Crash in event loop

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.26100
ChimeraX Version: 1.10.dev202503110047 (2025-03-11 00:47:19 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Windows fatal exception: code 0x8001010d

Thread 0x000092f8 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503110047\bin\Lib\threading.py", line 320 in wait
  File "C:\Program Files\ChimeraX 1.10.dev202503110047\bin\Lib\threading.py", line 622 in wait
  File "C:\Program Files\ChimeraX 1.10.dev202503110047\bin\Lib\multiprocessing\pool.py", line 765 in wait
  File "C:\Program Files\ChimeraX 1.10.dev202503110047\bin\Lib\multiprocessing\pool.py", line 768 in get
  File "C:\Program Files\ChimeraX 1.10.dev202503110047\bin\Lib\site-packages\chimerax\core\toolshed\__init__.py", line 1678 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503110047\bin\Lib\site-packages\chimerax\core\tasks.py", line 300 in _run_function
  File "C:\Program Files\ChimeraX 1.10.dev202503110047\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503110047\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503110047\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x000018d4 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503110047\bin\Lib\multiprocessing\pool.py", line 579 in _handle_results
  File "C:\Program Files\ChimeraX 1.10.dev202503110047\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503110047\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503110047\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x000019a8 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503110047\bin\Lib\multiprocessing\pool.py", line 531 in _handle_tasks
  File "C:\Program Files\ChimeraX 1.10.dev202503110047\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503110047\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503110047\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x0000844c (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503110047\bin\Lib\multiprocessing\connection.py", line 810 in _exhaustive_wait
  File "C:\Program Files\ChimeraX 1.10.dev202503110047\bin\Lib\multiprocessing\connection.py", line 878 in wait
  File "C:\Program Files\ChimeraX 1.10.dev202503110047\bin\Lib\multiprocessing\pool.py", line 502 in _wait_for_updates
  File "C:\Program Files\ChimeraX 1.10.dev202503110047\bin\Lib\multiprocessing\pool.py", line 522 in _handle_workers
  File "C:\Program Files\ChimeraX 1.10.dev202503110047\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503110047\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503110047\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00005284 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503110047\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503110047\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503110047\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503110047\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x0000a0dc (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503110047\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503110047\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503110047\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503110047\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00006b84 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503110047\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503110047\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503110047\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503110047\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00009fdc (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503110047\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503110047\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503110047\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503110047\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x0000570c (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503110047\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503110047\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503110047\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503110047\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00009b8c (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503110047\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503110047\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503110047\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503110047\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00009fc4 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503110047\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503110047\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503110047\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503110047\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x0000a1f8 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503110047\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503110047\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503110047\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503110047\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x0000988c (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503110047\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503110047\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503110047\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503110047\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00005e58 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503110047\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503110047\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503110047\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503110047\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00009dec (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503110047\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503110047\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503110047\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503110047\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x000098ac (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503110047\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503110047\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503110047\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503110047\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00008300 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503110047\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503110047\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503110047\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503110047\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x0000911c (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503110047\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503110047\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503110047\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503110047\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x0000973c (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503110047\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503110047\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503110047\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503110047\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00009fc8 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503110047\bin\Lib\socket.py", line 962 in getaddrinfo
  File "C:\Program Files\ChimeraX 1.10.dev202503110047\bin\Lib\site-packages\urllib3\util\connection.py", line 60 in create_connection
  File "C:\Program Files\ChimeraX 1.10.dev202503110047\bin\Lib\site-packages\urllib3\connection.py", line 198 in _new_conn
  File "C:\Program Files\ChimeraX 1.10.dev202503110047\bin\Lib\site-packages\urllib3\connection.py", line 276 in connect
  File "C:\Program Files\ChimeraX 1.10.dev202503110047\bin\Lib\http\client.py", line 979 in send
  File "C:\Program Files\ChimeraX 1.10.dev202503110047\bin\Lib\http\client.py", line 1041 in _send_output
  File "C:\Program Files\ChimeraX 1.10.dev202503110047\bin\Lib\http\client.py", line 1281 in endheaders
  File "C:\Program Files\ChimeraX 1.10.dev202503110047\bin\Lib\site-packages\urllib3\connection.py", line 445 in request
  File "C:\Program Files\ChimeraX 1.10.dev202503110047\bin\Lib\site-packages\urllib3\connectionpool.py", line 493 in _make_request
  File "C:\Program Files\ChimeraX 1.10.dev202503110047\bin\Lib\site-packages\urllib3\connectionpool.py", line 787 in urlopen
  File "C:\Program Files\ChimeraX 1.10.dev202503110047\bin\Lib\site-packages\urllib3\poolmanager.py", line 443 in urlopen
  File "C:\Program Files\ChimeraX 1.10.dev202503110047\bin\Lib\site-packages\urllib3\_request_methods.py", line 182 in request_encode_url
  File "C:\Program Files\ChimeraX 1.10.dev202503110047\bin\Lib\site-packages\urllib3\_request_methods.py", line 135 in request
  File "C:\Program Files\ChimeraX 1.10.dev202503110047\bin\Lib\site-packages\cxservices\rest.py", line 206 in request
  File "C:\Program Files\ChimeraX 1.10.dev202503110047\bin\Lib\site-packages\cxservices\rest.py", line 228 in GET
  File "C:\Program Files\ChimeraX 1.10.dev202503110047\bin\Lib\site-packages\cxservices\api_client.py", line 341 in request
  File "C:\Program Files\ChimeraX 1.10.dev202503110047\bin\Lib\site-packages\cxservices\api_client.py", line 151 in __call_api
  File "C:\Program Files\ChimeraX 1.10.dev202503110047\bin\Lib\multiprocessing\pool.py", line 125 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503110047\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503110047\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503110047\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00009f88 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503110047\bin\Lib\socket.py", line 836 in create_connection
  File "C:\Program Files\ChimeraX 1.10.dev202503110047\bin\Lib\http\client.py", line 945 in connect
  File "C:\Program Files\ChimeraX 1.10.dev202503110047\bin\Lib\http\client.py", line 1451 in connect
  File "C:\Program Files\ChimeraX 1.10.dev202503110047\bin\Lib\http\client.py", line 979 in send
  File "C:\Program Files\ChimeraX 1.10.dev202503110047\bin\Lib\http\client.py", line 1041 in _send_output
  File "C:\Program Files\ChimeraX 1.10.dev202503110047\bin\Lib\http\client.py", line 1281 in endheaders
  File "C:\Program Files\ChimeraX 1.10.dev202503110047\bin\Lib\http\client.py", line 1332 in _send_request
  File "C:\Program Files\ChimeraX 1.10.dev202503110047\bin\Lib\http\client.py", line 1286 in request
  File "C:\Program Files\ChimeraX 1.10.dev202503110047\bin\Lib\urllib\request.py", line 1348 in do_open
  File "C:\Program Files\ChimeraX 1.10.dev202503110047\bin\Lib\urllib\request.py", line 1391 in https_open
  File "C:\Program Files\ChimeraX 1.10.dev202503110047\bin\Lib\urllib\request.py", line 496 in _call_chain
  File "C:\Program Files\ChimeraX 1.10.dev202503110047\bin\Lib\urllib\request.py", line 536 in _open
  File "C:\Program Files\ChimeraX 1.10.dev202503110047\bin\Lib\urllib\request.py", line 519 in open
  File "C:\Program Files\ChimeraX 1.10.dev202503110047\bin\Lib\urllib\request.py", line 216 in urlopen
  File "C:\Program Files\ChimeraX 1.10.dev202503110047\bin\Lib\site-packages\chimerax\core\toolshed\available.py", line 62 in load
  File "C:\Program Files\ChimeraX 1.10.dev202503110047\bin\Lib\site-packages\chimerax\core\toolshed\__init__.py", line 516 in reload_available
  File "C:\Program Files\ChimeraX 1.10.dev202503110047\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503110047\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503110047\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00008acc (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503110047\bin\Lib\threading.py", line 324 in wait
  File "C:\Program Files\ChimeraX 1.10.dev202503110047\bin\Lib\threading.py", line 622 in wait
  File "C:\Program Files\ChimeraX 1.10.dev202503110047\bin\Lib\threading.py", line 1392 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503110047\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503110047\bin\Lib\threading.py", line 995 in _bootstrap

