #2/B:2-165,167-188
2907 atoms, 2984 bonds, 3 pseudobonds, 352 residues, 4 models selected
> select ::seq_identity color sel red
> delete solvent #1
Expected a keyword
> delete #1 & solvent
> select #1/A:201@C2
1 atom, 1 residue, 1 model selected
Drag select of 6 atoms, 5 bonds
> delete atoms sel
> delete bonds sel
> select #1/C
116 atoms, 115 bonds, 15 residues, 1 model selected
> hbonds sel reveal true
38 hydrogen bonds found
> hide #!2 models
Drag select of 3 atoms, 2 bonds
Drag select of 2 atoms, 3 bonds
> hide sel atoms
Drag select of 3 atoms, 2 bonds
> hide sel atoms
Drag select of 1 atoms, 1 residues, 1 bonds
> hide sel atoms
Drag select of 95 residues, 1 pseudobonds
> hide sel atoms
> hide sel cartoons
Drag select of 59 residues
> hide sel cartoons
Drag select of 33 residues
> hide sel surfaces
> hide sel cartoons
Drag select of 1 residues
> hide sel cartoons
> set bgColor white
> set bgColor #ffffff00
> lighting simple
> lighting soft
> lighting full
> lighting simple
> lighting full
> lighting soft
> lighting simple
> lighting soft
> select /A:1-184
2975 atoms, 3075 bonds, 366 residues, 2 models selected
> color sel white
> color (#!1 & sel) light gray
> style sel & #!1 stick
Changed 1496 atom styles
> style sel & #!1 stick
Changed 1496 atom styles
> color (#!1 & sel) byelement
> style sel & #!1 stick
Changed 1496 atom styles
> ui tool show "Color Actions"
> color sel light gray
> color sel byelement
> color sel dark gray
> color sel byelement
> color sel light gray
> color sel white
> color sel light gray
> color electrostatic #1/A & sidechain
Missing required "map" argument
> color electrostatic #1/A
Missing required "map" argument
> color Element #1/B & sidechain
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color byelement #1/B & sidechain
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> color byelement #1/B
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> color #1/B byelement
> color #1/A byelement
> color sel light gray
> color sel gray
> color sel dark gray
> color sel byelement
> color sel light gray
> color sel byelement
> color (#!1 & sel) light gray
> select /C:1-15
200 atoms, 198 bonds, 3 pseudobonds, 27 residues, 3 models selected
> hbonds sel & #!1 reveal true
38 hydrogen bonds found
> select #1/A
1496 atoms, 1546 bonds, 184 residues, 1 model selected
> select O
1130 atoms, 6 pseudobonds, 753 residues, 3 models selected
> color (#!1 & sel) red
> select sideonly
3138 atoms, 2572 bonds, 4 pseudobonds, 710 residues, 3 models selected
> select #1/A
1496 atoms, 1546 bonds, 184 residues, 1 model selected
> color sel bychain
> color sel byhetero
> color sel light gray
> color sel byhetero
> select #1/B:2-165,167-188 #2/B:2-165,167-188
2907 atoms, 2984 bonds, 3 pseudobonds, 352 residues, 4 models selected
> select ::seq_identity color (#!1 & sel) hot pink
> style sel & #!1 stick
Changed 143 atom styles
> color sel & #!1 byhetero
> save "D:/桌面/BLB4 and BLB21/BLB4_1.png" width 1979 height 1169 supersample 3
QDxgiVSyncService: DXGI Factory is no longer Current
> hide #!1 models
> hide #3 models
> show #!2 models
Drag select of 113 residues, 2 pseudobonds
Drag select of 29 residues
Drag select of 166 residues, 2 pseudobonds
> hide sel cartoons
Drag select of 8 residues
> hide sel cartoons
Drag select of 9 residues
> hide sel cartoons
Drag select of 1 residues
> hide sel cartoons
> view clip false
> select #2/C:4-17
104 atoms, 104 bonds, 14 residues, 1 model selected
> hbonds sel reveal true
45 hydrogen bonds found
> select #2/A
1479 atoms, 1529 bonds, 182 residues, 1 model selected
> color sel light gray
> color sel byhetero
> select #1/B:2-165,167-188 #2/B:2-165,167-188
2907 atoms, 2984 bonds, 3 pseudobonds, 352 residues, 4 models selected
> select ::seq_identity color (#!2 & sel) hot pink
> color sel & #!2 byhetero
> show #3 models
> color #3 #55ff7fff models
> color #3 #00aa00ff models
> show #!1 models
> hide #3 models
> show #3 models
> hide #!2 models
> hide #3 models
> hide #!1 models
> show #!2 models
> show #3 models
> color #3 #5555ffff models
> color #3 #55aaffff models
> color #3 #ffaa7fff models
> color #3 #ffaa00ff models
> color #3 #aaaa7fff models
> color #3 #aaaa00ff models
> color #3 #00aa00ff models
> color #3 #ff007fff models
> color #3 red models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #3 models
> hide #!2 models
> select /C:1-15
200 atoms, 198 bonds, 1 pseudobond, 27 residues, 3 models selected
> hbonds sel & #!1 reveal true
38 hydrogen bonds found
> show #3 models
> color #3 red models
> color #3 #00aaffff models
> color #3 #55aaffff models
> color #3 #0055ffff models
> color #3 #005500ff models
> color #3 #aa0000ff models
> color #3 black models
> color #3 #686868ff models
> color #3 #5d5d5dff models
> color #3 #515151ff models
> color #3 #818181ff models
> color #3 #474747ff models
> color #3 #383838ff models
> color #3 #5d5d5dff models
> color #3 #818181ff models
> color #3 #6f6f6fff models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #!1 models
> show #!1 models
> hide #3 models
> show #!2 models
> show #3 models
> hide #3 models
> hide #!2 models
> select /B:2-190
2955 atoms, 3036 bonds, 3 pseudobonds, 358 residues, 4 models selected
> hide sel & #!1 atoms
> select #1/C
116 atoms, 115 bonds, 2 pseudobonds, 15 residues, 2 models selected
> hbonds sel reveal true
38 hydrogen bonds found
> show #3 models
> color #3 black models
> color #3 #6c6c6cff models
> color #3 #595959ff models
> color #3 #3e3e3eff models
> color #3 #6f6f6fff models
> color #3 #7e7e7eff models
> color #3 #828282ff models
> save "D:/桌面/BLB4 and BLB21/BLB4_1.png" width 1979 height 1169 supersample 3
No model chosen to save relative to
> save image.png transparentBackground true
QDxgiVSyncService: DXGI Factory is no longer Current
> select clear
> save image.png transparentBackground true
> cd D:\桌面\BLB4 and BLB21
Expected name of a folder to open/read; a name of 'browse' will bring up a
file browser or a keyword
> cd "D:/桌面/BLB4 and BLB21"
Current working directory is: D:\桌面\BLB4 and BLB21
> save BLB4_1.png transparentBackground true
> hide #3 models
> hide #!1 models
> show #!2 models
No model chosen to save relative to
> save BLB21.cif
Not saving entity_poly_seq for non-authoritative sequences
> save project.cxs
> select #2/C
104 atoms, 104 bonds, 14 residues, 1 model selected
> hbonds sel reveal true
45 hydrogen bonds found
> show #3 models
> color #3 black models
> color #3 #828282ff models
> save BLB21_1.png transparentBackground true
QDxgiVSyncService: DXGI Factory is no longer Current
> hide #3 models
> show #!1 models
> hide #!2 models
> coulombic #!1
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for BL4R.pdb_A SES surface #1.2: minimum, -13.30, mean -2.41,
maximum 9.55
Coulombic values for BL4R.pdb_B SES surface #1.3: minimum, -14.87, mean -1.87,
maximum 11.23
Coulombic values for BL4R.pdb_C SES surface #1.4: minimum, -8.31, mean 2.68,
maximum 12.11
To also show corresponding color key, enter the above coulombic command and
add key true
> hide #1.4 models
> select #1/C
116 atoms, 115 bonds, 15 residues, 1 model selected
> show sel atoms
> lighting simple
> lighting soft
> lighting full
> lighting soft
> lighting full
> lighting soft
> lighting full
> lighting shadows false
> lighting soft
> lighting simple
> lighting soft
> hide #1.3 models
> hide #1.2 models
> interfaces select & ~solvent
Missing or invalid "atoms" argument: invalid atoms specifier
> select subtract #1.4
1 model selected
> select add #1.4
116 atoms, 15 residues, 1 model selected
> show #1.2 models
> show #1.3 models
> show #1.4 models
> hide #1.4 models
> lighting flat
> lighting full
> lighting flat
> lighting simple
> lighting shadows true
> lighting shadows false
> lighting flat
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting shadows false
> graphics silhouettes false
> lighting soft
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> ui tool show Contacts
> contacts ignoreHiddenModels true
2164 contacts
> contacts ignoreHiddenModels true
2164 contacts
> hide #1.3 models
> hide #1.2 models
> hide #1.1 models
> hide #4 models
> show #3 models
> hide #3 models
> ui tool show Contacts
Restriction atom specifier must not be blank
> contacts sel restrict cross ignoreHiddenModels true
140 contacts
> contacts sel ignoreHiddenModels true
143 contacts
> show #4 models
> contacts sel restrict cross ignoreHiddenModels true
140 contacts
> contacts sel ignoreHiddenModels true
143 contacts
> hide sel atoms
> show sel atoms
> sequence chain #1/C
Alignment identifier is 1/C
> select #1/C:1
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #1/C
116 atoms, 115 bonds, 3 pseudobonds, 15 residues, 2 models selected
> select #1/C:15
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #1/C
116 atoms, 115 bonds, 3 pseudobonds, 15 residues, 2 models selected
> select #1/C:15
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #1/C
116 atoms, 115 bonds, 3 pseudobonds, 15 residues, 2 models selected
Drag select of 9 atoms, 1 residues, 8 bonds
> hide sel atoms
Drag select of 2 atoms, 2 bonds
> hide sel atoms
Drag select of 2 atoms
> hide sel atoms
> select /C:1-15
200 atoms, 198 bonds, 4 pseudobonds, 27 residues, 4 models selected
> show sel & #!1 atoms
> save C:\Users\1/Desktop\image2.png supersample 3
> save BLB4_contacts.png transparentgroud true
Expected a keyword
> save BLB4_contacts.png transparentBackground true
> hide #!1 models
> show #!2 models
> select #2/C:4-17
104 atoms, 104 bonds, 14 residues, 1 model selected
> select #2/C:4-17
104 atoms, 104 bonds, 14 residues, 1 model selected
> select #2/B:2-190
1468 atoms, 1507 bonds, 2 pseudobonds, 179 residues, 2 models selected
> select #2/C:4-17
104 atoms, 104 bonds, 14 residues, 1 model selected
> ui tool show Contacts
> contacts sel ignoreHiddenModels true
121 contacts
> contacts sel ignoreHiddenModels true
121 contacts
> show sel atoms
QDxgiVSyncService: DXGI Factory is no longer Current
> save BLB21_contacts.png transparentBackground true
> show #!1 models
> hide #!1 models
> hide #4 models
> ui tool show Distances
Exactly two atoms must be selected!
