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Opened 7 months ago
Closed 7 months ago
#17282 closed defect (can't reproduce)
Crash closing dock widget
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Window Toolkit | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description (last modified by )
The following bug report has been submitted:
Platform: macOS-13.7.1-x86_64-i386-64bit
ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault
Thread 0x0000700092852000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 579 in _handle_results
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/ipykernel/ipkernel.py", line 761 in run_closure
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000070009184f000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 531 in _handle_tasks
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/ipykernel/ipkernel.py", line 761 in run_closure
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000070009084c000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/selectors.py", line 415 in select
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/connection.py", line 930 in wait
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 502 in _wait_for_updates
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 522 in _handle_workers
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/ipykernel/ipkernel.py", line 761 in run_closure
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000070008f849000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/ipykernel/ipkernel.py", line 761 in run_closure
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000070008e846000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/ipykernel/ipkernel.py", line 761 in run_closure
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000070008d843000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/ipykernel/ipkernel.py", line 761 in run_closure
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000070008c840000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/ipykernel/ipkernel.py", line 761 in run_closure
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000070008b03a000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/selectors.py", line 561 in select
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/asyncio/base_events.py", line 1884 in _run_once
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/asyncio/base_events.py", line 607 in run_forever
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/tornado/platform/asyncio.py", line 205 in start
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/ipykernel/iostream.py", line 92 in _thread_main
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000070008a037000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 320 in wait
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 622 in wait
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/IPython/core/history.py", line 894 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/IPython/core/history.py", line 60 in only_when_enabled
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/decorator.py", line 232 in fun
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000700089034000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 579 in _handle_results
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000700088031000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 531 in _handle_tasks
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000070008702e000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/selectors.py", line 415 in select
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/connection.py", line 930 in wait
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 502 in _wait_for_updates
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 522 in _handle_workers
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000070008602b000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000700085028000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000700068fd4000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000700060fbc000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000700084025000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 579 in _handle_results
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000700083022000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 531 in _handle_tasks
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000070008201f000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/selectors.py", line 415 in select
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/connection.py", line 930 in wait
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 502 in _wait_for_updates
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 522 in _handle_workers
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000070008101c000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000700079004000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000700070fec000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000700058fa4000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000700080019000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 579 in _handle_results
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000070007f016000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 531 in _handle_tasks
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000070007e013000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/selectors.py", line 415 in select
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/connection.py", line 930 in wait
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 502 in _wait_for_updates
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 522 in _handle_workers
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000070007d010000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000070007c00d000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000070007b00a000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000070007a007000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000700078001000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 579 in _handle_results
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000700076ffe000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 531 in _handle_tasks
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000700075ffb000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/selectors.py", line 415 in select
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/connection.py", line 930 in wait
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 502 in _wait_for_updates
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 522 in _handle_workers
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000700074ff8000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000700073ff5000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000700072ff2000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000700071fef000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000070006ffe9000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 579 in _handle_results
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000070006efe6000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 531 in _handle_tasks
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000070006dfe3000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/selectors.py", line 415 in select
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/connection.py", line 930 in wait
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 502 in _wait_for_updates
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 522 in _handle_workers
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000070006cfe0000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000070006bfdd000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000070006afda000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000700069fd7000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000700067fd1000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 579 in _handle_results
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000700066fce000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 531 in _handle_tasks
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000700065fcb000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/selectors.py", line 415 in select
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/connection.py", line 930 in wait
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 502 in _wait_for_updates
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 522 in _handle_workers
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000700064fc8000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000700063fc5000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000700062fc2000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000700061fbf000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000070005ffb9000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 579 in _handle_results
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000070005efb6000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 531 in _handle_tasks
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000070005dfb3000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/selectors.py", line 415 in select
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/connection.py", line 930 in wait
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 502 in _wait_for_updates
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 522 in _handle_workers
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000070005cfb0000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000070005bfad000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000070005afaa000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000700059fa7000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000700057fa1000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 579 in _handle_results
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000700056f9e000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 531 in _handle_tasks
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000700055f9b000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/selectors.py", line 415 in select
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/connection.py", line 930 in wait
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 502 in _wait_for_updates
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 522 in _handle_workers
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000700054f98000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000700053f95000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000070004bf7d000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000070004af7a000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000700052f92000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 579 in _handle_results
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000700051f8f000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 531 in _handle_tasks
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000700050f8c000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/selectors.py", line 415 in select
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/connection.py", line 930 in wait
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 502 in _wait_for_updates
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 522 in _handle_workers
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000070004ff89000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000070004ef86000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000070004df83000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000070004cf80000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000700049f77000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 579 in _handle_results
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000700041f5f000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 531 in _handle_tasks
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000700039f47000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/selectors.py", line 415 in select
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/connection.py", line 930 in wait
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 502 in _wait_for_updates
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 522 in _handle_workers
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000700031f2f000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000700029f17000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000700021eff000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000070000c107000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000700048f74000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 579 in _handle_results
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000700047f71000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 531 in _handle_tasks
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000700046f6e000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/selectors.py", line 415 in select
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/connection.py", line 930 in wait
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 502 in _wait_for_updates
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 522 in _handle_workers
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000700045f6b000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000700044f68000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000700043f65000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000700042f62000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000700040f5c000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 579 in _handle_results
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000070003ff59000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 531 in _handle_tasks
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000070003ef56000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/selectors.py", line 415 in select
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/connection.py", line 930 in wait
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 502 in _wait_for_updates
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 522 in _handle_workers
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000070003df53000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000070003cf50000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000070003bf4d000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000070003af4a000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000700038f44000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 579 in _handle_results
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000700037f41000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 531 in _handle_tasks
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000700036f3e000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/selectors.py", line 415 in select
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/connection.py", line 930 in wait
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 502 in _wait_for_updates
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 522 in _handle_workers
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000700035f3b000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000700034f38000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000700033f35000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000700032f32000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
...
Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, chimerax.pdb_lib._load_libs, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.surface._surface, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, PIL._imagingmath, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, zmq.backend.cython._zmq, tornado.speedups, psutil._psutil_osx, psutil._psutil_posix, PyQt6.QtSvg (total: 61)
{"app_name":"ChimeraX","timestamp":"2025-04-03 14:07:09.00 -0400","app_version":"1.8.0","slice_uuid":"194a3167-3db5-3029-8d22-1d742b826bb9","build_version":"1.8.0.0","platform":1,"bundleID":"edu.ucsf.cgl.ChimeraX","share_with_app_devs":0,"is_first_party":0,"bug_type":"309","os_version":"macOS 13.7.1 (22H221)","roots_installed":0,"name":"ChimeraX","incident_id":"FA371808-006B-4D85-A8DD-A26B41F5D6C5"}
{
"uptime" : 51000,
"procRole" : "Foreground",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "MacBookPro14,1",
"coalitionID" : 465,
"osVersion" : {
"train" : "macOS 13.7.1",
"build" : "22H221",
"releaseType" : "User"
},
"captureTime" : "2025-04-03 14:06:55.2345 -0400",
"incident" : "FA371808-006B-4D85-A8DD-A26B41F5D6C5",
"pid" : 450,
"cpuType" : "X86-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-04-01 12:18:45.6979 -0400",
"procStartAbsTime" : 27844219724,
"procExitAbsTime" : 51496820374870,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.8.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.8.0","CFBundleVersion":"1.8.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"6EE9740B-A496-5619-B776-963B1C600DE2","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "1BC9ED74-A73A-BB75-8E2C-1774CFA56FB6",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 0,
"wakeTime" : 3523,
"sleepWakeUUID" : "A4EFE7E4-36D4-4362-8DE6-5F84AEE1259B",
"sip" : "enabled",
"vmRegionInfo" : "0xf7 is not in any region. Bytes before following region: 140737486360329\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n shared memory 7fffffe19000-7fffffe1a000 [ 4K] r-x\/r-x SM=SHM ",
"exception" : {"codes":"0x0000000000000001, 0x00000000000000f7","rawCodes":[1,247],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x00000000000000f7"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":450},
"vmregioninfo" : "0xf7 is not in any region. Bytes before following region: 140737486360329\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n shared memory 7fffffe19000-7fffffe1a000 [ 4K] r-x\/r-x SM=SHM ",
"extMods" : {"caller":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"system":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"targeted":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"warnings":0},
"faultingThread" : 0,
[deleted to fit within ticket limits]
"usedImages" : [
[deleted to fit within ticket limits]
],
"sharedCache" : {
"base" : 140703265591296,
"size" : 21474836480,
"uuid" : "bdcffdbd-683c-3c37-808c-6ae85c95c7e8"
},
"vmSummary" : "ReadOnly portion of Libraries: Total=1.2G resident=0K(0%) swapped_out_or_unallocated=1.2G(100%)\nWritable regions: Total=4.4G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=4.4G(100%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 384K 3 \nActivity Tracing 256K 1 \nCG backing stores 2160K 4 \nCG image 588K 51 \nColorSync 264K 30 \nCoreAnimation 604K 35 \nCoreGraphics 12K 2 \nCoreUI image data 5148K 38 \nFoundation 32K 2 \nIOKit 7940K 1 \nKernel Alloc Once 8K 1 \nMALLOC 1.6G 829 \nMALLOC guard page 32K 7 \nMALLOC_LARGE (reserved) 384K 1 reserved VM address space (unallocated)\nMALLOC_NANO (reserved) 384.0M 1 reserved VM address space (unallocated)\nMach message 16K 2 \nOpenGL GLSL 384K 4 \nSTACK GUARD 636K 159 \nStack 2.2G 160 \nStack Guard 56.0M 1 \nVM_ALLOCATE 219.9M 335 \n__CTF 824 1 \n__DATA 41.8M 799 \n__DATA_CONST 50.1M 455 \n__DATA_DIRTY 1861K 239 \n__FONT_DATA 2352 1 \n__GLSLBUILTINS 5174K 1 \n__INFO_FILTER 8 1 \n__LINKEDIT 203.3M 167 \n__OBJC_RO 66.3M 1 \n__OBJC_RW 2013K 2 \n__TEXT 977.2M 807 \ndyld private memory 292K 4 \nmapped file 541.6M 87 \nshared memory 3000K 33 \n=========== ======= ======= \nTOTAL 6.3G 4265 \nTOTAL, minus reserved VM space 5.9G 4265 \n",
"legacyInfo" : {
"threadTriggered" : {
"name" : "CrBrowserMain",
"queue" : "com.apple.main-thread"
}
},
"logWritingSignature" : "fd9d4a9250f5cedda72a64d4902fe1ff6b26e0cb",
"trialInfo" : {
"rollouts" : [
{
"rolloutId" : "62c74108bcb0435c2153f963",
"factorPackIds" : {
"SIRI_TEXT_TO_SPEECH" : "657a4921d6ad146894c1b003"
},
"deploymentId" : 240000394
},
{
"rolloutId" : "6410af69ed1e1e7ab93ed169",
"factorPackIds" : {
},
"deploymentId" : 240000011
}
],
"experiments" : [
{
"treatmentId" : "28060e10-d4e5-4163-aa2b-d8bd088d5cbf",
"experimentId" : "6685b283afc7c17197d69eec",
"deploymentId" : 400000008
}
]
}
}
===== Log before crash start =====
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> ui tool show Registration
Registration server unavailable. Please try again later.