Current thread 0x00008f0c (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503110047\bin\Lib\site-packages\chimerax\ui\gui.py", line 339 in event_loop
  File "C:\Program Files\ChimeraX 1.10.dev202503110047\bin\Lib\site-packages\chimerax\core\__main__.py", line 1054 in init
  File "C:\Program Files\ChimeraX 1.10.dev202503110047\bin\Lib\site-packages\chimerax\core\__main__.py", line 1217 in 
  File "", line 88 in _run_code
  File "", line 198 in _run_module_as_main
===== Log before crash start =====
> open
> D:\DATA_Biken\AF\AF3\vesA_vscF2_vopW_oki\fold_vopw5_vesa5_vpa134325_model_0.cif
> format mmcif

Chain information for fold_vopw5_vesa5_vpa134325_model_0.cif #1  
---  
Chain | Description  
A B C D E | .  
AA BA CA DA EA FA GA HA IA K L M N O P Q R S T U V W X Y Z | .  
F G H I J | .  
  

monitorData: Unable to obtain handle for monitor '\\\\.\DISPLAY2', defaulting
to 96 DPI.  

monitorData: Unable to obtain handle for monitor '\\\\.\DISPLAY1', defaulting
to 96 DPI.  

monitorData: Unable to obtain handle for monitor '\\\\.\DISPLAY2', defaulting
to 96 DPI.  

monitorData: Unable to obtain handle for monitor '\\\\.\DISPLAY1', defaulting
to 96 DPI.  

monitorData: Unable to obtain handle for monitor '\\\\.\DISPLAY2', defaulting
to 96 DPI.  

monitorData: Unable to obtain handle for monitor '\\\\.\DISPLAY1', defaulting
to 96 DPI.  

monitorData: Unable to obtain handle for monitor '\\\\.\DISPLAY2', defaulting
to 96 DPI.  

monitorData: Unable to obtain handle for monitor '\\\\.\DISPLAY1', defaulting
to 96 DPI.  

Drag select of 36885 atoms  

> show sel atoms

> hide sel atoms

> select /F:1-165

1297 atoms, 1309 bonds, 165 residues, 1 model selected  

> show sel cartoons

Computing secondary structure  

> select /G:1-165

1297 atoms, 1309 bonds, 165 residues, 1 model selected  

> show sel cartoons

> select /H:1-165

1297 atoms, 1309 bonds, 165 residues, 1 model selected  

> show sel cartoons

> select /A:1-318

2525 atoms, 2571 bonds, 318 residues, 1 model selected  

> select /B:1-318

2525 atoms, 2571 bonds, 318 residues, 1 model selected  

> open
> D:\DATA_Biken\AF\AF3\vesA5_vscF2_25_vopW4_\fold_2025_05_02_19_24_model_0.cif
> format mmcif

Chain information for fold_2025_05_02_19_24_model_0.cif #2  
---  
Chain | Description  
A B C D E F G H I J K L M N O P Q R S T U V W X Y | .  
AA BA CA Z | .  
DA EA FA GA HA | .  
  

