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Opened 3 months ago
Closed 3 months ago
#18268 closed defect (duplicate)
Crash in garbage collection
| Reported by: | Owned by: | pett | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Core | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Linux-4.18.0-513.18.1.el8_9.x86_64-x86_64-with-glibc2.28
ChimeraX Version: 1.7.1 (2024-01-23 01:58:08 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault
Thread 0x00007f4c4bfff700 (most recent call first):
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/multiprocessing/pool.py", line 579 in _handle_results
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 975 in run
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00007f4c68ff9700 (most recent call first):
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/multiprocessing/pool.py", line 531 in _handle_tasks
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 975 in run
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00007f4c697fa700 (most recent call first):
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/selectors.py", line 415 in select
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/multiprocessing/connection.py", line 930 in wait
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/multiprocessing/pool.py", line 502 in _wait_for_updates
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/multiprocessing/pool.py", line 522 in _handle_workers
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 975 in run
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00007f4c69ffb700 (most recent call first):
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 975 in run
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00007f4c6a7fc700 (most recent call first):
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 975 in run
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00007f4c6affd700 (most recent call first):
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 975 in run
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00007f4c6b7fe700 (most recent call first):
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 975 in run
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00007f4c6bfff700 (most recent call first):
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 975 in run
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00007f4c88ff9700 (most recent call first):
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 975 in run
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00007f4c897fa700 (most recent call first):
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 975 in run
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00007f4c89ffb700 (most recent call first):
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 975 in run
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00007f4c8a7fc700 (most recent call first):
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 975 in run
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00007f4c8affd700 (most recent call first):
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 975 in run
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00007f4c8b7fe700 (most recent call first):
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 975 in run
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00007f4c8bfff700 (most recent call first):
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 975 in run
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00007f4ca8ff9700 (most recent call first):
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 975 in run
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00007f4ca97fa700 (most recent call first):
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 975 in run
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00007f4ca9ffb700 (most recent call first):
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 975 in run
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00007f4caa7fc700 (most recent call first):
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 975 in run
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00007f4caaffd700 (most recent call first):
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 975 in run
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00007f4cab7fe700 (most recent call first):
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 975 in run
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00007f4cabfff700 (most recent call first):
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 975 in run
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00007f4cc8ff9700 (most recent call first):
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 975 in run
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00007f4cc97fa700 (most recent call first):
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 975 in run
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00007f4cc9ffb700 (most recent call first):
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 975 in run
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00007f4cca7fc700 (most recent call first):
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 975 in run
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00007f4ccaffd700 (most recent call first):
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 975 in run
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00007f4ccb7fe700 (most recent call first):
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 975 in run
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00007f4ccbfff700 (most recent call first):
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 975 in run
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00007f4ce8ff9700 (most recent call first):
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 975 in run
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00007f4ce97fa700 (most recent call first):
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 975 in run
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00007f4ce9ffb700 (most recent call first):
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 975 in run
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00007f4cea7fc700 (most recent call first):
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 975 in run
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00007f4ceaffd700 (most recent call first):
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 975 in run
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00007f4ceb7fe700 (most recent call first):
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 975 in run
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00007f4cebfff700 (most recent call first):
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 975 in run
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00007f4d08ff9700 (most recent call first):
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 975 in run
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00007f4d097fa700 (most recent call first):
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 975 in run
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00007f4d09ffb700 (most recent call first):
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 975 in run
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00007f4d0a7fc700 (most recent call first):
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 975 in run
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00007f4d0affd700 (most recent call first):
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 975 in run
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00007f4d0b7fe700 (most recent call first):
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 975 in run
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00007f4d0bfff700 (most recent call first):
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 975 in run
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00007f4d28ff9700 (most recent call first):
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 975 in run
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00007f4d297fa700 (most recent call first):
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 975 in run
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00007f4d29ffb700 (most recent call first):
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 975 in run
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00007f4d2a7fc700 (most recent call first):
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 975 in run
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00007f4d2affd700 (most recent call first):
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 975 in run
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 995 in _bootstrap
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File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 995 in _bootstrap
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File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00007f4d48ff9700 (most recent call first):
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File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 995 in _bootstrap
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File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00007f4d49ffb700 (most recent call first):
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File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 995 in _bootstrap
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File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00007f4d4affd700 (most recent call first):
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File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 995 in _bootstrap
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File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00007f4d4bfff700 (most recent call first):
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File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00007f4d68ff9700 (most recent call first):
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File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00007f4d697fa700 (most recent call first):
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File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00007f4d69ffb700 (most recent call first):
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File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00007f4d6a7fc700 (most recent call first):
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File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00007f4d6affd700 (most recent call first):
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File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00007f4d6b7fe700 (most recent call first):
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File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00007f4d6bfff700 (most recent call first):
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File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00007f4d88ff9700 (most recent call first):
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File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00007f4d897fa700 (most recent call first):
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File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00007f4d89ffb700 (most recent call first):