> hide sel atoms
> interfaces select & ~solvent
Missing or invalid "atoms" argument: invalid atoms specifier
> show sel atoms
> interfaces select & ~solvent
Missing or invalid "atoms" argument: invalid atoms specifier
> hide #!2 models
> show #!1 models
> interfaces #!1 & ~solvent
3 buried areas: A B 2689, B C 723, A C 701
> show #4 models
> hide #4 models
> show #!1 cartoons
> undo
> show #1.2 models
> hide #1.2 models
> show #1.1 models
> hide #1.1 models
> select add #1
3203 atoms, 3294 bonds, 1 pseudobond, 392 residues, 3 models selected
> show sel & #!1 cartoons
Drag select of 149 residues
> hide sel cartoons
Drag select of 38 residues
> hide sel cartoons
Drag select of 1 residues
> hide sel cartoons
> show sel atoms
Drag select of 8 atoms, 7 bonds
> hide sel atoms
QDxgiVSyncService: DXGI Factory is no longer Current
> select clear
> select /A:1-184
2975 atoms, 3075 bonds, 366 residues, 2 models selected
> select /A:1-184
2975 atoms, 3075 bonds, 366 residues, 2 models selected
> select add #1
4578 atoms, 4719 bonds, 1 pseudobond, 560 residues, 4 models selected
> show sel & #!1 cartoons
Drag select of 179 residues
> hide sel cartoons
Drag select of 7 residues
> hide sel cartoons
Drag select of 2 residues
> hide sel cartoons
> save BLB4_neighbors.png transparentBackground true
> hide #!1 models
> show #!2 models
> select #2/C
104 atoms, 104 bonds, 6 pseudobonds, 14 residues, 2 models selected
> interfaces select & ~solvent
Missing or invalid "atoms" argument: invalid atoms specifier
> show #4 models
> hide #4 models
> select add #2
3051 atoms, 3140 bonds, 145 pseudobonds, 375 residues, 4 models selected
> interfaces select & ~solvent
Missing or invalid "atoms" argument: invalid atoms specifier
> select subtract #4
3051 atoms, 3140 bonds, 24 pseudobonds, 375 residues, 3 models selected
> select subtract #2.1
3051 atoms, 3140 bonds, 22 pseudobonds, 375 residues, 2 models selected
> hide #2.1 models
> select add #2.1
3051 atoms, 3140 bonds, 24 pseudobonds, 375 residues, 3 models selected
> show #2.1 models
> interfaces select & ~solvent
Missing or invalid "atoms" argument: invalid atoms specifier
> select #2
3051 atoms, 3140 bonds, 145 pseudobonds, 375 residues, 4 models selected
> interfaces select & ~solvent
Missing or invalid "atoms" argument: invalid atoms specifier
> select #2/C
104 atoms, 104 bonds, 6 pseudobonds, 14 residues, 2 models selected
> interfaces select & ~solvent
Missing or invalid "atoms" argument: invalid atoms specifier
> interfaces select & ~solvent
Missing or invalid "atoms" argument: invalid atoms specifier
> show #!1 models
> select add #1
3203 atoms, 3294 bonds, 7 pseudobonds, 392 residues, 4 models selected
> hide #2.1 models
> hide #!2 models
> select #1/C
116 atoms, 115 bonds, 15 residues, 1 model selected
> interfaces select & ~solvent
Missing or invalid "atoms" argument: invalid atoms specifier
> select add #2
3167 atoms, 3255 bonds, 145 pseudobonds, 390 residues, 6 models selected
> show #!2 models
> hide #!1 models
> interfaces #!2 & ~solvent
3 buried areas: A B 2621, B C 647, A C 642
> interfaces select & #!2 & ~solvent
Missing or invalid "atoms" argument: invalid atoms specifier
> select subtract #4
3167 atoms, 3255 bonds, 24 pseudobonds, 390 residues, 5 models selected
> select add #3
3167 atoms, 3255 bonds, 47 pseudobonds, 390 residues, 5 models selected
> select subtract #3
3167 atoms, 3255 bonds, 2 pseudobonds, 390 residues, 4 models selected
> show sel & #!2 cartoons
Drag select of 98 residues
> hide sel atoms
> hide sel cartoons
Drag select of 2 residues
> hide sel cartoons
Drag select of 2 residues
> hide sel cartoons
Drag select of 85 residues
> hide sel cartoons
> interfaces contact true
Expected an atoms specifier or a keyword
> interfaces contact true
Expected an atoms specifier or a keyword
> select add #2
3051 atoms, 3140 bonds, 145 pseudobonds, 375 residues, 4 models selected
> interfaces contact true
Expected an atoms specifier or a keyword
> interfaces contact true
Expected an atoms specifier or a keyword
> interfaces select contact true
Missing or invalid "atoms" argument: invalid atoms specifier
> interfaces select atoms contact true
Missing or invalid "atoms" argument: invalid atoms specifier
> ui tool show Contacts
> ui tool show Distances
Exactly two atoms must be selected!