Thank you for registering your copy of ChimeraX. By providing the information
requested you will be helping us document the impact this software is having
in the scientific community. The information you supplied will only be used
for reporting summary usage statistics; no individual data will be released.
bednova.op@gmail.com has been invited to the ChimeraX discussion list
bednova.op@gmail.com has been invited to the ChimeraX announcements list
> open /Users/olgabednova/Desktop/!LDI/NGF/!hNGF/1www_hNGF_prepared.pdb
Chain information for 1www_hNGF_prepared.pdb #1
---
Chain | Description
V W | No description available
> open /Users/olgabednova/Desktop/!LDI/NGF/PDB/1WWW_hNGF.pdb
Summary of feedback from opening
/Users/olgabednova/Desktop/!LDI/NGF/PDB/1WWW_hNGF.pdb
---
warnings | Start residue of secondary structure not found: HELIX 3 3 HIS X 353 ASN X 355 1 3
Start residue of secondary structure not found: HELIX 4 4 HIS Y 353 ASN Y 355
1 3
Start residue of secondary structure not found: SHEET 17 17 1 SER X 287 LEU X
290 0
Start residue of secondary structure not found: SHEET 18 18 1 TRP X 299 ASP X
306 0
Start residue of secondary structure not found: SHEET 19 19 1 SER X 312 PHE X
317 0
11 messages similar to the above omitted
Cannot find LINK/SSBOND residue CYS (300 )
Cannot find LINK/SSBOND residue CYS (300 )
Chain information for 1WWW_hNGF.pdb #2
---
Chain | Description
V W | No description available
> hide #!1 models
> hide #1.1 models
> hide #!2 models
> show #!1 models
> show #1.1 models
> ui tool show "Model Loops"
> select #1/V#2/V
2548 atoms, 2590 bonds, 2 pseudobonds, 216 residues, 4 models selected
> select #2/W:2-116
862 atoms, 883 bonds, 1 pseudobond, 109 residues, 2 models selected
> select #2/W:2-116
862 atoms, 883 bonds, 1 pseudobond, 109 residues, 2 models selected
> select #2/V:2-115
857 atoms, 878 bonds, 1 pseudobond, 108 residues, 2 models selected
> select #2/V:2-115
857 atoms, 878 bonds, 1 pseudobond, 108 residues, 2 models selected
> select #2/W:2-116
862 atoms, 883 bonds, 1 pseudobond, 109 residues, 2 models selected
> select all
5111 atoms, 5195 bonds, 4 pseudobonds, 434 residues, 4 models selected
> ui tool show "Model Loops"
No alignments chosen for modeling
> select /V:2-115
2548 atoms, 2590 bonds, 2 pseudobonds, 216 residues, 4 models selected
> ui tool show "Show Sequence Viewer"
> sequence chain #1/V
Alignment identifier is 1/V
> select clear
> select #1/V:4
17 atoms, 17 bonds, 1 residue, 1 model selected
> select #1/V:2-4
39 atoms, 39 bonds, 3 residues, 1 model selected
> ui tool show "Show Sequence Viewer"
> sequence chain #1/W
Alignment identifier is 1/W
> select all
5111 atoms, 5195 bonds, 4 pseudobonds, 434 residues, 4 models selected
> ui tool show "Model Loops"
> modeller refine 1/W:1:internal-missing 1/V:1:internal-missing numModels 5
> fast false adjacentFlexible 1 protocol DOPE
Webservices job id: AWTHDQLNGA4LA7O1
Modeller job (ID AWTHDQLNGA4LA7O1) finished
Parameters
---
Chain pairing | ss
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 1www_hNGF_prepared.pdb, chain V (#1) with chain_V, chain V (#),
sequence alignment score = 606.1
Matchmaker 1www_hNGF_prepared.pdb, chain W (#1) with chain_V, chain W (#),
sequence alignment score = 600.5
RMSD between 217 pruned atom pairs is 0.065 angstroms; (across all 217 pairs:
0.065)
Parameters
---
Chain pairing | ss
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 1www_hNGF_prepared.pdb, chain V (#1) with chain_V, chain V (#),
sequence alignment score = 606.1
Matchmaker 1www_hNGF_prepared.pdb, chain W (#1) with chain_V, chain W (#),
sequence alignment score = 600.5
RMSD between 217 pruned atom pairs is 0.100 angstroms; (across all 217 pairs:
0.100)
Parameters
---
Chain pairing | ss
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 1www_hNGF_prepared.pdb, chain V (#1) with chain_V, chain V (#),
sequence alignment score = 606.1
Matchmaker 1www_hNGF_prepared.pdb, chain W (#1) with chain_V, chain W (#),
sequence alignment score = 600.5
RMSD between 217 pruned atom pairs is 0.094 angstroms; (across all 217 pairs:
0.094)
Parameters
---
Chain pairing | ss
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 1www_hNGF_prepared.pdb, chain V (#1) with chain_V, chain V (#),
sequence alignment score = 606.1
Matchmaker 1www_hNGF_prepared.pdb, chain W (#1) with chain_V, chain W (#),
sequence alignment score = 600.5
RMSD between 217 pruned atom pairs is 0.060 angstroms; (across all 217 pairs:
0.060)
Parameters
---
Chain pairing | ss
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 1www_hNGF_prepared.pdb, chain V (#1) with chain_V, chain V (#),
sequence alignment score = 606.1
Matchmaker 1www_hNGF_prepared.pdb, chain W (#1) with chain_V, chain W (#),
sequence alignment score = 600.5
RMSD between 217 pruned atom pairs is 0.087 angstroms; (across all 217 pairs:
0.087)
Associated chain_V chain W to chain W with 0 mismatches
Associated chain_V chain V to chain W with 0 mismatches
Associated chain_V chain W to chain W with 0 mismatches
Associated chain_V chain V to chain W with 0 mismatches
Associated chain_V chain W to chain W with 0 mismatches
Associated chain_V chain V to chain W with 0 mismatches
Associated chain_V chain W to chain W with 0 mismatches
Associated chain_V chain V to chain W with 0 mismatches
Associated chain_V chain W to chain W with 0 mismatches
Associated chain_V chain V to chain W with 0 mismatches
Associated chain_V chain W to chain V with 0 mismatches
Associated chain_V chain V to chain V with 0 mismatches
Associated chain_V chain W to chain V with 0 mismatches
Associated chain_V chain V to chain V with 0 mismatches
Associated chain_V chain W to chain V with 0 mismatches
Associated chain_V chain V to chain V with 0 mismatches
Associated chain_V chain W to chain V with 0 mismatches
Associated chain_V chain V to chain V with 0 mismatches
Associated chain_V chain W to chain V with 0 mismatches
Associated chain_V chain V to chain V with 0 mismatches
Chain information for chain_V
---
Chain | Description
3.1/V 3.2/V 3.3/V 3.4/V 3.5/V | No description available
3.1/W 3.2/W 3.3/W 3.4/W 3.5/W | No description available
> ui tool show "Model Loops"
> modeller refine 1/W:1:all-missing 1/V:1:all-missing numModels 5 fast false
> adjacentFlexible 1 protocol DOPE
Webservices job id: NGQOJZ3X89CG8314
Webservices job id: OCSIZ8DFDG9YS6BY
Webservices job id: EZZX7UU75XAU1R8O
Webservices job id: WRUH2IREJMR6HYGH
Webservices job id: PGMBJ87EFSOBN1EV
Webservices job id: NTSM7C6V9BWV2E8Z
Modeller job (ID OCSIZ8DFDG9YS6BY) finished
Parameters
---
Chain pairing | ss
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 chain_V, chain V (#3.1) with chain_V, chain V (#), sequence
alignment score = 615.7
Matchmaker chain_V, chain W (#3.1) with chain_V, chain W (#), sequence
alignment score = 616.7
RMSD between 229 pruned atom pairs is 0.080 angstroms; (across all 229 pairs:
0.080)
Parameters
---
Chain pairing | ss
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 chain_V, chain V (#3.1) with chain_V, chain V (#), sequence
alignment score = 615.7
Matchmaker chain_V, chain W (#3.1) with chain_V, chain W (#), sequence
alignment score = 616.7
RMSD between 229 pruned atom pairs is 0.157 angstroms; (across all 229 pairs:
0.157)
Parameters
---
Chain pairing | ss
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 chain_V, chain V (#3.1) with chain_V, chain V (#), sequence
alignment score = 615.7
Matchmaker chain_V, chain W (#3.1) with chain_V, chain W (#), sequence
alignment score = 613.7
