Opened 6 months ago

Last modified 6 months ago

#17647 accepted defect

Crash using open/save dialog

Reported by: chimerax-bug-report@… Owned by: Eric Pettersen
Priority: normal Milestone:
Component: UI Version:
Keywords: Cc: Tom Goddard
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Windows-10-10.0.26100
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: code 0xc0000002

Thread 0x00005518 (most recent call first):
  File "C:\Program Files (x86)\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 135 in show_open_file_dialog
  File "C:\Program Files (x86)\ChimeraX 1.3\bin\lib\site-packages\chimerax\toolbar\providers.py", line 17 in _file_open
  File "C:\Program Files (x86)\ChimeraX 1.3\bin\lib\site-packages\chimerax\toolbar\providers.py", line 45 in run_provider
  File "C:\Program Files (x86)\ChimeraX 1.3\bin\lib\site-packages\chimerax\toolbar\__init__.py", line 37 in run_provider
  File "C:\Program Files (x86)\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\toolshed\__init__.py", line 1284 in run_provider
  File "C:\Program Files (x86)\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\toolshed\info.py", line 381 in run_provider
  File "C:\Program Files (x86)\ChimeraX 1.3\bin\lib\site-packages\chimerax\toolbar\tool.py", line 165 in callback
  File "C:\Program Files (x86)\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
  File "C:\Program Files (x86)\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
  File "C:\Program Files (x86)\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 1018 in 
  File "C:\Program Files (x86)\ChimeraX 1.3\bin\lib\runpy.py", line 87 in _run_code
  File "C:\Program Files (x86)\ChimeraX 1.3\bin\lib\runpy.py", line 197 in _run_module_as_main
Windows fatal exception: code 0xc0000002

Thread 0x00005518 (most recent call first):
  File "C:\Program Files (x86)\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 135 in show_open_file_dialog
  File "C:\Program Files (x86)\ChimeraX 1.3\bin\lib\site-packages\chimerax\toolbar\providers.py", line 17 in _file_open
  File "C:\Program Files (x86)\ChimeraX 1.3\bin\lib\site-packages\chimerax\toolbar\providers.py", line 45 in run_provider
  File "C:\Program Files (x86)\ChimeraX 1.3\bin\lib\site-packages\chimerax\toolbar\__init__.py", line 37 in run_provider
  File "C:\Program Files (x86)\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\toolshed\__init__.py", line 1284 in run_provider
  File "C:\Program Files (x86)\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\toolshed\info.py", line 381 in run_provider
  File "C:\Program Files (x86)\ChimeraX 1.3\bin\lib\site-packages\chimerax\toolbar\tool.py", line 165 in callback
  File "C:\Program Files (x86)\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
  File "C:\Program Files (x86)\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
  File "C:\Program Files (x86)\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 1018 in 
  File "C:\Program Files (x86)\ChimeraX 1.3\bin\lib\runpy.py", line 87 in _run_code
  File "C:\Program Files (x86)\ChimeraX 1.3\bin\lib\runpy.py", line 197 in _run_module_as_main
Windows fatal exception: code 0xc0000002

Thread 0x00005518 (most recent call first):
  File "C:\Program Files (x86)\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 135 in show_open_file_dialog
  File "C:\Program Files (x86)\ChimeraX 1.3\bin\lib\site-packages\chimerax\toolbar\providers.py", line 17 in _file_open
  File "C:\Program Files (x86)\ChimeraX 1.3\bin\lib\site-packages\chimerax\toolbar\providers.py", line 45 in run_provider
  File "C:\Program Files (x86)\ChimeraX 1.3\bin\lib\site-packages\chimerax\toolbar\__init__.py", line 37 in run_provider
  File "C:\Program Files (x86)\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\toolshed\__init__.py", line 1284 in run_provider
  File "C:\Program Files (x86)\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\toolshed\info.py", line 381 in run_provider
  File "C:\Program Files (x86)\ChimeraX 1.3\bin\lib\site-packages\chimerax\toolbar\tool.py", line 165 in callback
  File "C:\Program Files (x86)\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
  File "C:\Program Files (x86)\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
  File "C:\Program Files (x86)\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 1018 in 
  File "C:\Program Files (x86)\ChimeraX 1.3\bin\lib\runpy.py", line 87 in _run_code
  File "C:\Program Files (x86)\ChimeraX 1.3\bin\lib\runpy.py", line 197 in _run_module_as_main
Windows fatal exception: code 0xc0000002