> hide #1 models

> show #1 models

> hide #1 models

Drag select of 33838 atoms  

> hide sel atoms

> open
> C:\Users\ag141\Desktop\T3SS2needle_vcsf2_Ca_real_space_refined_005-coot-0_real_space_refined_013.pdb
> format pdb

No such file/path:
C:\Users\ag141\Desktop\T3SS2needle_vcsf2_Ca_real_space_refined_005-coot-0_real_space_refined_013.pdb  

> open
> D:\DATA_Biken\CryoEM\Oki\EM2\T3SS2needle_vcsf2_Ca_real_space_refined_005-coot-0_real_space_refined_013.pdb
> format pdb

Chain information for
T3SS2needle_vcsf2_Ca_real_space_refined_005-coot-0_real_space_refined_013.pdb
#3  
---  
Chain | Description  
A B C E O R S | No description available  
D F G H I J K L M N Q T V W X Y Z | No description available  
P | No description available  
U | No description available  
  

> hide #3 models

> show #1 models

> hide #2 models

> hide #1 models

> show #2 models

> show sel atoms

> hide sel atoms

> show sel cartoons

Computing secondary structure  

> show #3 models

> select clear

Drag select of 17200 atoms  

> hide sel cartoons

> show sel cartoons

> show sel atoms

> hide sel atoms

> select clear

> hide #2 models

> hide #3 models

> show #1 models

> show #1 cartoons

> hide #1 atoms

Drag select of 4840 residues  

> hide sel atoms

> hide sel cartoons

> select /F:1-165

2539 atoms, 2555 bonds, 332 residues, 3 models selected  

> sequence chain #1/F#1/G#1/H#1/I#1/J

Alignment identifier is 1  

> show sel & #1 cartoons

> select /J:1-165

2539 atoms, 2555 bonds, 332 residues, 3 models selected  

> show sel & #1 cartoons

> select /J:1-165

2539 atoms, 2555 bonds, 332 residues, 3 models selected  

> show sel & #1 cartoons

> select /J:1-165

2539 atoms, 2555 bonds, 332 residues, 3 models selected  

> show sel & #1 cartoons

> select /J:1-165

2539 atoms, 2555 bonds, 332 residues, 3 models selected  

> show sel & #1 cartoons

> select /F:1-165

2539 atoms, 2555 bonds, 332 residues, 3 models selected  

> select /G:1-165

2539 atoms, 2555 bonds, 332 residues, 3 models selected  

> show sel & #1 cartoons

> select clear

Drag select of 1 residues  

> select /AA:1-97

1443 atoms, 1455 bonds, 194 residues, 2 models selected  

> select /AA:1-97

1443 atoms, 1455 bonds, 194 residues, 2 models selected  

> select /AA:1-97

1443 atoms, 1455 bonds, 194 residues, 2 models selected  

> show sel & #1 atoms

> select clear

> select /AA:1-97

1443 atoms, 1455 bonds, 194 residues, 2 models selected  

> show sel & #1 cartoons

> show sel & #2 cartoons

> show sel & #3 cartoons

> show sel & #1 cartoons

> hide sel & #1 atoms

> select clear

> show sel & #3 cartoons

> open
> D:\DATA_Biken\CryoEM\Oki\EM2\T3SS2needle_vcsf2_Ca_real_space_refined_005-coot-0_real_space_refined_013.pdb
> format pdb

Chain information for
T3SS2needle_vcsf2_Ca_real_space_refined_005-coot-0_real_space_refined_013.pdb
#4  
---  
Chain | Description  
A B C E O R S | No description available  
D F G H I J K L M N Q T V W X Y Z | No description available  
P | No description available  
U | No description available  
  

> hide #1 models

Drag select of 17200 atoms  

> hide sel atoms

> show sel cartoons

> select ::name="THR"

8176 atoms, 7123 bonds, 1168 residues, 4 models selected  

> show sel & #4 atoms

> style sel & #4 stick

Changed 1757 atom styles  

> select clear

> select ::name="THR"

8176 atoms, 7123 bonds, 1168 residues, 4 models selected  

> color (#4 & sel) red

> select ::name="SER"