> select clear
> save BLB21_neighbors.png transparentBackground true
QDxgiVSyncService: DXGI Factory is no longer Current
> ui tool show Contacts
> contacts sel overlapCutoff -0.10000000000000003 ignoreHiddenModels true
No atoms match given atom specifier
> select #2/C
104 atoms, 104 bonds, 6 pseudobonds, 14 residues, 2 models selected
> contacts sel overlapCutoff -0.10000000000000003 ignoreHiddenModels true
38 contacts
> show #4 models
QDxgiVSyncService: DXGI Factory is no longer Current
> coulombic sel
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for BLB21_ABC.cif_C SES surface #2.2: minimum, -10.32, mean
-0.71, maximum 9.59
To also show corresponding color key, enter the above coulombic command and
add key true
> select add #4
104 atoms, 104 bonds, 38 pseudobonds, 14 residues, 3 models selected
> hide sel surfaces
> hide #4 models
> select subtract #4
104 atoms, 104 bonds, 14 residues, 2 models selected
> select add #2
3051 atoms, 3140 bonds, 62 pseudobonds, 375 residues, 5 models selected
> select subtract #4
3051 atoms, 3140 bonds, 24 pseudobonds, 375 residues, 4 models selected
> coulombic sel
The following residues are missing heavy (non-hydrogen) atoms, which may
result in inaccurate electrostatics:
BLB21_ABC.cif #2/B ARG 166
BLB21_ABC.cif #2/B ARG 167
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for BLB21_ABC.cif_A SES surface #2.3: minimum, -17.91, mean
-2.58, maximum 11.04
Coulombic values for BLB21_ABC.cif_B SES surface #2.4: minimum, -12.48, mean
-2.11, maximum 11.54
Coulombic values for BLB21_ABC.cif_C SES surface #2.2: minimum, -10.32, mean
-0.71, maximum 9.59
To also show corresponding color key, enter the above coulombic command and
add key true
> select subtract #2.4
1583 atoms, 1633 bonds, 11 pseudobonds, 196 residues, 5 models selected
> hide #2.4 models
> show #2.4 models
> select add #2.4
3051 atoms, 1633 bonds, 11 pseudobonds, 375 residues, 4 models selected
> select subtract #2.3
1572 atoms, 104 bonds, 193 residues, 4 models selected
> select add #2.3
3051 atoms, 104 bonds, 375 residues, 3 models selected
> select subtract #2.2
2947 atoms, 361 residues, 4 models selected
> hide #2.2 models
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting soft
> lighting simple
> lighting soft
> lighting flat
> lighting full
> lighting soft
> sequence chain #2/C
Alignment identifier is 2/C
> select #2/C:5
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #2/C:5-12
60 atoms, 59 bonds, 1 pseudobond, 8 residues, 2 models selected
> select #2/C:16
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #2/C:15-16
20 atoms, 20 bonds, 2 residues, 1 model selected
> select #2/C:16
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #2/C:15-16
20 atoms, 20 bonds, 2 residues, 1 model selected
> select #2/C:5
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #2/C:5
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #2/C:6
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/C:6-14
62 atoms, 61 bonds, 1 pseudobond, 9 residues, 2 models selected
QDxgiVSyncService: DXGI Factory is no longer Current
> select #1/B:2-165,167-188 #2/B:2-165,167-188
2907 atoms, 2984 bonds, 3 pseudobonds, 352 residues, 4 models selected
> select ::seq_identity color sel red
> lighting simple
> lighting shadows true
> lighting shadows false
> lighting flat
> graphics silhouettes false
> graphics silhouettes true
> lighting full
> lighting shadows false
> lighting soft
> graphics silhouettes false
> graphics silhouettes true
> select clear
> ui tool show "Side View"
> view
> view orient
> view
> hide #2.3 models
> hide #!2 models
> hide #2.4 models
> show #2.3 models
> hide #2.3 models
> show #2.2 models
> hide #2.2 models
> show #2.1 models
> hide #2.1 models
> show #2.1 models
> hide #2.1 models
> show #2.2 models
> hide #2.2 models
> show #2.3 models
> hide #2.3 models
> hide #!2 models
> show #2.2 models
> hide #2.2 models
> hide #!2 models
> show #2.3 models
> show #2.2 models
> hide #2.2 models
> show #2.4 models
> hide #2.4 models
> hide #2.3 models
> select add #2
3051 atoms, 3140 bonds, 62 pseudobonds, 375 residues, 4 models selected
> coulombic sel
Coulombic values for BLB21_ABC.cif_A SES surface #2.3: minimum, -17.91, mean
-2.58, maximum 11.04
Coulombic values for BLB21_ABC.cif_B SES surface #2.4: minimum, -12.48, mean
-2.11, maximum 11.54
Coulombic values for BLB21_ABC.cif_C SES surface #2.2: minimum, -10.32, mean
-0.71, maximum 9.59
To also show corresponding color key, enter the above coulombic command and
add key true
> hide #2.2 models
> graphics silhouettes false
> graphics silhouettes true
> select subtract #2
3 models selected
> transparency #2.3-4#!2 40
> transparency #2.3-4#!2 20
> lighting full
> graphics silhouettes false
> graphics silhouettes true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting flat
> lighting full
> lighting simple
> lighting soft
> transparency #2.3-4#!2 0
> lighting shadows true intensity 0.5
> lighting soft
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting soft
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting soft
> save BLB21_electr.png transparentBackground true
> show #!1 models
> hide #!2 models
> select add #1
3099 atoms, 3190 bonds, 1 pseudobond, 378 residues, 2 models selected
> coulombic sel
Coulombic values for BL4R.pdb_A SES surface #1.2: minimum, -13.30, mean -2.41,
maximum 9.55
Coulombic values for BL4R.pdb_B SES surface #1.3: minimum, -14.87, mean -1.87,
maximum 11.23
Coulombic values for BL4R.pdb_C SES surface #1.4: minimum, -8.31, mean 2.68,
maximum 12.11
To also show corresponding color key, enter the above coulombic command and
add key true
> hide #1.4 models
> show #1.1 models
> hide #1.1 models
> show #!2 models
> hide #!2 models
> hide #!1 models
> show #!2 models
> hide #!2 models
> show #!1 models
> select add #1
3099 atoms, 3190 bonds, 1 pseudobond, 378 residues, 7 models selected
> select subtract #1
3 models selected
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> save BLB4_electr.png transparentBackground true
> hide #!1 models
> show #!2 models
> hide #!2 surfaces
> coulombic sel
Coulombic values for BLB21_ABC.cif_A SES surface #2.3: minimum, -17.91, mean
-2.58, maximum 11.04
Coulombic values for BLB21_ABC.cif_B SES surface #2.4: minimum, -12.48, mean
-2.11, maximum 11.54
To also show corresponding color key, enter the above coulombic command and
add key true
> hide sel surfaces
> select add #4
2947 atoms, 38 pseudobonds, 361 residues, 4 models selected
> coulombic sel
Coulombic values for BLB21_ABC.cif_A SES surface #2.3: minimum, -17.91, mean
-2.58, maximum 11.04
Coulombic values for BLB21_ABC.cif_B SES surface #2.4: minimum, -12.48, mean
-2.11, maximum 11.54
To also show corresponding color key, enter the above coulombic command and
add key true
> coulombic sel
Coulombic values for BLB21_ABC.cif_A SES surface #2.3: minimum, -17.91, mean
-2.58, maximum 11.04
Coulombic values for BLB21_ABC.cif_B SES surface #2.4: minimum, -12.48, mean
-2.11, maximum 11.54
To also show corresponding color key, enter the above coulombic command and
add key true
> hide sel surfaces
> show sel cartoons
> hide sel cartoons
> show sel cartoons
> select subtract #4
2947 atoms, 361 residues, 3 models selected
> show #4 models
> hide #4 models
> coulombic sel
Coulombic values for BLB21_ABC.cif_A SES surface #2.3: minimum, -17.91, mean
-2.58, maximum 11.04
Coulombic values for BLB21_ABC.cif_B SES surface #2.4: minimum, -12.48, mean
-2.11, maximum 11.54
Coulombic values for BLB21_ABC.cif_C SES surface #2.2: minimum, -10.32, mean
-0.71, maximum 9.59
To also show corresponding color key, enter the above coulombic command and
add key true
> hide #!2.4 models
> show #2.4 models
> hide #!2.3 models
> show #2.3 models
> hide #2.2 models
> style sel sphere
Changed 344 atom styles
> hide sel atoms
> hide sel surfaces
> copy sel new
Unknown command: copy sel new