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File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00007f4d8a7fc700 (most recent call first):
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File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00007f4d8affd700 (most recent call first):
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File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00007f4d8b7fe700 (most recent call first):
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File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00007f4d8bfff700 (most recent call first):
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File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00007f4da8ff9700 (most recent call first):
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File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00007f4da97fa700 (most recent call first):
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File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00007f4da9ffb700 (most recent call first):
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File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00007f4daa7fc700 (most recent call first):
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File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00007f4daaffd700 (most recent call first):
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File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00007f4dab7fe700 (most recent call first):
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File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00007f4dabfff700 (most recent call first):
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File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00007f4dc8ff9700 (most recent call first):
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File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 995 in _bootstrap
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File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 995 in _bootstrap
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File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00007f4dca7fc700 (most recent call first):
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File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 995 in _bootstrap
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File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 995 in _bootstrap
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File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 995 in _bootstrap
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File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00007f4de8ff9700 (most recent call first):
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File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 995 in _bootstrap
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File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 995 in _bootstrap
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File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 995 in _bootstrap
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File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 995 in _bootstrap
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File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 995 in _bootstrap
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File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 995 in _bootstrap
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File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00007f4e14ff9700 (most recent call first):
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File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 995 in _bootstrap
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File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00007f4e15ffb700 (most recent call first):
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File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00007f4e167fc700 (most recent call first):
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File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00007f4e16ffd700 (most recent call first):
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File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00007f4e177fe700 (most recent call first):
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 975 in run
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00007f4e17fff700 (most recent call first):
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 975 in run
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 995 in _bootstrap
Current thread 0x00007f4eeff3b740 (most recent call first):
Garbage-collecting
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/functools.py", line 76 in wraps
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/scipy/_lib/deprecation.py", line 16 in wrap
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/scipy/__init__.py", line 71 in
File "", line 241 in _call_with_frames_removed
File "", line 940 in exec_module
File "", line 690 in _load_unlocked
File "", line 1149 in _find_and_load_unlocked
File "", line 1178 in _find_and_load
File "/home/spuser/.local/share/ChimeraX/1.7/lib/python3.11/site-packages/chimerax/isolde/manipulations/register_shift.py", line 15 in
File "", line 241 in _call_with_frames_removed
File "", line 940 in exec_module
File "", line 690 in _load_unlocked
File "", line 1149 in _find_and_load_unlocked
File "", line 1178 in _find_and_load
File "/home/spuser/.local/share/ChimeraX/1.7/lib/python3.11/site-packages/chimerax/isolde/manipulations/__init__.py", line 12 in
File "", line 241 in _call_with_frames_removed
File "", line 940 in exec_module
File "", line 690 in _load_unlocked
File "", line 1149 in _find_and_load_unlocked
File "", line 1178 in _find_and_load
File "", line 241 in _call_with_frames_removed
File "", line 1128 in _find_and_load_unlocked
File "", line 1178 in _find_and_load
File "/home/spuser/.local/share/ChimeraX/1.7/lib/python3.11/site-packages/chimerax/isolde/cmd/cmd.py", line 478 in register_isolde
File "/home/spuser/.local/share/ChimeraX/1.7/lib/python3.11/site-packages/chimerax/isolde/__init__.py", line 170 in register_command
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/chimerax/core/toolshed/__init__.py", line 1286 in register_command
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/chimerax/core/toolshed/info.py", line 330 in _register_cmd
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/chimerax/core/toolshed/info.py", line 320 in cb
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 2158 in call
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 2227 in lazy_register
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 2579 in _find_command_name
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 2843 in run
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/chimerax/core/commands/run.py", line 49 in run
File "/home/spuser/.local/share/ChimeraX/1.7/lib/python3.11/site-packages/chimerax/isolde/toolbar.py", line 19 in toolbar_command
File "/home/spuser/.local/share/ChimeraX/1.7/lib/python3.11/site-packages/chimerax/isolde/__init__.py", line 183 in run_provider
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/chimerax/core/toolshed/__init__.py", line 1302 in run_provider
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/chimerax/core/toolshed/info.py", line 397 in run_provider
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/chimerax/toolbar/tool.py", line 205 in callback
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/chimerax/ui/gui.py", line 275 in event_loop
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/chimerax/core/__main__.py", line 918 in init
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1069 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
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.QtWebChannel, PyQt6.QtNetwork, PyQt6.QtWebEngineCore, PyQt6.QtPrintSupport, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, openmm._openmm, openmm.app.internal.compiled, chimerax.surface._surface, chimerax.pdb_lib._load_libs, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, PIL._imagingmath, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw (total: 57)
===== Log before crash start =====
Startup Messages
---
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle
You can double click a model's Name or ID in the model panel to edit those
fields
UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /data-old/cryotransTest/TmrAB_0_3A.mrc
Opened TmrAB_0_3A.mrc as #1, grid size 160,160,160, pixel 1, shown at level
0.743, step 1, values float32
> open /data-old/cryotransTest/output/frame_10.mrc /data-
> old/cryotransTest/output/frame_09.mrc /data-
> old/cryotransTest/output/frame_08.mrc /data-
> old/cryotransTest/output/frame_07.mrc /data-
> old/cryotransTest/output/frame_06.mrc /data-
> old/cryotransTest/output/frame_05.mrc /data-
> old/cryotransTest/output/frame_04.mrc /data-
> old/cryotransTest/output/frame_03.mrc /data-
> old/cryotransTest/output/frame_02.mrc /data-
> old/cryotransTest/output/frame_01.mrc /data-
> old/cryotransTest/output/frame_00.mrc
Opened frame_10.mrc as #2.1, grid size 160,160,160, pixel 1, shown at level
0.679, step 1, values float32
Opened frame_09.mrc as #2.2, grid size 160,160,160, pixel 1, shown at level
0.684, step 1, values float32
Opened frame_08.mrc as #2.3, grid size 160,160,160, pixel 1, shown at level
0.692, step 1, values float32
Opened frame_07.mrc as #2.4, grid size 160,160,160, pixel 1, shown at level
0.683, step 1, values float32
Opened frame_06.mrc as #2.5, grid size 160,160,160, pixel 1, shown at level
0.681, step 1, values float32
Opened frame_05.mrc as #2.6, grid size 160,160,160, pixel 1, shown at level
0.688, step 1, values float32
Opened frame_04.mrc as #2.7, grid size 160,160,160, pixel 1, shown at level
0.7, step 1, values float32
Opened frame_03.mrc as #2.8, grid size 160,160,160, pixel 1, shown at level
0.692, step 1, values float32
Opened frame_02.mrc as #2.9, grid size 160,160,160, pixel 1, shown at level
0.693, step 1, values float32
Opened frame_01.mrc as #2.10, grid size 160,160,160, pixel 1, shown at level
0.707, step 1, values float32
Opened frame_00.mrc as #2.11, grid size 160,160,160, pixel 1, shown at level
0.743, step 1, values float32
> hide #!1 models
> hide #!2.1 models
> hide #!2.2 models
> hide #!2.3 models
> hide #!2.4 models
> hide #!2.5 models
> hide #!2.6 models
> hide #!2.7 models
> hide #!2.9 models
> hide #!2.8 models
> hide #!2.10 models
> open /data-old/cryotransTest/TmrAB_1_7A.mrc
Opened TmrAB_1_7A.mrc as #3, grid size 160,160,160, pixel 1, shown at level
0.452, step 1, values float32
> open /data-old/cryotransTest/TmrAB_1_5A.mrc /data-
> old/cryotransTest/TmrAB_1_3A.mrc
Opened TmrAB_1_5A.mrc as #4.1, grid size 160,160,160, pixel 1, shown at level
0.511, step 1, values float32
Opened TmrAB_1_3A.mrc as #4.2, grid size 160,160,160, pixel 1, shown at level
0.747, step 1, values float32
> hide #!3 models
> hide #!4.1 models
> hide #!2 models
> hide #!4.2 models
> show #!4.1 models
> clear
Unknown command: clear
> close
> open /data-old/cryotransTest/output/frame_01.mrc /data-
> old/cryotransTest/output/frame_00.mrc
Opened frame_01.mrc as #1.1, grid size 384,384,384, pixel 0.842, shown at
level 0.0793, step 2, values float32