RMSD between 229 pruned atom pairs is 0.157 angstroms; (across all 229 pairs:
0.157)
Parameters
---
Chain pairing | ss
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 chain_V, chain V (#3.1) with chain_V, chain V (#), sequence
alignment score = 615.7
Matchmaker chain_V, chain W (#3.1) with chain_V, chain W (#), sequence
alignment score = 616.7
RMSD between 229 pruned atom pairs is 0.138 angstroms; (across all 229 pairs:
0.138)
Parameters
---
Chain pairing | ss
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 chain_V, chain V (#3.1) with chain_V, chain V (#), sequence
alignment score = 615.7
Matchmaker chain_V, chain W (#3.1) with chain_V, chain W (#), sequence
alignment score = 616.7
RMSD between 229 pruned atom pairs is 0.086 angstroms; (across all 229 pairs:
0.086)
Associated chain_V chain V to chain W with 0 mismatches
Associated chain_V chain W to chain W with 0 mismatches
Associated chain_V chain V to chain W with 0 mismatches
Associated chain_V chain W to chain W with 0 mismatches
Associated chain_V chain V to chain W with 0 mismatches
Associated chain_V chain W to chain W with 0 mismatches
Associated chain_V chain V to chain W with 0 mismatches
Associated chain_V chain W to chain W with 0 mismatches
Associated chain_V chain V to chain W with 0 mismatches
Associated chain_V chain W to chain W with 0 mismatches
Associated chain_V chain V to chain V with 0 mismatches
Associated chain_V chain W to chain V with 0 mismatches
Associated chain_V chain V to chain V with 0 mismatches
Associated chain_V chain W to chain V with 0 mismatches
Associated chain_V chain V to chain V with 0 mismatches
Associated chain_V chain W to chain V with 0 mismatches
Associated chain_V chain V to chain V with 0 mismatches
Associated chain_V chain W to chain V with 0 mismatches
Associated chain_V chain V to chain V with 0 mismatches
Associated chain_V chain W to chain V with 0 mismatches
Chain information for chain_V
---
Chain | Description
4.1/V 4.2/V 4.3/V 4.4/V 4.5/V 4.1/W 4.2/W 4.3/W 4.4/W 4.5/W | No description available
Modeller job (ID WRUH2IREJMR6HYGH) finished
Parameters
---
Chain pairing | ss
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 chain_V, chain V (#3.2) with chain_V, chain V (#), sequence
alignment score = 610.3
Matchmaker chain_V, chain W (#3.2) with chain_V, chain W (#), sequence
alignment score = 616.7
RMSD between 229 pruned atom pairs is 0.137 angstroms; (across all 229 pairs:
0.137)
Parameters
---
Chain pairing | ss
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 chain_V, chain V (#3.2) with chain_V, chain V (#), sequence
alignment score = 613.3
Matchmaker chain_V, chain W (#3.2) with chain_V, chain W (#), sequence
alignment score = 616.7
RMSD between 229 pruned atom pairs is 0.122 angstroms; (across all 229 pairs:
0.122)
Parameters
---
Chain pairing | ss
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 chain_V, chain V (#3.2) with chain_V, chain V (#), sequence
alignment score = 613.3
Matchmaker chain_V, chain W (#3.2) with chain_V, chain W (#), sequence
alignment score = 616.7
RMSD between 229 pruned atom pairs is 0.133 angstroms; (across all 229 pairs:
0.133)
Parameters
---
Chain pairing | ss
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 chain_V, chain V (#3.2) with chain_V, chain V (#), sequence
alignment score = 610.3
Matchmaker chain_V, chain W (#3.2) with chain_V, chain W (#), sequence
alignment score = 616.7
RMSD between 229 pruned atom pairs is 0.152 angstroms; (across all 229 pairs:
0.152)
Parameters
---
Chain pairing | ss
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 chain_V, chain V (#3.2) with chain_V, chain V (#), sequence
alignment score = 613.3
Matchmaker chain_V, chain W (#3.2) with chain_V, chain W (#), sequence
alignment score = 613.7
RMSD between 229 pruned atom pairs is 0.055 angstroms; (across all 229 pairs:
0.055)
Associated chain_V chain V to chain W with 0 mismatches
Associated chain_V chain W to chain W with 0 mismatches
Associated chain_V chain V to chain W with 0 mismatches
Associated chain_V chain W to chain W with 0 mismatches
Associated chain_V chain V to chain W with 0 mismatches
Associated chain_V chain W to chain W with 0 mismatches
Associated chain_V chain V to chain W with 0 mismatches
Associated chain_V chain W to chain W with 0 mismatches
Associated chain_V chain V to chain W with 0 mismatches
Associated chain_V chain W to chain W with 0 mismatches
Associated chain_V chain V to chain V with 0 mismatches
Associated chain_V chain W to chain V with 0 mismatches
Associated chain_V chain V to chain V with 0 mismatches
Associated chain_V chain W to chain V with 0 mismatches
Associated chain_V chain V to chain V with 0 mismatches
Associated chain_V chain W to chain V with 0 mismatches
Associated chain_V chain V to chain V with 0 mismatches
Associated chain_V chain W to chain V with 0 mismatches
Associated chain_V chain V to chain V with 0 mismatches
Associated chain_V chain W to chain V with 0 mismatches
[deleted to fit within ticket limits]
# Code #_Res #_Segm PDB_code Name
\-------------------------------------------------------------------------------
1 chain_W_3 229 2 chain_W_3.3
2 chain_W 229 2 chain_W
check_a_343_> >> BEGINNING OF COMMAND
openf___224_> Open ./chain_W_3.3.pdb
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 477814 466.615
0.456
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 477814 466.615 0.456
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 477985 466.782
0.456
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 478835 467.612
0.457
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 480093 468.841
0.458
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 481997 470.700
0.460
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 481997 470.700 0.460
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 482087 470.788
0.460
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 484943 473.577
0.462
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 484943 473.577 0.462
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 485078 473.709
0.463
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 489362 477.893
0.467
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 489362 477.893 0.467
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 489560 478.086
0.467
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 495986 484.361
0.473
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 495986 484.361 0.473
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 496283 484.651
0.473
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 505905 494.048
0.482
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 505905 494.048 0.482
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 506355 494.487
0.483
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 520805 508.599
0.497
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 520805 508.599 0.497
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 520805 508.599
0.497
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 520805 508.599 0.497
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 521480 509.258
0.497
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 543138 530.408
0.518
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 543138 530.408 0.518
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 544146 531.393
0.519
Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 543174 530.443
0.518
check_ali___> Checking the sequence-structure alignment.