> copy sel #3
Unknown command: copy sel #3
> clone fromAtoms sel
Unknown command: clone fromAtoms sel
> save fragment_BLB21.pdb selectedOnly
Missing "selectedOnly" keyword's argument
> show sel cartoons
> show sel atoms
> hide sel atoms
> style sel stick
Changed 344 atom styles
> show sel atoms
> save fragment_BLB21.pdb selectedOnly
Missing "selectedOnly" keyword's argument
> show #2.1 models
> hide #2.1 models
> select add #2
3051 atoms, 3140 bonds, 62 pseudobonds, 375 residues, 6 models selected
> select subtract #2
3 models selected
> show sel surfaces
> ui tool show "Side View"
> surface (#!2 & sel)
> color byattribute curvature surfaces
No known/registered numeric attribute curvature
> select add #1
6046 atoms, 3190 bonds, 1 pseudobond, 739 residues, 5 models selected
> select subtract #1
2947 atoms, 361 residues, 6 models selected
> select add #2
3051 atoms, 3140 bonds, 62 pseudobonds, 375 residues, 10 models selected
> select subtract #2
3 models selected
> select add #2.2
104 atoms, 14 residues, 1 model selected
> surface zone sel distance 4
Missing required "near_atoms" argument
> surface zone distance 4 sel
Missing or invalid "surfaces" argument: invalid surfaces specifier
> surface zone sel distance 4
Missing required "near_atoms" argument
> select add #1
6150 atoms, 6330 bonds, 63 pseudobonds, 753 residues, 13 models selected
> select subtract #1
3051 atoms, 3140 bonds, 62 pseudobonds, 375 residues, 14 models selected
> select subtract #2
3 models selected
> ui mousemode right "mark surface"
> marker #5 position -22.51,-5.704,-20.31 color yellow radius 1
> ui mousemode right "mark surface"
> marker #5 position -16.61,-8.177,-23.34 color yellow radius 1
> marker #5 position -12.35,-3.246,-26.32 color yellow radius 1
> marker #5 position -11.93,-8.299,-26.45 color yellow radius 1
> marker #5 position -17.66,-9.161,-25.46 color yellow radius 1
> marker #5 position -24.66,-5.167,-24.74 color yellow radius 1
> marker #5 position -23.41,-4.978,-22.98 color yellow radius 1
> marker #5 position -22.68,-5.823,-21.79 color yellow radius 1
> marker #5 position -24.81,-4.865,-20.94 color yellow radius 1
> marker #5 position -24.97,-3.806,-22.63 color yellow radius 1
> marker #5 position -24.36,-5.637,-21.4 color yellow radius 1
> marker #5 position -23.74,-5.002,-20.21 color yellow radius 1
> marker #5 position -19.6,0.1163,-19.46 color yellow radius 1
> marker #5 position -20.45,-1.697,-19.34 color yellow radius 1
> marker #5 position -18.15,0.458,-19.37 color yellow radius 1
> marker #5 position -19.38,-3.857,-21 color yellow radius 1
> ui mousemode right "mark point"
> marker #5 position -27.75,-0.7166,-17.02 color yellow radius 1
> marker #5 position -26.43,-1.228,-17.8 color yellow radius 1
> ui mousemode right "delete markers"
> hide #5 models
> select #2/C
104 atoms, 104 bonds, 2 pseudobonds, 14 residues, 2 models selected
> surface zone #2 nearAtoms sel distance 4
> surface zone #2 nearAtoms sel distance 5
> surface zone #2 nearAtoms sel distance 6
> surface zone #2 nearAtoms sel distance 7
> surface zone #2 nearAtoms sel distance 8
> hide sel surfaces
Drag select of BLB21_ABC.cif_A SES surface, 27669 of 188428 triangles,
BLB21_ABC.cif_B SES surface, 27475 of 190786 triangles, 301 atoms, 14
residues, 278 bonds
> hide sel surfaces
> select add #2
3051 atoms, 3140 bonds, 62 pseudobonds, 375 residues, 11 models selected
> hide sel surfaces
Drag select of 301 atoms, 14 residues, 278 bonds
> select add #2.3
1719 atoms, 278 bonds, 210 residues, 6 models selected
> select subtract #2.3
240 atoms, 181 bonds, 28 residues, 4 models selected
> select add #2.3
1719 atoms, 181 bonds, 210 residues, 5 models selected
> select subtract #2.2
1615 atoms, 132 bonds, 196 residues, 6 models selected
> select add #2.2
1719 atoms, 132 bonds, 210 residues, 5 models selected
> select subtract #2.2
1615 atoms, 132 bonds, 196 residues, 6 models selected
> select clear
Drag select of 301 atoms, 14 residues, 278 bonds
> select subtract #2.2
240 atoms, 229 bonds, 27 residues, 4 models selected
> show sel surfaces
> undo
> select clear
> select #2/C
104 atoms, 104 bonds, 2 pseudobonds, 14 residues, 2 models selected
> surface zone #2 nearAtoms sel distance 7
> surface zone #2 nearAtoms sel distance 8
> hide sel cartoons
> hide sel surfaces
> show sel cartoons
> select up
3051 atoms, 3140 bonds, 38 pseudobonds, 375 residues, 3 models selected
> select #2/C
104 atoms, 104 bonds, 2 pseudobonds, 14 residues, 2 models selected
> select zone sel 8
Selected 1475 atoms
> show sel & #!2 atoms
> select sel up
Expected a keyword
> select up
1940 atoms, 1947 bonds, 248 residues, 8 models selected
> hide sel & #!2 atoms
> show sel & #!2 atoms
QDxgiVSyncService: DXGI Factory is no longer Current
> select subtract #5
1922 atoms, 1947 bonds, 230 residues, 7 models selected
> save "D:/桌面/BLB4 and BLB21/BLB21_cavity.cxs"
No model chosen to save relative to
> save fragment_BLB21.pdb selectedOnly
Missing "selectedOnly" keyword's argument
> save fragment_BLB21.pdb #2 selectedOnly true
> open "D:/桌面/BLB4 and BLB21/fragment_BLB21.pdb"
Summary of feedback from opening D:/桌面/BLB4 and BLB21/fragment_BLB21.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 PRO A 49 ARG A 53 1 5
Start residue of secondary structure not found: HELIX 7 7 ALA B 65 LEU B 71 1
7
Start residue of secondary structure not found: SHEET 1 1 1 HIS A 4 GLU A 16 0
Start residue of secondary structure not found: SHEET 2 2 1 LYS A 20 PHE A 29
0
Start residue of secondary structure not found: SHEET 3 3 1 ASP A 32 GLU A 38
0
12 messages similar to the above omitted
End residue of secondary structure not found: SHEET 16 16 1 PHE B 47 ALA B 49
0
Start residue of secondary structure not found: SHEET 17 17 1 LYS B 98 SER B
102 0
Start residue of secondary structure not found: SHEET 18 18 1 LEU B 115 PHE B
122 0
Start residue of secondary structure not found: SHEET 19 19 1 ILE B 127 LEU B
133 0
Start residue of secondary structure not found: SHEET 20 20 1 VAL B 142 SER B
144 0
Start residue of secondary structure not found: SHEET 21 21 1 TYR B 155 LEU B
161 0
2 messages similar to the above omitted
Cannot find LINK/SSBOND residue CYS (110 )
Cannot find LINK/SSBOND residue CYS (117 )
Chain information for fragment_BLB21.pdb #6
---
Chain | Description
A | No description available
B | No description available
Associated fragment_BLB21.pdb chain B to BLB21_ABC.cif, chain B with 0
mismatches
Chains used in RMSD evaluation for alignment 1: BL4R.pdb #1/B, BLB21_ABC.cif
#2/B, fragment_BLB21.pdb #6/B
> hide #!2 models
> hide #2.4 models
> hide #2.3 models
> select subtract #2.4
1467 atoms, 1488 bonds, 177 residues, 7 models selected
> select subtract #2.3
1026 atoms, 1040 bonds, 123 residues, 5 models selected
> coulombic #!6
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for fragment_BLB21.pdb_A SES surface #6.2: minimum, -9.25,
mean -1.00, maximum 7.98
Coulombic values for fragment_BLB21.pdb_B SES surface #6.3: minimum, -21.44,
mean -7.09, maximum 5.10
To also show corresponding color key, enter the above coulombic command and
add key true
> show #!6 atoms
> transparency #6 20
> lighting shadows true intensity 0.5
> lighting soft
> lighting full
> lighting shadows false
> transparency #6 40
> hide #!6.1 models
Drag select of fragment_BLB21.pdb_A SES surface, 1657 of 68844 triangles, 7
atoms, 7 bonds
> delete sel
Drag select of fragment_BLB21.pdb_A SES surface, 585 of 67838 triangles, 2
atoms, 3 bonds
> delete sel
Drag select of fragment_BLB21.pdb_A SES surface, 427 of 67564 triangles, 2
atoms, 1 bonds
> delete sel
Drag select of fragment_BLB21.pdb_A SES surface, 328 of 67054 triangles, 1
atoms
> delete sel
Drag select of fragment_BLB21.pdb_A SES surface, 751 of 66772 triangles
> delete sel
> hide #!6 surfaces
> hide #!6 cartoons
Drag select of 3 atoms, 1 bonds
> delete sel
> coulombic #!6
