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Opened 4 years ago
Closed 4 years ago
#5833 closed defect (duplicate)
Long atom spec crashes ChimeraX
| Reported by: | Owned by: | pett | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Command Line | Version: | |
| Keywords: | Cc: | chimera-programmers | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Windows-10-10.0.22000
ChimeraX Version: 1.3 (2021-12-08 23:08:33 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Windows fatal exception: stack overflow
Thread 0x00027e5c (most recent call first):
File "E:\Program Files\ChimeraX 1.4.dev202112160537\bin\lib\multiprocessing\pool.py", line 576 in _handle_results
File "E:\Program Files\ChimeraX 1.4.dev202112160537\bin\lib\threading.py", line 910 in run
File "E:\Program Files\ChimeraX 1.4.dev202112160537\bin\lib\threading.py", line 973 in _bootstrap_inner
File "E:\Program Files\ChimeraX 1.4.dev202112160537\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x00027f1c (most recent call first):
File "E:\Program Files\ChimeraX 1.4.dev202112160537\bin\lib\multiprocessing\pool.py", line 528 in _handle_tasks
File "E:\Program Files\ChimeraX 1.4.dev202112160537\bin\lib\threading.py", line 910 in run
File "E:\Program Files\ChimeraX 1.4.dev202112160537\bin\lib\threading.py", line 973 in _bootstrap_inner
File "E:\Program Files\ChimeraX 1.4.dev202112160537\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x00025e80 (most recent call first):
File "E:\Program Files\ChimeraX 1.4.dev202112160537\bin\lib\multiprocessing\connection.py", line 816 in _exhaustive_wait
File "E:\Program Files\ChimeraX 1.4.dev202112160537\bin\lib\multiprocessing\connection.py", line 884 in wait
File "E:\Program Files\ChimeraX 1.4.dev202112160537\bin\lib\multiprocessing\pool.py", line 499 in _wait_for_updates
File "E:\Program Files\ChimeraX 1.4.dev202112160537\bin\lib\multiprocessing\pool.py", line 519 in _handle_workers
File "E:\Program Files\ChimeraX 1.4.dev202112160537\bin\lib\threading.py", line 910 in run
File "E:\Program Files\ChimeraX 1.4.dev202112160537\bin\lib\threading.py", line 973 in _bootstrap_inner
File "E:\Program Files\ChimeraX 1.4.dev202112160537\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x0002652c (most recent call first):
File "E:\Program Files\ChimeraX 1.4.dev202112160537\bin\lib\multiprocessing\pool.py", line 114 in worker
File "E:\Program Files\ChimeraX 1.4.dev202112160537\bin\lib\threading.py", line 910 in run
File "E:\Program Files\ChimeraX 1.4.dev202112160537\bin\lib\threading.py", line 973 in _bootstrap_inner
File "E:\Program Files\ChimeraX 1.4.dev202112160537\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x000208a0 (most recent call first):
File "E:\Program Files\ChimeraX 1.4.dev202112160537\bin\lib\multiprocessing\pool.py", line 114 in worker
File "E:\Program Files\ChimeraX 1.4.dev202112160537\bin\lib\threading.py", line 910 in run
File "E:\Program Files\ChimeraX 1.4.dev202112160537\bin\lib\threading.py", line 973 in _bootstrap_inner
File "E:\Program Files\ChimeraX 1.4.dev202112160537\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x00025d5c (most recent call first):
File "E:\Program Files\ChimeraX 1.4.dev202112160537\bin\lib\multiprocessing\pool.py", line 114 in worker
File "E:\Program Files\ChimeraX 1.4.dev202112160537\bin\lib\threading.py", line 910 in run
File "E:\Program Files\ChimeraX 1.4.dev202112160537\bin\lib\threading.py", line 973 in _bootstrap_inner
File "E:\Program Files\ChimeraX 1.4.dev202112160537\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x00027ae4 (most recent call first):
File "E:\Program Files\ChimeraX 1.4.dev202112160537\bin\lib\multiprocessing\pool.py", line 114 in worker
File "E:\Program Files\ChimeraX 1.4.dev202112160537\bin\lib\threading.py", line 910 in run
File "E:\Program Files\ChimeraX 1.4.dev202112160537\bin\lib\threading.py", line 973 in _bootstrap_inner
File "E:\Program Files\ChimeraX 1.4.dev202112160537\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x00025f48 (most recent call first):
File "E:\Program Files\ChimeraX 1.4.dev202112160537\bin\lib\multiprocessing\pool.py", line 114 in worker
File "E:\Program Files\ChimeraX 1.4.dev202112160537\bin\lib\threading.py", line 910 in run
File "E:\Program Files\ChimeraX 1.4.dev202112160537\bin\lib\threading.py", line 973 in _bootstrap_inner
File "E:\Program Files\ChimeraX 1.4.dev202112160537\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x00020e08 (most recent call first):
File "E:\Program Files\ChimeraX 1.4.dev202112160537\bin\lib\multiprocessing\pool.py", line 114 in worker
File "E:\Program Files\ChimeraX 1.4.dev202112160537\bin\lib\threading.py", line 910 in run
File "E:\Program Files\ChimeraX 1.4.dev202112160537\bin\lib\threading.py", line 973 in _bootstrap_inner
File "E:\Program Files\ChimeraX 1.4.dev202112160537\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x00027090 (most recent call first):
File "E:\Program Files\ChimeraX 1.4.dev202112160537\bin\lib\multiprocessing\pool.py", line 114 in worker
File "E:\Program Files\ChimeraX 1.4.dev202112160537\bin\lib\threading.py", line 910 in run
File "E:\Program Files\ChimeraX 1.4.dev202112160537\bin\lib\threading.py", line 973 in _bootstrap_inner
File "E:\Program Files\ChimeraX 1.4.dev202112160537\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x00027e28 (most recent call first):
File "E:\Program Files\ChimeraX 1.4.dev202112160537\bin\lib\multiprocessing\pool.py", line 114 in worker
File "E:\Program Files\ChimeraX 1.4.dev202112160537\bin\lib\threading.py", line 910 in run
File "E:\Program Files\ChimeraX 1.4.dev202112160537\bin\lib\threading.py", line 973 in _bootstrap_inner
File "E:\Program Files\ChimeraX 1.4.dev202112160537\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x00025bac (most recent call first):
File "E:\Program Files\ChimeraX 1.4.dev202112160537\bin\lib\multiprocessing\pool.py", line 114 in worker
File "E:\Program Files\ChimeraX 1.4.dev202112160537\bin\lib\threading.py", line 910 in run
File "E:\Program Files\ChimeraX 1.4.dev202112160537\bin\lib\threading.py", line 973 in _bootstrap_inner
File "E:\Program Files\ChimeraX 1.4.dev202112160537\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x00022f68 (most recent call first):
File "E:\Program Files\ChimeraX 1.4.dev202112160537\bin\lib\multiprocessing\pool.py", line 114 in worker
File "E:\Program Files\ChimeraX 1.4.dev202112160537\bin\lib\threading.py", line 910 in run