Opened frame_00.mrc as #1.2, grid size 384,384,384, pixel 0.842, shown at
level 0.0825, step 2, values float32
> volume #1.1 step 1
> volume #1.2 step 1
> volume #1.1 level 0.4941
> volume #1.2 level 0.3782
> volume #1.2 level 0.6272
> surface dust #1.1 size 8.42
> open /data-old/cryotransTest/output/net.pt
Unrecognized file suffix '.pt'
> open /data-old/cryotransTest/output/net_400.pt
Unrecognized file suffix '.pt'
> open /data-old/cryotransTest/cryosparc_P2_J520_006_volume_map_sharp.mrc
Opened cryosparc_P2_J520_006_volume_map_sharp.mrc as #2, grid size
384,384,384, pixel 0.842, shown at level 0.083, step 2, values float32
> volume #2 step 1
> volume #2 level 0.4667
> volume #1.1 level 0.5
> volume #1.2 level 0.5
> volume #2 level 0.5
> surface dust #2 size 8.42
> surface dust #1.2 size 8.42
> close #2
> close #1.2
> close #1.1
> open /data-old/cryotransTest/J520EMready.mrc
Opened J520EMready.mrc as #2, grid size 645,645,645, pixel 0.5, shown at level
-0.0742, step 4, values float32
> volume #2 step 1
> volume #2 level 0.4908
> volume #2 level 0.7598
> surface dust #2 size 5
> volume #2 level 2.213
> open /data-old/5B10-PT/last_frame_rsr-3.pdb
Chain information for last_frame_rsr-3.pdb #3
---
Chain | Description
A | No description available
B | No description available
C | No description available
> fitmap #3 inMap #2
Fit molecule last_frame_rsr-3.pdb (#3) to map J520EMready.mrc (#2) using 4502
atoms
average map value = 2.144, steps = 44
shifted from previous position = 0.0992
rotated from previous position = 0.254 degrees
atoms outside contour = 2969, contour level = 2.2127
Position of last_frame_rsr-3.pdb (#3) relative to J520EMready.mrc (#2)
coordinates:
Matrix rotation and translation
0.99999414 -0.00323442 -0.00112466 0.77057805
0.00323758 0.99999078 0.00281950 -1.00140034
0.00111553 -0.00282313 0.99999539 0.35949089
Axis -0.63587382 -0.25245024 0.72933762
Axis point 308.04582207 242.60001400 0.00000000
Rotation angle (degrees) 0.25421686
Shift along axis 0.02500358
> volume #2 level 4.688
> show target ab
> volume #2 level 0.5446
> volume #2 level 2.589
> volume #2 level 4.096
> hide target a
> volume #2 level 2.32
> open /data-old/5B10-PT/oPT.pdb
Chain information for oPT.pdb #4
---
Chain | Description
A | No description available
> ui tool show "Model Panel"
> select add #4
4414 atoms, 4520 bonds, 1 pseudobond, 550 residues, 2 models selected
> ui mousemode right "translate selected models"
> view matrix models #4,1,0,0,1.9304,0,1,0,-4.7511,0,0,1,-6.8528
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.99996,-0.0080428,-0.0033828,2.0455,0.0080433,0.99997,0.00013628,-4.4911,0.0033816,-0.00016349,0.99999,-6.7413
> select subtract #4
Nothing selected
> select add #4
4414 atoms, 4520 bonds, 1 pseudobond, 550 residues, 2 models selected
> view matrix models
> #4,0.99954,-0.024375,-0.01798,2.4206,0.024119,0.99961,-0.014367,-3.6775,0.018323,0.013926,0.99974,-6.3351
> view matrix models
> #4,0.99899,-0.035373,-0.027576,2.66,0.03471,0.99911,-0.024163,-3.1351,0.028406,0.023181,0.99933,-6.0548
> view matrix models
> #4,0.99821,-0.0179,0.057141,0.85265,0.020685,0.99861,-0.048525,-3.1084,-0.056193,0.04962,0.99719,-8.9365
> view matrix models
> #4,0.98291,0.064043,0.17258,-2.4316,-0.06256,0.99794,-0.014025,-6.5034,-0.17312,0.0029892,0.9849,-12.224
> view matrix models
> #4,0.94212,0.0010622,0.33526,-6.5908,0.061156,0.98267,-0.17497,0.80941,-0.32964,0.18535,0.92574,-17.285
> view matrix models
> #4,0.80981,-0.041396,0.58523,-15.589,0.31398,0.87322,-0.3727,13.643,-0.4956,0.48557,0.72014,-20.485
> view matrix models
> #4,0.45559,0.20038,0.86734,-34.213,0.63648,0.60787,-0.47476,27.818,-0.62236,0.76834,0.1494,-15.082
> view matrix models
> #4,0.37254,0.25825,0.89136,-37.754,0.70843,0.54129,-0.45291,30.144,-0.59945,0.80019,0.018699,-11.947
> view matrix models
> #4,0.33142,0.28913,0.89809,-39.419,0.74239,0.50753,-0.43735,31.153,-0.58226,0.81167,-0.046444,-10.169
> view matrix models
> #4,0.32643,0.2939,0.89837,-39.617,0.74595,0.50362,-0.4358,31.262,-0.58052,0.8124,-0.054845,-9.9504
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.32643,0.2939,0.89837,-39.481,0.74595,0.50362,-0.4358,31.122,-0.58052,0.8124,-0.054845,-9.7958
> view matrix models
> #4,0.32643,0.2939,0.89837,-44.687,0.74595,0.50362,-0.4358,27.025,-0.58052,0.8124,-0.054845,-12.131
> view matrix models
> #4,0.32643,0.2939,0.89837,-44.384,0.74595,0.50362,-0.4358,26.785,-0.58052,0.8124,-0.054845,-8.8298
> view matrix models
> #4,0.32643,0.2939,0.89837,59.642,0.74595,0.50362,-0.4358,187.1,-0.58052,0.8124,-0.054845,144.44
> view matrix models
> #4,0.32643,0.2939,0.89837,101.1,0.74595,0.50362,-0.4358,170.37,-0.58052,0.8124,-0.054845,128.87
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.25772,0.3139,0.91381,98.432,0.78743,0.47985,-0.38691,170.9,-0.55994,0.81927,-0.12351,130.86
> view matrix models
> #4,0.081022,0.47836,0.87442,92.432,0.94972,0.22915,-0.21336,174.31,-0.30244,0.84774,-0.43574,145.26
> view matrix models
> #4,0.025097,0.57212,0.81979,91.11,0.99108,0.093134,-0.095338,174.17,-0.13089,0.81487,-0.56468,153.61
> view matrix models
> #4,0.02164,0.67137,0.74081,91.948,0.99526,-0.084741,0.047725,172.57,0.094818,0.73626,-0.67002,163.54
> view matrix models
> #4,0.028925,0.65198,0.75769,91.971,0.99778,-0.064324,0.01726,173.13,0.05999,0.75551,-0.65239,161.94
> view matrix models
> #4,0.028899,0.65527,0.75484,92.006,0.99731,-0.069827,0.022435,173.04,0.067409,0.75216,-0.65552,162.26
> view matrix models
> #4,0.076415,0.6829,0.72651,93.947,0.97873,-0.1905,0.076119,172.12,0.19038,0.70524,-0.68293,167.11
> view matrix models
> #4,0.69159,0.033744,0.7215,118.12,0.33925,0.8667,-0.36572,153.48,-0.63766,0.49769,0.58795,116.24
> view matrix models
> #4,0.65776,0.049138,0.75162,116.32,0.39365,0.82832,-0.39864,156.14,-0.64218,0.55809,0.5255,116.95
> mopmap #4 3
Unknown command: mopmap #4 3
> molmap #4 3
Opened oPT.pdb map 3 as #5, grid size 90,121,69, pixel 1, shown at level
0.111, step 1, values float32
> hide #!2 models
> hide #3 models
> volume #5 level 0.4629
> volume #5 level 0.2224
> molmap #4 4
Opened oPT.pdb map 4 as #5, grid size 72,95,57, pixel 1.33, shown at level
0.102, step 1, values float32
> volume #5 level 0.4162
> volume #5 level 0.2191
> volume #5 level 0.3219
> molmap #4 3
Opened oPT.pdb map 3 as #5, grid size 90,121,69, pixel 1, shown at level
0.111, step 1, values float32
> volume #5 level 0.5978
> volume #5 level 0.328
> fitmap #4 inMap #5
Fit molecule oPT.pdb (#4) to map oPT.pdb map 3 (#5) using 4414 atoms
average map value = 1.217, steps = 40
shifted from previous position = 0.0103
rotated from previous position = 0.00906 degrees
atoms outside contour = 0, contour level = 0.32797
Position of oPT.pdb (#4) relative to oPT.pdb map 3 (#5) coordinates:
Matrix rotation and translation
0.99999999 -0.00009703 0.00012437 -0.00752869
0.00009703 1.00000000 0.00001214 -0.00410795
-0.00012438 -0.00001212 0.99999999 0.00154398
Axis -0.07666672 0.78613898 0.61327622
Axis point 20.81879759 0.00000000 61.58590513
Rotation angle (degrees) 0.00906474
Shift along axis -0.00170534
> select add #5
4414 atoms, 4520 bonds, 1 pseudobond, 550 residues, 4 models selected
> fitmap #4 inMap #5
Fit molecule oPT.pdb (#4) to map oPT.pdb map 3 (#5) using 4414 atoms
average map value = 1.217, steps = 44
shifted from previous position = 0.00868
rotated from previous position = 0.00137 degrees
atoms outside contour = 0, contour level = 0.32797
Position of oPT.pdb (#4) relative to oPT.pdb map 3 (#5) coordinates:
Matrix rotation and translation
0.99999999 -0.00007905 0.00012846 -0.00750408
0.00007905 1.00000000 0.00002732 -0.00973471
-0.00012846 -0.00002731 0.99999999 -0.00588941
Axis -0.17819368 0.83802851 0.51570847
Axis point -6.27565982 0.00000000 72.09059790
Rotation angle (degrees) 0.00878274
Shift along axis -0.00985801
> select subtract #4
2 models selected
> select subtract #5
Nothing selected
> volume #5 level 0.369
> volume #5 level 0.1403
> volume #5 level 0.2693
> molmap #4 2
Opened oPT.pdb map 2 as #5, grid size 126,172,95, pixel 0.667, shown at level
0.192, step 1, values float32
> volume #5 level 0.7861
> hide #!4 models
> volume #5 level 0.05946
> molmap #4 2.5
Opened oPT.pdb map 2.5 as #5, grid size 105,141,80, pixel 0.833, shown at
level 0.136, step 1, values float32
> volume #5 level 0.462
> close #5
> show #!4 models
> ui tool show "Show Sequence Viewer"
> sequence chain #4/A
Alignment identifier is 4/A
> select #4/A:568
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #4/A:241-568
2514 atoms, 2577 bonds, 1 pseudobond, 310 residues, 2 models selected
> color (#!4 & sel) orange red
> select #4/A:568
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #4/A:181-568
2977 atoms, 3051 bonds, 1 pseudobond, 370 residues, 2 models selected
> select #4/A:180
14 atoms, 15 bonds, 1 residue, 1 model selected
> select #4/A:171-180
76 atoms, 79 bonds, 10 residues, 1 model selected
> select #4/A:568
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #4/A:151-568
3208 atoms, 3288 bonds, 1 pseudobond, 400 residues, 2 models selected
> color (#!4 & sel) orange red
> cartoon hide (#!4 & sel)
> molmap #4 5
Opened oPT.pdb map 5 as #5, grid size 62,80,49, pixel 1.67, shown at level
0.101, step 1, values float32
> volume #5 level 0.299
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!2 models
> view matrix models
> #4,0.28886,-0.30593,0.90717,118.66,0.72221,0.69167,0.0032926,159.45,-0.62847,0.65422,0.42074,115.87
> view matrix models
> #4,0.95241,-0.0084885,0.30471,131.25,0.29215,-0.25993,-0.92037,199.09,0.087017,0.96559,-0.24508,130.04
> view matrix models
> #4,0.95751,0.00080164,0.28841,131.32,0.28818,-0.042797,-0.95662,192.54,0.011576,0.99908,-0.041209,124.04
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.95751,0.00080164,0.28841,133.49,0.28818,-0.042797,-0.95662,192.23,0.011576,0.99908,-0.041209,123.11
> view matrix models
> #4,0.95751,0.00080164,0.28841,139.91,0.28818,-0.042797,-0.95662,191.03,0.011576,0.99908,-0.041209,118.74
> view matrix models
> #4,0.95751,0.00080164,0.28841,164.98,0.28818,-0.042797,-0.95662,187.17,0.011576,0.99908,-0.041209,106.06
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.95843,0.0034808,0.28532,164.96,0.28526,-0.035158,-0.95781,186.88,0.006697,0.99938,-0.034689,105.85
> view matrix models
> #4,0.95658,0.019044,0.29084,164.32,0.29104,-0.0083802,-0.95667,186.09,-0.015782,0.99978,-0.013559,105.07
> view matrix models
> #4,0.92898,0.10208,0.35577,159.97,0.34226,0.12897,-0.93071,182.05,-0.14089,0.98638,0.084872,101.56
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.92676,0.12917,0.35275,159.1,0.32706,0.18447,-0.92682,179.89,-0.18479,0.97431,0.12871,100.41
> view matrix models
> #4,0.14107,0.18922,0.97175,132.33,-0.98677,0.10605,0.1226,140.74,-0.079858,-0.97619,0.20168,164.93
> view matrix models
> #4,-0.08576,0.97119,0.22234,115.74,0.68855,0.21906,-0.69131,181.09,-0.7201,0.093803,-0.6875,133.97
> view matrix models
> #4,-0.89414,-0.37872,-0.23891,153.63,-0.13653,0.73872,-0.66004,148.81,0.42646,-0.55755,-0.71222,176.18
> fitmap #4 inMap #2
Fit molecule oPT.pdb (#4) to map J520EMready.mrc (#2) using 4414 atoms
average map value = 0.422, steps = 328
shifted from previous position = 4.97
rotated from previous position = 11.4 degrees
atoms outside contour = 4100, contour level = 2.3203
Position of oPT.pdb (#4) relative to J520EMready.mrc (#2) coordinates:
Matrix rotation and translation
-0.96252184 -0.24712194 -0.11172490 148.30734612
-0.12327757 0.76560864 -0.63138422 147.47745989
0.24156644 -0.59394793 -0.76737963 175.70258505