Thread 0x00005518 (most recent call first):
  File "C:\Program Files (x86)\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 135 in show_open_file_dialog
  File "C:\Program Files (x86)\ChimeraX 1.3\bin\lib\site-packages\chimerax\toolbar\providers.py", line 17 in _file_open
  File "C:\Program Files (x86)\ChimeraX 1.3\bin\lib\site-packages\chimerax\toolbar\providers.py", line 45 in run_provider
  File "C:\Program Files (x86)\ChimeraX 1.3\bin\lib\site-packages\chimerax\toolbar\__init__.py", line 37 in run_provider
  File "C:\Program Files (x86)\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\toolshed\__init__.py", line 1284 in run_provider
  File "C:\Program Files (x86)\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\toolshed\info.py", line 381 in run_provider
  File "C:\Program Files (x86)\ChimeraX 1.3\bin\lib\site-packages\chimerax\toolbar\tool.py", line 165 in callback
  File "C:\Program Files (x86)\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
  File "C:\Program Files (x86)\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
  File "C:\Program Files (x86)\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 1018 in 
  File "C:\Program Files (x86)\ChimeraX 1.3\bin\lib\runpy.py", line 87 in _run_code
  File "C:\Program Files (x86)\ChimeraX 1.3\bin\lib\runpy.py", line 197 in _run_module_as_main
Windows fatal exception: code 0xc0000002

Thread 0x00005518 (most recent call first):
  File "C:\Program Files (x86)\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\updateloop.py", line 141 in _redraw_timer_callback
Windows fatal exception: access violation

===== Log before crash start =====
> open "C:/Users/L/Downloads/AF-Q05940-F1-model_v4 (1).pdb"

AF-Q05940-F1-model_v4 (1).pdb title:  
Alphafold monomer V2.0 prediction for synaptic vesicular amine transporter
(Q05940) [more info...]  
  
Chain information for AF-Q05940-F1-model_v4 (1).pdb #1  
---  
Chain | Description | UniProt  
A | synaptic vesicular amine transporter | VMAT2_HUMAN  
  