File "E:\Program Files\ChimeraX 1.4.dev202112160537\bin\lib\threading.py", line 973 in _bootstrap_inner
File "E:\Program Files\ChimeraX 1.4.dev202112160537\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x00027130 (most recent call first):
File "E:\Program Files\ChimeraX 1.4.dev202112160537\bin\lib\multiprocessing\pool.py", line 114 in worker
File "E:\Program Files\ChimeraX 1.4.dev202112160537\bin\lib\threading.py", line 910 in run
File "E:\Program Files\ChimeraX 1.4.dev202112160537\bin\lib\threading.py", line 973 in _bootstrap_inner
File "E:\Program Files\ChimeraX 1.4.dev202112160537\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x000257a4 (most recent call first):
File "E:\Program Files\ChimeraX 1.4.dev202112160537\bin\lib\multiprocessing\pool.py", line 114 in worker
File "E:\Program Files\ChimeraX 1.4.dev202112160537\bin\lib\threading.py", line 910 in run
File "E:\Program Files\ChimeraX 1.4.dev202112160537\bin\lib\threading.py", line 973 in _bootstrap_inner
File "E:\Program Files\ChimeraX 1.4.dev202112160537\bin\lib\threading.py", line 930 in _bootstrap
Current thread 0x000150e4 (most recent call first):
File "E:\Program Files\ChimeraX 1.4.dev202112160537\bin\lib\site-packages\grako\ast.py", line 52 in
File "E:\Program Files\ChimeraX 1.4.dev202112160537\bin\lib\site-packages\grako\ast.py", line 90 in
File "E:\Program Files\ChimeraX 1.4.dev202112160537\bin\lib\site-packages\grako\ast.py", line 60 in upairs
File "E:\Program Files\ChimeraX 1.4.dev202112160537\bin\lib\site-packages\grako\ast.py", line 67 in update
File "E:\Program Files\ChimeraX 1.4.dev202112160537\bin\lib\site-packages\grako\ast.py", line 19 in __init__
File "E:\Program Files\ChimeraX 1.4.dev202112160537\bin\lib\site-packages\grako\ast.py", line 90 in copy
File "E:\Program Files\ChimeraX 1.4.dev202112160537\bin\lib\site-packages\grako\contexts.py", line 642 in _try
File "E:\Program Files\ChimeraX 1.4.dev202112160537\bin\lib\contextlib.py", line 117 in __enter__
File "E:\Program Files\ChimeraX 1.4.dev202112160537\bin\lib\site-packages\grako\contexts.py", line 679 in _choice
File "E:\Program Files\ChimeraX 1.4.dev202112160537\bin\lib\contextlib.py", line 117 in __enter__
File "E:\Program Files\ChimeraX 1.4.dev202112160537\bin\lib\site-packages\grako\contexts.py", line 688 in _optional
File "E:\Program Files\ChimeraX 1.4.dev202112160537\bin\lib\contextlib.py", line 117 in __enter__
File "E:\Program Files\ChimeraX 1.4.dev202112160537\bin\lib\site-packages\chimerax\core\commands\_atomspec.py", line 427 in _part_range_list_
File "E:\Program Files\ChimeraX 1.4.dev202112160537\bin\lib\site-packages\grako\contexts.py", line 497 in _invoke_rule
File "E:\Program Files\ChimeraX 1.4.dev202112160537\bin\lib\site-packages\grako\contexts.py", line 458 in _call
File "E:\Program Files\ChimeraX 1.4.dev202112160537\bin\lib\site-packages\grako\contexts.py", line 59 in wrapper
File "E:\Program Files\ChimeraX 1.4.dev202112160537\bin\lib\site-packages\chimerax\core\commands\_atomspec.py", line 409 in _part_list_
File "E:\Program Files\ChimeraX 1.4.dev202112160537\bin\lib\site-packages\grako\contexts.py", line 497 in _invoke_rule
File "E:\Program Files\ChimeraX 1.4.dev202112160537\bin\lib\site-packages\grako\contexts.py", line 458 in _call
File "E:\Program Files\ChimeraX 1.4.dev202112160537\bin\lib\site-packages\grako\contexts.py", line 59 in wrapper
File "E:\Program Files\ChimeraX 1.4.dev202112160537\bin\lib\site-packages\chimerax\core\commands\_atomspec.py", line 412 in _part_list_
File "E:\Program Files\ChimeraX 1.4.dev202112160537\bin\lib\site-packages\grako\contexts.py", line 497 in _invoke_rule
File "E:\Program Files\ChimeraX 1.4.dev202112160537\bin\lib\site-packages\grako\contexts.py", line 458 in _call
File "E:\Program Files\ChimeraX 1.4.dev202112160537\bin\lib\site-packages\grako\contexts.py", line 59 in wrapper
File "E:\Program Files\ChimeraX 1.4.dev202112160537\bin\lib\site-packages\chimerax\core\commands\_atomspec.py", line 412 in _part_list_
File "E:\Program Files\ChimeraX 1.4.dev202112160537\bin\lib\site-packages\grako\contexts.py", line 497 in _invoke_rule
File "E:\Program Files\ChimeraX 1.4.dev202112160537\bin\lib\site-packages\grako\contexts.py", line 458 in _call
File "E:\Program Files\ChimeraX 1.4.dev202112160537\bin\lib\site-packages\grako\contexts.py", line 59 in wrapper
File "E:\Program Files\ChimeraX 1.4.dev202112160537\bin\lib\site-packages\chimerax\core\commands\_atomspec.py", line 412 in _part_list_
File "E:\Program Files\ChimeraX 1.4.dev202112160537\bin\lib\site-packages\grako\contexts.py", line 497 in _invoke_rule
File "E:\Program Files\ChimeraX 1.4.dev202112160537\bin\lib\site-packages\grako\contexts.py", line 458 in _call
File "E:\Program Files\ChimeraX 1.4.dev202112160537\bin\lib\site-packages\grako\contexts.py", line 59 in wrapper
File "E:\Program Files\ChimeraX 1.4.dev202112160537\bin\lib\site-packages\chimerax\core\commands\_atomspec.py", line 412 in _part_list_
File "E:\Program Files\ChimeraX 1.4.dev202112160537\bin\lib\site-packages\grako\contexts.py", line 497 in _invoke_rule
File "E:\Program Files\ChimeraX 1.4.dev202112160537\bin\lib\site-packages\grako\contexts.py", line 458 in _call
File "E:\Program Files\ChimeraX 1.4.dev202112160537\bin\lib\site-packages\grako\contexts.py", line 59 in wrapper
File "E:\Program Files\ChimeraX 1.4.dev202112160537\bin\lib\site-packages\chimerax\core\commands\_atomspec.py", line 412 in _part_list_
File "E:\Program Files\ChimeraX 1.4.dev202112160537\bin\lib\site-packages\grako\contexts.py", line 497 in _invoke_rule
File "E:\Program Files\ChimeraX 1.4.dev202112160537\bin\lib\site-packages\grako\contexts.py", line 458 in _call
File "E:\Program Files\ChimeraX 1.4.dev202112160537\bin\lib\site-packages\grako\contexts.py", line 59 in wrapper
File "E:\Program Files\ChimeraX 1.4.dev202112160537\bin\lib\site-packages\chimerax\core\commands\_atomspec.py", line 412 in _part_list_
File "E:\Program Files\ChimeraX 1.4.dev202112160537\bin\lib\site-packages\grako\contexts.py", line 497 in _invoke_rule
File "E:\Program Files\ChimeraX 1.4.dev202112160537\bin\lib\site-packages\grako\contexts.py", line 458 in _call
File "E:\Program Files\ChimeraX 1.4.dev202112160537\bin\lib\site-packages\grako\contexts.py", line 59 in wrapper
File "E:\Program Files\ChimeraX 1.4.dev202112160537\bin\lib\site-packages\chimerax\core\commands\_atomspec.py", line 412 in _part_list_
File "E:\Program Files\ChimeraX 1.4.dev202112160537\bin\lib\site-packages\grako\contexts.py", line 497 in _invoke_rule