Axis 0.09950210 -0.93901476 0.32916655
Axis point 71.99215428 0.00000000 121.52604387
Rotation angle (degrees) 169.15702112
Shift along axis -65.89120451
> ui mousemode right "rotate selected models"
> view matrix models
> #4,-0.65334,-0.71681,0.24356,163.01,-0.70219,0.69402,0.15893,125.71,-0.28296,-0.067193,-0.95677,152.4
> view matrix models
> #4,-0.71196,-0.63933,0.29047,158.6,-0.63219,0.76362,0.13122,125.16,-0.3057,-0.09021,-0.94784,152.59
> view matrix models
> #4,-0.79688,-0.48919,0.35451,151.05,-0.50302,0.86225,0.059136,125.49,-0.33461,-0.1312,-0.93318,153.17
> view matrix models
> #4,-0.66163,-0.71451,0.22743,163.07,-0.71615,0.69202,0.090714,126.72,-0.2222,-0.10285,-0.96956,154.88
> view matrix models
> #4,-0.27542,-0.86465,0.42014,171.5,-0.42424,0.50151,0.754,126.59,-0.86265,0.029425,-0.50495,131.02
> view matrix models
> #4,-0.28439,-0.80658,0.51822,167.73,-0.38604,0.59112,0.7082,125.13,-0.87755,0.0013493,-0.47948,131.23
> view matrix models
> #4,-0.29348,-0.74662,0.59702,164.23,-0.36044,0.66485,0.65426,124.11,-0.88541,-0.023182,-0.46423,131.63
> view matrix models
> #4,-0.38868,-0.42985,0.81496,148.34,-0.36275,0.88446,0.2935,123.17,-0.84696,-0.18155,-0.4997,138.12
> view matrix models
> #4,-0.51068,-0.27509,0.81458,141.11,-0.467,0.88424,0.0058348,126.34,-0.72188,-0.37743,-0.58003,148.17
> view matrix models
> #4,-0.70655,-0.64709,0.28648,159.02,-0.52172,0.2028,-0.82866,162.27,0.47812,-0.73495,-0.48089,179.54
> view matrix models
> #4,-0.72914,-0.50265,0.46443,150.78,-0.58547,0.80955,-0.043014,127.53,-0.35436,-0.30328,-0.88456,157.6
> view matrix models
> #4,-0.77466,-0.48743,0.40287,150.55,-0.59498,0.77762,-0.20322,131.21,-0.21423,-0.39713,-0.89241,163.31
> ui mousemode right "translate selected models"
> view matrix models
> #4,-0.77466,-0.48743,0.40287,144.44,-0.59498,0.77762,-0.20322,136.47,-0.21423,-0.39713,-0.89241,149.93
> fitmap #4 inMap #2
Fit molecule oPT.pdb (#4) to map J520EMready.mrc (#2) using 4414 atoms
average map value = 0.7471, steps = 460
shifted from previous position = 16.9
rotated from previous position = 37.8 degrees
atoms outside contour = 3934, contour level = 2.3203
Position of oPT.pdb (#4) relative to J520EMready.mrc (#2) coordinates:
Matrix rotation and translation
-0.70345958 0.01035174 0.71065987 127.96923742
-0.52090935 0.67273751 -0.52543094 149.80376422
-0.48352668 -0.73980880 -0.46785133 139.68560748
Axis -0.16185673 0.90161888 -0.40110570
Axis point 111.66863195 0.00000000 74.31620731
Rotation angle (degrees) 138.52862740
Shift along axis 58.32452613
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> view matrix models
> #4,-0.70346,0.010352,0.71066,164.75,-0.52091,0.67274,-0.52543,128.13,-0.48353,-0.73981,-0.46785,149.26
> view matrix models
> #4,-0.70346,0.010352,0.71066,164.99,-0.52091,0.67274,-0.52543,127.92,-0.48353,-0.73981,-0.46785,148.89
> view matrix models
> #4,-0.70346,0.010352,0.71066,164.78,-0.52091,0.67274,-0.52543,127.97,-0.48353,-0.73981,-0.46785,148.34
> ui mousemode right "rotate selected models"
> view matrix models
> #4,-0.7642,-0.0018922,0.64498,165.24,-0.52631,0.57986,-0.6219,132.6,-0.37282,-0.81471,-0.44412,152.35
> view matrix models
> #4,-0.54376,-0.80874,0.2242,202.96,-0.83877,0.51479,-0.17735,121.41,0.028017,-0.28449,-0.95827,151.09
> view matrix models
> #4,-0.12745,-0.99107,0.039167,219.58,-0.99152,0.12631,-0.030446,128.85,0.025227,-0.042716,-0.99877,143.83
> view matrix models
> #4,0.73107,-0.62731,0.26837,218.95,0.6694,0.58329,-0.46008,150.97,0.13207,0.516,0.84634,95.218
> view matrix models
> #4,0.70552,-0.68401,0.18539,221.8,0.68993,0.60312,-0.40031,149.64,0.162,0.41033,0.89743,98.322
> view matrix models
> #4,0.62929,-0.77606,-0.041495,227.42,0.74612,0.61822,-0.24719,147.48,0.21749,0.1246,0.96808,107.44
> view matrix models
> #4,0.7342,-0.67892,0.0038974,225.32,0.67555,0.72996,-0.10387,140.06,0.067676,0.078896,0.99458,105.81
> view matrix models
> #4,0.90902,-0.14766,-0.38971,217.89,0.055095,0.9695,-0.23883,123.51,0.41308,0.19563,0.88943,109.97
> view matrix models
> #4,0.6674,0.27556,-0.69184,204.99,-0.51322,0.84336,-0.15919,116.12,0.5396,0.46131,0.70429,106.75
> view matrix models
> #4,0.80658,-0.5762,-0.13195,225.61,-0.35166,-0.28832,-0.89062,168.86,0.47514,0.76476,-0.43518,115.55
> view matrix models
> #4,0.86634,-0.058403,0.49603,198.75,0.47846,-0.18786,-0.85778,179.78,0.14328,0.98046,-0.13481,97.322
> view matrix models
> #4,0.85126,-0.064451,0.52078,198.24,0.49787,-0.21439,-0.84034,180.69,0.16581,0.97462,-0.15041,98.187
> view matrix models
> #4,0.65499,0.32055,0.68428,179.28,0.67529,0.15804,-0.72042,169.55,-0.33907,0.93396,-0.11295,89.871
> view matrix models
> #4,0.70349,0.30352,0.64263,181.43,0.64325,0.11256,-0.75734,171.12,-0.3022,0.94615,-0.11605,90.182
> view matrix models
> #4,0.92683,0.16728,0.33616,195.22,0.37018,-0.25714,-0.89266,180.73,-0.062888,0.95178,-0.30025,97.477
> view matrix models
> #4,0.91994,-0.043438,-0.38964,214.67,-0.38549,-0.28134,-0.87877,167.82,-0.07145,0.95862,-0.27556,96.669
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.91994,-0.043438,-0.38964,236.32,-0.38549,-0.28134,-0.87877,196.54,-0.07145,0.95862,-0.27556,110.19
> view matrix models
> #4,0.91994,-0.043438,-0.38964,235.11,-0.38549,-0.28134,-0.87877,197.46,-0.07145,0.95862,-0.27556,110.09
> view matrix models
> #4,0.91994,-0.043438,-0.38964,220.55,-0.38549,-0.28134,-0.87877,208.23,-0.07145,0.95862,-0.27556,113.65
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.95961,-0.15347,-0.23579,222.18,-0.25661,-0.13389,-0.9572,207.06,0.11533,0.97904,-0.16787,114.43
> view matrix models
> #4,0.55144,-0.20448,-0.80877,226.58,-0.4301,0.76102,-0.48566,166.42,0.7148,0.61566,0.33171,128.3
> view matrix models
> #4,0.53717,-0.17743,-0.8246,225.71,-0.45625,0.76114,-0.46099,165.52,0.70943,0.62385,0.32791,128
> view matrix models
> #4,0.61203,0.13756,-0.77878,215.92,-0.70203,0.5479,-0.45493,168.02,0.36411,0.82516,0.4319,113.43
> view matrix models
> #4,0.42942,-0.088286,-0.89878,222.17,-0.72622,0.55784,-0.40177,166.33,0.53685,0.82524,0.17543,120.98
> view matrix models
> #4,-0.12264,-0.62181,-0.77351,227.63,-0.98262,-0.033368,0.18262,170.94,-0.13937,0.78246,-0.60691,123.99
> view matrix models
> #4,0.31864,-0.36669,0.87408,198.37,0.52973,0.83359,0.15659,169.93,-0.78604,0.41312,0.45986,105.96
> view matrix models
> #4,0.52875,-0.42203,0.73642,206.33,0.32794,0.90183,0.28136,161.92,-0.78287,0.092732,0.61524,113.8
> view matrix models
> #4,0.54336,-0.4239,0.72462,206.86,0.31399,0.90312,0.29288,161.43,-0.77857,0.068377,0.62382,114.52
> view matrix models
> #4,0.97547,0.21759,0.033294,205.6,-0.085133,0.23345,0.96864,164.47,0.20299,-0.94771,0.24625,171.9
> view matrix models
> #4,0.91312,0.35688,0.19711,197.07,-0.25657,0.12727,0.95811,165.08,0.31684,-0.92544,0.20778,173.87
> view matrix models
> #4,0.45289,0.4218,0.78548,176.47,-0.87252,0.028558,0.48774,165.55,0.1833,-0.90624,0.38096,167.84
> view matrix models
> #4,-0.48803,0.76811,0.41451,154.83,-0.42015,-0.62301,0.6598,191.96,0.76505,0.14785,0.62677,139.37
> view matrix models
> #4,0.20759,0.93503,-0.28746,174.01,-0.56813,0.35446,0.74269,155.84,0.79633,0.0091369,0.6048,144.86
> view matrix models
> #4,-0.84892,0.52694,-0.04092,164.25,-0.28059,-0.38372,0.87979,182.76,0.44789,0.75835,0.4736,116.39
> view matrix models
> #4,-0.87891,0.47161,0.071379,163.57,-0.18467,-0.47443,0.86071,187.78,0.43978,0.74331,0.50407,116.2
> view matrix models
> #4,-0.97315,-0.05002,0.22468,176.31,0.17402,-0.79877,0.57592,209.77,0.15066,0.59956,0.78602,110.84
> view matrix models
> #4,0.64043,0.76168,-0.098476,184.1,-0.47994,0.49701,0.72294,153.08,0.59959,-0.41573,0.68386,153.9
> view matrix models
> #4,-0.99158,0.096456,0.086444,173.6,-0.099021,-0.13431,-0.98598,210.39,-0.083493,-0.98623,0.14273,169.87
> view matrix models
> #4,-0.90448,0.17253,-0.39007,180.97,0.37801,-0.099341,-0.92045,216.6,-0.19755,-0.97998,0.024634,169.69
> view matrix models
> #4,-0.90275,0.19694,-0.38244,180.07,0.36441,-0.12231,-0.92317,217.16,-0.22859,-0.97276,0.038646,168.66
> view matrix models
> #4,-0.037789,0.21326,-0.97626,205.31,0.97598,-0.20191,-0.081883,215.98,-0.21458,-0.95591,-0.20051,172.53
> view matrix models
> #4,-0.036547,0.21929,-0.97497,205.11,0.97466,-0.20765,-0.08324,216.16,-0.22071,-0.95331,-0.20614,172.43
> view matrix models
> #4,-0.0064896,0.27093,-0.96258,203.74,0.96206,-0.26087,-0.079912,217.63,-0.27276,-0.92658,-0.25896,171.55
> view matrix models
> #4,0.62578,0.37489,-0.684,206.74,0.57626,-0.81319,0.081514,226.03,-0.52566,-0.44517,-0.72491,159.4
> view matrix models
> #4,0.65624,0.063281,-0.7519,218.68,0.55723,-0.71254,0.42637,216.38,-0.50877,-0.69877,-0.50285,164.14
> view matrix models
> #4,0.92637,-0.31127,-0.21202,226.34,-0.14276,-0.81118,0.5671,204.68,-0.34851,-0.49508,-0.79589,165.43
> view matrix models
> #4,0.82901,-0.37455,-0.41529,230.23,0.012159,-0.73034,0.68297,202.77,-0.55911,-0.57124,-0.60091,160.77
> view matrix models
> #4,0.89727,-0.062287,-0.43706,221.59,0.12956,-0.90925,0.39557,215.74,-0.42204,-0.41156,-0.80778,161.59
> view matrix models
> #4,0.9324,-0.27545,-0.234,225.66,-0.13538,-0.86647,0.48052,208.14,-0.33512,-0.41636,-0.84519,163.95
> view matrix models
> #4,0.93214,-0.28151,-0.22774,225.74,-0.14298,-0.86399,0.48278,207.88,-0.33268,-0.41745,-0.84561,164.04
> view matrix models
> #4,-0.051977,-0.63961,0.76694,202.58,-0.97451,0.20031,0.10101,164.85,-0.21823,-0.74215,-0.63372,173.02
> view matrix models
> #4,0.17311,-0.76837,0.61615,213.44,-0.6928,0.34966,0.63069,155.73,-0.70004,-0.53605,-0.47179,154.85
> view matrix models
> #4,0.83762,-0.52481,-0.15154,230.7,-0.32363,-0.70027,0.63631,196.62,-0.44006,-0.48395,-0.7564,162.75
> view matrix models
> #4,0.8391,-0.52027,-0.15884,230.71,-0.31684,-0.70479,0.63473,196.91,-0.44218,-0.48227,-0.75624,162.65
> view matrix models
> #4,-0.92799,0.15669,0.33806,168.36,-0.3107,0.17541,-0.93418,195.56,-0.20568,-0.97195,-0.1141,171.7
> view matrix models
> #4,-0.92002,0.17294,0.35164,167.74,-0.32829,0.14984,-0.93262,196.06,-0.21397,-0.97347,-0.081082,171.03
> view matrix models
> #4,-0.83368,0.22947,0.50231,164.79,-0.42732,0.30812,-0.84997,187.67,-0.34982,-0.92326,-0.15882,168.32
> view matrix models
> #4,-0.77664,-0.32949,0.5369,183.52,-0.38135,0.9243,0.015598,153.19,-0.5014,-0.19263,-0.8435,153.63
> view matrix models
> #4,-0.76314,-0.2951,0.57492,181.97,-0.35085,0.93631,0.014889,153.35,-0.5427,-0.19035,-0.81807,152.37
> view matrix models
> #4,-0.7675,-0.29375,0.56979,181.94,-0.35166,0.93609,0.0089139,153.44,-0.53599,-0.19353,-0.82174,152.66
> view matrix models
> #4,-0.84736,-0.051427,0.52853,173.3,-0.21137,0.94572,-0.24686,160.09,-0.48714,-0.3209,-0.81223,157.54
> view matrix models
> #4,-0.8679,-0.12573,0.48057,176.2,-0.26869,0.93252,-0.24129,159.41,-0.4178,-0.33854,-0.84311,159.89
> view matrix models
> #4,-0.86827,-0.11717,0.48206,175.89,-0.26231,0.93319,-0.24565,159.57,-0.42107,-0.33974,-0.841,159.84
> view matrix models
> #4,-0.95679,0.20586,0.20535,168.56,0.038715,0.79013,-0.61172,176.02,-0.28818,-0.57734,-0.76396,168.65
> view matrix models
> #4,-0.95089,0.022738,0.30869,172.86,-0.13919,0.85935,-0.49207,168.49,-0.27646,-0.51087,-0.81399,167.55
> view matrix models
> #4,-0.94672,0.023935,0.32117,172.68,-0.15381,0.84254,-0.5162,169.2,-0.28295,-0.5381,-0.79397,167.98
> view matrix models
> #4,-0.92574,0.060294,0.37332,170.95,-0.21045,0.73806,-0.64107,173.79,-0.31418,-0.67203,-0.67057,169.66
> view matrix models
> #4,-0.93744,0.08465,0.3377,170.56,-0.15651,0.764,-0.62595,173.64,-0.31099,-0.63964,-0.70295,169.22
> view matrix models