Coulombic values for fragment_BLB21.pdb_A SES surface #6.2: minimum, -9.68,
mean -1.84, maximum 7.37
Coulombic values for fragment_BLB21.pdb_B SES surface #6.3: minimum, -21.44,
mean -7.09, maximum 5.10
To also show corresponding color key, enter the above coulombic command and
add key true
> mlp #!6
Map values for surface "fragment_BLB21.pdb_A SES surface": minimum -25.44,
mean -2.388, maximum 21.85
Map values for surface "fragment_BLB21.pdb_B SES surface": minimum -27.12,
mean -1.969, maximum 22.43
To also show corresponding color key, enter the above mlp command and add key
true
> coulombic #!6
Coulombic values for fragment_BLB21.pdb_A SES surface #6.2: minimum, -9.68,
mean -1.84, maximum 7.37
Coulombic values for fragment_BLB21.pdb_B SES surface #6.3: minimum, -21.44,
mean -7.09, maximum 5.10
To also show corresponding color key, enter the above coulombic command and
add key true
> show #!2 models
> select add #2
3051 atoms, 3140 bonds, 62 pseudobonds, 375 residues, 4 models selected
> coulombic sel
Coulombic values for BLB21_ABC.cif_A SES surface #2.3: minimum, -17.91, mean
-2.58, maximum 11.04
Coulombic values for BLB21_ABC.cif_B SES surface #2.4: minimum, -12.48, mean
-2.11, maximum 11.54
Coulombic values for BLB21_ABC.cif_C SES surface #2.2: minimum, -10.32, mean
-0.71, maximum 9.59
To also show corresponding color key, enter the above coulombic command and
add key true
> hide #!2.3 models
> show #2.3 models
> hide #2.2 models
> hide #!6 models
> show #!6 models
> hide #!2 models
> show #!2 models
> hide #!6 models
> hide #!2 models
> show #!2 models
> select add #2
3051 atoms, 3140 bonds, 62 pseudobonds, 375 residues, 9 models selected
> select add #2
3051 atoms, 3140 bonds, 62 pseudobonds, 375 residues, 10 models selected
> select subtract #2
3 models selected
> select add #2
3051 atoms, 3140 bonds, 62 pseudobonds, 375 residues, 7 models selected
> hide sel atoms
> show #!6 models
> select add #6
3932 atoms, 4033 bonds, 75 pseudobonds, 481 residues, 13 models selected
> select subtract #2
881 atoms, 893 bonds, 13 pseudobonds, 106 residues, 8 models selected
> hide sel surfaces
> show sel atoms
> transparency (#!6 & sel) 30
> select add #2
3932 atoms, 4033 bonds, 75 pseudobonds, 481 residues, 12 models selected
> hide sel surfaces
> show sel surfaces
> hide #!2 models
> select subtract #2
881 atoms, 893 bonds, 13 pseudobonds, 106 residues, 8 models selected
> hide sel surfaces
> hide #!6 models
> select subtract #6
2 models selected
> show #!6 models
> show #!2 models
> hide #2.2 models
> select add #2.3
1479 atoms, 182 residues, 2 models selected
> show sel atoms
> hide sel atoms
> select subtract #2.3
1 model selected
> select add #2.4
1468 atoms, 179 residues, 3 models selected
> select subtract #2.4
1 model selected
> select add #3
45 pseudobonds, 1 model selected
> select subtract #3
Nothing selected
> select add #2.4
1468 atoms, 179 residues, 3 models selected
> select subtract #2.4
1 model selected
> select add #2.3
1479 atoms, 182 residues, 2 models selected
> select subtract #2.3
1 model selected
> select add #2.2
104 atoms, 14 residues, 1 model selected
> show sel atoms
> select subtract #2.2
1 model selected
> select add #2
3051 atoms, 3140 bonds, 62 pseudobonds, 375 residues, 7 models selected
> hide sel surfaces
> show sel surfaces
> select subtract #2.2
2947 atoms, 3036 bonds, 2 pseudobonds, 361 residues, 8 models selected
> select add #2.2
3051 atoms, 3036 bonds, 2 pseudobonds, 375 residues, 7 models selected
> hide #2.2 models
> show #2.2 models
> show #2.1 models
> transparency (#!2 & sel) 20
> hide #2.2 models
> lighting soft
> lighting flat
> lighting full
> lighting shadows false
> hide #!2 models
> show #2.2 models
> hide #2.2 models
> hide #!2 models
> hide #2.1 models
> select subtract #2.1
3051 atoms, 3036 bonds, 375 residues, 4 models selected
> select subtract #2.2
2947 atoms, 3036 bonds, 361 residues, 4 models selected
> select subtract #2.3
1468 atoms, 1507 bonds, 179 residues, 3 models selected
> select subtract #2.4
1 model selected
> hide #2.4 models
> hide #2.3 models
> show #2.2 models
> select add #6.2
426 atoms, 53 residues, 1 model selected
> select subtract #6.2
1 model selected
> select add #6.3
455 atoms, 53 residues, 1 model selected
> select subtract #6.3
1 model selected
> select add #6
881 atoms, 893 bonds, 13 pseudobonds, 106 residues, 3 models selected
> show sel surfaces
> select subtract #6
2 models selected
> hide #2.2 models
Drag select of fragment_BLB21.pdb_A SES surface, 1574 of 65676 triangles, 3
atoms, 2 bonds
Drag select of fragment_BLB21.pdb_A SES surface, 1953 of 65676 triangles, 8
atoms, 7 bonds
> select #6/A:64@OE1
1 atom, 1 residue, 1 model selected
> delete sel
Drag select of fragment_BLB21.pdb_A SES surface, 8268 of 65642 triangles, 37
atoms, 33 bonds
> delete sel
Drag select of fragment_BLB21.pdb_A SES surface, 3150 of 61468 triangles, 8
atoms, 6 bonds
> delete sel
Drag select of fragment_BLB21.pdb_B SES surface, 15874 of 71448 triangles, 58
atoms, 53 bonds
> delete sel
Drag select of fragment_BLB21.pdb_B SES surface, 2297 of 66068 triangles, 8
atoms, 5 bonds
> delete sel
Drag select of fragment_BLB21.pdb_B SES surface, 1140 of 64948 triangles, 5
atoms, 5 bonds
> delete sel
Drag select of fragment_BLB21.pdb_A SES surface, 334 of 60258 triangles,
fragment_BLB21.pdb_B SES surface, 1845 of 63936 triangles, 8 atoms, 7 bonds
> delete sel
> hide #!2,6 surfaces
Drag select of 1 atoms
> delete sel
> show #!2,6 surfaces
> undo
Undo failed, probably because structures have been modified.
> undo
> hide #!2,6 surfaces
> select add #6
755 atoms, 759 bonds, 17 pseudobonds, 102 residues, 7 models selected
> show sel surfaces
Drag select of fragment_BLB21.pdb_B SES surface, 208 of 62230 triangles, 2
atoms, 1 bonds
> delete sel
Drag select of fragment_BLB21.pdb_B SES surface, 123 of 61982 triangles, 1
atoms
> delete sel
Drag select of fragment_BLB21.pdb_A SES surface, 70 of 60258 triangles,
fragment_BLB21.pdb_B SES surface, 252 of 61862 triangles, 1 atoms, 2 bonds
Drag select of fragment_BLB21.pdb_A SES surface, 291 of 60258 triangles,
fragment_BLB21.pdb_B SES surface, 757 of 61862 triangles, 6 atoms, 8 bonds
> hide sel surfaces
> select add #6
752 atoms, 758 bonds, 17 pseudobonds, 102 residues, 8 models selected
> hide sel surfaces
Drag select of 2 atoms, 2 bonds
> delete sel
Drag select of 3 atoms, 2 bonds
> delete sel
Drag select of 1 atoms
> delete sel
Drag select of 3 atoms, 2 bonds
Drag select of 2 atoms, 4 bonds
> delete sel
Drag select of 2 atoms
> delete sel
Drag select of 2 atoms, 3 bonds
> delete sel
Drag select of 1 atoms
> delete sel
Drag select of 5 atoms, 5 bonds
Drag select of 4 atoms, 5 bonds
Drag select of 6 atoms, 8 bonds
> delete sel
Drag select of 3 atoms, 2 bonds
> delete sel
Drag select of 10 atoms, 10 bonds
> delete sel
Drag select of 1 atoms
> delete sel
Drag select of 1 atoms
> delete sel
Drag select of 6 atoms, 7 bonds
> delete sel
Drag select of 13 atoms, 13 bonds
> delete sel
Drag select of 1 atoms
> delete sel
Drag select of 10 atoms, 7 bonds
> delete sel
Drag select of 3 atoms, 3 bonds
> delete sel
Drag select of 5 atoms, 4 bonds
> delete sel
> show #!2,6 surfaces
> hide #!2,6 surfaces
> select add #6
680 atoms, 683 bonds, 15 pseudobonds, 99 residues, 7 models selected
> show sel surfaces
Drag select of fragment_BLB21.pdb_B SES surface, 1442 of 56944 triangles, 9
atoms, 8 bonds
> delete sel
Drag select of fragment_BLB21.pdb_B SES surface, 1729 of 55662 triangles, 7
atoms, 6 bonds
> delete sel
Drag select of fragment_BLB21.pdb_B SES surface, 635 of 53984 triangles, 3
atoms, 3 bonds
> delete sel
Drag select of fragment_BLB21.pdb_B SES surface, 63 of 53608 triangles, 1
atoms
> delete sel
Drag select of fragment_BLB21.pdb_B SES surface, 590 of 53934 triangles, 2
atoms, 2 bonds
> delete sel
> undo
Undo failed, probably because structures have been modified.