Implied intrachain target CA(i)-CA(i+1) distances longer than 8.0 angstroms:
ALN_POS TMPL RID1 RID2 NAM1 NAM2 DIST
\----------------------------------------------
END OF TABLE
check_a_344_> Open ${LIB}/top_heav.lib
read_to_681_> topology.submodel read from topology file: 3
openf___224_> Open ${LIB}/par.lib
Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 682426 666.432
0.651
Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 684026 667.994
0.652
Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 688006 671.881
0.656
Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 690006 673.834
0.658
Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 693006 676.764
0.661
Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 697506 681.158
0.665
Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 703078 686.600
0.671
Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 705878 689.334
0.673
Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 710078 693.436
0.677
Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 716378 699.588
0.683
Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 719150 702.295
0.686
Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 720550 703.662
0.687
read_pa_232_> parameters BONDS ANGLS DIHEDS IMPROPS MODE
227 561 661 112 0
Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 738291 720.987 0.704
Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 828353 808.938 0.790
Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 841945 822.212 0.803
mkilst______> segment topology constructed from sequence and RTF:
segments residues atoms bonds angles dihedrals impropers:
1 114 900 921 0 0 389
Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 880665 860.024 0.840
patch_______> segment topology patched using RTF: 1 ; SER ; NTER
segments residues atoms bonds angles dihedrals impropers:
1 114 900 921 1245 1488 389
Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 917761 896.251 0.875
patch_______> segment topology patched using RTF: 114 ; LYS ; CTER
segments residues atoms bonds angles dihedrals impropers:
1 114 901 922 1247 1490 390
genseg______> segment topology constructed from sequence and RTF:
segments residues atoms bonds angles dihedrals impropers:
1 114 901 922 1247 1490 390
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 917789 896.278 0.875
Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 935844 913.910 0.892
Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 1024632 1000.617 0.977
Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 1038320 1013.984 0.990
mkilst______> segment topology constructed from sequence and RTF:
segments residues atoms bonds angles dihedrals impropers:
2 229 1806 1848 1247 1490 781
Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 1077280 1052.031 1.027
patch_______> segment topology patched using RTF: 115 ; SER ; NTER
segments residues atoms bonds angles dihedrals impropers:
2 229 1806 1848 2499 2986 781
Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 1117016 1090.836 1.065
patch_______> segment topology patched using RTF: 229 ; ALA ; CTER
segments residues atoms bonds angles dihedrals impropers:
2 229 1807 1849 2501 2988 782
genseg______> segment topology constructed from sequence and RTF:
segments residues atoms bonds angles dihedrals impropers:
2 229 1807 1849 2501 2988 782
Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 1135520 1108.906 1.083
patch_______> segment topology patched using RTF: 14 79 ; CYS CYS ; DISU
segments residues atoms bonds angles dihedrals impropers:
2 229 1807 1850 2503 2991 782
patch_______> segment topology patched using RTF: 57 107 ; CYS CYS ; DISU
segments residues atoms bonds angles dihedrals impropers:
2 229 1807 1851 2505 2994 782
Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 1135768 1109.148 1.083
patch_______> segment topology patched using RTF: 67 109 ; CYS CYS ; DISU
segments residues atoms bonds angles dihedrals impropers:
2 229 1807 1852 2507 2997 782
patch_______> segment topology patched using RTF: 128 193 ; CYS CYS ; DISU
segments residues atoms bonds angles dihedrals impropers:
2 229 1807 1853 2509 3000 782
patch_______> segment topology patched using RTF: 171 221 ; CYS CYS ; DISU
segments residues atoms bonds angles dihedrals impropers:
2 229 1807 1854 2511 3003 782
patch_______> segment topology patched using RTF: 181 223 ; CYS CYS ; DISU
segments residues atoms bonds angles dihedrals impropers:
2 229 1807 1855 2513 3006 782
patch_s_522_> Number of disulfides patched in MODEL: 6
transfe_506_> MODEL is an average of all templates.
transfe_511_> Number of templates for coordinate transfer: 1
After transferring coordinates of the equivalent template atoms,
there are defined, undefined atoms in MODEL: 1807 0
openf___224_> Open chain_W.ini
wrpdb___568_> Residues, atoms, selected atoms: 229 1807 1807
make_re_417_> Restraint type to be calculated: stereo
Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1243217 1214.079
1.186
Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1251409 1222.079
1.193
Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1267793 1238.079
1.209
Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1300561 1270.079
1.240
Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1333329 1302.079
1.272
Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1398865 1366.079
1.334
Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1431633 1398.079
1.365
Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1464401 1430.079
1.397
Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1529937 1494.079
1.459
Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1661009 1622.079
1.584
Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1726545 1686.079
1.647
r_stere_606_> Stereochemical restraints were constructed from RTF & PRMF.
Added bond,angle,dihedral,improper restraints : 1855 2513 2847 776
Total number of restraints before, now : 0 7991
make_re_422_> Number of previous, current restraints : 0 7991
make_re_423_> Number of previous, current selected restraints: 0 7991
make_re_417_> Restraint type to be calculated: phi-psi_binormal
Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 1857779 1814.237
1.772
openf___224_> Open ${MODINSTALL10v6}/modlib/mnch1.bin
openf___224_> Open ${MODINSTALL10v6}/modlib/mnch1.mdt
getdata_643_> Protein accepted: chain_W_3.3
getdata_289_> Proteins (all/accepted): 1 1
Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1923331 1878.253
1.834
Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 2054403 2006.253
1.959
make_re_422_> Number of previous, current restraints : 7991 8216
make_re_423_> Number of previous, current selected restraints: 7991 8216
make_re_417_> Restraint type to be calculated: omega_dihedral
Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 2054403 2006.253
1.959
openf___224_> Open ${MODINSTALL10v6}/modlib/omega.bin
openf___224_> Open ${MODINSTALL10v6}/modlib/omega.mdt
getdata_643_> Protein accepted: chain_W_3.3
getdata_289_> Proteins (all/accepted): 1 1
omgdel__425_> Unselected all O C +N +CA dihedrals: 233
(This is to avoid clashes between STEREO
and OMEGA_DIHEDRAL restraints)
make_re_422_> Number of previous, current restraints : 8216 8443
make_re_423_> Number of previous, current selected restraints: 8216 8210
make_re_417_> Restraint type to be calculated: chi1_dihedral
Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 2054403 2006.253
1.959
openf___224_> Open ${MODINSTALL10v6}/modlib/chi1234.bin
openf___224_> Open ${MODINSTALL10v6}/modlib/chi1.mdt
getdata_643_> Protein accepted: chain_W_3.3
getdata_289_> Proteins (all/accepted): 1 1
make_re_422_> Number of previous, current restraints : 8443 8647
make_re_423_> Number of previous, current selected restraints: 8210 8414
make_re_417_> Restraint type to be calculated: chi2_dihedral
Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 2054403 2006.253
1.959
openf___224_> Open ${MODINSTALL10v6}/modlib/chi1234.bin
openf___224_> Open ${MODINSTALL10v6}/modlib/chi2.mdt
getdata_643_> Protein accepted: chain_W_3.3
getdata_289_> Proteins (all/accepted): 1 1
Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 2185475 2134.253
2.084
make_re_422_> Number of previous, current restraints : 8647 8775
make_re_423_> Number of previous, current selected restraints: 8414 8542
make_re_417_> Restraint type to be calculated: chi3_dihedral
Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 2185475 2134.253
2.084
openf___224_> Open ${MODINSTALL10v6}/modlib/chi1234.bin
openf___224_> Open ${MODINSTALL10v6}/modlib/chi3.mdt
getdata_643_> Protein accepted: chain_W_3.3
getdata_289_> Proteins (all/accepted): 1 1
make_re_422_> Number of previous, current restraints : 8775 8827
make_re_423_> Number of previous, current selected restraints: 8542 8594
make_re_417_> Restraint type to be calculated: chi4_dihedral
Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 2185475 2134.253
2.084
openf___224_> Open ${MODINSTALL10v6}/modlib/chi1234.bin
openf___224_> Open ${MODINSTALL10v6}/modlib/chi4.mdt
mdtrsr__446W> A potential that relies on one protein is used, yet you have at
least one known structure available. MDT, not library, potential is used.
getdata_643_> Protein accepted: chain_W_3.3
getdata_289_> Proteins (all/accepted): 1 1
make_re_422_> Number of previous, current restraints : 8827 8857
make_re_423_> Number of previous, current selected restraints: 8594 8624
make_re_417_> Restraint type to be calculated: DISTANCE
Dynamically allocated memory at amaxhash_contac [B,KiB,MiB]: 2705855 2642.437
2.581
Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 2967999 2898.437
2.831
Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 3099071 3026.437
2.956
make_re_422_> Number of previous, current restraints : 8857 13020
make_re_423_> Number of previous, current selected restraints: 8624 12787
make_re_417_> Restraint type to be calculated: DISTANCE
Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 3361215 3282.437
3.206
make_re_422_> Number of previous, current restraints : 13020 17466
make_re_423_> Number of previous, current selected restraints: 12787 17233
make_re_417_> Restraint type to be calculated: DISTANCE
Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 3885503 3794.437
3.706
make_re_422_> Number of previous, current restraints : 17466 21524
make_re_423_> Number of previous, current selected restraints: 17233 21291
make_re_417_> Restraint type to be calculated: DISTANCE
Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 4147647 4050.437
3.956
make_re_422_> Number of previous, current restraints : 21524 23508
make_re_423_> Number of previous, current selected restraints: 21291 23275
0 atoms in HETATM/BLK residues constrained
to protein atoms within 2.30 angstroms
and protein CA atoms within 10.00 angstroms
make_re_417_> Restraint type to be calculated: DISTANCE
make_re_422_> Number of previous, current restraints : 23508 23508
make_re_423_> Number of previous, current selected restraints: 23275 23275
make_re_417_> Restraint type to be calculated: DISTANCE
make_re_422_> Number of previous, current restraints : 23508 23508
make_re_423_> Number of previous, current selected restraints: 23275 23275
make_re_417_> Restraint type to be calculated: DISTANCE
make_re_422_> Number of previous, current restraints : 23508 23508
make_re_423_> Number of previous, current selected restraints: 23275 23275
make_re_417_> Restraint type to be calculated: DISTANCE
make_re_422_> Number of previous, current restraints : 23508 23508
make_re_423_> Number of previous, current selected restraints: 23275 23275
0 atoms in residues without defined topology
constrained to be rigid bodies
make_re_417_> Restraint type to be calculated: DISTANCE
make_re_422_> Number of previous, current restraints : 23508 23508
make_re_423_> Number of previous, current selected restraints: 23275 23275
rmdupl__427_> 1360 redundant cosine dihedral restraints were unselected.
condens_443_> Restraints marked for deletion were removed.
Total number of restraints before, now: 23508 21915
openf___224_> Open chain_W.rsr
openf___224_> Open chain_W.rsr
Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 4260279 4160.429
4.063
rdcsr2__307_> Number of restraints read : 21915
Number of excluded pairs read: 0
Number of pseudo atoms read : 0
rdcsrs__304_> Restraints in memory, selected restraints: 21915 21915
Explicitly excluded atom pairs in memory : 0
Pseudo atoms in memory : 0
No output models from Modeller; see log for Modeller text output.