> #4,-0.91647,0.016515,0.39977,172.09,-0.25577,0.74417,-0.61709,172.37,-0.30769,-0.66779,-0.67778,169.76
> ui mousemode right "translate selected models"
> view matrix models
> #4,-0.91647,0.016515,0.39977,158,-0.25577,0.74417,-0.61709,166.52,-0.30769,-0.66779,-0.67778,165.94
> view matrix models
> #4,-0.91647,0.016515,0.39977,127.77,-0.25577,0.74417,-0.61709,153.86,-0.30769,-0.66779,-0.67778,156.57
> view matrix models
> #4,-0.91647,0.016515,0.39977,127.77,-0.25577,0.74417,-0.61709,153.99,-0.30769,-0.66779,-0.67778,157.11
> view matrix models
> #4,-0.91647,0.016515,0.39977,132.52,-0.25577,0.74417,-0.61709,145.06,-0.30769,-0.66779,-0.67778,154.99
> fitmap #4 inMap #2
Fit molecule oPT.pdb (#4) to map J520EMready.mrc (#2) using 4414 atoms
average map value = 0.5728, steps = 180
shifted from previous position = 5.84
rotated from previous position = 7.34 degrees
atoms outside contour = 4022, contour level = 2.3203
Position of oPT.pdb (#4) relative to J520EMready.mrc (#2) coordinates:
Matrix rotation and translation
-0.90338760 -0.01838387 0.42843071 129.78958982
-0.33305783 0.65940132 -0.67398989 148.60258244
-0.27011724 -0.75156632 -0.60181787 154.19153746
Axis -0.10073951 0.90712325 -0.40863060
Axis point 92.81238970 0.00000000 95.58858383
Rotation angle (degrees) 157.35410205
Shift along axis 58.71853696
> ui mousemode right "rotate selected models"
> view matrix models
> #4,-0.90553,-0.02229,0.4237,129.96,-0.33031,0.66379,-0.67102,148.46,-0.26629,-0.74758,-0.60845,154.24
> view matrix models
> #4,-0.86361,0.051265,0.50156,126.94,-0.38165,0.58356,-0.7168,150.97,-0.32943,-0.81045,-0.4844,153.01
> view matrix models
> #4,-0.86619,0.046883,0.49751,127.11,-0.37861,0.58821,-0.71461,150.83,-0.32614,-0.80735,-0.49175,153.1
> view matrix models
> #4,-0.8698,0.04073,0.49172,127.35,-0.37434,0.59476,-0.71143,150.64,-0.32143,-0.80287,-0.50207,153.22
> view matrix models
> #4,-0.82692,0.11193,0.55107,124.74,-0.42354,0.52065,-0.74131,152.71,-0.36989,-0.8464,-0.38312,151.7
> view matrix models
> #4,-0.97878,-0.20394,0.020065,141.66,-0.19692,0.9089,-0.3676,137.5,0.056731,-0.36375,-0.92977,153.03
> view matrix models
> #4,-0.97864,-0.19452,0.066548,140.54,-0.20463,0.89051,-0.40634,138.65,0.019781,-0.41128,-0.91129,153.61
> view matrix models
> #4,-0.9653,-0.21751,0.14453,140.17,-0.25386,0.91137,-0.32398,135.65,-0.061251,-0.34943,-0.93496,150.55
> view matrix models
> #4,-0.96595,-0.25723,0.027834,143.49,-0.24196,0.86001,-0.44925,139.73,0.091623,-0.44069,-0.89297,155.53
> view matrix models
> #4,-0.85973,-0.24682,-0.44715,153.34,-0.26879,0.96309,-0.014804,128.29,0.4343,0.10746,-0.89434,143.7
> view matrix models
> #4,-0.8411,-0.19073,-0.50614,152.86,-0.18526,0.98075,-0.061706,130.02,0.50817,0.041869,-0.86024,146.57
> view matrix models
> #4,-0.82025,-0.15527,-0.55052,152.84,-0.12344,0.98782,-0.094678,131.46,0.55852,-0.009702,-0.82943,148.62
> view matrix models
> #4,-0.85536,-0.16624,-0.49063,151.53,-0.1723,0.98449,-0.033173,129.63,0.48853,0.056162,-0.87074,145.93
> view matrix models
> #4,-0.92226,-0.36512,-0.12699,150.51,-0.38558,0.84521,0.37006,123.35,-0.027784,0.39026,-0.92029,126.65
> view matrix models
> #4,-0.87795,-0.47263,0.076286,151.27,-0.34066,0.7287,0.59409,124.06,-0.33637,0.4956,-0.80077,115.61
> view matrix models
> #4,-0.92983,-0.087673,0.35739,132.83,0.046832,0.93511,0.35124,128.44,-0.36499,0.34333,-0.86539,121.22
> view matrix models
> #4,-0.94143,-0.067971,0.33028,132.45,0.041474,0.9487,0.31345,128.56,-0.33464,0.30879,-0.89031,123.33
> view matrix models
> #4,-0.96159,-0.03057,0.27277,131.87,0.074398,0.92754,0.36623,128.92,-0.2642,0.37246,-0.88965,122.49
> view matrix models
> #4,-0.97157,-0.0046984,0.23672,131.47,0.093076,0.91173,0.4001,129.18,-0.21771,0.41076,-0.88537,121.98
> view matrix models
> #4,-0.98245,0.037825,0.18266,130.83,0.1181,0.88411,0.45211,129.62,-0.14439,0.46575,-0.87306,121.27
> view matrix models
> #4,-0.9798,-0.031041,0.19754,132.87,0.076932,0.85333,0.51566,128.79,-0.18458,0.52045,-0.83371,118.08
> view matrix models
> #4,-0.77456,-0.17074,-0.60902,155.19,-0.1385,0.98529,-0.10009,131.37,0.61715,0.0068231,-0.78681,148.38
> view matrix models
> #4,-0.89285,-0.18978,-0.4084,150.2,-0.065472,0.95193,-0.29923,137.24,0.44556,-0.24043,-0.86236,154.74
> view matrix models
> #4,-0.89802,-0.18715,-0.39816,149.84,-0.071264,0.95494,-0.28811,136.85,0.43414,-0.23036,-0.87089,154.36
> view matrix models
> #4,-0.92606,-0.37114,-0.068282,149.62,-0.37362,0.92717,0.027556,126.86,0.053081,0.05103,-0.99729,140.55
> view matrix models
> #4,-0.92724,-0.27543,0.25369,140.84,-0.23695,0.95617,0.17205,125.82,-0.28996,0.099426,-0.95186,132.06
> view matrix models
> #4,-0.92546,-0.28357,0.25123,141.18,-0.2447,0.95367,0.17502,125.71,-0.28922,0.1005,-0.95197,132.04
> ui mousemode right "translate selected models"
> view matrix models
> #4,-0.92546,-0.28357,0.25123,138.23,-0.2447,0.95367,0.17502,130.13,-0.28922,0.1005,-0.95197,140.42
> view matrix models
> #4,-0.92546,-0.28357,0.25123,138.12,-0.2447,0.95367,0.17502,130.14,-0.28922,0.1005,-0.95197,139.96
> fitmap #4 inMap #2
Fit molecule oPT.pdb (#4) to map J520EMready.mrc (#2) using 4414 atoms
average map value = 0.3692, steps = 280
shifted from previous position = 7.47
rotated from previous position = 4.76 degrees
atoms outside contour = 4124, contour level = 2.3203
Position of oPT.pdb (#4) relative to J520EMready.mrc (#2) coordinates:
Matrix rotation and translation
-0.93152775 -0.28358863 0.22766979 141.19128042
-0.26754708 0.95843035 0.09914540 128.46483843
-0.24632215 0.03144430 -0.96867779 148.01350010
Axis -0.14131743 0.98939788 0.03348468
Axis point 88.63044300 0.00000000 62.18794053
Rotation angle (degrees) 166.14086971
Shift along axis 112.10623521
> view matrix models
> #4,-0.93153,-0.28359,0.22767,138.52,-0.26755,0.95843,0.099145,128.67,-0.24632,0.031444,-0.96868,143.48
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.073838,-0.36447,-0.92828,179.26,0.59107,-0.73372,0.3351,195.3,-0.80324,-0.57342,0.16125,133.66
> view matrix models
> #4,0.046904,-0.48114,-0.87539,181.68,0.40482,-0.79201,0.457,191.76,-0.91319,-0.37581,0.15763,125.29
> view matrix models
> #4,-0.22157,0.23138,-0.9473,154.8,0.83616,0.54492,-0.062474,164.71,0.50174,-0.80593,-0.31421,172.83
> view matrix models
> #4,-0.20339,0.21518,-0.95516,155.79,0.86475,0.49699,-0.072177,166.95,0.45917,-0.84065,-0.28716,172.74
> view matrix models
> #4,-0.17229,0.20783,-0.96287,156.72,0.89223,0.44715,-0.063135,168.92,0.41743,-0.86998,-0.26247,172.52
> view matrix models
> #4,0.09988,-0.010713,-0.99494,169.29,0.97834,-0.18114,0.10016,188.19,-0.1813,-0.9834,-0.0076115,161.12
> view matrix models
> #4,0.096569,-0.0033092,-0.99532,169,0.98147,-0.16596,0.095777,187.83,-0.1655,-0.98613,-0.012778,161.59
> view matrix models
> #4,0.24371,-0.095503,-0.96513,174.11,0.91839,-0.29713,0.26131,188.11,-0.31172,-0.95005,0.015294,157.31
> ui tool show "Fit in Map"
> fitmap #4 inMap #2
Fit molecule oPT.pdb (#4) to map J520EMready.mrc (#2) using 4414 atoms
average map value = 0.9812, steps = 232
shifted from previous position = 9.19
rotated from previous position = 5.35 degrees
atoms outside contour = 3801, contour level = 2.3203
Position of oPT.pdb (#4) relative to J520EMready.mrc (#2) coordinates:
Matrix rotation and translation
0.32290981 -0.05151188 -0.94502687 185.17764289
0.90278331 -0.28296877 0.32389962 183.74864857
-0.28409777 -0.95774485 -0.04486933 158.30765045
Axis -0.74117937 -0.38221755 0.55187216
Axis point 0.00000000 131.31594976 94.58529611
Rotation angle (degrees) 120.16316055
Shift along axis -120.11622141
> view matrix models
> #4,0.49872,0.0012553,-0.86676,185.21,0.86608,-0.040435,0.49827,172.1,-0.034422,-0.99918,-0.021253,163.7
> view matrix models
> #4,0.48293,-0.012294,-0.87557,185.53,0.87309,-0.069816,0.48254,173.47,-0.067061,-0.99748,-0.022982,163.09
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.48293,-0.012294,-0.87557,181.32,0.87309,-0.069816,0.48254,176.43,-0.067061,-0.99748,-0.022982,156.51
> view matrix models
> #4,0.48293,-0.012294,-0.87557,183.68,0.87309,-0.069816,0.48254,180.51,-0.067061,-0.99748,-0.022982,157.05
> view matrix models
> #4,0.48293,-0.012294,-0.87557,183.64,0.87309,-0.069816,0.48254,183.53,-0.067061,-0.99748,-0.022982,158.42
> view matrix models
> #4,0.48293,-0.012294,-0.87557,183.64,0.87309,-0.069816,0.48254,183.58,-0.067061,-0.99748,-0.022982,158.41
> view matrix models
> #4,0.48293,-0.012294,-0.87557,183.92,0.87309,-0.069816,0.48254,184.97,-0.067061,-0.99748,-0.022982,158.57
> view matrix models
> #4,0.48293,-0.012294,-0.87557,183.9,0.87309,-0.069816,0.48254,184.91,-0.067061,-0.99748,-0.022982,158.54
> view matrix models
> #4,0.48293,-0.012294,-0.87557,183.77,0.87309,-0.069816,0.48254,184.84,-0.067061,-0.99748,-0.022982,158.47
> view matrix models
> #4,0.48293,-0.012294,-0.87557,180.51,0.87309,-0.069816,0.48254,182.8,-0.067061,-0.99748,-0.022982,157.15
> view matrix models
> #4,0.48293,-0.012294,-0.87557,180.75,0.87309,-0.069816,0.48254,183.05,-0.067061,-0.99748,-0.022982,156.84
> volume #2 level 1.244
> fitmap #4 inMap #2
Fit molecule oPT.pdb (#4) to map J520EMready.mrc (#2) using 4414 atoms
average map value = 0.9889, steps = 168
shifted from previous position = 11.2
rotated from previous position = 10.7 degrees
atoms outside contour = 3338, contour level = 1.244
Position of oPT.pdb (#4) relative to J520EMready.mrc (#2) coordinates:
Matrix rotation and translation
0.41409030 -0.14994664 -0.89780022 188.62781502
0.88231146 -0.17631493 0.43639379 183.39337350
-0.22373137 -0.97284585 0.05928934 155.04601176
Axis -0.75263811 -0.36000258 0.55130211
Axis point 0.00000000 149.01935971 82.50680250
Rotation angle (degrees) 110.57710945
Shift along axis -122.51337783
> view matrix models
> #4,0.41409,-0.14995,-0.8978,188.19,0.88231,-0.17631,0.43639,183.59,-0.22373,-0.97285,0.059289,153.81
> view matrix models
> #4,0.41409,-0.14995,-0.8978,182.41,0.88231,-0.17631,0.43639,183.97,-0.22373,-0.97285,0.059289,127.13
> view matrix models
> #4,0.41409,-0.14995,-0.8978,182.3,0.88231,-0.17631,0.43639,184.04,-0.22373,-0.97285,0.059289,126.92
> show #3 models
> show #!5 models
> hide #!2 models
> hide #3 models
> select add #4
4414 atoms, 4520 bonds, 1 pseudobond, 550 residues, 2 models selected
> select subtract #4
Nothing selected
> hide #!4 models
> volume #5 level 0.4085
> volume #5 level 0.1553
> show #!4 models
> hide #!5 models
> select #4/A:539-568
268 atoms, 276 bonds, 30 residues, 1 model selected
> select #4/A:151-568
3208 atoms, 3288 bonds, 1 pseudobond, 400 residues, 2 models selected
> cartoon (#!4 & sel)
> morph #4
Require at least 2 structures for morph
> open 6C2W
Summary of feedback from opening 6C2W fetched from pdb
---
notes | Fetching compressed mmCIF 6c2w from
http://files.rcsb.org/download/6c2w.cif
Fetching CCD MG from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/G/MG/MG.cif
6c2w title:
Crystal structure of human prothrombin mutant S101C/A470C [more info...]
Chain information for 6c2w #6
---
Chain | Description | UniProt
A B | Prothrombin | THRB_HUMAN 1-579
Non-standard residues in 6c2w #6
---
BMA — beta-D-mannopyranose (beta-D-mannose; D-mannose; mannose)
CGU — γ-carboxy-glutamic acid
MG — magnesium ion
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)
6c2w mmCIF Assemblies
---
1| author_defined_assembly
2| author_defined_assembly
> select add #6
12486 atoms, 12804 bonds, 27 pseudobonds, 1568 residues, 5 models selected
> select add #4
13692 atoms, 14036 bonds, 27 pseudobonds, 1718 residues, 5 models selected
> select subtract #4
9278 atoms, 9516 bonds, 26 pseudobonds, 1168 residues, 3 models selected