> hide #!6 models
> hide #!2 models
> hide #2.2 models
> hide #2.3 models
> hide #2.4 models
> hide #6.2 models
> hide #6.3 models
> view #6 clip false
> show #!6 models
> show #!6 surfaces
Drag select of fragment_BLB21.pdb_A SES surface, 11841 of 57024 triangles,
fragment_BLB21.pdb_B SES surface, 734 of 53716 triangles, 48 atoms, 45 bonds
> delete sel
Drag select of fragment_BLB21.pdb_A SES surface, 473 of 50668 triangles, 1
atoms
> delete sel
Drag select of fragment_BLB21.pdb_A SES surface, 214 of 50286 triangles, 1
atoms
> delete sel
Drag select of fragment_BLB21.pdb_A SES surface, 830 of 50162 triangles, 3
atoms, 2 bonds
> delete sel
> hide #!6 models
> show #!6 models
> select add #6
605 atoms, 607 bonds, 15 pseudobonds, 94 residues, 2 models selected
> coulombic sel
Coulombic values for fragment_BLB21.pdb_A SES surface #6.2: minimum, -8.25,
mean -0.98, maximum 4.17
Coulombic values for fragment_BLB21.pdb_B SES surface #6.3: minimum, -7.04,
mean -0.70, maximum 8.27
To also show corresponding color key, enter the above coulombic command and
add key true
> lighting soft
> lighting shadows true intensity 0.5
> lighting soft
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting soft
> graphics silhouettes false
> ui tool show "Color Zone"
> ui tool show "Volume Viewer"
> select add #6
605 atoms, 607 bonds, 15 pseudobonds, 94 residues, 7 models selected
No surface chosen for color zoning
> color bychain surfaces
> color byattribute attribute residueType surfaces
Expected a collection of one of 'atoms', 'cartoons', 'ribbons', or 'surfaces'
or a keyword
> color electrostatic surfaces
Missing or invalid "surfaces" argument: invalid surfaces specifier
> select add #6
605 atoms, 607 bonds, 15 pseudobonds, 94 residues, 8 models selected
> color electrostatic surfaces
Missing or invalid "surfaces" argument: invalid surfaces specifier
> color electrostatic surfaces sel
Missing or invalid "surfaces" argument: invalid surfaces specifier
> surface dust
Missing or invalid "surfaces" argument: empty atom specifier
> ui mousemode right distance
> hide #!6 models
> select subtract #6
2 models selected
> show #2.4 models
> show #2.3 models
> show #2.2 models
> select add #2
3051 atoms, 3140 bonds, 62 pseudobonds, 375 residues, 4 models selected
> coulombic sel
Coulombic values for BLB21_ABC.cif_A SES surface #2.3: minimum, -17.91, mean
-2.58, maximum 11.04
Coulombic values for BLB21_ABC.cif_B SES surface #2.4: minimum, -12.48, mean
-2.11, maximum 11.54
Coulombic values for BLB21_ABC.cif_C SES surface #2.2: minimum, -10.32, mean
-0.71, maximum 9.59
To also show corresponding color key, enter the above coulombic command and
add key true
> hide #!2.4 models
> show #2.4 models
> hide #!2.3 models
> show #2.3 models
> hide #2.2 models
> ui tool show "Side View"
> select add #2
3051 atoms, 3140 bonds, 62 pseudobonds, 375 residues, 11 models selected
> select subtract #2
3 models selected
> lighting soft
> lighting full
> lighting shadows false
> lighting soft
> save "D:/桌面/BLB4 and BLB21/BLB21_electr_1.png" width 1979 height 1169
> supersample 3 transparentBackground true
QDxgiVSyncService: DXGI Factory is no longer Current
> graphics silhouettes true
> save "D:/桌面/BLB4 and BLB21/BLB21_electr_1.png" width 1979 height 1169
> supersample 3 transparentBackground true
> save C:\Users\1/Desktop\image3.png supersample 3
> save "D:/桌面/BLB4 and BLB21/BLB21_electr_1.png" width 1979 height 1169
> supersample 3 transparentBackground true
> hide #!2 models
> show #!1 models
> select add #1
3099 atoms, 3190 bonds, 1 pseudobond, 378 residues, 4 models selected
> coulombic sel
Coulombic values for BL4R.pdb_A SES surface #1.2: minimum, -13.30, mean -2.41,
maximum 9.55
Coulombic values for BL4R.pdb_B SES surface #1.3: minimum, -14.87, mean -1.87,
maximum 11.23
Coulombic values for BL4R.pdb_C SES surface #1.4: minimum, -8.31, mean 2.68,
maximum 12.11
To also show corresponding color key, enter the above coulombic command and
add key true
> select subtract #1
3 models selected
> hide #1.4 models
> save "D:/桌面/BLB4 and BLB21/BLB4_electr_1.png" width 1979 height 1169
> supersample 3
QDxgiVSyncService: DXGI Factory is no longer Current
> select #1/B:2-165,167-188 #2/B:2-165,167-188 #6/B
3209 atoms, 3287 bonds, 11 pseudobonds, 399 residues, 6 models selected
> select #2/B:2-8,16,18-25,32-36,38-39,41-46,48-51,65,69,72,88,91-190
1021 atoms, 1035 bonds, 2 pseudobonds, 127 residues, 2 models selected
> ui mousemode right clip
> hide #!1.3 models
> hide #!1.2 models
> show #1.1 models
> hide #1.1 models
> show #1.2 models
> hide #!1.2 models
> show #1.4 models
> hide #!1 models
> hide #1.4 models
> show #1.4 models
> select add #1
4120 atoms, 4225 bonds, 3 pseudobonds, 505 residues, 5 models selected
> hide sel & #!1 surfaces
> hide sel & #!1 cartoons
> show sel & #!1 cartoons
> hide sel & #!1 cartoons
> select subtract #1.3
2633 atoms, 2696 bonds, 2 pseudobonds, 326 residues, 7 models selected
> select subtract #1.2
1137 atoms, 1150 bonds, 2 pseudobonds, 142 residues, 6 models selected
> show sel & #!1 cartoons
QDxgiVSyncService: DXGI Factory is no longer Current
> hide #1.5 models
> hide #1.4 models
> select subtract #1.4
1021 atoms, 1035 bonds, 2 pseudobonds, 127 residues, 4 models selected
> open 7pdy
Summary of feedback from opening 7pdy fetched from pdb
---
notes | Fetching compressed mmCIF 7pdy from http://files.rcsb.org/download/7pdy.cif
Fetching CCD ACT from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/T/ACT/ACT.cif
Fetching CCD GOL from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/L/GOL/GOL.cif
Fetching CCD PEG from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/G/PEG/PEG.cif
7pdy title:
A viral peptide from Marek's disease virus bound to chicken MHC-II molecule
[more info...]
Chain information for 7pdy #7
---
Chain | Description | UniProt
A C E | MHC class II alpha chain | Q4U5Z6_CHICK 5-192
B D F | 38 kDa phosphoprotein,MHC class II beta chain | VP38_GAHVN -26--12 -26--10, Q4U5Z9_CHICK 6-197
Non-standard residues in 7pdy #7
---
ACT — acetate ion
GOL — glycerol (glycerin; propane-1,2,3-triol)
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)
PEG — di(hydroxyethyl)ether
7pdy mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
3| author_and_software_defined_assembly
9378 atoms have anisotropic B-factors. Depict anisotropic information with
Thermal Ellipsoids [start tool...] or the aniso command.
> select add #1
4120 atoms, 4225 bonds, 4 pseudobonds, 505 residues, 6 models selected
> show sel & #!1 cartoons
> mmaker #7 to #1
Parameters
---
Chain pairing | bb
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 BL4R.pdb, chain A (#1) with 7pdy, chain E (#7), sequence alignment
score = 955.4
RMSD between 178 pruned atom pairs is 0.440 angstroms; (across all 181 pairs:
0.632)
> select add #7
13645 atoms, 13862 bonds, 8 pseudobonds, 1837 residues, 10 models selected
> select subtract #1
10546 atoms, 10672 bonds, 7 pseudobonds, 1459 residues, 8 models selected
> hide #!1 models
> hide sel & #!7 surfaces
> hide sel & #!7 cartoons
> hide sel & #!7 atoms
> show sel & #!7 cartoons
> show #!1 models
> select #7/B:-27-190
1598 atoms, 1640 bonds, 1 pseudobond, 204 residues, 2 models selected
> select #7/D:-27-190
1579 atoms, 1621 bonds, 1 pseudobond, 202 residues, 2 models selected
> select #7/F:-28-189
1606 atoms, 1647 bonds, 1 pseudobond, 204 residues, 2 models selected
> show #!2 models
Drag select of 389 residues, 1 pseudobonds
No model chosen to save relative to
> close #5
> close #7
> close #6
> open 7pdy
7pdy title:
A viral peptide from Marek's disease virus bound to chicken MHC-II molecule
[more info...]
Chain information for 7pdy #5
---
Chain | Description | UniProt
A C E | MHC class II alpha chain | Q4U5Z6_CHICK 5-192
B D F | 38 kDa phosphoprotein,MHC class II beta chain | VP38_GAHVN -26--12 -26--10, Q4U5Z9_CHICK 6-197
Non-standard residues in 7pdy #5
---
ACT — acetate ion
GOL — glycerol (glycerin; propane-1,2,3-triol)
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)
PEG — di(hydroxyethyl)ether
7pdy mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
3| author_and_software_defined_assembly
9378 atoms have anisotropic B-factors. Depict anisotropic information with
Thermal Ellipsoids [start tool...] or the aniso command.