> select all
14146 atoms, 14440 bonds, 4 pseudobonds, 1579 residues, 10 models selected
> ui tool show "Model Loops"
> close #3
> ui tool show "Model Loops"
> modeller refine 1/V:1:internal-missing 1/W:1:internal-missing numModels 10
> fast false adjacentFlexible 1 protocol DOPE
Webservices job id: I6W67AQ1SKUDJUZW
Modeller job (ID 8EF664GPC52WVSQB) finished
Parameters
---
Chain pairing | ss
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 1www_hNGF_prepared.pdb, chain V (#1) with chain_W, chain V (#),
sequence alignment score = 606.1
Matchmaker 1www_hNGF_prepared.pdb, chain W (#1) with chain_W, chain W (#),
sequence alignment score = 600.5
RMSD between 217 pruned atom pairs is 0.065 angstroms; (across all 217 pairs:
0.065)
Parameters
---
Chain pairing | ss
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 1www_hNGF_prepared.pdb, chain V (#1) with chain_W, chain V (#),
sequence alignment score = 606.1
Matchmaker 1www_hNGF_prepared.pdb, chain W (#1) with chain_W, chain W (#),
sequence alignment score = 600.5
RMSD between 217 pruned atom pairs is 0.100 angstroms; (across all 217 pairs:
0.100)
Parameters
---
Chain pairing | ss
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 1www_hNGF_prepared.pdb, chain V (#1) with chain_W, chain V (#),
sequence alignment score = 606.1
Matchmaker 1www_hNGF_prepared.pdb, chain W (#1) with chain_W, chain W (#),
sequence alignment score = 600.5
RMSD between 217 pruned atom pairs is 0.094 angstroms; (across all 217 pairs:
0.094)
Parameters
---
Chain pairing | ss
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 1www_hNGF_prepared.pdb, chain V (#1) with chain_W, chain V (#),
sequence alignment score = 606.1
Matchmaker 1www_hNGF_prepared.pdb, chain W (#1) with chain_W, chain W (#),
sequence alignment score = 600.5
RMSD between 217 pruned atom pairs is 0.060 angstroms; (across all 217 pairs:
0.060)
Parameters
---
Chain pairing | ss
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 1www_hNGF_prepared.pdb, chain V (#1) with chain_W, chain V (#),
sequence alignment score = 606.1
Matchmaker 1www_hNGF_prepared.pdb, chain W (#1) with chain_W, chain W (#),
sequence alignment score = 600.5
RMSD between 217 pruned atom pairs is 0.087 angstroms; (across all 217 pairs:
0.087)
Parameters
---
Chain pairing | ss
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 1www_hNGF_prepared.pdb, chain V (#1) with chain_W, chain V (#),
sequence alignment score = 606.1
Matchmaker 1www_hNGF_prepared.pdb, chain W (#1) with chain_W, chain W (#),
sequence alignment score = 600.5
RMSD between 217 pruned atom pairs is 0.067 angstroms; (across all 217 pairs:
0.067)
Parameters
---
Chain pairing | ss
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 1www_hNGF_prepared.pdb, chain V (#1) with chain_W, chain V (#),
sequence alignment score = 606.1
Matchmaker 1www_hNGF_prepared.pdb, chain W (#1) with chain_W, chain W (#),
sequence alignment score = 600.5
RMSD between 217 pruned atom pairs is 0.080 angstroms; (across all 217 pairs:
0.080)
Parameters
---
Chain pairing | ss
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 1www_hNGF_prepared.pdb, chain V (#1) with chain_W, chain V (#),
sequence alignment score = 606.1
Matchmaker 1www_hNGF_prepared.pdb, chain W (#1) with chain_W, chain W (#),
sequence alignment score = 600.5
RMSD between 217 pruned atom pairs is 0.106 angstroms; (across all 217 pairs:
0.106)
Parameters
---
Chain pairing | ss
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 1www_hNGF_prepared.pdb, chain V (#1) with chain_W, chain V (#),
sequence alignment score = 606.1
Matchmaker 1www_hNGF_prepared.pdb, chain W (#1) with chain_W, chain W (#),
sequence alignment score = 600.5
RMSD between 217 pruned atom pairs is 0.061 angstroms; (across all 217 pairs:
0.061)
Parameters
---
Chain pairing | ss
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 1www_hNGF_prepared.pdb, chain V (#1) with chain_W, chain V (#),
sequence alignment score = 606.1
Matchmaker 1www_hNGF_prepared.pdb, chain W (#1) with chain_W, chain W (#),
sequence alignment score = 600.5
RMSD between 217 pruned atom pairs is 0.087 angstroms; (across all 217 pairs:
0.087)
Associated chain_W chain W to chain V with 0 mismatches
Associated chain_W chain V to chain V with 0 mismatches
Associated chain_W chain W to chain V with 0 mismatches
Associated chain_W chain V to chain V with 0 mismatches
Associated chain_W chain W to chain V with 0 mismatches
Associated chain_W chain V to chain V with 0 mismatches
Associated chain_W chain W to chain V with 0 mismatches
Associated chain_W chain V to chain V with 0 mismatches
Associated chain_W chain W to chain V with 0 mismatches
Associated chain_W chain V to chain V with 0 mismatches
Associated chain_W chain W to chain V with 0 mismatches
Associated chain_W chain V to chain V with 0 mismatches
Associated chain_W chain W to chain V with 0 mismatches
Associated chain_W chain V to chain V with 0 mismatches
Associated chain_W chain W to chain V with 0 mismatches
Associated chain_W chain V to chain V with 0 mismatches
Associated chain_W chain W to chain V with 0 mismatches
Associated chain_W chain V to chain V with 0 mismatches
Associated chain_W chain W to chain V with 0 mismatches
Associated chain_W chain V to chain V with 0 mismatches
Associated chain_W chain W to chain W with 0 mismatches
Associated chain_W chain V to chain W with 0 mismatches
Associated chain_W chain W to chain W with 0 mismatches
Associated chain_W chain V to chain W with 0 mismatches
Associated chain_W chain W to chain W with 0 mismatches
Associated chain_W chain V to chain W with 0 mismatches
Associated chain_W chain W to chain W with 0 mismatches
Associated chain_W chain V to chain W with 0 mismatches
Associated chain_W chain W to chain W with 0 mismatches
Associated chain_W chain V to chain W with 0 mismatches
Associated chain_W chain W to chain W with 0 mismatches
Associated chain_W chain V to chain W with 0 mismatches
Associated chain_W chain W to chain W with 0 mismatches
Associated chain_W chain V to chain W with 0 mismatches
Associated chain_W chain W to chain W with 0 mismatches
Associated chain_W chain V to chain W with 0 mismatches
Associated chain_W chain W to chain W with 0 mismatches
Associated chain_W chain V to chain W with 0 mismatches
Associated chain_W chain W to chain W with 0 mismatches
Associated chain_W chain V to chain W with 0 mismatches
Chain information for chain_W
---
Chain | Description
3.1/V 3.2/V 3.3/V 3.4/V 3.5/V 3.6/V 3.7/V 3.8/V 3.9/V 3.10/V | No description available
3.1/W 3.2/W 3.3/W 3.4/W 3.5/W 3.6/W 3.7/W 3.8/W 3.9/W 3.10/W | No description available
> hide #3.3 models
> hide #3.7 models
> hide #3.6 models
> hide #3.5 models
Modeller job (ID I6W67AQ1SKUDJUZW) finished
Parameters
---
Chain pairing | ss
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 1www_hNGF_prepared.pdb, chain V (#1) with chain_W, chain V (#),
sequence alignment score = 606.1
Matchmaker 1www_hNGF_prepared.pdb, chain W (#1) with chain_W, chain W (#),
sequence alignment score = 600.5
RMSD between 217 pruned atom pairs is 0.065 angstroms; (across all 217 pairs:
0.065)
Parameters
---
Chain pairing | ss
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 1www_hNGF_prepared.pdb, chain V (#1) with chain_W, chain V (#),
sequence alignment score = 606.1
Matchmaker 1www_hNGF_prepared.pdb, chain W (#1) with chain_W, chain W (#),
sequence alignment score = 600.5