> view matrix models #6,1,0,0,4.0036,0,1,0,6.1338,0,0,1,4.9424
> view matrix models #6,1,0,0,-1.8882,0,1,0,-3.4643,0,0,1,-3.9731
> view matrix models #6,1,0,0,150.36,0,1,0,220.27,0,0,1,156.61
> view matrix models #6,1,0,0,150.48,0,1,0,220.47,0,0,1,156.8
> ui tool show "Show Sequence Viewer"
> sequence chain #6/A #6/B
Alignment identifier is 1
> select #6/A-B:552-582
552 atoms, 568 bonds, 62 residues, 1 model selected
> select #6/A-B:1-582
9188 atoms, 9432 bonds, 2 pseudobonds, 1150 residues, 2 models selected
> select #6/A-B:376-406
534 atoms, 538 bonds, 62 residues, 1 model selected
> select #6/A-B:376-406
534 atoms, 538 bonds, 62 residues, 1 model selected
> delete chain B, #6
Missing or invalid "atoms" argument: invalid atoms specifier
> close #6
> show #!5 models
> select add #4
4414 atoms, 4520 bonds, 1 pseudobond, 550 residues, 2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.41807,-0.1451,-0.89675,182.38,0.88331,-0.16555,0.43859,183.97,-0.21209,-0.97547,0.058955,127.32
> view matrix models
> #4,-0.070411,0.86316,-0.49999,152.39,0.021518,0.50243,0.86435,143.31,0.99729,0.050101,-0.05395,162.73
> view matrix models
> #4,-0.024672,0.85735,-0.51415,154.2,0.042985,0.51474,0.85627,144.1,0.99877,-0.00097447,-0.049553,163
> view matrix models
> #4,-0.022015,0.85789,-0.51337,154.27,0.03476,0.51384,0.85718,143.82,0.99915,0.0010261,-0.041133,162.84
> view matrix models
> #4,-0.74859,0.5963,-0.2899,127.74,0.56947,0.80218,0.1795,172.89,0.33959,-0.030714,-0.94007,159.27
> view matrix models
> #4,-0.69488,0.56973,-0.43881,132.6,0.5315,0.81791,0.22029,170.75,0.48441,-0.080149,-0.87116,162.94
> view matrix models
> #4,-0.68446,0.58009,-0.4416,132.93,0.50043,0.81431,0.29405,168.3,0.53017,-0.019726,-0.84766,163.59
> view matrix models
> #4,0.74438,-0.19432,0.63885,162.98,0.59418,0.62933,-0.5009,188.21,-0.30471,0.75245,0.58392,103.3
> view matrix models
> #4,0.70738,-0.12765,0.69522,160.25,0.61646,0.59264,-0.51842,189.51,-0.34583,0.79529,0.49791,103.4
> view matrix models
> #4,0.95559,-0.19214,0.22346,178.07,0.29375,0.68189,-0.66988,181.42,-0.023662,0.70577,0.70804,110.31
> view matrix models
> #4,0.14531,0.59899,-0.78746,166.74,0.20157,0.7613,0.61628,152.5,0.96864,-0.24828,-0.010113,162.76
> view matrix models
> #4,0.14806,0.59914,-0.78683,166.81,0.19341,0.7627,0.61716,152.21,0.96988,-0.24356,-0.002959,162.63
> view matrix models
> #4,0.23725,0.56706,-0.78877,169.96,0.15178,0.78034,0.60666,150.95,0.95952,-0.26365,0.099068,160.4
> view matrix models
> #4,-0.6154,0.56236,-0.55231,137.48,0.53168,0.81345,0.23585,170.47,0.5819,-0.14851,-0.79958,165.12
> view matrix models
> #4,-0.61175,0.55942,-0.5593,137.76,0.53175,0.81427,0.23283,170.53,0.58567,-0.15497,-0.7956,165.21
> ui mousemode right "translate selected models"
> view matrix models
> #4,-0.61175,0.55942,-0.5593,128.98,0.53175,0.81427,0.23283,164.99,0.58567,-0.15497,-0.7956,165.77
> view matrix models
> #4,-0.61175,0.55942,-0.5593,124.19,0.53175,0.81427,0.23283,162.55,0.58567,-0.15497,-0.7956,166.19
> view matrix models
> #4,-0.61175,0.55942,-0.5593,97.308,0.53175,0.81427,0.23283,146.05,0.58567,-0.15497,-0.7956,168
> view matrix models
> #4,-0.61175,0.55942,-0.5593,97.296,0.53175,0.81427,0.23283,145.96,0.58567,-0.15497,-0.7956,167.72
> view matrix models
> #4,-0.61175,0.55942,-0.5593,97.849,0.53175,0.81427,0.23283,146.25,0.58567,-0.15497,-0.7956,167.81
> view matrix models
> #4,-0.61175,0.55942,-0.5593,100.61,0.53175,0.81427,0.23283,153.64,0.58567,-0.15497,-0.7956,186.32
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.87575,0.15152,0.45838,131.56,0.20254,0.74657,-0.63373,160.43,-0.43823,0.64783,0.62312,119.92
> fitmap #4 inMap #5
Fit molecule oPT.pdb (#4) to map oPT.pdb map 5 (#5) using 4414 atoms
average map value = 0.5437, steps = 104
shifted from previous position = 7.2
rotated from previous position = 22.4 degrees
atoms outside contour = 0, contour level = 0.15527
Position of oPT.pdb (#4) relative to oPT.pdb map 5 (#5) coordinates:
Matrix rotation and translation
0.99999993 0.00035634 0.00010411 -0.00293197
-0.00035633 0.99999993 -0.00007620 -0.01890754
-0.00010414 0.00007616 0.99999999 -0.00509083
Axis 0.20102022 0.27475385 -0.94026655
Axis point -52.29410182 7.65517913 -0.00000000
Rotation angle (degrees) 0.02171346
Shift along axis -0.00099757
> volume #5 level 0.3531
> show #!2 models
> select subtract #4
Nothing selected
> select add #2
2 models selected
> view matrix models
> #2,0.87179,0.45973,0.16922,-80.323,-0.43548,0.88548,-0.16212,117.4,-0.22437,0.067645,0.97215,31.002
> view matrix models
> #2,0.9585,0.26474,0.10575,-52.994,-0.2569,0.96293,-0.082233,62.159,-0.1236,0.051654,0.99099,13.728
> view matrix models
> #2,0.69432,0.68442,0.22246,-95.659,-0.6266,0.72696,-0.28087,194.14,-0.35395,0.055622,0.93361,60.803
> view matrix models
> #2,0.3044,0.89769,0.31859,-81.03,-0.4259,-0.1709,0.88848,110.91,0.85203,-0.40614,0.3303,34.559
> view matrix models
> #2,0.30429,0.94154,0.14458,-59.218,-0.3388,-0.034883,0.94021,66.128,0.89029,-0.33508,0.30838,20.47
> view matrix models
> #2,0.15056,0.98492,-0.085205,-2.6118,-0.91457,0.1715,0.36627,223.64,0.37536,0.022779,0.9266,-53.752
> view matrix models
> #2,0.31821,-0.48696,-0.81339,325.7,0.22721,0.87216,-0.43326,54.51,0.92039,-0.046945,0.38817,-43.846
> view matrix models
> #2,0.27822,0.93384,-0.22479,7.5009,-0.85721,0.34699,0.38052,183.68,0.43334,0.086826,0.89704,-68.725
> view matrix models
> #2,0.30959,0.92589,-0.21654,2.2035,-0.87782,0.36583,0.30919,195.89,0.36549,0.094355,0.92602,-63.474
> view matrix models
> #2,-0.34732,0.75361,0.55807,10.475,0.9187,0.39278,0.041353,-62.06,-0.18804,0.52706,-0.82876,249.65
> view matrix models
> #2,-0.28306,0.79764,0.53259,-3.0115,0.94572,0.32456,0.016544,-51.516,-0.15966,0.50837,-0.84621,250.83
> view matrix models
> #2,0.84096,0.53502,-0.080866,-45.849,0.53878,-0.84178,0.033615,199.81,-0.050087,-0.071837,-0.99616,350.33
> view matrix models
> #2,0.83098,0.55389,-0.051778,-52.029,0.55449,-0.81719,0.15729,172.79,0.044806,-0.15941,-0.98619,346.96
> view matrix models
> #2,-0.37794,0.92519,0.034506,74.789,-0.078492,0.0051169,-0.9969,337.3,-0.9225,-0.37948,0.070686,367.62
> view matrix models
> #2,-0.50596,0.82982,-0.23539,155.97,0.22323,-0.13763,-0.965,304.81,-0.83317,-0.54079,-0.11561,409.47
> ui mousemode right "translate selected models"
> view matrix models
> #2,-0.50596,0.82982,-0.23539,156.04,0.22323,-0.13763,-0.965,304.84,-0.83317,-0.54079,-0.11561,409.49
> view matrix models
> #2,-0.50596,0.82982,-0.23539,97.125,0.22323,-0.13763,-0.965,284.93,-0.83317,-0.54079,-0.11561,385.62
> view matrix models
> #2,-0.50596,0.82982,-0.23539,97.136,0.22323,-0.13763,-0.965,284.87,-0.83317,-0.54079,-0.11561,385.59
> view matrix models
> #2,-0.50596,0.82982,-0.23539,88.333,0.22323,-0.13763,-0.965,283.8,-0.83317,-0.54079,-0.11561,392.76
> view matrix models
> #2,-0.50596,0.82982,-0.23539,89.942,0.22323,-0.13763,-0.965,280.2,-0.83317,-0.54079,-0.11561,394.33
> view matrix models
> #2,-0.50596,0.82982,-0.23539,90.416,0.22323,-0.13763,-0.965,281.22,-0.83317,-0.54079,-0.11561,391.91
> view matrix models
> #2,-0.50596,0.82982,-0.23539,90.417,0.22323,-0.13763,-0.965,281.24,-0.83317,-0.54079,-0.11561,391.77
> view matrix models
> #2,-0.50596,0.82982,-0.23539,90.455,0.22323,-0.13763,-0.965,281.3,-0.83317,-0.54079,-0.11561,391.78
> fitmap #2 inMap #5
Fit map J520EMready.mrc in map oPT.pdb map 5 using 215994 points
correlation = 0.6949, correlation about mean = 0.07485, overlap = 1.908e+05
steps = 96, shift = 5.92, angle = 12.3 degrees
Position of J520EMready.mrc (#2) relative to oPT.pdb map 5 (#5) coordinates:
Matrix rotation and translation
0.43273136 0.84490080 -0.31446181 -186.43116058
-0.18617502 -0.25754146 -0.94816206 229.13575447
-0.88208982 0.46884439 0.04585315 76.71666881
Axis 0.76924631 0.30814663 -0.55973723
Axis point 0.00000000 146.76844310 84.62146499
Rotation angle (degrees) 112.92205204
Shift along axis -115.74524859
> fitmap #2 inMap #5
Fit map J520EMready.mrc in map oPT.pdb map 5 using 215994 points
correlation = 0.6949, correlation about mean = 0.07477, overlap = 1.908e+05
steps = 60, shift = 0.0308, angle = 0.0249 degrees
Position of J520EMready.mrc (#2) relative to oPT.pdb map 5 (#5) coordinates:
Matrix rotation and translation
0.43305560 0.84481763 -0.31423882 -186.48686155
-0.18592324 -0.25740619 -0.94824819 229.07179642
-0.88198380 0.46906849 0.04560003 76.68696816
Axis 0.76937828 0.30819552 -0.55952890
Axis point 0.00000000 146.76025654 84.59818430
Rotation angle (degrees) 112.91563275
Shift along axis -115.78861289
> view matrix models
> #2,-0.38731,0.89558,-0.21891,59.861,0.36806,-0.067507,-0.92735,245.16,-0.8453,-0.43974,-0.30348,403.14
> ui mousemode right "rotate selected models"
> view matrix models
> #2,-0.39638,0.90395,-0.16047,50.349,0.2471,-0.063298,-0.96692,271.1,-0.88421,-0.42292,-0.19828,389.48
> view matrix models
> #2,-0.37847,0.91168,-0.15997,46.058,0.24842,-0.066439,-0.96637,271.3,-0.89165,-0.40548,-0.20134,388.43
> view matrix models
> #2,-0.15414,0.9361,-0.31617,30.806,0.20714,-0.28227,-0.9367,307.77,-0.96609,-0.20988,-0.1504,361.04
> ui mousemode right "translate selected models"
> view matrix models
> #2,-0.15414,0.9361,-0.31617,27.212,0.20714,-0.28227,-0.9367,310.46,-0.96609,-0.20988,-0.1504,363.08
> view matrix models
> #2,-0.15414,0.9361,-0.31617,26.906,0.20714,-0.28227,-0.9367,309.26,-0.96609,-0.20988,-0.1504,363.24
> view matrix models
> #2,-0.15414,0.9361,-0.31617,26.312,0.20714,-0.28227,-0.9367,307.18,-0.96609,-0.20988,-0.1504,363.45
> view matrix models
> #2,-0.15414,0.9361,-0.31617,24.906,0.20714,-0.28227,-0.9367,304.5,-0.96609,-0.20988,-0.1504,364.53
> view matrix models
> #2,-0.15414,0.9361,-0.31617,24.958,0.20714,-0.28227,-0.9367,304.79,-0.96609,-0.20988,-0.1504,364.54
> view matrix models
> #2,-0.15414,0.9361,-0.31617,25.045,0.20714,-0.28227,-0.9367,304.9,-0.96609,-0.20988,-0.1504,364.61
> view matrix models
> #2,-0.15414,0.9361,-0.31617,24.692,0.20714,-0.28227,-0.9367,300.73,-0.96609,-0.20988,-0.1504,364.57
> view matrix models
> #2,-0.15414,0.9361,-0.31617,25.218,0.20714,-0.28227,-0.9367,305.12,-0.96609,-0.20988,-0.1504,364.76
> view matrix models
> #2,-0.15414,0.9361,-0.31617,25.356,0.20714,-0.28227,-0.9367,305.28,-0.96609,-0.20988,-0.1504,364.76
> view matrix models
> #2,-0.15414,0.9361,-0.31617,25.342,0.20714,-0.28227,-0.9367,305.11,-0.96609,-0.20988,-0.1504,364.66
> view matrix models
> #2,-0.15414,0.9361,-0.31617,26.408,0.20714,-0.28227,-0.9367,305.98,-0.96609,-0.20988,-0.1504,364.45
> view matrix models
> #2,-0.15414,0.9361,-0.31617,53.162,0.20714,-0.28227,-0.9367,292.61,-0.96609,-0.20988,-0.1504,334.86
> volume #5 level 0.3391
> open /data-old/5B10-PT/k1.pdb
Chain information for k1.pdb #6
---
Chain | Description
? | No description available
> select subtract #2
Nothing selected
> select add #6
616 atoms, 633 bonds, 78 residues, 1 model selected
> view matrix models #6,1,0,0,0.99149,0,1,0,1.5041,0,0,1,1.0837
> view matrix models #6,1,0,0,156.76,0,1,0,166.4,0,0,1,124.98
> color #6 #cc0000ff
> ui mousemode right "rotate selected models"
> view matrix models
> #6,0.88584,-0.40603,0.22455,184.28,-0.058048,0.38318,0.92185,233.36,-0.46034,-0.82965,0.31587,131.69
> view matrix models
> #6,0.88458,-0.40965,0.22294,184.37,-0.05201,0.38838,0.92003,233.04,-0.46348,-0.82544,0.32225,131.79
> view matrix models
> #6,0.73268,-0.071931,-0.67676,130.76,0.68056,0.071193,0.72923,237.29,-0.0042732,-0.99487,0.10112,128.75
> view matrix models
> #6,0.72928,-0.42207,0.53852,198.91,-0.27636,0.5383,0.79615,221.51,-0.62592,-0.72944,0.27593,125.87