7559 atoms, 6412 bonds, 1259 residues, 4 models selected  

> show sel & #4 atoms

> style sel & #4 stick

Changed 1248 atom styles  

> color (#4 & sel) blue

> select clear

Drag select of 1628 atoms, 2250 residues, 1169 bonds  

> hide sel cartoons

> hide sel atoms

> hide sel surfaces

> select #3/D:12-98

645 atoms, 647 bonds, 87 residues, 1 model selected  

> select #3/D:12-98

645 atoms, 647 bonds, 87 residues, 1 model selected  

> show #4 atoms

> undo

> select clear

> select #3/D:12-98

645 atoms, 647 bonds, 87 residues, 1 model selected  

> show #4 cartoons

> undo

> select clear

> select #4/F:12-98

645 atoms, 647 bonds, 87 residues, 1 model selected  

> show sel cartoons

> show sel atoms

> undo

> select ::name="THR"

8176 atoms, 7123 bonds, 1168 residues, 4 models selected  

> style sel & #4 stick

Changed 1757 atom styles  

> show sel & #4 atoms

> undo

> select clear

> select ::name="THR"

8176 atoms, 7123 bonds, 1168 residues, 4 models selected  

> show sel & #4 atoms

> select #4::name="THR"

1757 atoms, 1532 bonds, 251 residues, 1 model selected  

> select clear

> select #4::name="THR"

1757 atoms, 1532 bonds, 251 residues, 1 model selected  

> select #4/F::name="THR"

70 atoms, 61 bonds, 10 residues, 1 model selected  

> select ::name="THR"

8176 atoms, 7123 bonds, 1168 residues, 4 models selected  

> hide sel & #4 atoms

> select #4/F::name="THR"

70 atoms, 61 bonds, 10 residues, 1 model selected  

> show sel atoms

> select #4/F::name="SER"

48 atoms, 41 bonds, 8 residues, 1 model selected  

> show sel atoms

> style sel stick

Changed 48 atom styles  


===== Log before crash end =====

Log:
You can double click a model's Name or ID in the model panel to edit those
fields  
UCSF ChimeraX version: 1.10.dev202503110047 (2025-03-11)  
© 2016-2025 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 3.3.0 NVIDIA 472.12
OpenGL renderer: NVIDIA T600/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.11.4
Locale: ja_JP.cp932
Qt version: PyQt6 6.8.1, Qt 6.8.2
Qt runtime version: 6.8.2
Qt platform: windows

Manufacturer: To Be Filled By O.E.M.
Model: To Be Filled By O.E.M.
OS: Microsoft Windows 11 Education (Build 26100)
Memory: 34,207,977,472
MaxProcessMemory: 137,438,953,344
CPU: 16 11th Gen Intel(R) Core(TM) i7-11700 @ 2.50GHz
OSLanguage: ja-JP