> cartoon style modeHelix tube

> set bgColor white

> rainbow

Alignment identifier is 1/A  

> color #1 #aaaaff transparency 0

> color #1 #ffaaff transparency 0

> select add /A:328

14 atoms, 15 bonds, 1 residue, 1 model selected  

> select add /A:327

23 atoms, 23 bonds, 2 residues, 1 model selected  

> select add /A:329

32 atoms, 31 bonds, 3 residues, 1 model selected  

> select add /A:333

37 atoms, 35 bonds, 4 residues, 1 model selected  

> select add /A:334

48 atoms, 46 bonds, 5 residues, 1 model selected  

> select add /A:336

55 atoms, 53 bonds, 6 residues, 1 model selected  

> select add /A:338

61 atoms, 58 bonds, 7 residues, 1 model selected  

> select add /A:337

66 atoms, 62 bonds, 8 residues, 1 model selected  

> select add /A:339

74 atoms, 69 bonds, 9 residues, 1 model selected  

> select add /A:342

82 atoms, 76 bonds, 10 residues, 1 model selected  

> select add /A:341

94 atoms, 88 bonds, 11 residues, 1 model selected  

> select add /A:340

100 atoms, 93 bonds, 12 residues, 1 model selected  

> select add /A:344

104 atoms, 96 bonds, 13 residues, 1 model selected  

> select add /A:343

112 atoms, 103 bonds, 14 residues, 1 model selected  

> select add /A:345

119 atoms, 109 bonds, 15 residues, 1 model selected  

> select add /A:347

127 atoms, 116 bonds, 16 residues, 1 model selected  

> select add /A:346

135 atoms, 123 bonds, 17 residues, 1 model selected  

> select add /A:349

139 atoms, 126 bonds, 18 residues, 1 model selected  

> select add /A:348

150 atoms, 137 bonds, 19 residues, 1 model selected  

> select add /A:350

158 atoms, 144 bonds, 20 residues, 1 model selected  

> select add /A:351

166 atoms, 151 bonds, 21 residues, 1 model selected  

> select add /A:352

171 atoms, 155 bonds, 22 residues, 1 model selected  

> select add /A:353

181 atoms, 165 bonds, 23 residues, 1 model selected  

> select add /A:354

190 atoms, 173 bonds, 24 residues, 1 model selected  

> select add /A:355

198 atoms, 180 bonds, 25 residues, 1 model selected  

> select add /A:356

202 atoms, 183 bonds, 26 residues, 1 model selected  

> select add /A:357

213 atoms, 193 bonds, 27 residues, 1 model selected  

> select add /A:358

227 atoms, 208 bonds, 28 residues, 1 model selected  

> select add /A:360

233 atoms, 213 bonds, 29 residues, 1 model selected  

> select add /A:359

241 atoms, 220 bonds, 30 residues, 1 model selected  

> select add /A:361

246 atoms, 224 bonds, 31 residues, 1 model selected  

> select add /A:362

254 atoms, 231 bonds, 32 residues, 1 model selected  

> select add /A:363

262 atoms, 238 bonds, 33 residues, 1 model selected  

> select add /A:365

270 atoms, 245 bonds, 34 residues, 1 model selected  

> select add /A:364

274 atoms, 248 bonds, 35 residues, 1 model selected  

> select add /A:366

282 atoms, 255 bonds, 36 residues, 1 model selected  

> select add /A:367

290 atoms, 262 bonds, 37 residues, 1 model selected  

> select add /A:368

297 atoms, 268 bonds, 38 residues, 1 model selected  

> select add /A:371

303 atoms, 273 bonds, 39 residues, 1 model selected  

> select add /A:370

310 atoms, 279 bonds, 40 residues, 1 model selected  

> select add /A:369

314 atoms, 282 bonds, 41 residues, 1 model selected  

> select add /A:372

322 atoms, 289 bonds, 42 residues, 1 model selected  

> select add /A:373

330 atoms, 296 bonds, 43 residues, 1 model selected  

> select add /A:374

336 atoms, 301 bonds, 44 residues, 1 model selected  

> select add /A:375

344 atoms, 308 bonds, 45 residues, 1 model selected  

> select add /A:376

351 atoms, 315 bonds, 46 residues, 1 model selected  

> select add /A:377

362 atoms, 326 bonds, 47 residues, 1 model selected  

> hide sel cartoons

> select add /A:335

370 atoms, 333 bonds, 48 residues, 1 model selected  

> hide sel cartoons

> open "C:\Users\L\Downloads\AF-Q05940-F1-model_v4 (1).pdb" format pdb

AF-Q05940-F1-model_v4 (1).pdb title:  
Alphafold monomer V2.0 prediction for synaptic vesicular amine transporter
(Q05940) [more info...]  
  
Chain information for AF-Q05940-F1-model_v4 (1).pdb #2  
---  
Chain | Description | UniProt  
A | synaptic vesicular amine transporter | VMAT2_HUMAN  
  

> cartoon style modeHelix tube

> hide #2 models

> select add #1/A:332

377 atoms, 339 bonds, 49 residues, 1 model selected  

> hide sel cartoons

> show #2 models

> save C:\Users\L\Desktop\image1.png supersample 3

> hide #2 models

> hide #1 models

> open C:/Users/L/Downloads/3s22.cif

Summary of feedback from opening C:/Users/L/Downloads/3s22.cif  
---  
note | Fetching CCD CL from http://ligand-expo.rcsb.org/reports/C/CL/CL.cif  
  
3s22.cif title:  
AMP-C BETA-LACTAMASE (PSEUDOMONAS AERUGINOSA) in complex with an inhibitor
[more info...]  
  
Chain information for 3s22.cif #3  
---  
Chain | Description | UniProt  
A | Beta-lactamase | AMPC_PSEAE  
  
Non-standard residues in 3s22.cif #3  
---  
3S2 —
[(2S,3R)-2-formyl-1-{[4-(methylamino)butyl]carbamoyl}pyrrolidin-3-yl]sulfamic
acid  
CL — chloride ion  
  