> view matrix models
> #6,0.70893,-0.47224,0.52384,200.47,-0.21992,0.55769,0.80038,220.77,-0.67011,-0.68262,0.29151,124.6
> view matrix models
> #6,0.6107,-0.74565,-0.26655,177.95,-0.57489,-0.64898,0.49831,260.27,-0.54456,-0.15108,-0.82501,52.727
> view matrix models
> #6,0.59306,0.081598,-0.80101,118.92,-0.55335,0.76398,-0.33187,162.97,0.58488,0.64005,0.49824,74.534
> view matrix models
> #6,0.5895,0.78147,0.20442,132.55,0.63385,-0.6044,0.48264,255.8,0.50072,-0.15495,-0.85163,50.119
> view matrix models
> #6,0.60014,0.7774,0.18835,132.01,0.71579,-0.62704,0.30735,249,0.35704,-0.049638,-0.93277,42.251
> view matrix models
> #6,0.61936,0.77101,0.1481,130.5,0.78502,-0.60538,-0.13137,228.82,-0.01163,0.19763,-0.98021,30.067
> view matrix models
> #6,0.27261,0.9176,-0.28929,105.62,0.91656,-0.15626,0.3681,231,0.29256,-0.3655,-0.88364,58.141
> ui mousemode right "translate selected models"
> view matrix models
> #6,0.27261,0.9176,-0.28929,62.063,0.91656,-0.15626,0.3681,181.6,0.29256,-0.3655,-0.88364,130.87
> view matrix models
> #6,0.27261,0.9176,-0.28929,62.073,0.91656,-0.15626,0.3681,181.7,0.29256,-0.3655,-0.88364,130.88
> hide #!5 models
> show #!5 models
> ui tool show Matchmaker
> matchmaker #!4 to #6
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 k1.pdb, chain (blank) (#6) with oPT.pdb, chain A (#4), sequence
alignment score = 408.7
RMSD between 78 pruned atom pairs is 0.057 angstroms; (across all 78 pairs:
0.057)
> matchmaker #6 to #4
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 oPT.pdb, chain A (#4) with k1.pdb, chain (blank) (#6), sequence
alignment score = 408.7
RMSD between 78 pruned atom pairs is 0.057 angstroms; (across all 78 pairs:
0.057)
> matchmaker #6 to #4
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 oPT.pdb, chain A (#4) with k1.pdb, chain (blank) (#6), sequence
alignment score = 408.7
RMSD between 78 pruned atom pairs is 0.057 angstroms; (across all 78 pairs:
0.057)
> hide #!5 models
> show #!5 models
> select subtract #6
Nothing selected
> fitmap #4 inMap #5
Fit molecule oPT.pdb (#4) to map oPT.pdb map 5 (#5) using 4414 atoms
average map value = 0.5437, steps = 104
shifted from previous position = 8.05
rotated from previous position = 16.6 degrees
atoms outside contour = 131, contour level = 0.33913
Position of oPT.pdb (#4) relative to oPT.pdb map 5 (#5) coordinates:
Matrix rotation and translation
0.99999997 0.00019458 0.00012690 -0.00986317
-0.00019458 0.99999997 -0.00000146 -0.02636922
-0.00012690 0.00000143 0.99999999 -0.01015472
Axis 0.00621476 0.54624137 -0.83760476
Axis point -118.79119390 50.48178785 0.00000000
Rotation angle (degrees) 0.01331035
Shift along axis -0.00595962
> fitmap #6 inMap #5
Fit molecule k1.pdb (#6) to map oPT.pdb map 5 (#5) using 616 atoms
average map value = 0.5547, steps = 64
shifted from previous position = 3.29
rotated from previous position = 16.4 degrees
atoms outside contour = 13, contour level = 0.33913
Position of k1.pdb (#6) relative to oPT.pdb map 5 (#5) coordinates:
Matrix rotation and translation
0.29803519 0.62077653 0.72512862 -21.87515184
0.93596344 -0.33924355 -0.09426687 33.37417713
0.18747655 0.70678873 -0.68213066 -46.13345664
Axis 0.78926422 0.52973794 0.31054742
Axis point 0.00000000 31.24865652 -11.72728126
Rotation angle (degrees) 149.50455549
Shift along axis -13.91233275
> select add #2
2 models selected
> view matrix models
> #2,-0.15414,0.9361,-0.31617,26.948,0.20714,-0.28227,-0.9367,306.2,-0.96609,-0.20988,-0.1504,352.62
> view matrix models
> #2,-0.15414,0.9361,-0.31617,26.879,0.20714,-0.28227,-0.9367,306.37,-0.96609,-0.20988,-0.1504,352.73
> view matrix models
> #2,-0.15414,0.9361,-0.31617,17.754,0.20714,-0.28227,-0.9367,307.28,-0.96609,-0.20988,-0.1504,359.56
> view matrix models
> #2,-0.15414,0.9361,-0.31617,27.398,0.20714,-0.28227,-0.9367,301.01,-0.96609,-0.20988,-0.1504,368.95
> view matrix models
> #2,-0.15414,0.9361,-0.31617,26.565,0.20714,-0.28227,-0.9367,302.72,-0.96609,-0.20988,-0.1504,367.93
> view matrix models
> #2,-0.15414,0.9361,-0.31617,26.495,0.20714,-0.28227,-0.9367,303.43,-0.96609,-0.20988,-0.1504,367.75
> view matrix models
> #2,-0.15414,0.9361,-0.31617,26.352,0.20714,-0.28227,-0.9367,303.91,-0.96609,-0.20988,-0.1504,367.54
> view matrix models
> #2,-0.15414,0.9361,-0.31617,25.819,0.20714,-0.28227,-0.9367,305.24,-0.96609,-0.20988,-0.1504,366.85
> view matrix models
> #2,-0.15414,0.9361,-0.31617,27.772,0.20714,-0.28227,-0.9367,305.69,-0.96609,-0.20988,-0.1504,363.43
> view matrix models
> #2,-0.15414,0.9361,-0.31617,27.744,0.20714,-0.28227,-0.9367,305,-0.96609,-0.20988,-0.1504,363.34
> view matrix models
> #2,-0.15414,0.9361,-0.31617,27.733,0.20714,-0.28227,-0.9367,304.93,-0.96609,-0.20988,-0.1504,363.33
> hide #!5 models
> hide #!4 models
> select subtract #2
Nothing selected
> fitmap #6 inMap #2
Fit molecule k1.pdb (#6) to map J520EMready.mrc (#2) using 616 atoms
average map value = 2.817, steps = 100
shifted from previous position = 2.78
rotated from previous position = 19.6 degrees
atoms outside contour = 218, contour level = 1.244
Position of k1.pdb (#6) relative to J520EMready.mrc (#2) coordinates:
Matrix rotation and translation
-0.19593601 -0.00025241 0.98061664 203.65194146
0.34712852 0.93523130 0.06960013 123.11024788
-0.91712096 0.35403717 -0.18315787 120.29854053
Axis 0.14585583 0.97313659 0.17813268
Axis point 129.43797100 0.00000000 -24.39321727
Rotation angle (degrees) 102.82249252
Shift along axis 170.93601253
> volume #2 level 3.692
> select add #6
616 atoms, 633 bonds, 78 residues, 1 model selected
> view matrix models
> #6,0.64512,0.76357,-0.028092,76.978,0.7205,-0.59567,0.35505,201.49,0.25437,-0.24929,-0.93443,127.2
> view matrix models
> #6,0.64512,0.76357,-0.028092,76.654,0.7205,-0.59567,0.35505,201.3,0.25437,-0.24929,-0.93443,126.77
> view matrix models
> #6,0.64512,0.76357,-0.028092,81.185,0.7205,-0.59567,0.35505,199.76,0.25437,-0.24929,-0.93443,124.21
> view matrix models
> #6,0.64512,0.76357,-0.028092,81.959,0.7205,-0.59567,0.35505,198.86,0.25437,-0.24929,-0.93443,122.85
> view matrix models
> #6,0.64512,0.76357,-0.028092,81.767,0.7205,-0.59567,0.35505,198.86,0.25437,-0.24929,-0.93443,122.97
> view matrix models
> #6,0.64512,0.76357,-0.028092,81.77,0.7205,-0.59567,0.35505,198.87,0.25437,-0.24929,-0.93443,122.94
> view matrix models
> #6,0.64512,0.76357,-0.028092,77.648,0.7205,-0.59567,0.35505,198.92,0.25437,-0.24929,-0.93443,126.1
> fitmap #6 inMap #2
Fit molecule k1.pdb (#6) to map J520EMready.mrc (#2) using 616 atoms
average map value = 2.082, steps = 120
shifted from previous position = 1.95
rotated from previous position = 10.4 degrees
atoms outside contour = 491, contour level = 3.6923
Position of k1.pdb (#6) relative to J520EMready.mrc (#2) coordinates:
Matrix rotation and translation
-0.20813384 -0.16331562 0.96436937 206.71210370
0.24112689 0.94696371 0.21240889 132.15075409
-0.94791250 0.27674487 -0.15771541 121.92439966
Axis 0.03289763 0.97782829 0.20680807
Axis point 137.75272156 0.00000000 -36.27665368
Rotation angle (degrees) 102.08969956
Shift along axis 161.23603430
> volume #2 level 1.809
> show #3 models
> select subtract #6
Nothing selected
> select add #3
4502 atoms, 4622 bonds, 582 residues, 1 model selected
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.95382,-0.17692,0.24275,-2.7133,0.1341,0.97394,0.18292,-46.786,-0.26879,-0.14192,0.95269,74.083
> view matrix models
> #3,0.83969,-0.44072,0.31731,46.306,0.23911,0.82465,0.51262,-92.428,-0.48759,-0.35457,0.79783,168.46
> view matrix models
> #3,-0.32993,-0.93874,-0.099574,382.74,-0.12906,-0.059633,0.98984,33.316,-0.93514,0.33943,-0.10148,273.07
> view matrix models
> #3,-0.25298,-0.96702,-0.02957,363.62,-0.039663,-0.020172,0.99901,10.995,-0.96666,0.2539,-0.033252,281.05
> view matrix models
> #3,-0.25395,-0.96641,-0.039554,365.27,-0.055968,-0.026144,0.99809,14.749,-0.9656,0.25568,-0.047449,282.86
> view matrix models
> #3,-0.40848,-0.90995,-0.071719,386.43,-0.061521,-0.050948,0.9968,19.84,-0.91069,0.41158,-0.03517,246.94
> view matrix models
> #3,0.22087,0.97239,-0.075303,-17.533,-0.54781,0.059809,-0.83446,372.98,-0.80692,0.22556,0.5459,167.33
> view matrix models
> #3,0.22572,0.97168,-0.069964,-19.058,-0.54229,0.065662,-0.83762,371.65,-0.8093,0.22701,0.54175,168.14
> view matrix models
> #3,0.067929,0.75144,-0.6563,135.42,0.4308,-0.61543,-0.66005,294.66,-0.89989,-0.2379,-0.36552,402.16
> view matrix models
> #3,0.081257,0.77742,-0.62371,123.88,0.38309,-0.60207,-0.70054,306.72,-0.92013,-0.18201,-0.34674,393.48
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.081257,0.77742,-0.62371,77.012,0.38309,-0.60207,-0.70054,282.2,-0.92013,-0.18201,-0.34674,411.36
> view matrix models
> #3,0.081257,0.77742,-0.62371,63.868,0.38309,-0.60207,-0.70054,293.46,-0.92013,-0.18201,-0.34674,387.29
> fitmap #3 inMap #2
Fit molecule last_frame_rsr-3.pdb (#3) to map J520EMready.mrc (#2) using 4502
atoms
average map value = 2.144, steps = 328
shifted from previous position = 5.53
rotated from previous position = 26.1 degrees
atoms outside contour = 2711, contour level = 1.809
Position of last_frame_rsr-3.pdb (#3) relative to J520EMready.mrc (#2)
coordinates:
Matrix rotation and translation
0.99999426 -0.00317245 -0.00117778 0.77147674
0.00317569 0.99999114 0.00275787 -0.97766286
0.00116902 -0.00276159 0.99999549 0.34435124
Axis -0.63200033 -0.26871887 0.72688772
Axis point 306.39507456 247.69656859 0.00000000
Rotation angle (degrees) 0.25019188
Shift along axis 0.02544759
> select subtract #3
Nothing selected
> select add #6
616 atoms, 633 bonds, 78 residues, 1 model selected
> view matrix models
> #6,0.5575,0.82412,0.10005,81.23,0.77674,-0.56036,0.28754,198.66,0.29303,-0.082591,-0.95253,116
> view matrix models
> #6,0.5575,0.82412,0.10005,80.945,0.77674,-0.56036,0.28754,198.93,0.29303,-0.082591,-0.95253,115.07
> view matrix models
> #6,0.5575,0.82412,0.10005,80.837,0.77674,-0.56036,0.28754,199.65,0.29303,-0.082591,-0.95253,115.61
> view matrix models
> #6,0.5575,0.82412,0.10005,81.07,0.77674,-0.56036,0.28754,199.67,0.29303,-0.082591,-0.95253,115.46
> view matrix models
> #6,0.5575,0.82412,0.10005,81.007,0.77674,-0.56036,0.28754,199.63,0.29303,-0.082591,-0.95253,115.48
> fitmap #6 inMap #2
Fit molecule k1.pdb (#6) to map J520EMready.mrc (#2) using 616 atoms
average map value = 2.817, steps = 152
shifted from previous position = 6.21
rotated from previous position = 10.4 degrees
atoms outside contour = 286, contour level = 1.809
Position of k1.pdb (#6) relative to J520EMready.mrc (#2) coordinates:
Matrix rotation and translation
-0.19616140 -0.00015716 0.98057160 203.64307238
0.34699138 0.93528482 0.06956484 123.10593242
-0.91712467 0.35389583 -0.18341224 120.29402950
Axis 0.14580871 0.97316384 0.17802238
Axis point 129.43557345 0.00000000 -24.37051910
Rotation angle (degrees) 102.83501603
Shift along axis 170.91020405
> view matrix models
> #6,0.64502,0.76365,-0.028038,79.701,0.7205,-0.59553,0.35529,202.3,0.25462,-0.24937,-0.93434,122.25
> select subtract #6
Nothing selected
> ui tool show Matchmaker
> matchmaker #3 to #6
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 k1.pdb, chain (blank) (#6) with last_frame_rsr-3.pdb, chain C (#3),
sequence alignment score = 382.9
RMSD between 39 pruned atom pairs is 1.296 angstroms; (across all 78 pairs:
2.677)
> matchmaker #6 to #3
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 last_frame_rsr-3.pdb, chain C (#3) with k1.pdb, chain (blank) (#6),
sequence alignment score = 382.9