File "E:\Program Files\ChimeraX 1.4.dev202112160537\bin\lib\site-packages\grako\contexts.py", line 458 in _call
File "E:\Program Files\ChimeraX 1.4.dev202112160537\bin\lib\site-packages\grako\contexts.py", line 59 in wrapper
File "E:\Program Files\ChimeraX 1.4.dev202112160537\bin\lib\site-packages\chimerax\core\commands\_atomspec.py", line 412 in _part_list_
File "E:\Program Files\ChimeraX 1.4.dev202112160537\bin\lib\site-packages\grako\contexts.py", line 497 in _invoke_rule
File "E:\Program Files\ChimeraX 1.4.dev202112160537\bin\lib\site-packages\grako\contexts.py", line 458 in _call
File "E:\Program Files\ChimeraX 1.4.dev202112160537\bin\lib\site-packages\grako\contexts.py", line 59 in wrapper
File "E:\Program Files\ChimeraX 1.4.dev202112160537\bin\lib\site-packages\chimerax\core\commands\_atomspec.py", line 412 in _part_list_
File "E:\Program Files\ChimeraX 1.4.dev202112160537\bin\lib\site-packages\grako\contexts.py", line 497 in _invoke_rule
File "E:\Program Files\ChimeraX 1.4.dev202112160537\bin\lib\site-packages\grako\contexts.py", line 458 in _call
File "E:\Program Files\ChimeraX 1.4.dev202112160537\bin\lib\site-packages\grako\contexts.py", line 59 in wrapper
File "E:\Program Files\ChimeraX 1.4.dev202112160537\bin\lib\site-packages\chimerax\core\commands\_atomspec.py", line 412 in _part_list_
File "E:\Program Files\ChimeraX 1.4.dev202112160537\bin\lib\site-packages\grako\contexts.py", line 497 in _invoke_rule
File "E:\Program Files\ChimeraX 1.4.dev202112160537\bin\lib\site-packages\grako\contexts.py", line 458 in _call
File "E:\Program Files\ChimeraX 1.4.dev202112160537\bin\lib\site-packages\grako\contexts.py", line 59 in wrapper
File "E:\Program Files\ChimeraX 1.4.dev202112160537\bin\lib\site-packages\chimerax\core\commands\_atomspec.py", line 412 in _part_list_
File "E:\Program Files\ChimeraX 1.4.dev202112160537\bin\lib\site-packages\grako\contexts.py", line 497 in _invoke_rule
File "E:\Program Files\ChimeraX 1.4.dev202112160537\bin\lib\site-packages\grako\contexts.py", line 458 in _call
File "E:\Program Files\ChimeraX 1.4.dev202112160537\bin\lib\site-packages\grako\contexts.py", line 59 in wrapper
File "E:\Program Files\ChimeraX 1.4.dev202112160537\bin\lib\site-packages\chimerax\core\commands\_atomspec.py", line 412 in _part_list_
File "E:\Program Files\ChimeraX 1.4.dev202112160537\bin\lib\site-packages\grako\contexts.py", line 497 in _invoke_rule
File "E:\Program Files\ChimeraX 1.4.dev202112160537\bin\lib\site-packages\grako\contexts.py", line 458 in _call
File "E:\Program Files\ChimeraX 1.4.dev202112160537\bin\lib\site-packages\grako\contexts.py", line 59 in wrapper
File "E:\Program Files\ChimeraX 1.4.dev202112160537\bin\lib\site-packages\chimerax\core\commands\_atomspec.py", line 412 in _part_list_
File "E:\Program Files\ChimeraX 1.4.dev202112160537\bin\lib\site-packages\grako\contexts.py", line 497 in _invoke_rule
File "E:\Program Files\ChimeraX 1.4.dev202112160537\bin\lib\site-packages\grako\contexts.py", line 458 in _call
File "E:\Program Files\ChimeraX 1.4.dev202112160537\bin\lib\site-packages\grako\contexts.py", line 59 in wrapper
File "E:\Program Files\ChimeraX 1.4.dev202112160537\bin\lib\site-packages\chimerax\core\commands\_atomspec.py", line 412 in _part_list_
File "E:\Program Files\ChimeraX 1.4.dev202112160537\bin\lib\site-packages\grako\contexts.py", line 497 in _invoke_rule
File "E:\Program Files\ChimeraX 1.4.dev202112160537\bin\lib\site-packages\grako\contexts.py", line 458 in _call
File "E:\Program Files\ChimeraX 1.4.dev202112160537\bin\lib\site-packages\grako\contexts.py", line 59 in wrapper
File "E:\Program Files\ChimeraX 1.4.dev202112160537\bin\lib\site-packages\chimerax\core\commands\_atomspec.py", line 412 in _part_list_
File "E:\Program Files\ChimeraX 1.4.dev202112160537\bin\lib\site-packages\grako\contexts.py", line 497 in _invoke_rule
File "E:\Program Files\ChimeraX 1.4.dev202112160537\bin\lib\site-packages\grako\contexts.py", line 458 in _call
File "E:\Program Files\ChimeraX 1.4.dev202112160537\bin\lib\site-packages\grako\contexts.py", line 59 in wrapper
File "E:\Program Files\ChimeraX 1.4.dev202112160537\bin\lib\site-packages\chimerax\core\commands\_atomspec.py", line 412 in _part_list_
File "E:\Program Files\ChimeraX 1.4.dev202112160537\bin\lib\site-packages\grako\contexts.py", line 497 in _invoke_rule
File "E:\Program Files\ChimeraX 1.4.dev202112160537\bin\lib\site-packages\grako\contexts.py", line 458 in _call
File "E:\Program Files\ChimeraX 1.4.dev202112160537\bin\lib\site-packages\grako\contexts.py", line 59 in wrapper
File "E:\Program Files\ChimeraX 1.4.dev202112160537\bin\lib\site-packages\chimerax\core\commands\_atomspec.py", line 412 in _part_list_
File "E:\Program Files\ChimeraX 1.4.dev202112160537\bin\lib\site-packages\grako\contexts.py", line 497 in _invoke_rule
File "E:\Program Files\ChimeraX 1.4.dev202112160537\bin\lib\site-packages\grako\contexts.py", line 458 in _call
File "E:\Program Files\ChimeraX 1.4.dev202112160537\bin\lib\site-packages\grako\contexts.py", line 59 in wrapper
File "E:\Program Files\ChimeraX 1.4.dev202112160537\bin\lib\site-packages\chimerax\core\commands\_atomspec.py", line 412 in _part_list_
File "E:\Program Files\ChimeraX 1.4.dev202112160537\bin\lib\site-packages\grako\contexts.py", line 497 in _invoke_rule
File "E:\Program Files\ChimeraX 1.4.dev202112160537\bin\lib\site-packages\grako\contexts.py", line 458 in _call
File "E:\Program Files\ChimeraX 1.4.dev202112160537\bin\lib\site-packages\grako\contexts.py", line 59 in wrapper
File "E:\Program Files\ChimeraX 1.4.dev202112160537\bin\lib\site-packages\chimerax\core\commands\_atomspec.py", line 412 in _part_list_
File "E:\Program Files\ChimeraX 1.4.dev202112160537\bin\lib\site-packages\grako\contexts.py", line 497 in _invoke_rule
File "E:\Program Files\ChimeraX 1.4.dev202112160537\bin\lib\site-packages\grako\contexts.py", line 458 in _call
File "E:\Program Files\ChimeraX 1.4.dev202112160537\bin\lib\site-packages\grako\contexts.py", line 59 in wrapper
File "E:\Program Files\ChimeraX 1.4.dev202112160537\bin\lib\site-packages\chimerax\core\commands\_atomspec.py", line 412 in _part_list_
File "E:\Program Files\ChimeraX 1.4.dev202112160537\bin\lib\site-packages\grako\contexts.py", line 497 in _invoke_rule
File "E:\Program Files\ChimeraX 1.4.dev202112160537\bin\lib\site-packages\grako\contexts.py", line 458 in _call
File "E:\Program Files\ChimeraX 1.4.dev202112160537\bin\lib\site-packages\grako\contexts.py", line 59 in wrapper
...