RMSD between 217 pruned atom pairs is 0.100 angstroms; (across all 217 pairs:
0.100)
Parameters
---
Chain pairing | ss
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 1www_hNGF_prepared.pdb, chain V (#1) with chain_W, chain V (#),
sequence alignment score = 606.1
Matchmaker 1www_hNGF_prepared.pdb, chain W (#1) with chain_W, chain W (#),
sequence alignment score = 600.5
RMSD between 217 pruned atom pairs is 0.094 angstroms; (across all 217 pairs:
0.094)
Parameters
---
Chain pairing | ss
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 1www_hNGF_prepared.pdb, chain V (#1) with chain_W, chain V (#),
sequence alignment score = 606.1
Matchmaker 1www_hNGF_prepared.pdb, chain W (#1) with chain_W, chain W (#),
sequence alignment score = 600.5
RMSD between 217 pruned atom pairs is 0.060 angstroms; (across all 217 pairs:
0.060)
Parameters
---
Chain pairing | ss
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 1www_hNGF_prepared.pdb, chain V (#1) with chain_W, chain V (#),
sequence alignment score = 606.1
Matchmaker 1www_hNGF_prepared.pdb, chain W (#1) with chain_W, chain W (#),
sequence alignment score = 600.5
RMSD between 217 pruned atom pairs is 0.087 angstroms; (across all 217 pairs:
0.087)
Parameters
---
Chain pairing | ss
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 1www_hNGF_prepared.pdb, chain V (#1) with chain_W, chain V (#),
sequence alignment score = 606.1
Matchmaker 1www_hNGF_prepared.pdb, chain W (#1) with chain_W, chain W (#),
sequence alignment score = 600.5
RMSD between 217 pruned atom pairs is 0.067 angstroms; (across all 217 pairs:
0.067)
Parameters
---
Chain pairing | ss
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 1www_hNGF_prepared.pdb, chain V (#1) with chain_W, chain V (#),
sequence alignment score = 606.1
Matchmaker 1www_hNGF_prepared.pdb, chain W (#1) with chain_W, chain W (#),
sequence alignment score = 600.5
RMSD between 217 pruned atom pairs is 0.080 angstroms; (across all 217 pairs:
0.080)
Parameters
---
Chain pairing | ss
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 1www_hNGF_prepared.pdb, chain V (#1) with chain_W, chain V (#),
sequence alignment score = 606.1
Matchmaker 1www_hNGF_prepared.pdb, chain W (#1) with chain_W, chain W (#),
sequence alignment score = 600.5
RMSD between 217 pruned atom pairs is 0.106 angstroms; (across all 217 pairs:
0.106)
Parameters
---
Chain pairing | ss
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 1www_hNGF_prepared.pdb, chain V (#1) with chain_W, chain V (#),
sequence alignment score = 606.1
Matchmaker 1www_hNGF_prepared.pdb, chain W (#1) with chain_W, chain W (#),
sequence alignment score = 600.5
RMSD between 217 pruned atom pairs is 0.061 angstroms; (across all 217 pairs:
0.061)
Parameters
---
Chain pairing | ss
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 1www_hNGF_prepared.pdb, chain V (#1) with chain_W, chain V (#),
sequence alignment score = 606.1
Matchmaker 1www_hNGF_prepared.pdb, chain W (#1) with chain_W, chain W (#),
sequence alignment score = 600.5
RMSD between 217 pruned atom pairs is 0.087 angstroms; (across all 217 pairs:
0.087)
Associated chain_W chain W to chain V with 0 mismatches
Associated chain_W chain V to chain V with 0 mismatches
Associated chain_W chain W to chain V with 0 mismatches
Associated chain_W chain V to chain V with 0 mismatches
Associated chain_W chain W to chain V with 0 mismatches
Associated chain_W chain V to chain V with 0 mismatches
Associated chain_W chain W to chain V with 0 mismatches
Associated chain_W chain V to chain V with 0 mismatches
Associated chain_W chain W to chain V with 0 mismatches
Associated chain_W chain V to chain V with 0 mismatches
Associated chain_W chain W to chain V with 0 mismatches
Associated chain_W chain V to chain V with 0 mismatches
Associated chain_W chain W to chain V with 0 mismatches
Associated chain_W chain V to chain V with 0 mismatches
Associated chain_W chain W to chain V with 0 mismatches
Associated chain_W chain V to chain V with 0 mismatches
Associated chain_W chain W to chain V with 0 mismatches
Associated chain_W chain V to chain V with 0 mismatches
Associated chain_W chain W to chain V with 0 mismatches
Associated chain_W chain V to chain V with 0 mismatches
Associated chain_W chain W to chain W with 0 mismatches
Associated chain_W chain V to chain W with 0 mismatches
Associated chain_W chain W to chain W with 0 mismatches
Associated chain_W chain V to chain W with 0 mismatches
Associated chain_W chain W to chain W with 0 mismatches
Associated chain_W chain V to chain W with 0 mismatches
Associated chain_W chain W to chain W with 0 mismatches
Associated chain_W chain V to chain W with 0 mismatches
Associated chain_W chain W to chain W with 0 mismatches
Associated chain_W chain V to chain W with 0 mismatches
Associated chain_W chain W to chain W with 0 mismatches
Associated chain_W chain V to chain W with 0 mismatches
Associated chain_W chain W to chain W with 0 mismatches
Associated chain_W chain V to chain W with 0 mismatches
Associated chain_W chain W to chain W with 0 mismatches
Associated chain_W chain V to chain W with 0 mismatches
Associated chain_W chain W to chain W with 0 mismatches
Associated chain_W chain V to chain W with 0 mismatches
Associated chain_W chain W to chain W with 0 mismatches
Associated chain_W chain V to chain W with 0 mismatches
Chain information for chain_W
---
Chain | Description
4.1/V 4.2/V 4.3/V 4.4/V 4.5/V 4.6/V 4.7/V 4.8/V 4.9/V 4.10/V | No description available
4.1/W 4.2/W 4.3/W 4.4/W 4.5/W 4.6/W 4.7/W 4.8/W 4.9/W 4.10/W | No description available
> show #!2 models
> hide #!2 models
> hide #4.3 models
> hide #4.7 models
> hide #4.6 models
> hide #4.5 models
> hide #3.8 models
> hide #4.8 models
> hide #3.1 models
> open 4edx fromDatabase pdb format mmcif
Summary of feedback from opening 4edx fetched from pdb
---
note | Fetching compressed mmCIF 4edx from http://files.rcsb.org/download/4edx.cif
4edx title:
Nerve Growth Factor in Complex with Fab from mouse mAb 911 [more info...]
Chain information for 4edx #5
---
Chain | Description | UniProt
A L | light chain of FAB of murine anti-NGF |
B H | heavy chain of Fab of murine anti-NGF |
V W | Beta-nerve growth factor | NGF_HUMAN 1-120
> preset cartoons/nucleotides ribbons/slabs
Using preset: Cartoons/Nucleotides / Ribbons/Slabs
Changed 8200 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
~worm
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
nucleotides tube/slab shape box
> close #5
> open 5jz7 fromDatabase pdbe_bio format mmcif
Summary of feedback from opening 5jz7 fetched from pdbe_bio
---
warnings | Missing or incomplete sequence information. Inferred polymer connectivity.
Missing or incomplete sequence information. Inferred polymer connectivity.
notes | Fetching compressed 5jz7 bioassembly 1 from https://www.ebi.ac.uk/pdbe/static/entry/download/5jz7-assembly-1.cif.gz
Fetching compressed 5jz7 bioassembly 2 from
https://www.ebi.ac.uk/pdbe/static/entry/download/5jz7-assembly-2.cif.gz
5jz7 bioassembly 1 title:
NGF IN COMPLEX WITH MEDI578 scFv [more info...]
Chain information for 5jz7 bioassembly 1 #5.1
---
Chain | Description
A B | Beta-nerve growth factor
C H | MEDI578 scFv, heavy chain
D L | MEDI578 scFv, light chain
5jz7 bioassembly 1 mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
5jz7 bioassembly 2 title:
NGF IN COMPLEX WITH MEDI578 scFv [more info...]