RMSD between 39 pruned atom pairs is 1.296 angstroms; (across all 78 pairs:
2.677)
> matchmaker #6 to #3
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 last_frame_rsr-3.pdb, chain C (#3) with k1.pdb, chain (blank) (#6),
sequence alignment score = 382.9
RMSD between 39 pruned atom pairs is 1.296 angstroms; (across all 78 pairs:
2.677)
> hide #3 models
> fitmap #6 inMap #2
Fit molecule k1.pdb (#6) to map J520EMready.mrc (#2) using 616 atoms
average map value = 2.817, steps = 128
shifted from previous position = 6.7
rotated from previous position = 0.0104 degrees
atoms outside contour = 286, contour level = 1.809
Position of k1.pdb (#6) relative to J520EMready.mrc (#2) coordinates:
Matrix rotation and translation
-0.19623104 -0.00015146 0.98055766 203.64266200
0.34683492 0.93534368 0.06955373 123.10496976
-0.91716896 0.35374024 -0.18349094 120.29902736
Axis 0.14573614 0.97318958 0.17794108
Axis point 129.44687784 0.00000000 -24.36330675
Rotation angle (degrees) 102.83764511
Shift along axis 170.88870681
> volume #2 level 0.7059
> select add #6
616 atoms, 633 bonds, 78 residues, 1 model selected
> view matrix models
> #6,0.6449,0.76375,-0.028021,79.119,0.72057,-0.5954,0.35536,204.18,0.25472,-0.24936,-0.93431,127.05
> view matrix models
> #6,0.6449,0.76375,-0.028021,81.056,0.72057,-0.5954,0.35536,203.77,0.25472,-0.24936,-0.93431,123.34
> view matrix models
> #6,0.6449,0.76375,-0.028021,77.306,0.72057,-0.5954,0.35536,203.94,0.25472,-0.24936,-0.93431,121.61
> fitmap #6 inMap #2
Fit molecule k1.pdb (#6) to map J520EMready.mrc (#2) using 616 atoms
average map value = 2.817, steps = 140
shifted from previous position = 5.78
rotated from previous position = 0.00513 degrees
atoms outside contour = 141, contour level = 0.70586
Position of k1.pdb (#6) relative to J520EMready.mrc (#2) coordinates:
Matrix rotation and translation
-0.19624246 -0.00014754 0.98055538 203.64222841
0.34691620 0.93531229 0.06957046 123.10600705
-0.91713577 0.35382323 -0.18349680 120.29447294
Axis 0.14577095 0.97317692 0.17798177
Axis point 129.43831090 0.00000000 -24.36422873
Rotation angle (degrees) 102.83907519
Shift along axis 170.89926820
> volume #2 level 3.558
> volume #2 level 6.598
> volume #2 level 2.697
> volume #2 level 1.352
> transparency #2.1 50
> view matrix models
> #6,0.64497,0.7637,-0.028003,76.549,0.72051,-0.59547,0.35536,200.75,0.25471,-0.24937,-0.93431,123.32
> view matrix models
> #6,0.64497,0.7637,-0.028003,77.144,0.72051,-0.59547,0.35536,201,0.25471,-0.24937,-0.93431,123.45
> view matrix models
> #6,0.64497,0.7637,-0.028003,77.202,0.72051,-0.59547,0.35536,201,0.25471,-0.24937,-0.93431,123.47
> view matrix models
> #6,0.64497,0.7637,-0.028003,78.602,0.72051,-0.59547,0.35536,200.94,0.25471,-0.24937,-0.93431,124.14
> select subtract #6
Nothing selected
> hide #6 models
> close #3
> close #6
> close #5
> close #4
> open /data-old/5B10-PT/BestFitModel-coot-2.pdb
Chain information for BestFitModel-coot-2.pdb #3
---
Chain | Description
A | No description available
B | No description available
C | No description available
> select add #3
8792 atoms, 8912 bonds, 582 residues, 1 model selected
> view matrix models #3,1,0,0,-0.40849,0,1,0,-0.46145,0,0,1,0.13197
> view matrix models #3,1,0,0,-26.179,0,1,0,-33.161,0,0,1,7.246
> view matrix models #3,1,0,0,-26.934,0,1,0,-32.463,0,0,1,8.0136
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.99931,-0.036406,-0.0072579,-19.827,0.036104,0.99862,-0.038059,-32.054,0.0086334,0.03777,0.99925,0.67054
> view matrix models
> #3,0.99677,-0.075172,-0.028119,-9.8481,0.07325,0.99525,-0.064076,-33.436,0.032802,0.061809,0.99755,-6.8775
> view matrix models
> #3,0.96116,-0.26251,-0.085188,35.174,0.23919,0.94632,-0.21742,-28.214,0.13769,0.1886,0.97235,-40.361
> view matrix models
> #3,0.36291,0.90213,-0.23334,-28.949,-0.47932,-0.034011,-0.87698,353,-0.79909,0.43011,0.42007,163.97
> view matrix models
> #3,0.41185,0.90284,-0.12355,-54.783,-0.30829,0.010454,-0.95124,329.71,-0.85752,0.42986,0.28264,195.74
> view matrix models
> #3,-0.12137,0.42949,-0.89488,232.83,0.09813,-0.89194,-0.44138,325.2,-0.98774,-0.14139,0.066111,343.43
> view matrix models
> #3,-0.13931,0.45461,-0.87973,229.32,0.14661,-0.86913,-0.47235,318.56,-0.97934,-0.19478,0.054425,352.47
> ui mousemode right "translate selected models"
> view matrix models
> #3,-0.13931,0.45461,-0.87973,205.74,0.14661,-0.86913,-0.47235,329.16,-0.97934,-0.19478,0.054425,325.6
> view matrix models
> #3,-0.13931,0.45461,-0.87973,205.58,0.14661,-0.86913,-0.47235,331.51,-0.97934,-0.19478,0.054425,326.65
> ui mousemode right "rotate selected models"
> view matrix models
> #3,-0.22131,0.43888,-0.87087,220.16,0.17043,-0.86186,-0.47765,327.28,-0.96019,-0.25414,0.11594,323.1
> view matrix models
> #3,0.21149,0.73798,-0.64082,64.083,0.42053,-0.66057,-0.62194,277.16,-0.88228,-0.13795,-0.45005,382.8
> view matrix models
> #3,0.016966,0.86623,-0.49936,52.786,0.27773,-0.48386,-0.8299,305.85,-0.96051,-0.12461,-0.24879,361.14
> view matrix models
> #3,0.025361,0.86676,-0.49809,51.115,0.27584,-0.48497,-0.82989,306.34,-0.96087,-0.11635,-0.25139,360.29
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.025361,0.86676,-0.49809,46.001,0.27584,-0.48497,-0.82989,307.84,-0.96087,-0.11635,-0.25139,366.49
> view matrix models
> #3,0.025361,0.86676,-0.49809,41.306,0.27584,-0.48497,-0.82989,310.8,-0.96087,-0.11635,-0.25139,363.61
> fitmap #3 inMap #2
Fit molecule BestFitModel-coot-2.pdb (#3) to map J520EMready.mrc (#2) using
8792 atoms
average map value = 2.191, steps = 160
shifted from previous position = 2.3
rotated from previous position = 15.5 degrees
atoms outside contour = 4282, contour level = 1.3516
Position of BestFitModel-coot-2.pdb (#3) relative to J520EMready.mrc (#2)
coordinates:
Matrix rotation and translation
0.99999844 0.00045807 0.00170144 -0.35873299
-0.00045703 0.99999970 -0.00061273 0.16067883
-0.00170172 0.00061195 0.99999836 0.22331071
Axis 0.32826188 0.91218382 -0.24528515
Axis point 127.28595407 0.00000000 205.94740681
Rotation angle (degrees) 0.10687921
Shift along axis -0.02596454
> transparency 0
> volume #2 level 1
> volume #2 level 0.4619
===== Log before crash end =====
Log:
Startup Messages
---
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle
UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 3.3.0 NVIDIA 570.172.08
OpenGL renderer: NVIDIA GeForce RTX 3090/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Python: 3.11.2
Locale: en_US.UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: xcb
XDG_SESSION_TYPE=x11
DESKTOP_SESSION=gnome-classic
XDG_SESSION_DESKTOP=gnome-classic
XDG_CURRENT_DESKTOP=GNOME-Classic:GNOME
DISPLAY=:1
Manufacturer: Supermicro
Model: SYS-7049GP-TRT
OS: Rocky Linux 8.9 Green Obsidian
Architecture: 64bit ELF
Virtual Machine: none
CPU: 96 Intel(R) Xeon(R) Gold 5220R CPU @ 2.20GHz
Cache Size: 36608 KB
Memory:
total used free shared buff/cache available
Mem: 1.0Ti 25Gi 877Gi 670Mi 103Gi 974Gi
Swap: 4.0Gi 0B 4.0Gi
Graphics:
04:00.0 VGA compatible controller [0300]: ASPEED Technology, Inc. ASPEED Graphics Family [1a03:2000] (rev 41)
DeviceName: ASPEED Video AST2500
Subsystem: Super Micro Computer Inc Device [15d9:096d]
Installed Packages:
alabaster: 0.7.16
appdirs: 1.4.4
asttokens: 2.4.1
Babel: 2.14.0
backcall: 0.2.0
beautifulsoup4: 4.11.2
blockdiag: 3.0.0
blosc2: 2.0.0
build: 0.10.0
certifi: 2023.11.17
cftime: 1.6.3
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.13
ChimeraX-AddH: 2.2.5
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.4.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.2
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.49.1
ChimeraX-AtomicLibrary: 12.1.5
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3.2
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.10.5
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.2
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.3.2
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-Clipper: 0.22.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.5
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.7.1
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2
ChimeraX-DistMonitor: 1.4
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-ISOLDE: 1.7.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-Label: 1.1.8
ChimeraX-LinuxSupport: 1.0.1
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.1.4
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: 2.1.2
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.6.1
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.12.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.14
ChimeraX-ModelPanel: 1.4
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: 1.1
ChimeraX-NRRD: 1.1
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.1
ChimeraX-PDB: 2.7.3
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
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.1
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-SelInspector: 1.0
ChimeraX-SeqView: 2.11
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.2
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.12.4
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1.2
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.2.2
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: 1.33.3
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.3.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.3
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.1
contourpy: 1.2.0
cxservices: 1.2.2
cycler: 0.12.1
Cython: 0.29.33
debugpy: 1.8.0
decorator: 5.1.1
distro: 1.7.0
docutils: 0.19
executing: 2.0.1
filelock: 3.9.0
fonttools: 4.47.2
funcparserlib: 2.0.0a0
glfw: 2.6.4
grako: 3.16.5
h5py: 3.10.0
html2text: 2020.1.16
idna: 3.6
ihm: 0.38
imagecodecs: 2023.9.18
imagesize: 1.4.1
ipykernel: 6.23.2
ipython: 8.14.0
ipython-genutils: 0.2.0
ipywidgets: 8.1.1
jedi: 0.18.2
Jinja2: 3.1.2
jupyter-client: 8.2.0
jupyter-core: 5.7.1
jupyterlab-widgets: 3.0.9
kiwisolver: 1.4.5
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.4
matplotlib: 3.7.2
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.6.0
netCDF4: 1.6.2
networkx: 3.1
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.8.8
numpy: 1.25.1
openvr: 1.23.701
packaging: 23.2
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pexpect: 4.9.0
pickleshare: 0.7.5
pillow: 10.2.0
pip: 23.0
pkginfo: 1.9.6
platformdirs: 4.1.0
prompt-toolkit: 3.0.43
psutil: 5.9.5
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.16.1
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.2801
pyparsing: 3.0.9
pyproject-hooks: 1.0.0
PyQt6-commercial: 6.3.1
PyQt6-Qt6: 6.3.2
PyQt6-sip: 13.4.0
PyQt6-WebEngine-commercial: 6.3.1
PyQt6-WebEngine-Qt6: 6.3.2
python-dateutil: 2.8.2
pytz: 2023.3.post1
pyzmq: 25.1.2
qtconsole: 5.4.3
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.11.1
setuptools: 67.4.0
sfftk-rw: 0.7.3
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 6.1.3
sphinx-autodoc-typehints: 1.22
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: 0.5.0
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2023.7.18
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.4
traitlets: 5.9.0
typing-extensions: 4.9.0
tzdata: 2023.4
urllib3: 2.1.0
wcwidth: 0.2.13
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.9
Change History (2)
comment:1 by , 3 months ago
| Component: | Unassigned → Core |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Crash in garbage collection |
comment:2 by , 3 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | accepted → closed |
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