===== Log before crash start =====
> open D:/EM/HRD/300_2021/pp/837_inverted_C2.mrc
Opened 837_inverted_C2.mrc as #1, grid size 256,256,256, pixel 0.86, shown at
level 0.0062, step 1, values float32
> open D:/EM/HRD/300_2021/pp/837_C2.pdb
Chain information for 837_C2.pdb #2
---
Chain | Description
B U | No description available
> volume #1 level 0.01354
> open D:/EM/HRD/AF2/analysis.cxs
Opened 837_inverted_C2.mrc as #4, grid size 256,256,256, pixel 0.86, shown at
level 0.017, step 1, values float32
Opened 837postprocess.mrc as #3, grid size 256,256,256, pixel 0.86, shown at
level 0.0151, step 1, values float32
Opened 923postprocess.mrc as #5, grid size 256,256,256, pixel 0.86, shown at
level 0.0126, step 1, values float32
Opened 923postprocess.mrc z flip as #6, grid size 256,256,256, pixel 0.86,
shown at level 0.0185, step 1, values float32
opened ChimeraX session
> show #!15 models
> hide #!15 models
> show #!13 models
> show #!6 models
> hide #!6 models
> hide #!5 models
> show #!6 models
> hide #!6 models
> show #!5 models
> show #!4 models
> hide #!5 models
> volume #4 level 0.01096
> hide #!4 models
> show #!5 models
> show #!15 models
> hide #!15 models
> volume #4 level 0.01503
> hide #!4 models
> show #!4 models
> hide #!4 models
> volume zone #5 nearAtoms #14 range 2.5 newMap true
Opened 923postprocess.mrc zone as #16, grid size 256,256,256, pixel 0.86,
shown at step 1, values float32
> show #!5 models
> select #5
3 models selected
> volume sel style mesh
> volume sel style surface
> transparency sel 0
> select #16
2 models selected
> volume sel style mesh
> volume #5 level 0.006824
> transparency sel 50
> transparency sel 0
> transparency sel 50
> transparency sel 0
> transparency sel 50
> transparency sel 0
> select #5
2 models selected
> transparency sel 50
> volume #5 level 0.002504
> volume #5 level 0.004738
> select #16
2 models selected
> transparency sel 50
> transparency sel 0
> select clear
> color #16 #55ffff models transparency 0
> transparency #5 sel 50
Missing or invalid "percent" argument: Expected a number
> transparency #5 50
> transparency #5 25
> transparency #5 80
> set bgColor white
> select #16
2 models selected
> color #16 yellow models transparency 0
> select clear
> select #14
11099 atoms, 11247 bonds, 675 residues, 1 model selected
> cartoon style sel modeHelix tube sides 20
> select clear
> color #14 yellow transparency 0
> select clear
> volume #16 level 0.009803
> select #5
3 models selected
> ~select #5
Nothing selected
> select #14
11099 atoms, 11247 bonds, 675 residues, 1 model selected
> cartoon style (sel & coil) xsection oval
> cartoon style sel xsection barbell modeHelix default
> cartoon style width 1
> select clear
> volume #16 level 0.01293
> lighting full
> lighting soft
> ui tool show "Side View"
> save D:\EM\HRD\AF2\HRD1_dimer.png supersample 8 transparentBackground true
> save D:/EM/HRD/AF2/analysis.cxs includeMaps true
> open D:/EM/YYT/ALPL_Xray/YDQ/apo/final/FINAL_ANA.cxs
opened ChimeraX session
> close session
> open E:/writing/ALPL/models/YDQ/basic_inhibito/basic_lei5_1.cxs
Opened inhi_lei5_1_refine_5_2mFo-DFc.ccp4 as #2, grid size 321,305,285, pixel
0.317,0.31,0.315, shown at level 2.81, step 2, values float32
Opened density_A as #3, grid size 321,305,285, pixel 0.317,0.31,0.315, shown
at level 2.16, step 2, values float32
Opened density_B as #4, grid size 321,305,285, pixel 0.317,0.31,0.315, shown
at level 2.81, step 2, values float32
opened ChimeraX session
> close session
> open E:/writing/ALPL/2in1.cxs
Opened LPCAT_Ara_map_968_006 as #1, grid size 272,272,272, pixel 0.86, shown
at level 0.399, step 1, values float32
Opened LPCAT_Ara_map_968_006 zone as #16, grid size 272,272,272, pixel 0.86,
shown at step 1, values float32
Opened LPCAT_Ara_map_968_006 zone as #17, grid size 272,272,272, pixel 0.86,
shown at level 0.3, step 1, values float32
opened ChimeraX session
> close session
> open "E:/writing/ALPL/ALPL analysis_0510.cxs"
opened ChimeraX session
> open D:/EM/YYT/ALPL_Xray/figure/disease.cxs
Opened 117inverted.mrc as #3, grid size 192,192,192, pixel 1.24, shown at
level 0.0529, step 1, values float32
opened ChimeraX session
> close session
> open "D:/EM/YYT/ALPL_Xray/YDQ/pH_sensor/acidic analysis/0322b.cxs"
opened ChimeraX session
> close session
> open "D:/EM/YYT/ALPL_Xray/YDQ/pH_sensor/acidic analysis/0322.cxs"
opened ChimeraX session
> close session
> open "D:/EM/YYT/ALPL_Xray/YDQ/pH_sensor/acidic analysis/acidic_0320.cxs"
registering illegal selector name "mut_2"
registering illegal selector name "muts_2"
opened ChimeraX session
> hide #!3 models
> show #!3 models
> set bgColor white
> graphics silhouettes true
> lighting shadows false
> lighting shadows true
> lighting flat
> lighting full
> lighting soft
> lighting simple
> lighting soft
> save E:\PPT\SHIP-M\2022年会\alpl "原始数据整理\\\alpl_tetramer.png" supersample 8
> transparentbackground 1
Cannot determine format for 'E:\PPT\SHIP-M\2022年会\alpl'
> save E:\PPT\SHIP-M\2022年会\alpl_tetramer.png supersample 8
> transparentBackground true
> ui tool show "Side View"
> save E:\PPT\SHIP-M\2022年会\alpl_tetramer2.png supersample 8
> transparentBackground true
> open 1EW2
1ew2 title:
Crystal structure of A human phosphatase [more info...]
Chain information for 1ew2 #5
---
Chain | Description | UniProt
A | phosphatase | PPB1_HUMAN
Non-standard residues in 1ew2 #5
---
MG — magnesium ion
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose
PO4 — phosphate ion
ZN — zinc ion
1ew2 mmCIF Assemblies
---
1| author_and_software_defined_assembly
> hide #!3 models
> select #5
4277 atoms, 3755 bonds, 24 pseudobonds, 1087 residues, 2 models selected
> ui tool show "Crystal Contacts"
> crystalcontacts #5
8 pairs of asymmetric units of 1ew2 contact at distance 3.0 A
Atoms MTRIX SMTRY Unit cell MTRIXref Copies
92 0 2 1 0 0 0 1
22 0 3 0 0 0 0 1
11 0 1 1 0 0 0 1
10 0 1 1 0 -1 0 1
9 0 7 0 0 0 0 1
8 0 7 -1 0 0 0 1
1 0 5 1 0 0 0 1
1 0 5 1 0 -1 0 1
> select clear
> ui tool show "Unit Cell"
> unitcell outline #5
> unitcell delete #5
> ui tool show "Cage Builder"
Drag select of 4 atoms, 1 bonds, 12 residues
Drag select of 23 residues
Drag select of 49 residues
> select up
622 atoms, 98 bonds, 85 residues, 3 models selected
> select up
1363 atoms, 1387 bonds, 180 residues, 3 models selected
> select up
12831 atoms, 11265 bonds, 3261 residues, 3 models selected
> cartoon hide sel
> hide sel target a
> hide #7 target m
> select #6.4
4277 atoms, 3755 bonds, 24 pseudobonds, 1087 residues, 2 models selected
> ~select #6.4
Nothing selected
> hide #!6.8 models
> show #!6.8 models
Drag select of 732 atoms, 2874 residues, 144 pseudobonds, 594 bonds
> surface (#!5#!6.1-2,4-5,8 & sel)
> color sel bypolymer
> rainbow sel
> color sel bychain
> color #6.1 #55ff00 transparency 0
> color #6.4 #ffff7f transparency 0
> color #6.8 #55ffff transparency 0
> color #6.5 #aa007f transparency 0
> color #6.5 #aa0000 transparency 0
> color #6.2 #ffaa00 transparency 0
> select clear
> lighting full
> lighting soft
> lighting simple
> lighting soft
> lighting flat
> lighting shadows true intensity 0.5
> lighting full
> hide #!6 models
> hide #!5 models
> show #!1 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> hide #!1 models
> select #1
30062 atoms, 30756 bonds, 1 pseudobond, 3877 residues, 2 models selected
No visible models!