Chain information for 5jz7 bioassembly 2 #5.2
---
Chain | Description
E F | Beta-nerve growth factor
G J | MEDI578 scFv, heavy chain
I K | MEDI578 scFv, light chain
5jz7 bioassembly 2 mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
Opened 2 biological assemblies for 5jz7
> preset cartoons/nucleotides ribbons/slabs
Using preset: Cartoons/Nucleotides / Ribbons/Slabs
Changed 10556 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
~worm
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
nucleotides tube/slab shape box
> hide #5.2 models
> show #5.2 models
> hide #5.1 models
> hide #!1 models
> hide #1.1 models
> hide #!3 models
> hide #3.2 models
> hide #!4 models
> show #5.1 models
> hide #5.1 models
> show #5.1 models
> hide #5.2 models
> hide #!5 models
> show #5.2 models
> ui tool show Matchmaker
> matchmaker #5.2 to #5.1
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 5jz7 bioassembly 1, chain C (#5.1) with 5jz7 bioassembly 2, chain G
(#5.2), sequence alignment score = 655.3
RMSD between 128 pruned atom pairs is 0.097 angstroms; (across all 128 pairs:
0.097)
> matchmaker #5.2 to #5.1
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 5jz7 bioassembly 1, chain C (#5.1) with 5jz7 bioassembly 2, chain G
(#5.2), sequence alignment score = 655.3
RMSD between 128 pruned atom pairs is 0.097 angstroms; (across all 128 pairs:
0.097)
> hide #5.2 models
> ui tool show "Show Sequence Viewer"
> sequence chain #5.1/A
Alignment identifier is 5.1/A
> sequence chain #5.1/B
Alignment identifier is 5.1/B
> close #3-4
> ui tool show Matchmaker
> matchmaker #5.1 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 1www_hNGF_prepared.pdb, chain W (#1) with 5jz7 bioassembly 1, chain
B (#5.1), sequence alignment score = 570.8
RMSD between 95 pruned atom pairs is 0.778 angstroms; (across all 104 pairs:
2.381)
> matchmaker #5.1 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 1www_hNGF_prepared.pdb, chain W (#1) with 5jz7 bioassembly 1, chain
B (#5.1), sequence alignment score = 570.8
RMSD between 95 pruned atom pairs is 0.778 angstroms; (across all 104 pairs:
2.381)
> show #!1 models
> close #5.2
> ui tool show "Model Loops"
> modeller refine 1/W:1:internal-missing 1/V:1:internal-missing numModels 10
> fast false adjacentFlexible 1 protocol DOPE
Webservices job id: 7V2XH8IUSJTY5ND7
> select clear
> ui tool show "Show Sequence Viewer"
> sequence chain #5.1/C
Alignment identifier is 5.1/C
> sequence chain #5.1/D
Alignment identifier is 5.1/D
> sequence chain #5.1/H
Alignment identifier is 5.1/H
> sequence chain #5.1/L
Alignment identifier is 5.1/L
> select chain D
Expected an objects specifier or a keyword
> select medi578
Expected an objects specifier or a keyword
> select
> #5.1/H:3-6,10-12,18-25,34-39,45-52,56-59,67-72,77-82,88-93,97-99,107-111
461 atoms, 458 bonds, 59 residues, 1 model selected
> select #5.1/L:1
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #5.1/L:1-97
738 atoms, 756 bonds, 100 residues, 1 model selected
> delete
Missing or invalid "atoms" argument: empty atom specifier
Modeller job (ID 7V2XH8IUSJTY5ND7) finished
Parameters
---
Chain pairing | ss
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 1www_hNGF_prepared.pdb, chain V (#1) with chain_V, chain V (#),
sequence alignment score = 606.1
Matchmaker 1www_hNGF_prepared.pdb, chain W (#1) with chain_V, chain W (#),
sequence alignment score = 600.5
RMSD between 217 pruned atom pairs is 0.065 angstroms; (across all 217 pairs:
0.065)
Parameters
---
Chain pairing | ss
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 1www_hNGF_prepared.pdb, chain V (#1) with chain_V, chain V (#),
sequence alignment score = 606.1
Matchmaker 1www_hNGF_prepared.pdb, chain W (#1) with chain_V, chain W (#),
sequence alignment score = 600.5
RMSD between 217 pruned atom pairs is 0.100 angstroms; (across all 217 pairs:
0.100)
Parameters
---
Chain pairing | ss
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 1www_hNGF_prepared.pdb, chain V (#1) with chain_V, chain V (#),
sequence alignment score = 606.1
Matchmaker 1www_hNGF_prepared.pdb, chain W (#1) with chain_V, chain W (#),
sequence alignment score = 600.5
RMSD between 217 pruned atom pairs is 0.094 angstroms; (across all 217 pairs:
0.094)
Parameters
---
Chain pairing | ss
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 1www_hNGF_prepared.pdb, chain V (#1) with chain_V, chain V (#),
sequence alignment score = 606.1
Matchmaker 1www_hNGF_prepared.pdb, chain W (#1) with chain_V, chain W (#),
sequence alignment score = 600.5
RMSD between 217 pruned atom pairs is 0.060 angstroms; (across all 217 pairs:
0.060)
Parameters
---
Chain pairing | ss
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 1www_hNGF_prepared.pdb, chain V (#1) with chain_V, chain V (#),
sequence alignment score = 606.1
Matchmaker 1www_hNGF_prepared.pdb, chain W (#1) with chain_V, chain W (#),
sequence alignment score = 600.5
RMSD between 217 pruned atom pairs is 0.087 angstroms; (across all 217 pairs:
0.087)
Parameters
---
Chain pairing | ss
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 1www_hNGF_prepared.pdb, chain V (#1) with chain_V, chain V (#),
sequence alignment score = 606.1
Matchmaker 1www_hNGF_prepared.pdb, chain W (#1) with chain_V, chain W (#),
sequence alignment score = 600.5
RMSD between 217 pruned atom pairs is 0.067 angstroms; (across all 217 pairs:
0.067)
Parameters
---
Chain pairing | ss
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 1www_hNGF_prepared.pdb, chain V (#1) with chain_V, chain V (#),
sequence alignment score = 606.1
Matchmaker 1www_hNGF_prepared.pdb, chain W (#1) with chain_V, chain W (#),
sequence alignment score = 600.5
RMSD between 217 pruned atom pairs is 0.080 angstroms; (across all 217 pairs:
0.080)
Parameters
---
Chain pairing | ss
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 1www_hNGF_prepared.pdb, chain V (#1) with chain_V, chain V (#),
sequence alignment score = 606.1
Matchmaker 1www_hNGF_prepared.pdb, chain W (#1) with chain_V, chain W (#),
sequence alignment score = 600.5
RMSD between 217 pruned atom pairs is 0.106 angstroms; (across all 217 pairs:
0.106)
Parameters
---
Chain pairing | ss
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 1www_hNGF_prepared.pdb, chain V (#1) with chain_V, chain V (#),
sequence alignment score = 606.1
Matchmaker 1www_hNGF_prepared.pdb, chain W (#1) with chain_V, chain W (#),
sequence alignment score = 600.5
RMSD between 217 pruned atom pairs is 0.061 angstroms; (across all 217 pairs:
0.061)
Parameters
---
Chain pairing | ss
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 1www_hNGF_prepared.pdb, chain V (#1) with chain_V, chain V (#),
sequence alignment score = 606.1
Matchmaker 1www_hNGF_prepared.pdb, chain W (#1) with chain_V, chain W (#),
sequence alignment score = 600.5
RMSD between 217 pruned atom pairs is 0.087 angstroms; (across all 217 pairs:
0.087)
Associated chain_V chain W to chain W with 0 mismatches
Associated chain_V chain V to chain W with 0 mismatches
Associated chain_V chain W to chain W with 0 mismatches
Associated chain_V chain V to chain W with 0 mismatches
Associated chain_V chain W to chain W with 0 mismatches
Associated chain_V chain V to chain W with 0 mismatches
Associated chain_V chain W to chain W with 0 mismatches
Associated chain_V chain V to chain W with 0 mismatches
Associated chain_V chain W to chain W with 0 mismatches
Associated chain_V chain V to chain W with 0 mismatches
Associated chain_V chain W to chain W with 0 mismatches
Associated chain_V chain V to chain W with 0 mismatches
Associated chain_V chain W to chain W with 0 mismatches
Associated chain_V chain V to chain W with 0 mismatches
Associated chain_V chain W to chain W with 0 mismatches
Associated chain_V chain V to chain W with 0 mismatches
Associated chain_V chain W to chain W with 0 mismatches
Associated chain_V chain V to chain W with 0 mismatches
Associated chain_V chain W to chain W with 0 mismatches
Associated chain_V chain V to chain W with 0 mismatches
Associated chain_V chain W to chain V with 0 mismatches
Associated chain_V chain V to chain V with 0 mismatches
Associated chain_V chain W to chain V with 0 mismatches
Associated chain_V chain V to chain V with 0 mismatches
Associated chain_V chain W to chain V with 0 mismatches
Associated chain_V chain V to chain V with 0 mismatches
Associated chain_V chain W to chain V with 0 mismatches
Associated chain_V chain V to chain V with 0 mismatches
Associated chain_V chain W to chain V with 0 mismatches
Associated chain_V chain V to chain V with 0 mismatches
Associated chain_V chain W to chain V with 0 mismatches
Associated chain_V chain V to chain V with 0 mismatches
Associated chain_V chain W to chain V with 0 mismatches
Associated chain_V chain V to chain V with 0 mismatches
Associated chain_V chain W to chain V with 0 mismatches
Associated chain_V chain V to chain V with 0 mismatches
Associated chain_V chain W to chain V with 0 mismatches
Associated chain_V chain V to chain V with 0 mismatches
Associated chain_V chain W to chain V with 0 mismatches
Associated chain_V chain V to chain V with 0 mismatches
Chain information for chain_V
---
Chain | Description
3.1/V 3.2/V 3.3/V 3.4/V 3.5/V 3.6/V 3.7/V 3.8/V 3.9/V 3.10/V | No description available
3.1/W 3.2/W 3.3/W 3.4/W 3.5/W 3.6/W 3.7/W 3.8/W 3.9/W 3.10/W | No description available
> ui tool show Shell
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/qtconsole/base_frontend_mixin.py", line 138, in _dispatch
handler(msg)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/qtconsole/jupyter_widget.py", line 190, in _handle_execute_reply
self._show_interpreter_prompt(number)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/qtconsole/jupyter_widget.py", line 384, in _show_interpreter_prompt
self._show_prompt(self._make_in_prompt(number), html=True)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/qtconsole/console_widget.py", line 2489, in _show_prompt
cursor = self._get_end_cursor()
^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/qtconsole/console_widget.py", line 1691, in _get_end_cursor
cursor = self._control.textCursor()
^^^^^^^^^^^^^^^^^^^^^^^^^^
RuntimeError: wrapped C/C++ object of type QTextEdit has been deleted
RuntimeError: wrapped C/C++ object of type QTextEdit has been deleted
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/qtconsole/console_widget.py", line 1691, in _get_end_cursor
cursor = self._control.textCursor()
^^^^^^^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