> mmaker #5 to #1
Parameters
---
Chain pairing | bb
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 BL4R.pdb, chain A (#1) with 7pdy, chain E (#5), sequence alignment
score = 955.4
RMSD between 178 pruned atom pairs is 0.440 angstroms; (across all 181 pairs:
0.632)
> select add #5
9525 atoms, 9637 bonds, 5 pseudobonds, 1332 residues, 2 models selected
> hide sel atoms
> show sel cartoons
> select #5/B:-27-190
1598 atoms, 1640 bonds, 1 pseudobond, 204 residues, 2 models selected
> select #5/D:-27-190
1579 atoms, 1621 bonds, 1 pseudobond, 202 residues, 2 models selected
> select #5/B:-27-190
1598 atoms, 1640 bonds, 1 pseudobond, 204 residues, 2 models selected
> select #5/B:-27-190
1598 atoms, 1640 bonds, 1 pseudobond, 204 residues, 2 models selected
> select #5/D:-27-190
1579 atoms, 1621 bonds, 1 pseudobond, 202 residues, 2 models selected
> select #5/C:3-188
1452 atoms, 1498 bonds, 1 pseudobond, 184 residues, 2 models selected
> select #5/A:3-189
1517 atoms, 1568 bonds, 187 residues, 1 model selected
> select #5/E:3-188
1472 atoms, 1519 bonds, 1 pseudobond, 184 residues, 2 models selected
> select #5/C:3-188
1452 atoms, 1498 bonds, 1 pseudobond, 184 residues, 2 models selected
> select #5/D:-27-190
1579 atoms, 1621 bonds, 1 pseudobond, 202 residues, 2 models selected
> delete #5/C #5/D
> select #5/E #5/F
3143 atoms, 3189 bonds, 2 pseudobonds, 432 residues, 2 models selected
> select #5/F:-28-189
1606 atoms, 1647 bonds, 1 pseudobond, 204 residues, 2 models selected
> select #5/E:3-188
1472 atoms, 1519 bonds, 1 pseudobond, 184 residues, 2 models selected
> select #5/B:-27-190
1598 atoms, 1640 bonds, 1 pseudobond, 204 residues, 2 models selected
> select #5/A:3-189
1517 atoms, 1568 bonds, 187 residues, 1 model selected
> select #5/A #5/B
3247 atoms, 3257 bonds, 1 pseudobond, 476 residues, 2 models selected
> save BLB21_7pdy_10.pdb selectedOnly
Missing "selectedOnly" keyword's argument
> save BLB21_7pdy_10.pdb selectedOnly true
> save BLB21_7pdy_10.pdb
> save BLB21_7pdy_10.pdb #5 selctedOnly true
Expected a keyword
> save BLB21_7pdy_10.pdb #5 selectedOnly true
> delete sel
> open "D:/桌面/BLB4 and BLB21/BLB21_7pdy_10.pdb"
Chain information for BLB21_7pdy_10.pdb #6
---
Chain | Description
A | No description available
B | No description available
3115 atoms have anisotropic B-factors. Depict anisotropic information with
Thermal Ellipsoids [start tool...] or the aniso command.
Computing secondary structure
> mmaker #6 to #1
Parameters
---
Chain pairing | bb
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 BL4R.pdb, chain A (#1) with BLB21_7pdy_10.pdb, chain A (#6),
sequence alignment score = 946.8
RMSD between 178 pruned atom pairs is 0.486 angstroms; (across all 183 pairs:
0.768)
> hide surfaces
> save my_session.cxs
> hide atoms
> ui tool show "Model Panel"
> hide #5.1 models
> hide #6.1 models
> hide #!2 models
> hide #!1 models
> select #5/A #6/A
1517 atoms, 1567 bonds, 187 residues, 1 model selected
> color sel light gray
> color sel byhetero
> hide #!5 models
> show #!5 models
> hide #!6 models
> select #5/A
Nothing selected
> select #5/E
1499 atoms, 1524 bonds, 1 pseudobond, 206 residues, 2 models selected
> color (#!5 & sel) light gray
> show #!2 models
> hide #!2 models
> show #!6 models
> hide #!6 models
> show #!6 models
> select #5/F #6/B
3242 atoms, 3303 bonds, 2 pseudobonds, 430 residues, 4 models selected
> color #6 #aaffffff
> undo
> ui tool show "Color Actions"
> color sel pale turquoise
> color sel powder blue
> color sel light blue
> color sel light sky blue
> color sel sky blue
> color sel light blue
> show #!2 models
> color sel light sky blue
> hide #!2 models
> color (#!5-6 & sel) cornflower blue
> ui tool show "Color Actions"
> color sel light cyan
> color sel sky blue
> color sel light steel blue
> show #!1 models
> show #!2 models
> show #3 models
> show #4 models
> hide #4 models
> hide #3 models
> select clear
> hide #!6 models
> hide #!5 models
> show #!1-2 cartoons
> show #!5 models
> show #!6 models
> hide #!6 models
> hide #!5 models
> hide #!2 models
> show #1.4 models
> hide #1.4 models
> select #1/A
1496 atoms, 1546 bonds, 184 residues, 1 model selected
> ui tool show "Color Actions"
> color sel wheat
> color sel moccasin
> color sel navajo white
> color sel peach puff
> color sel antique white
> color sel wheat
> color sel burly wood
> color sel tan
> color sel burly wood
> color sel tan
> select add #1
3099 atoms, 3190 bonds, 1 pseudobond, 378 residues, 3 models selected
> color sel tan
> select #1/A
1496 atoms, 1546 bonds, 184 residues, 1 model selected
> color sel light gray
> show #!2 models
> show #!5 models
> show #!6 models
> select clear
> hide #!6 models
> hide #!5 models
> hide #!1 models
> show #!1 target m
> hide #!2 target m
> show #!2 target m
> hide #!1 target m
> select #2/A
1479 atoms, 1529 bonds, 182 residues, 1 model selected
> ui tool show "Color Actions"
> color sel sky blue
> color sel light sky blue
> color sel powder blue
> color sel pale turquoise
> color sel light blue
> color sel sky blue
> color sel light cyan
> color sel powder blue
> color sel pale turquoise
> color sel light sky blue
> hide #!2 models
> show #!2 models
> select add #2
3051 atoms, 3140 bonds, 62 pseudobonds, 375 residues, 5 models selected
> select subtract #2
3 models selected
> color light sky blue
> color sky blue
> color light blue
> color light sky blue
> select #2/A
1479 atoms, 1529 bonds, 182 residues, 1 model selected
> color sel sky blue
> color sel light sky blue
> color sel sky blue
> color sel light sky blue
> show #!1 models
> undo
> select #2/A
1479 atoms, 1529 bonds, 182 residues, 1 model selected
> color sel light gray
> hide #!2 models
> select subtract #2.3
1 model selected
> select add #2.4
1468 atoms, 179 residues, 1 model selected
> show #2.2 models
> hide #2.3 models
> hide #2.4 models
> select subtract #2.4
1 model selected
> hide #2.2 models
> select #2/B
1468 atoms, 1507 bonds, 2 pseudobonds, 179 residues, 2 models selected
> color #2 #aaffffff
> undo
> ui tool show "Color Actions"
> color sel sky blue
> show #!1 models
> show #!5 models
> show #!6 models
> select clear
> open 6T3Y
Summary of feedback from opening 6T3Y fetched from pdb
---
note | Fetching compressed mmCIF 6t3y from http://files.rcsb.org/download/6t3y.cif
6t3y title:
Improved High Resolution Structure of MHC Class II complex [more info...]
Chain information for 6t3y #7
---
Chain | Description | UniProt
A | MHC class II alpha chain | Q4U5Z6_CHICK 6-186
B | MHC class II beta chain 2 | B5BSA0_CHICK 39-224
Non-standard residues in 6t3y #7
---
ACT — acetate ion
GOL — glycerol (glycerin; propane-1,2,3-triol)
3027 atoms have anisotropic B-factors. Depict anisotropic information with
Thermal Ellipsoids [start tool...] or the aniso command.
> open 6KVM
Summary of feedback from opening 6KVM fetched from pdb
---
note | Fetching compressed mmCIF 6kvm from http://files.rcsb.org/download/6kvm.cif
6kvm title:
Crystal structure of Chicken MHC Class II for 1.9 angstrom [more info...]
Chain information for 6kvm #8
---
Chain | Description | UniProt
A | MHC class II alpha chain | Q4U5Z6_CHICK 1-194
B | MHC class II beta chain 2 | Q4U600_CHICK 1-198
C | peptide from 60S ribosomal protein L30 | RL30_CHICK 1-17
Non-standard residues in 6kvm #8
---
GOL — glycerol (glycerin; propane-1,2,3-triol)
> open 1DLH
Summary of feedback from opening 1DLH fetched from pdb
---
notes | Fetching compressed mmCIF 1dlh from http://files.rcsb.org/download/1dlh.cif
Fetching CCD NDG from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/G/NDG/NDG.cif
1dlh title:
Crystal structure of the human class II MHC protein hla-DR1 complexed with an
influenza virus peptide [more info...]