> show #!1 models
> hide #1.1 models
> ~select #1
8 models selected
> select #1
30062 atoms, 30756 bonds, 1 pseudobond, 3877 residues, 2 models selected
> cartoon (#!1 & sel)
> hide (#!1 & sel) target a
> select clear
> show #!2 models
> select #2
30712 atoms, 31438 bonds, 3941 residues, 1 model selected
> hide #2.1-8 target m
> hide (#!2 & sel) target a
> cartoon (#!2 & sel)
> select clear
> ui tool show Matchmaker
> matchmaker #!2 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker acid_oct.pdb, chain G (#1) with basic_oct.pdb, chain E (#2),
sequence alignment score = 2485
RMSD between 484 pruned atom pairs is 0.284 angstroms; (across all 484 pairs:
0.284)
> matchmaker #2/A to #1/A pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker acid_oct.pdb, chain A (#1) with basic_oct.pdb, chain A (#2),
sequence alignment score = 2400.2
RMSD between 482 pruned atom pairs is 0.279 angstroms; (across all 482 pairs:
0.279)
> matchmaker #2/A to #1/B pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker acid_oct.pdb, chain B (#1) with basic_oct.pdb, chain A (#2),
sequence alignment score = 2467.4
RMSD between 482 pruned atom pairs is 0.236 angstroms; (across all 482 pairs:
0.236)
> show #2.1-8 target m
> color #2#!1 cornflower blue
> show #1.1-8 target m
> color #1-2 orange red
> undo
> select #1.8
3749 atoms, 484 residues, 1 model selected
> ui tool show "Color Actions"
> hide #!2 models
> select clear
Drag select of acid_oct.pdb_E SES surface, acid_oct.pdb_H SES surface,
acid_oct.pdb_D SES surface, acid_oct.pdb_G SES surface, acid_oct.pdb_A SES
surface, acid_oct.pdb_F SES surface, acid_oct.pdb_B SES surface,
acid_oct.pdb_C SES surface, 3872 residues
> color sel fire brick
> hide #!1 models
> show #!2 models
> show #!1 models
> select clear
Drag select of acid_oct.pdb_G SES surface, 80 of 380044 triangles,
acid_oct.pdb_F SES surface, 376 of 376746 triangles, basic_oct.pdb_C SES
surface, 292 of 377278 triangles, basic_oct.pdb_H SES surface, 135 of 375036
triangles
> lighting shadows false
> lighting shadows true
> lighting flat
> lighting full
> lighting soft
> lighting simple
> lighting soft
> select #1.8
3749 atoms, 484 residues, 1 model selected
> ~select #1.8
1 model selected
> select #1.7
3749 atoms, 484 residues, 1 model selected
> ~select #1.7
1 model selected
> select #1.6
3749 atoms, 484 residues, 1 model selected
> ~select #1.6
1 model selected
> select #1.5
3749 atoms, 484 residues, 1 model selected
> ~select #1.5
1 model selected
> select #1.4
3749 atoms, 484 residues, 1 model selected
> volume style mesh
No volumes specified
> volume style mesh
No volumes specified
> volume style mesh
No volumes specified
> transparency sel 50
> select clear
> select add #1/D:388@CA
1 atom, 1 residue, 1 model selected
> select up
7 atoms, 6 bonds, 1 residue, 2 models selected
> select up
199 atoms, 204 bonds, 27 residues, 2 models selected
> transparency sel 50
> select clear
> select add #1/E:265@CB
1 atom, 1 residue, 1 model selected
> select add #1/E:211@CG
2 atoms, 2 residues, 2 models selected
> select add #1/E:22@CE1
3 atoms, 3 residues, 2 models selected
> select up
27 atoms, 26 bonds, 3 residues, 2 models selected
> select up
378 atoms, 385 bonds, 45 residues, 2 models selected
> select up
3749 atoms, 3835 bonds, 484 residues, 2 models selected
> transparency sel 50
> select clear
> ui tool show Matchmaker
> matchmaker #2/C to #1/F pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker acid_oct.pdb, chain F (#1) with basic_oct.pdb, chain C (#2),
sequence alignment score = 2477.2
RMSD between 483 pruned atom pairs is 0.286 angstroms; (across all 484 pairs:
0.335)
> select add #1/H:381@CD1
1 atom, 1 residue, 1 model selected
> select add #1/H:4@OE1
2 atoms, 2 residues, 2 models selected
> select add #1/D:177@CG
3 atoms, 3 residues, 2 models selected
> select add #1/D:220@OE2
4 atoms, 4 residues, 3 models selected
> select add #1/D:421@CE1
5 atoms, 5 residues, 3 models selected
> select up
43 atoms, 40 bonds, 5 residues, 3 models selected
> select up
671 atoms, 682 bonds, 86 residues, 3 models selected
> select up
7498 atoms, 7670 bonds, 968 residues, 3 models selected
> transparency sel 0
> transparency sel 50
> select clear
> hide #!2 models
> show #!2 models
> hide #!1 models
> show #!1 models
> save E:\PPT\SHIP-M\2022年会\basci_acid_ALPL.png supersample 8
> transparentBackground true
> hide #2.1-8 target m
> hide #1.1-8 target m
Drag select of 7740 residues
> cartoon hide (#!1-2 & sel)
> select #1/F
3749 atoms, 3835 bonds, 484 residues, 1 model selected
> cartoon (#!1 & sel)
> select #2/C
3840 atoms, 3930 bonds, 493 residues, 1 model selected
> cartoon (#!2 & sel)
> ui mousemode right pivot
> select up
30712 atoms, 31438 bonds, 3941 residues, 2 models selected
> cartoon (#!2 & sel)
Drag select of 1145 residues
Drag select of 302 residues
> select up
13724 atoms, 14008 bonds, 1770 residues, 7 models selected
> select up
23032 atoms, 23578 bonds, 2955 residues, 7 models selected
> cartoon hide (#!2 & sel)
> select #1/F:181
6 atoms, 5 bonds, 1 residue, 1 model selected
> select up
44 atoms, 44 bonds, 6 residues, 2 models selected
> select up
3749 atoms, 3835 bonds, 484 residues, 2 models selected
> select up
30062 atoms, 30756 bonds, 3877 residues, 2 models selected
> cartoon (#!1 & sel)
> select clear
Drag select of 792 residues
Drag select of 51 residues
> select add #1/C:1
6486 atoms, 7 bonds, 844 residues, 6 models selected
Drag select of 55 residues
> select up
9767 atoms, 9973 bonds, 1271 residues, 7 models selected
> select up
22494 atoms, 23010 bonds, 2904 residues, 7 models selected
> cartoon hide (#!1 & sel)
Drag select of 1936 residues
> show (#!1-2 & sel) target ab
> select clear
> select ::name="CA"
8 atoms, 8 residues, 1 model selected
> show sel target ab
> style sel sphere
Changed 8 atom styles
> color sel yellow
> select ions
60 atoms, 60 residues, 10 models selected
> show (#!2 & sel) target ab
> style (#!2 & sel) sphere
Changed 24 atom styles
> select clear
> select ::name="MG"
26 atoms, 26 residues, 10 models selected
> color (#!2 & sel) lime
> select clear
> select ::name="ZN"
26 atoms, 26 residues, 10 models selected
> color (#!2 & sel) dim gray
> select clear
> select ::name="PO4"
45 atoms, 36 bonds, 9 residues, 9 models selected
> style #!1-2 sphere
Changed 60774 atom styles
> undo
> select ::name="PO4"
45 atoms, 36 bonds, 9 residues, 9 models selected
> show #!1-2 target ab
> undo
> select ::name="NAG"
952 atoms, 971 bonds, 68 residues, 12 models selected
> show (#!1-2 & sel) target ab
> color (#!1-2 & sel) byelement
> show #1.1 models
> show #1.2 models
> show #1.3 models
> show #1.4 models
> show #1.6 models
> show #1.7 models
> show #1.8 models
> show #1.5 models
> select #1
30062 atoms, 30756 bonds, 1 pseudobond, 3877 residues, 2 models selected
> transparency sel 0
> transparency sel 50
> transparency sel 90
> transparency sel 100
> graphics silhouettes false
> graphics silhouettes true
> select clear
Drag select of acid_oct.pdb_E SES surface, 375545 of 378314 triangles,
acid_oct.pdb_H SES surface, 175242 of 378990 triangles, acid_oct.pdb_D SES
surface, 18370 of 376744 triangles, acid_oct.pdb_G SES surface, 56367 of
380044 triangles, 196 atoms, 197 bonds
> select up