Installed Packages:
    alabaster: 1.0.0
    appdirs: 1.4.4
    asttokens: 3.0.0
    auditwheel: 6.2.0
    babel: 2.17.0
    beautifulsoup4: 4.13.3
    blockdiag: 3.0.0
    blosc2: 3.2.0
    build: 1.2.2.post1
    certifi: 2025.1.31
    cftime: 1.6.4.post1
    charset-normalizer: 3.4.1
    ChimeraX-AddCharge: 1.5.18
    ChimeraX-AddH: 2.2.6
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.6
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.19.1
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Aniso: 1.1.1
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.60.5
    ChimeraX-AtomicLibrary: 14.1.13
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.3
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 3.0.0
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.2
    ChimeraX-BuildStructure: 2.13.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.4.0
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.4
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.3
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.8
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.10.dev202503110047
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.5
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.4
    ChimeraX-Dicom: 1.2.7
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.4
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.4.1
    ChimeraX-Hbonds: 2.5
    ChimeraX-Help: 1.3
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.3
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-KVFinder: 1.5.1
    ChimeraX-Label: 1.1.14
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.3
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.1.7
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.7.2
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.15
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.18
    ChimeraX-ModelPanel: 1.5
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-MutationScores: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.2
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.2
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.14.1
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.7
    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: 1.1.2
    ChimeraX-ProfileGrids: 1.0.2
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.6.3
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.3.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.3
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.5.7
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.17
    ChimeraX-Shape: 1.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.2.0
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-SimilarStructures: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.19.1
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.2.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.5.2
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.2.3
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.44
    ChimeraX-Umap: 1.0
    ChimeraX-uniprot: 2.3.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.4
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.4
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    comtypes: 1.4.5
    contourpy: 1.3.1
    coverage: 7.6.12
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.0.12
    debugpy: 1.8.13
    decorator: 5.2.1
    docutils: 0.21.2
    executing: 2.2.0
    filelock: 3.17.0
    fonttools: 4.56.0
    funcparserlib: 2.0.0a0
    glfw: 2.8.0
    grako: 3.16.5
    h5py: 3.13.0
    html2text: 2024.2.26
    idna: 3.10
    ihm: 2.2
    imagecodecs: 2024.6.1
    imagesize: 1.4.1
    iniconfig: 2.0.0
    ipykernel: 6.29.5
    ipython: 8.26.0
    ipywidgets: 8.1.5
    jedi: 0.19.1
    Jinja2: 3.1.6
    jupyter_client: 8.6.2
    jupyter_core: 5.7.2
    jupyterlab_widgets: 3.0.13
    kiwisolver: 1.4.8
    line_profiler: 4.2.0
    lxml: 5.3.1
    lz4: 4.4.3
    MarkupSafe: 3.0.2
    matplotlib: 3.9.2
    matplotlib-inline: 0.1.7
    msgpack: 1.1.0
    ndindex: 1.9.2
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.10.2
    numpy: 1.26.4
    OpenMM: 8.2.0
    openvr: 1.26.701
    packaging: 24.2
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pickleshare: 0.7.5
    pillow: 10.4.0
    pip: 25.0.1
    pkginfo: 1.11.1
    platformdirs: 4.3.6
    pluggy: 1.5.0
    prompt_toolkit: 3.0.50
    psutil: 6.0.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    pyelftools: 0.32
    Pygments: 2.18.0
    pynmrstar: 3.3.5
    pynrrd: 1.0.0
    PyOpenGL: 3.1.9
    PyOpenGL-accelerate: 3.1.9
    pyopenxr: 1.1.4501
    pyparsing: 3.2.1
    pyproject_hooks: 1.2.0
    PyQt6-commercial: 6.8.1
    PyQt6-Qt6: 6.8.2
    PyQt6-WebEngine-commercial: 6.8.0
    PyQt6-WebEngine-Qt6: 6.8.2
    PyQt6_sip: 13.10.0
    pytest: 8.3.5
    pytest-cov: 6.0.0
    python-dateutil: 2.9.0.post0
    pytz: 2025.1
    pywin32: 306
    pyzmq: 26.2.1
    qtconsole: 5.5.2
    QtPy: 2.4.3
    qtshim: 1.1
    RandomWords: 0.4.0
    requests: 2.32.3
    scipy: 1.14.0
    setuptools: 75.8.2
    sfftk-rw: 0.8.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.6
    Sphinx: 8.1.3
    sphinx-autodoc-typehints: 3.0.1
    sphinxcontrib-applehelp: 2.0.0
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 2.0.0
    sphinxcontrib-htmlhelp: 2.1.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 2.0.0
    sphinxcontrib-serializinghtml: 2.0.0
    stack-data: 0.6.3
    superqt: 0.7.1
    tables: 3.10.2
    tcia_utils: 1.5.1
    tifffile: 2024.7.24
    tinyarray: 1.2.4
    tornado: 6.4.2
    traitlets: 5.14.3
    typing_extensions: 4.12.2
    tzdata: 2025.1
    urllib3: 2.3.0
    wcwidth: 0.2.13
    webcolors: 24.11.1
    wheel: 0.45.1
    wheel-filename: 1.4.2
    widgetsnbextension: 4.0.13
    WMI: 1.5.1