> rainbow #3

> hide #3 cartoons

> show #3 cartoons

> hide #3 atoms

> cartoon style modeHelix tube

> save C:\Users\L\Desktop\image2.png supersample 3

> color #3 #ffaaff transparency 0

> select add #3/A:389

382 atoms, 343 bonds, 50 residues, 2 models selected  

> select add #3/A:387

390 atoms, 350 bonds, 51 residues, 2 models selected  

> select add #3/A:388

395 atoms, 354 bonds, 52 residues, 2 models selected  

> select add #3/A:385

401 atoms, 359 bonds, 53 residues, 2 models selected  

> select add #3/A:386

405 atoms, 362 bonds, 54 residues, 2 models selected  

> select add #3/A:384

413 atoms, 369 bonds, 55 residues, 2 models selected  

> select add #3/A:383

421 atoms, 376 bonds, 56 residues, 2 models selected  

> select add #3/A:382

426 atoms, 380 bonds, 57 residues, 2 models selected  

> select add #3/A:381

438 atoms, 392 bonds, 58 residues, 2 models selected  

> select add #3/A:380

443 atoms, 396 bonds, 59 residues, 2 models selected  

> select subtract #3/A:380

438 atoms, 392 bonds, 58 residues, 2 models selected  

> select add #3/A:379

446 atoms, 399 bonds, 59 residues, 2 models selected  

> select add #3/A:380

451 atoms, 403 bonds, 60 residues, 2 models selected  

> select add #3/A:378

460 atoms, 411 bonds, 61 residues, 2 models selected  

> select add #3/A:377

467 atoms, 417 bonds, 62 residues, 2 models selected  

> select add #3/A:376

478 atoms, 427 bonds, 63 residues, 2 models selected  

> select add #3/A:374

483 atoms, 431 bonds, 64 residues, 2 models selected  

> select add #3/A:375

492 atoms, 439 bonds, 65 residues, 2 models selected  

> select add #3/A:373

500 atoms, 446 bonds, 66 residues, 2 models selected  

> select add #3/A:372

507 atoms, 453 bonds, 67 residues, 2 models selected  

> select add #3/A:49

515 atoms, 460 bonds, 68 residues, 2 models selected  

> select add #3/A:47

521 atoms, 465 bonds, 69 residues, 2 models selected  

> select add #3/A:48

526 atoms, 469 bonds, 70 residues, 2 models selected  

> select add #3/A:46

534 atoms, 476 bonds, 71 residues, 2 models selected  

> select add #3/A:45

541 atoms, 482 bonds, 72 residues, 2 models selected  

> select add #3/A:44

548 atoms, 489 bonds, 73 residues, 2 models selected  

> select add #3/A:43

557 atoms, 497 bonds, 74 residues, 2 models selected  

> select add #3/A:42

564 atoms, 503 bonds, 75 residues, 2 models selected  

> select add #3/A:41

569 atoms, 507 bonds, 76 residues, 2 models selected  

> select add #3/A:39

577 atoms, 514 bonds, 77 residues, 2 models selected  

> select add #3/A:40

582 atoms, 518 bonds, 78 residues, 2 models selected  

> select add #3/A:38

589 atoms, 524 bonds, 79 residues, 2 models selected  

> select add #3/A:37

597 atoms, 531 bonds, 80 residues, 2 models selected  

> select add #3/A:36

602 atoms, 535 bonds, 81 residues, 2 models selected  

> select add #3/A:35

611 atoms, 543 bonds, 82 residues, 2 models selected  

> select add #3/A:34

619 atoms, 550 bonds, 83 residues, 2 models selected  

> select add #3/A:33

630 atoms, 560 bonds, 84 residues, 2 models selected  

> select add #3/A:32

638 atoms, 567 bonds, 85 residues, 2 models selected  

> select add #3/A:30

645 atoms, 574 bonds, 86 residues, 2 models selected  

> select add #3/A:31

650 atoms, 578 bonds, 87 residues, 2 models selected  

> select add #3/A:29

655 atoms, 582 bonds, 88 residues, 2 models selected  

> hide sel & #3 cartoons

> open C:/Users/L/Downloads/3s22.cif

3s22.cif title:  
AMP-C BETA-LACTAMASE (PSEUDOMONAS AERUGINOSA) in complex with an inhibitor
[more info...]  
  
Chain information for 3s22.cif #4  
---  
Chain | Description | UniProt  
A | Beta-lactamase | AMPC_PSEAE  
  
Non-standard residues in 3s22.cif #4  
---  
3S2 —
[(2S,3R)-2-formyl-1-{[4-(methylamino)butyl]carbamoyl}pyrrolidin-3-yl]sulfamic
acid  
CL — chloride ion  
  

> cartoon style modeHelix tube

> hide sel & #3 atoms

> select #3

3164 atoms, 2848 bonds, 749 residues, 1 model selected  

> ~select #3

Nothing selected  

> hide #3-4 atoms

Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps,
got 2 atomic models, 0 maps.  

> ui tool show Matchmaker

> matchmaker #4 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 3s22.cif, chain A (#3) with 3s22.cif, chain A (#4), sequence
alignment score = 1917.2  
RMSD between 361 pruned atom pairs is 0.000 angstroms; (across all 361 pairs:
0.000)  
  

> color #4 #aaffff transparency 0

> save C:\Users\L\Desktop\image3.png supersample 3

> hide #3 models

> hide #4 models

> show #2 models

> show #1 models

> color #2 #55ffff transparency 0

> color #2 cyan transparency 0

> color #2 #aaffff transparency 0

> save C:\Users\L\Desktop\image4.png supersample 3

> close session

> open "C:\Users\L\Downloads\8xit (1).cif" format mmcif

8xit (1).cif title:  
Cryo-EM structure of sheep VMAT2 dimer in an atypical fold [more info...]  
  