199 atoms, 197 bonds, 19 residues, 5 models selected
> select up
214 atoms, 215 bonds, 19 residues, 5 models selected
> hide (#!2 & sel) target a
> select clear
Drag select of acid_oct.pdb_E SES surface, 146123 of 378314 triangles,
acid_oct.pdb_H SES surface, 127114 of 378990 triangles, acid_oct.pdb_D SES
surface, acid_oct.pdb_G SES surface, 351584 of 380044 triangles,
acid_oct.pdb_B SES surface, 121020 of 375170 triangles, acid_oct.pdb_C SES
surface, 35923 of 376450 triangles, 185 atoms, 184 bonds
> select up
186 atoms, 184 bonds, 20 residues, 7 models selected
> hide (#!2 & sel) target a
> select up
189 atoms, 187 bonds, 20 residues, 7 models selected
> hide (#!2 & sel) target a
> select clear
Drag select of acid_oct.pdb_G SES surface, 880 of 380044 triangles,
acid_oct.pdb_B SES surface, 126774 of 375170 triangles, acid_oct.pdb_C SES
surface, 356379 of 376450 triangles, 88 atoms, 86 bonds
> select up
7669 atoms, 7851 bonds, 984 residues, 4 models selected
> select up
30712 atoms, 31438 bonds, 3941 residues, 6 models selected
> select down
7669 atoms, 7851 bonds, 984 residues, 12 models selected
> hide (#!2 & sel) target a
> select clear
Drag select of acid_oct.pdb_E SES surface, 31742 of 378314 triangles,
acid_oct.pdb_H SES surface, 98290 of 378990 triangles, acid_oct.pdb_D SES
surface, 110152 of 376744 triangles, acid_oct.pdb_G SES surface, 754 of 380044
triangles, 29 atoms, 29 bonds
> select up
3843 atoms, 3935 bonds, 492 residues, 5 models selected
> hide (#!2 & sel) target a
> select clear
> select add #2/C:632@C5
1 atom, 2 bonds, 1 residue, 2 models selected
> select add #2/C:621@C2
2 atoms, 2 bonds, 2 residues, 2 models selected
> select up
6 atoms, 2 bonds, 4 residues, 2 models selected
> select up
56 atoms, 56 bonds, 4 residues, 2 models selected
> surface sel
> color (#!1-2 & sel) orange
> select clear
> undo
> transparency sel 50
> select clear
> select #2/C:601@C1
1 atom, 1 residue, 1 model selected
> select add #1/A:485@C7
2 atoms, 2 residues, 2 models selected
> select up
28 atoms, 28 bonds, 2 residues, 2 models selected
> select up
7659 atoms, 7841 bonds, 982 residues, 2 models selected
> select down
28 atoms, 28 bonds, 2 residues, 6 models selected
> select up
7659 atoms, 7841 bonds, 982 residues, 2 models selected
> select clear
Drag select of 1 bonds
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
14 atoms, 14 bonds, 1 residue, 1 model selected
> surface sel
> transparency sel 50
> color sel orange
> transparency sel 50
> select #2/C:601@C5
1 atom, 1 residue, 1 model selected
> select up
14 atoms, 14 bonds, 1 residue, 1 model selected
> volume style surface
No volumes specified
> transparency #1.1-9#2.9-11 0
> undo
> transparency sel 50
> transparency sel 0
> select #1
30062 atoms, 30756 bonds, 1 pseudobond, 3877 residues, 2 models selected
> transparency sel 100
> select clear
> select #2/C:601@C4
1 atom, 1 residue, 1 model selected
> select up
14 atoms, 14 bonds, 1 residue, 1 model selected
> surface sel
> color sel orange
> select add #1/A:489@O4
15 atoms, 14 bonds, 2 residues, 3 models selected
> select add #2/C:632@C6
16 atoms, 14 bonds, 3 residues, 4 models selected
> select add #2/B:621@C5
17 atoms, 14 bonds, 4 residues, 5 models selected
> select add #2/C:621@C8
18 atoms, 14 bonds, 5 residues, 6 models selected
> select add #2/B:601@C3
19 atoms, 14 bonds, 6 residues, 6 models selected
> select up
84 atoms, 84 bonds, 6 residues, 7 models selected
> transparency sel 0
> transparency sel 50
> select clear
> select add #2/B:612@C5
1 atom, 1 residue, 1 model selected
> select add #2/C:612@C4
2 atoms, 2 residues, 1 model selected
> select up
28 atoms, 28 bonds, 2 residues, 1 model selected
> select up
7680 atoms, 7860 bonds, 986 residues, 1 model selected
> select down
28 atoms, 28 bonds, 2 residues, 7 models selected
> surface sel
> color sel orange
> transparency sel 50
> select clear
> select add #1/A:304@CB
1 atom, 1 residue, 1 model selected
> select add #1/A:304@CZ
2 atoms, 1 residue, 2 models selected
> select up
11 atoms, 10 bonds, 1 residue, 2 models selected
> select up
56 atoms, 56 bonds, 7 residues, 2 models selected
> select up
3819 atoms, 3911 bonds, 489 residues, 2 models selected
> cartoon style (#!1 & sel) modeHelix tube sides 20
> select #1/A:293@C
1 atom, 1 residue, 1 model selected
> select up
6 atoms, 5 bonds, 1 residue, 2 models selected
> select up
82 atoms, 81 bonds, 11 residues, 2 models selected
> select up
3819 atoms, 3911 bonds, 489 residues, 2 models selected
> cartoon style (#!1 & sel) modeHelix tube sides 20
> select clear
> cartoon style (#1#2.9-14#!2 & coil) xsection oval
> cartoon style #1#2.9-14#!2 xsection barbell modeHelix default
> select #1.2
3749 atoms, 484 residues, 1 model selected
> transparency sel 0
> select #1.3
3749 atoms, 484 residues, 1 model selected
> transparency sel 0
> select #1.4
3749 atoms, 484 residues, 1 model selected
> transparency sel 0
> select #1.5
3749 atoms, 484 residues, 1 model selected
> transparency sel 0
> undo
> select #1.5
3749 atoms, 484 residues, 1 model selected
> transparency sel 100
> select clear
> select #1.6
3749 atoms, 484 residues, 1 model selected
> select #1.7
3749 atoms, 484 residues, 1 model selected
> transparency sel 0
> select #1.8
3749 atoms, 484 residues, 1 model selected
> transparency sel 0
> select clear
> select #1/H:221@CA
1 atom, 1 residue, 1 model selected
> select up
6 atoms, 5 bonds, 1 residue, 2 models selected
> select up
203 atoms, 205 bonds, 25 residues, 2 models selected
> select up
3749 atoms, 3835 bonds, 484 residues, 2 models selected
> transparency sel 50
> select clear
Drag select of acid_oct.pdb_A SES surface, 9519 of 375256 triangles, 88 atoms,
26 residues, 73 bonds
> select up
221 atoms, 211 bonds, 30 residues, 4 models selected
> select up
258 atoms, 252 bonds, 30 residues, 4 models selected
> select clear
> cartoon style #1#2.9-14#!2 modeHelix tube sides 20
> select clear
Drag select of acid_oct.pdb_A SES surface, 3404 of 375256 triangles,
acid_oct.pdb_F SES surface, 701 of 376746 triangles, 31 atoms, 8 residues, 27
bonds
> select up
88 atoms, 85 bonds, 13 residues, 5 models selected
> select up
119 atoms, 118 bonds, 13 residues, 5 models selected
> select up
723 atoms, 740 bonds, 95 residues, 5 models selected
> select up
11499 atoms, 11771 bonds, 1475 residues, 5 models selected
> hide (#!1-2 & sel) target a
> select clear
Drag select of acid_oct.pdb_A SES surface, 3681 of 375256 triangles,
acid_oct.pdb_F SES surface, 4439 of 376746 triangles, 14 atoms, 16 residues,
13 bonds
> select up
124 atoms, 61 bonds, 17 residues, 6 models selected
> select up
131 atoms, 68 bonds, 17 residues, 6 models selected
> select up
1008 atoms, 1030 bonds, 134 residues, 6 models selected
> select up
15248 atoms, 15606 bonds, 1959 residues, 6 models selected
> hide (#!1-2 & sel) target a
> select clear
> select ::name="NAG"
952 atoms, 971 bonds, 68 residues, 12 models selected
> surface (#!1-2 & sel)
> undo
> select ::name="NAG"
952 atoms, 971 bonds, 68 residues, 12 models selected
> surface hidePatches (#!1-2 & sel)
> select ::name="NAG"
952 atoms, 971 bonds, 68 residues, 12 models selected
> select intersect #1/A
71 bonds, 1 model selected
> surface sel
No atoms specified by sel
> show sel target ab
> surface sel
No atoms specified by sel