Chain information for 1dlh #9
---
Chain | Description | UniProt
A D | CLASS II HISTOCOMPATIBILITY ANTIGEN (HLA-DR1) (ALPHA CHAIN) | HA2R_HUMAN 3-182
B E | CLASS II HISTOCOMPATIBILITY ANTIGEN (HLA-DR1) (BETA CHAIN) | HB2F_HUMAN 3-190
C F | ENTEROTOXIN TYPE B PRECURSOR | HEMA_IAZH2 306-318
Non-standard residues in 1dlh #9
---
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)
NDG — 2-acetamido-2-deoxy-alpha-D-glucopyranose (N-acetyl-alpha-D-glucosamine;
2-acetamido-2-deoxy-alpha-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE)
> mmaker #7-#9 to #1
> matchmaker #7-#9 to #1
Missing or invalid "matchAtoms" argument: only initial part "#7" of atom
specifier valid
> mmaker #7-9 to #1
Parameters
---
Chain pairing | bb
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 BL4R.pdb, chain A (#1) with 6t3y, chain A (#7), sequence alignment
score = 929.7
RMSD between 174 pruned atom pairs is 0.624 angstroms; (across all 183 pairs:
1.085)
Matchmaker BL4R.pdb, chain A (#1) with 6kvm, chain A (#8), sequence alignment
score = 953.8
RMSD between 184 pruned atom pairs is 0.381 angstroms; (across all 184 pairs:
0.381)
Matchmaker BL4R.pdb, chain B (#1) with 1dlh, chain B (#9), sequence alignment
score = 614.8
RMSD between 154 pruned atom pairs is 0.997 angstroms; (across all 177 pairs:
1.754)
> hide atoms
> hide #!8.1 models
> hide #!7.1 models
> hide #!1 models
> hide #!2 models
> hide #!5 models
> hide #!6 models
> select #7/A #8/A #9/A
4846 atoms, 4643 bonds, 897 residues, 3 models selected
> color sel light gray
> hide #9 models
> show #9 models
> show #!1 models
> show #!2 models
> show #3 models
> hide #3 models
> show #!6 models
> show #!5 models
> hide #9 models
> select clear
> select #7/B
1713 atoms, 1606 bonds, 3 pseudobonds, 341 residues, 2 models selected
> ui tool show "Color Actions"
> color sel pink
> select #8/B
1538 atoms, 1516 bonds, 1 pseudobond, 242 residues, 2 models selected
> color sel khaki
> select #8/C
143 atoms, 131 bonds, 30 residues, 1 model selected
> color sel khaki
> select clear
> save "D:/桌面/BLB4 and BLB21/BLB_comparison.png" width 1979 height 1169
> supersample 3 transparentBackground true
> save my_session.cxs
QDxgiVSyncService: DXGI Factory is no longer Current
> close #9
> hide #!1 models
> hide #!8 models
> hide #!7 models
> select #2/B
1468 atoms, 1507 bonds, 2 pseudobonds, 179 residues, 2 models selected
> show sel atoms
> undo
> select #2/C
104 atoms, 104 bonds, 2 pseudobonds, 14 residues, 2 models selected
> show sel atoms
> select #5/C
Nothing selected
> show #!7 target m
> hide #!7 models
> select add #6
3115 atoms, 3205 bonds, 1 pseudobond, 391 residues, 2 models selected
> view #7 clip false
No displayed objects specified.
> show #!7 target m
> hide #!7 models
> select subtract #6
Nothing selected
> select #5/B
Nothing selected
> select #5/F
1644 atoms, 1665 bonds, 1 pseudobond, 226 residues, 2 models selected
> sequence chain #5/F
Alignment identifier is 5/F
> select #5/F:-28
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #5/F:-28--12
120 atoms, 121 bonds, 17 residues, 1 model selected
> show sel atoms
> hide sel atoms
> style sel stick
Changed 120 atom styles
> show sel atoms
> color sel byhetero
Drag select of 27 atoms, 48 residues, 22 bonds
> hide sel atoms
> undo
Drag select of 26 atoms, 41 residues, 22 bonds
> hide sel atoms
> undo
Drag select of 21 atoms, 36 residues, 18 bonds
> hide sel atoms
Drag select of 24 atoms, 51 residues, 20 bonds
> hide sel atoms
> select #6/B
1598 atoms, 1638 bonds, 1 pseudobond, 204 residues, 2 models selected
> sequence chain #6/B
Alignment identifier is 6/B
> select #6/B:-27
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #6/B:-27--12
112 atoms, 113 bonds, 16 residues, 1 model selected
> show sel atoms
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.11.dev202508300055 (2025-08-30)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 3.3.0 NVIDIA 576.97
OpenGL renderer: NVIDIA GeForce RTX 3080/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Python: 3.11.9
Locale: zh_CN.cp936
Qt version: PyQt6 6.9.1, Qt 6.9.0
Qt runtime version: 6.9.1
Qt platform: windows
Manufacturer: HP
Model: OMEN by HP 45L Gaming Desktop GT22-0xxx
OS: Microsoft Windows 11 家庭中文版 (Build 22621)
Memory: 34,105,032,704
MaxProcessMemory: 137,438,953,344
CPU: 20 12th Gen Intel(R) Core(TM) i7-12700K
OSLanguage: zh-CN
Installed Packages:
alabaster: 1.0.0
appdirs: 1.4.4
asttokens: 3.0.0
babel: 2.17.0
beautifulsoup4: 4.13.5
blockdiag: 3.0.0
blosc2: 3.7.2
build: 1.3.0
certifi: 2025.8.3
cftime: 1.6.4.post1
charset-normalizer: 3.4.3
ChimeraX-AddCharge: 1.5.20
ChimeraX-AddH: 2.2.7
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.6.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 3.0.2
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Aniso: 1.3.2
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.60.16
ChimeraX-AtomicLibrary: 14.1.23
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.3
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-Boltz: 1.1
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.2
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.6.0
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.5
ChimeraX-ChemGroup: 2.0.2
ChimeraX-Clashes: 2.3
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.8
ChimeraX-CommandLine: 1.3.0
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.11.dev202508300055
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.5
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.4
ChimeraX-Dicom: 1.2.7
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.4
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.4.1
ChimeraX-Hbonds: 2.5.3
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.4
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.7.1
ChimeraX-Label: 1.1.14
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.2
ChimeraX-Map: 1.3
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.2.2
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.17.1
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-Minimize: 1.2
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.16
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.22
ChimeraX-ModelPanel: 1.5.1
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0.1
ChimeraX-MutationScores: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.15.1
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.10
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.3
ChimeraX-ProfileGrids: 1.3.1
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.5
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.2
ChimeraX-Scenes: 0.2.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.3
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.7
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.17.2
ChimeraX-Shape: 1.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-SimilarStructures: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.19.1
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5.2
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.2.3
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.48.2
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDock: 1.3.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.5
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.3
comtypes: 1.4.11
contourpy: 1.3.3
coverage: 7.10.6
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.1.3
debugpy: 1.8.16
decorator: 5.2.1
docutils: 0.21.2
executing: 2.2.0
filelock: 3.19.1
fonttools: 4.59.2
funcparserlib: 2.0.0a0
glfw: 2.9.0
grako: 3.16.5
h5py: 3.14.0
html2text: 2025.4.15
idna: 3.10
ihm: 2.2
imagecodecs: 2024.6.1
imagesize: 1.4.1
iniconfig: 2.1.0
ipykernel: 6.30.1
ipython: 9.5.0
ipython_pygments_lexers: 1.1.1
ipywidgets: 8.1.7
jedi: 0.19.2
Jinja2: 3.1.6
jupyter_client: 8.6.3
jupyter_core: 5.8.1
jupyterlab_widgets: 3.0.15
kiwisolver: 1.4.9
line_profiler: 5.0.0
lxml: 6.0.1
lz4: 4.3.2
Markdown: 3.8.2
MarkupSafe: 3.0.2
matplotlib: 3.10.5
matplotlib-inline: 0.1.7
msgpack: 1.1.1
narwhals: 2.3.0
ndindex: 1.10.0
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.11.0
numpy: 2.2.6
numpy: 1.26.4
nvidia-nvjitlink-cu12: 12.9.86
OpenMM: 8.2.0
OpenMM-CUDA-12: 8.2.0
openvr: 1.26.701
packaging: 25.0
ParmEd: 4.2.2
parso: 0.8.5
pep517: 0.13.1
pickleshare: 0.7.5
pillow: 11.3.0
pip: 25.2
pkginfo: 1.12.1.2
platformdirs: 4.4.0
plotly: 6.0.1
pluggy: 1.6.0
prompt_toolkit: 3.0.52
psutil: 7.0.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pybind11: 3.0.1
pycollada: 0.8
pydicom: 2.4.4
Pygments: 2.18.0
pyKVFinder: 0.8.1
pynmrstar: 3.3.5
pynrrd: 1.0.0
PyOpenGL: 3.1.10
PyOpenGL-accelerate: 3.1.10
pyopenxr: 1.1.4501
pyparsing: 3.2.3
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.9.1
PyQt6-Qt6: 6.9.1
PyQt6-WebEngine-commercial: 6.9.0
PyQt6-WebEngine-Qt6: 6.9.1
PyQt6_sip: 13.10.2
pytest: 8.4.1
pytest-cov: 6.2.1
python-dateutil: 2.9.0.post0
pytz: 2025.2
pywin32: 311
pyzmq: 27.0.2
qtconsole: 5.6.1
QtPy: 2.4.3
qtshim: 1.2
RandomWords: 0.4.0
requests: 2.32.4
roman-numerals-py: 3.1.0
scipy: 1.14.0
setuptools: 80.9.0
sfftk-rw: 0.8.1
six: 1.17.0
snowballstemmer: 3.0.1
sortedcontainers: 2.4.0
soupsieve: 2.8
Sphinx: 8.2.3
sphinx-autodoc-typehints: 3.2.0
sphinxcontrib-applehelp: 2.0.0
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 2.0.0
sphinxcontrib-htmlhelp: 2.1.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 2.0.0
sphinxcontrib-serializinghtml: 2.0.0
stack-data: 0.6.3
superqt: 0.7.6
tables: 3.10.2
tcia_utils: 1.5.1
tifffile: 2025.3.13
tinyarray: 1.2.5
tomlkit: 0.13.2
tornado: 6.5.2
traitlets: 5.14.3
typing_extensions: 4.15.0
tzdata: 2025.2
urllib3: 2.5.0
wcwidth: 0.2.13
webcolors: 24.11.1
wheel: 0.45.1
wheel-filename: 1.4.2
widgetsnbextension: 4.0.14
WMI: 1.5.1
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