> select #5.1/C#5.1/H
1928 atoms, 1966 bonds, 256 residues, 1 model selected
> delete
Missing or invalid "atoms" argument: empty atom specifier
> delete
Missing or invalid "atoms" argument: empty atom specifier
> delete #5.1/C#5.1/H
> select #5.1/D#5.1/L
1614 atoms, 1652 bonds, 220 residues, 1 model selected
> delete #5.1/D#5.1/L
> ui mousemode right zoom
> hide #3.9 models
> hide #3.8 models
> hide #3.7 models
> show #3.7 models
> hide #3.10 models
> hide #3.3 models
> hide #3.7 models
> hide #3.6 models
> hide #3.1 models
> hide #3.5 models
> hide #3.4 models
> show #3.4 models
> hide #3.4 models
> ui tool show "Modeller Comparative"
> ui tool show "Model Loops"
> close #3
> select clear
> show #1.1 models
> ui tool show "Modeller Comparative"
> modeller comparative 1/V:1 1/W:1 numModels 5 fast false multichain true
> hetPreserve false hydrogens false waterPreserve false
Webservices job id: MB9OO9NFC3B5017B
> ui tool show "Modeller Comparative"
Modeller job (ID MB9OO9NFC3B5017B) finished
Parameters
---
Chain pairing | ss
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 1www_hNGF_prepared.pdb, chain V (#1) with target, chain V (#),
sequence alignment score = 607.5
Matchmaker 1www_hNGF_prepared.pdb, chain W (#1) with target, chain W (#),
sequence alignment score = 603.9
RMSD between 213 pruned atom pairs is 0.318 angstroms; (across all 217 pairs:
0.608)
Parameters
---
Chain pairing | ss
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 1www_hNGF_prepared.pdb, chain V (#1) with target, chain V (#),
sequence alignment score = 607.5
Matchmaker 1www_hNGF_prepared.pdb, chain W (#1) with target, chain W (#),
sequence alignment score = 603.9
RMSD between 215 pruned atom pairs is 0.308 angstroms; (across all 217 pairs:
0.708)
Parameters
---
Chain pairing | ss
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 1www_hNGF_prepared.pdb, chain V (#1) with target, chain V (#),
sequence alignment score = 607.5
Matchmaker 1www_hNGF_prepared.pdb, chain W (#1) with target, chain W (#),
sequence alignment score = 603.9
RMSD between 215 pruned atom pairs is 0.369 angstroms; (across all 217 pairs:
0.620)
Parameters
---
Chain pairing | ss
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 1www_hNGF_prepared.pdb, chain V (#1) with target, chain V (#),
sequence alignment score = 607.5
Matchmaker 1www_hNGF_prepared.pdb, chain W (#1) with target, chain W (#),
sequence alignment score = 603.9
RMSD between 214 pruned atom pairs is 0.363 angstroms; (across all 217 pairs:
0.645)
Parameters
---
Chain pairing | ss
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 1www_hNGF_prepared.pdb, chain V (#1) with target, chain V (#),
sequence alignment score = 607.5
Matchmaker 1www_hNGF_prepared.pdb, chain W (#1) with target, chain W (#),
sequence alignment score = 603.9
RMSD between 214 pruned atom pairs is 0.331 angstroms; (across all 217 pairs:
0.585)
Associated target chain V to chain V with 0 mismatches
Associated target chain W to chain V with 0 mismatches
Associated target chain V to chain V with 0 mismatches
Associated target chain W to chain V with 0 mismatches
Associated target chain V to chain V with 0 mismatches
Associated target chain W to chain V with 0 mismatches
Associated target chain V to chain V with 0 mismatches
Associated target chain W to chain V with 0 mismatches
Associated target chain V to chain V with 0 mismatches
Associated target chain W to chain V with 0 mismatches
Associated target chain V to chain W with 0 mismatches
Associated target chain W to chain W with 0 mismatches
Associated target chain V to chain W with 0 mismatches
Associated target chain W to chain W with 0 mismatches
Associated target chain V to chain W with 0 mismatches
Associated target chain W to chain W with 0 mismatches
Associated target chain V to chain W with 0 mismatches
Associated target chain W to chain W with 0 mismatches
Associated target chain V to chain W with 0 mismatches
Associated target chain W to chain W with 0 mismatches
Chain information for target
---
Chain | Description
3.1/V 3.2/V 3.3/V 3.4/V 3.5/V 3.1/W 3.2/W 3.3/W 3.4/W 3.5/W | No description available
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #3.1 models
> show #3.1 models
> hide #3.1 models
> hide #3.2 models
> hide #3.3 models
> hide #3.5 models
> hide #!5 models
> show #!5 models
===== Log before crash end =====
Log:
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/olgabednova/Desktop/!LDI/NGF/PDB/1WWW_hNGF.pdb
Summary of feedback from opening
/Users/olgabednova/Desktop/!LDI/NGF/PDB/1WWW_hNGF.pdb
---
warnings | Start residue of secondary structure not found: HELIX 3 3 HIS X 353 ASN X 355 1 3
Start residue of secondary structure not found: HELIX 4 4 HIS Y 353 ASN Y 355
1 3
Start residue of secondary structure not found: SHEET 17 17 1 SER X 287 LEU X
290 0
Start residue of secondary structure not found: SHEET 18 18 1 TRP X 299 ASP X
306 0
Start residue of secondary structure not found: SHEET 19 19 1 SER X 312 PHE X
317 0
11 messages similar to the above omitted
Cannot find LINK/SSBOND residue CYS (300 )
Cannot find LINK/SSBOND residue CYS (300 )
Chain information for 1WWW_hNGF.pdb #1
---
Chain | Description
V W | No description available
OpenGL version: 4.1 INTEL-20.7.3
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 640
OpenGL vendor: Intel Inc.
Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro14,1
Processor Name: Dual-Core Intel Core i5
Processor Speed: 2.3 GHz
Number of Processors: 1
Total Number of Cores: 2
L2 Cache (per Core): 256 KB
L3 Cache: 4 MB
Hyper-Threading Technology: Enabled
Memory: 8 GB
System Firmware Version: 529.140.2.0.0
OS Loader Version: 577.140.2~30
SMC Version (system): 2.43f11
Software:
System Software Overview:
System Version: macOS 13.7.1 (22H221)
Kernel Version: Darwin 22.6.0
Time since boot: 2 days, 1 hour, 49 minutes
Graphics/Displays:
Intel Iris Plus Graphics 640:
Chipset Model: Intel Iris Plus Graphics 640
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x5926
Revision ID: 0x0006
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2560 x 1600 Retina
Framebuffer Depth: 24-Bit Color (ARGB8888)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
alabaster: 0.7.16
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 2.4.1
Babel: 2.15.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 2.0.0
build: 1.2.1
certifi: 2023.11.17
cftime: 1.6.4
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.17
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.7
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.57.1
ChimeraX-AtomicLibrary: 14.0.6
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.4.6
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.12.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.7
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.6
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.8
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.3
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.4
ChimeraX-DiffPlot: 1.0
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.3
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: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-Label: 1.1.10
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.2
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: 2.1.3
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.1
ChimeraX-MedicalToolbar: 1.0.3
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.17
ChimeraX-ModelPanel: 1.5
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
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.5
ChimeraX-PDB: 2.7.5
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: 1.1.1
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.4.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.2
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.0.15
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.11.2
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.16.5
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
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.39.1
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.3
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: 1.1.4
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.2.1
cxservices: 1.2.2
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.1
decorator: 5.1.1
docutils: 0.20.1
executing: 2.0.1
filelock: 3.13.4
fonttools: 4.53.0
funcparserlib: 2.0.0a0
glfw: 2.7.0
grako: 3.16.5
h5py: 3.11.0
html2text: 2024.2.26
idna: 3.7
ihm: 1.0
imagecodecs: 2024.1.1
imagesize: 1.4.1
ipykernel: 6.29.2
ipython: 8.21.0
ipywidgets: 8.1.3
jedi: 0.19.1
jinja2: 3.1.4
jupyter-client: 8.6.0
jupyter-core: 5.7.2
jupyterlab-widgets: 3.0.11
kiwisolver: 1.4.5
line-profiler: 4.1.2
lxml: 5.2.1
lz4: 4.3.3
MarkupSafe: 2.1.5
matplotlib: 3.8.4
matplotlib-inline: 0.1.7
msgpack: 1.0.8
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.0
numpy: 1.26.4
openvr: 1.26.701
packaging: 23.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pillow: 10.3.0
pip: 24.0
pkginfo: 1.10.0
platformdirs: 4.2.2
prompt-toolkit: 3.0.47
psutil: 5.9.8
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pygments: 2.17.2
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.1.2
pyproject-hooks: 1.1.0
PyQt6-commercial: 6.6.1
PyQt6-Qt6: 6.6.3
PyQt6-sip: 13.6.0
PyQt6-WebEngine-commercial: 6.6.0
PyQt6-WebEngine-Qt6: 6.6.3
python-dateutil: 2.9.0.post0
pytz: 2024.1
pyzmq: 26.0.3
qtconsole: 5.5.1
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.13.0
setuptools: 69.5.1
setuptools-scm: 8.0.4
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 7.2.6
sphinx-autodoc-typehints: 2.0.1
sphinxcontrib-applehelp: 1.0.8
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.6
sphinxcontrib-htmlhelp: 2.0.5
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.7
sphinxcontrib-serializinghtml: 1.1.10
stack-data: 0.6.3
superqt: 0.6.3
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2024.1.30
tinyarray: 1.2.4
tornado: 6.4.1
traitlets: 5.14.2
typing-extensions: 4.12.2
tzdata: 2024.1
urllib3: 2.2.1
wcwidth: 0.2.13
webcolors: 1.13
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.11
Change History (2)
comment:1 by , 7 months ago
| Component: | Unassigned → Window Toolkit |
|---|---|
| Description: | modified (diff) |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Crash closing dock widget |
comment:2 by , 7 months ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | accepted → closed |
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