> select up
70 atoms, 71 bonds, 5 residues, 1 model selected
> surface (#!1 & sel)
> color sel orange
> transparency sel 50
> select clear
> select intersect #1/F
Nothing selected
> select intersect ::name="NAG"
Nothing selected
> show #1#2.9-16#!2 target ab
> undo
> select clear
> select intersect ::name="NAG"
Nothing selected
> select clear
> select ::name="NAG"
952 atoms, 971 bonds, 68 residues, 12 models selected
> select intersect #1/F
Nothing selected
> select clear
> select ::name="NAG"
952 atoms, 971 bonds, 68 residues, 12 models selected
> select intersect #1/F
Nothing selected
> hide #!1 models
> show #!1 models
> select clear
> select intersect #2/C
Nothing selected
> select clear
> select #1/F
3749 atoms, 3835 bonds, 484 residues, 1 model selected
> select intersect ::name="NAG"
Nothing selected
> select #1/F:178@CA
1 atom, 1 residue, 1 model selected
> select up
9 atoms, 8 bonds, 1 residue, 2 models selected
> select up
44 atoms, 44 bonds, 6 residues, 2 models selected
> select clear
> select #1/F:182@CA
1 atom, 1 residue, 1 model selected
> select up
9 atoms, 8 bonds, 1 residue, 2 models selected
> select up
44 atoms, 44 bonds, 6 residues, 2 models selected
> select up
3749 atoms, 3835 bonds, 484 residues, 2 models selected
> show (#!1 & sel) target ab
> hide (#!1 & sel) target a
> select #1/F:280@CD2
1 atom, 1 residue, 1 model selected
> select up
12 atoms, 12 bonds, 1 residue, 2 models selected
> select up
68 atoms, 70 bonds, 8 residues, 2 models selected
> select up
3749 atoms, 3835 bonds, 484 residues, 2 models selected
> show (#!1 & sel) target ab
> hide (#!1 & sel) target a
> select ::name="NAG"
952 atoms, 971 bonds, 68 residues, 12 models selected
> show (#!1-2 & sel) target ab
> select clear
> select add #1/F:220@CB
1 atom, 1 residue, 1 model selected
> select clear
Drag select of 2 atoms, 3 bonds
> select add #2/C:621@C2
3 atoms, 3 bonds, 2 residues, 2 models selected
> select up
9 atoms, 5 bonds, 4 residues, 2 models selected
> select up
56 atoms, 56 bonds, 4 residues, 2 models selected
> surface (#!2 & sel)
> color (#!2 & sel) orange
> transparency sel 50
> select #1/A:307@CB
1 atom, 1 residue, 1 model selected
> select add #2/G:612@O5
2 atoms, 2 residues, 3 models selected
> select clear
> select #2/A:611@C4
1 atom, 1 residue, 1 model selected
> select #2/G:612@O6
1 atom, 1 residue, 1 model selected
> select #2/G:612@O6
1 atom, 1 residue, 1 model selected
> select add #2/A:611@C5
2 atoms, 2 residues, 2 models selected
> select add #2/G:704@O3
3 atoms, 3 residues, 3 models selected
> select add #2/G:601@C4
4 atoms, 4 residues, 3 models selected
> select add #2/A:621@C3
5 atoms, 5 residues, 3 models selected
> select up
70 atoms, 70 bonds, 5 residues, 3 models selected
> select up
7672 atoms, 7855 bonds, 983 residues, 3 models selected
> hide (#!2 & sel) target a
> select clear
> hide #!1.3 models
> show #!1.3 models
> hide #1.5 models
> show #1.5 models
> hide #1.6 models
> show #1.6 models
> hide #!1.7 models
> show #!1.7 models
> hide #!1.8 models
> show #!1.8 models
> hide #!1.1 models
> show #!1.1 models
> hide #!1.2 models
Drag select of acid_oct.pdb_E SES surface, 678 of 378314 triangles
> select #1.1
3749 atoms, 484 residues, 2 models selected
> transparency sel 0
> select clear
Drag select of acid_oct.pdb_F SES surface, 347 of 376746 triangles
> select up
26313 atoms, 3393 residues, 10 models selected
> select down
Nothing selected
> select clear
> hide #!1.3 models
> show #!1.3 models
> hide #!1.4 models
> show #!1.4 models
> select #1.4
3749 atoms, 484 residues, 2 models selected
> transparency sel 50
> transparency sel 0
> color #1.4 #ffaa7f transparency 0
> color #1.4 #ffcdbe transparency 0
> select add #1/E:12@CB
3750 atoms, 485 residues, 3 models selected
> select add #1/B:240@CD
3751 atoms, 486 residues, 4 models selected
> select #1.5
3749 atoms, 484 residues, 1 model selected
> ~select #1.5
1 model selected
> select #1.6
3749 atoms, 484 residues, 1 model selected
> select #1.7
3749 atoms, 484 residues, 2 models selected
> color #1.7 #ffcdbe transparency 0
> color #1.8 #ffcdbe transparency 0
> color #1.3 #ffcdbe transparency 0
> color #1.2 #ffcdbe80
> color #1.1 #ffcdbe transparency 0
> select clear
> lighting flat
> lighting full
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting simple
> save E:\PPT\SHIP-M\2022年会\basci_acid_ALPLb.png supersample 8
> transparentBackground true
> hide #1.5-6,9#!1.1-4,7-8 target m
> select clear
> select #1
30062 atoms, 30756 bonds, 1 pseudobond, 3877 residues, 8 models selected
> cartoon (#!1 & sel)
> select #2
30712 atoms, 31438 bonds, 3941 residues, 1 model selected
> cartoon (#!2 & sel)
> select clear
> hide #!2 models
> show #!2 models
> hide #!1 models
> show #!1 models
> hide #!2 models
> show #!2 models
> hide #!1 models
> show #!1 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!1.1 models
> hide #!1.1 models
> show #!2 models
> hide #!1 models
> show #!1 models
> hide #!2 models
> select add #1/F:482
7 atoms, 7 bonds, 1 residue, 1 model selected
> select add #1/G:482
14 atoms, 14 bonds, 2 residues, 2 models selected
> show (#!1 & sel) target ab
> color (#!1 & sel) byelement
> select add #1/H:482
21 atoms, 21 bonds, 3 residues, 3 models selected
> select add #1/B:482
28 atoms, 28 bonds, 4 residues, 4 models selected
> color (#!1 & sel) byelement
> show (#!1 & sel) target ab
> hide #!1 models
> show #!2 models
> select #2/pro
Nothing selected
> select #2:pro
1232 atoms, 1240 bonds, 176 residues, 1 model selected
> select clear
> show #!1 models
> hide #!2 models
> show #!2 models
> hide #!1 models
> select #2:pro
1232 atoms, 1240 bonds, 176 residues, 1 model selected
> select clear
> select #2:264
72 atoms, 64 bonds, 8 residues, 1 model selected
> show (#!2 & sel) target ab
> hide #!2 models
> show #!1 models
> select #1:264
80 atoms, 80 bonds, 8 residues, 1 model selected
> show (#!1 & sel) target ab
> color (#!1 & sel) byelement
> select clear
> select #1:pro
1232 atoms, 1240 bonds, 176 residues, 1 model selected
> hide (#!1 & sel) target a
> select clear
> hide #!1 models
> show #!2 models
> select #1:264
80 atoms, 80 bonds, 8 residues, 1 model selected
> select #2:264
72 atoms, 64 bonds, 8 residues, 1 model selected
> show (#!2 & sel) target ab
> color (#!2 & sel) byelement
> select clear
> hide #!2 models
> show #!1 models
> select #1:264
80 atoms, 80 bonds, 8 residues, 1 model selected
> hide (#!1 & sel) target a
> select #1/B:247
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1:247
72 atoms, 64 bonds, 8 residues, 1 model selected
> show (#!1 & sel) target ab
> color (#!1 & sel) byelement
> select clear
> show #!2 models
> hide #!1 models
> select #2/H:264@CE
1 atom, 1 residue, 1 model selected
> select up
9 atoms, 8 bonds, 1 residue, 2 models selected
> select up
115 atoms, 121 bonds, 12 residues, 2 models selected
> select down
9 atoms, 8 bonds, 1 residue, 2 models selected
> select sel : select clear
> select #2:glu
2088 atoms, 1864 bonds, 232 residues, 1 model selected
> select #2:asp
1856 atoms, 1624 bonds, 232 residues, 1 model selected
> select clear
> hide #!2 models
> show #!1 models
> hide #!1 models
> show #!2 models
Drag select of basic_oct.pdb_C SES surface, 293 of 13522 triangles, 2 atoms,
355 residues, 2 bonds
> select clear
Drag select of 100 atoms, 913 residues, 101 bonds
> select up
6473 atoms, 6595 bonds, 840 residues, 8 models selected
> select up
6493 atoms, 6617 bonds, 840 residues, 8 models selected
> select up
7890 atoms, 8062 bonds, 1013 residues, 8 models selected
> select up
15363 atoms, 15727 bonds, 1971 residues, 8 models selected
> hide (#!2 & sel) target a
> cartoon hide (#!2 & sel)
Drag select of 76 atoms, 425 residues, 77 bonds
> select up
3741 atoms, 3826 bonds, 479 residues, 4 models selected
> select up
7669 atoms, 7851 bonds, 984 residues, 4 models selected
> hide (#!2 & sel) target a
> cartoon hide (#!2 & sel)
> select clear
Drag select of 10 residues
> select up
285 atoms, 285 bonds, 39 residues, 3 models selected
> select up
7680 atoms, 7860 bonds, 986 residues, 3 models selected
> select down
285 atoms, 285 bonds, 39 residues, 5 models selected
> select up
7680 atoms, 7860 bonds, 986 residues, 3 models selected
> select down
285 atoms, 285 bonds, 39 residues, 5 models selected
> select clear
> select #2/C:207
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
60 atoms, 61 bonds, 7 residues, 2 models selected
> select up
3840 atoms, 3930 bonds, 493 residues, 2 models selected
> color (#!2 & sel) forest green
> surface hidePatches (#!2 & sel)
> select clear
Drag select of 180 atoms, 1084 residues, 182 bonds
> select intersect ::name="NAG"
28 atoms, 172 bonds, 2 residues, 1 model selected
> select up
168 atoms, 172 bonds, 12 residues, 1 model selected
> color (#!2 & sel) byhetero
> color (#!2 & sel) byelement
> surface (#!2 & sel)
> transparency sel 50
> hide #2.11 models
> show #2.11 models
> color #2.11 #ffaa0080
> hide #2.10 models
> show #2.10 models
> color #2.10 #ffaa0080
> select clear
> select #2/C:264@CD
1 atom, 1 residue, 1 model selected
> select up
9 atoms, 8 bonds, 1 residue, 2 models selected
> select clear
===== Log before crash end =====
Log:
Startup Messages
---
warning | Unable to enumerate family ' "WenYue XinQingNianTi (Authorization
Required)" '
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 3.3.0 NVIDIA 497.09
OpenGL renderer: NVIDIA GeForce GTX 1070/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Dell Inc.
Model: XPS 8930
OS: Microsoft Windows 11 家庭中文版 (Build 22000)
Memory: 34,159,972,352
MaxProcessMemory: 137,438,953,344
CPU: 12 Intel(R) Core(TM) i7-8700 CPU @ 3.20GHz
OSLanguage: zh-CN
Locale: ('zh_CN', 'cp936')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
Babel: 2.9.1
backcall: 0.2.0
blockdiag: 2.0.1
certifi: 2021.10.8
cftime: 1.5.1.1
charset-normalizer: 2.0.9
ChimeraX-AddCharge: 1.2.2
ChimeraX-AddH: 2.1.11
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.2.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.31
ChimeraX-AtomicLibrary: 4.2
ChimeraX-AtomSearch: 2.0
ChimeraX-AtomSearchLibrary: 1.0
ChimeraX-AxesPlanes: 2.0
ChimeraX-BasicActions: 1.1
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.0
ChimeraX-BondRot: 2.0
ChimeraX-BugReporter: 1.0
ChimeraX-BuildStructure: 2.6.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.1
ChimeraX-ButtonPanel: 1.0
ChimeraX-CageBuilder: 1.0
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.2
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.2.2
ChimeraX-ColorActions: 1.0
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5
ChimeraX-CommandLine: 1.1.5
ChimeraX-ConnectStructure: 2.0
ChimeraX-Contacts: 1.0
ChimeraX-Core: 1.3
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.3.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0
ChimeraX-DataFormats: 1.2.2
ChimeraX-Dicom: 1.0
ChimeraX-DistMonitor: 1.1.5
ChimeraX-DistUI: 1.0
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0
ChimeraX-FunctionKey: 1.0
ChimeraX-Geometry: 1.1
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1
ChimeraX-Hbonds: 2.1.2
ChimeraX-Help: 1.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0
ChimeraX-Label: 1.1
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.4
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.1
ChimeraX-Map: 1.1
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1
ChimeraX-Markers: 1.0
ChimeraX-Mask: 1.0
ChimeraX-MatchMaker: 2.0.4
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.1
ChimeraX-Meeting: 1.0
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.4
ChimeraX-MMTF: 2.1
ChimeraX-Modeller: 1.2.6
ChimeraX-ModelPanel: 1.2.1
ChimeraX-ModelSeries: 1.0
ChimeraX-Mol2: 2.0
ChimeraX-Morph: 1.0
ChimeraX-MouseModes: 1.1
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0.2
ChimeraX-OpenCommand: 1.7
ChimeraX-PDB: 2.6.5
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.0.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-ResidueFit: 1.0
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0.1
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.4.6
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0
ChimeraX-Shortcuts: 1.1
ChimeraX-ShowAttr: 1.0
ChimeraX-ShowSequences: 1.0
ChimeraX-SideView: 1.0
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.6.1
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-Struts: 1.0
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0
ChimeraX-SwapRes: 2.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1
ChimeraX-ToolshedUtils: 1.2
ChimeraX-Tug: 1.0
ChimeraX-UI: 1.13.7
ChimeraX-uniprot: 2.2
ChimeraX-UnitCell: 1.0
ChimeraX-ViewDockX: 1.0.1
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0
ChimeraX-WebServices: 1.0
ChimeraX-Zone: 1.0
colorama: 0.4.4
comtypes: 1.1.10
cxservices: 1.1
cycler: 0.11.0
Cython: 0.29.24
decorator: 5.1.0
docutils: 0.17.1
filelock: 3.0.12
funcparserlib: 0.3.6
grako: 3.16.5
h5py: 3.6.0
html2text: 2020.1.16
idna: 3.3
ihm: 0.21
imagecodecs: 2021.4.28
imagesize: 1.3.0
ipykernel: 5.5.5
ipython: 7.23.1
ipython-genutils: 0.2.0
jedi: 0.18.0
Jinja2: 3.0.1
jupyter-client: 6.1.12
jupyter-core: 4.9.1
kiwisolver: 1.3.2
lxml: 4.6.3
lz4: 3.1.3
MarkupSafe: 2.0.1
matplotlib: 3.4.3
matplotlib-inline: 0.1.3
msgpack: 1.0.2
netCDF4: 1.5.7
networkx: 2.6.3
numexpr: 2.8.0
numpy: 1.21.2
openvr: 1.16.801
packaging: 21.3
ParmEd: 3.2.0
parso: 0.8.3
pickleshare: 0.7.5
Pillow: 8.3.2
pip: 21.2.4
pkginfo: 1.7.1
prompt-toolkit: 3.0.23
psutil: 5.8.0
pycollada: 0.7.1
pydicom: 2.1.2
Pygments: 2.10.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.6
PyQt5-commercial: 5.15.2
PyQt5-sip: 12.8.1
PyQtWebEngine-commercial: 5.15.2
python-dateutil: 2.8.2
pytz: 2021.3
pywin32: 228
pyzmq: 22.3.0
qtconsole: 5.1.1
QtPy: 1.11.3
RandomWords: 0.3.0
requests: 2.26.0
scipy: 1.7.1
setuptools: 57.5.0
sfftk-rw: 0.7.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
Sphinx: 4.2.0
sphinx-autodoc-typehints: 1.12.0
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 2.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
suds-jurko: 0.6
tables: 3.6.1
tifffile: 2021.4.8
tinyarray: 1.2.3
tornado: 6.1
traitlets: 5.1.1
urllib3: 1.26.7
wcwidth: 0.2.5
webcolors: 1.11.1
wheel: 0.37.0
wheel-filename: 1.3.0
WMI: 1.5.1
Change History (2)
comment:1 by , 4 years ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Command Line |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Long atom spec crashes ChimeraX |
comment:2 by , 4 years ago
| Resolution: | → duplicate |
|---|---|
| Status: | accepted → closed |
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