Chain information for 8xit (1).cif #1  
---  
Chain | Description  
A B | OaVMAT2-BRIL  
  

> delete bonds

> select /B:16-584

3001 atoms, 1175 pseudobonds, 392 residues, 2 models selected  

> delete /b

> cartoon style modeHelix tube

> rainbow

> select add /A:566

7 atoms, 2 pseudobonds, 1 residue, 2 models selected  

> select add /A:565

18 atoms, 4 pseudobonds, 2 residues, 2 models selected  

> select add /A:564

22 atoms, 6 pseudobonds, 3 residues, 2 models selected  

> select add /A:563

30 atoms, 8 pseudobonds, 4 residues, 2 models selected  

> select add /A:548

34 atoms, 11 pseudobonds, 5 residues, 2 models selected  

> hide sel cartoons

> select add /A:547

42 atoms, 13 pseudobonds, 6 residues, 2 models selected  

> hide sel cartoons

> select add /A:133

51 atoms, 15 pseudobonds, 7 residues, 2 models selected  

> select add /A:49

63 atoms, 17 pseudobonds, 8 residues, 2 models selected  

> hide sel cartoons

> select add /A:17

73 atoms, 20 pseudobonds, 9 residues, 2 models selected  

> select #1

3001 atoms, 1175 pseudobonds, 392 residues, 2 models selected  

> ~select #1

Nothing selected  

> select add /A:297

8 atoms, 2 pseudobonds, 1 residue, 2 models selected  

> select add /A:296

20 atoms, 4 pseudobonds, 2 residues, 2 models selected  

> select add /A:274

29 atoms, 7 pseudobonds, 3 residues, 2 models selected  

> select add /A:272

36 atoms, 9 pseudobonds, 4 residues, 2 models selected  

> select add /A:273

44 atoms, 11 pseudobonds, 5 residues, 2 models selected  

> hide sel cartoons

> select add /A:426

52 atoms, 13 pseudobonds, 6 residues, 2 models selected  

> select add /A:423

56 atoms, 15 pseudobonds, 7 residues, 2 models selected  

> select #1

3001 atoms, 1175 pseudobonds, 392 residues, 2 models selected  

> ~select #1

Nothing selected  

> select add /A:423

4 atoms, 2 pseudobonds, 1 residue, 2 models selected  

> select add /A:424

15 atoms, 4 pseudobonds, 2 residues, 2 models selected  

> select add /A:394

20 atoms, 6 pseudobonds, 3 residues, 2 models selected  

> hide sel cartoons

Alignment identifier is 1/A  
Drag select of 33 residues, 57 pseudobonds  

> select
> /A:16-49,134-159,161-182,184-214,216-249,252-272,297-314,321-328,330-371,385-394,424-433,454-494,497-519,524-547,567-584

2775 atoms, 1071 pseudobonds, 362 residues, 2 models selected  

> select #1

3001 atoms, 1175 pseudobonds, 392 residues, 2 models selected  

> ~select #1

Nothing selected  

> select /A:297

8 atoms, 2 pseudobonds, 1 residue, 2 models selected  

> select /A:297-584

1657 atoms, 644 pseudobonds, 215 residues, 2 models selected  

> hide sel cartoons

> select #1

3001 atoms, 1175 pseudobonds, 392 residues, 2 models selected  

> ~select #1

Nothing selected  

> save C:\Users\L\Desktop\image5.png supersample 3

> open "C:\Users\L\Downloads\8xit (1).cif" format mmcif

8xit (1).cif title:  
Cryo-EM structure of sheep VMAT2 dimer in an atypical fold [more info...]  
  
Chain information for 8xit (1).cif #2  
---  
Chain | Description  
A B | OaVMAT2-BRIL  
  

> hide #!1 models

> delete /b

> cartoon style modeHelix tube

> rainbow #!2

Alignment identifier is 1  

> select #1/A:16-274 #2/A:16-274

2664 atoms, 1360 bonds, 528 pseudobonds, 352 residues, 4 models selected  
Seqview [ID: 1] region 2 chains [1-295] RMSD: 0.000  
  

> hide sel & #!2 cartoons

> select #2

3001 atoms, 3062 bonds, 6 pseudobonds, 392 residues, 2 models selected  

> ~select #2

Nothing selected  

> select add #2/A:567

14 atoms, 15 bonds, 1 residue, 1 model selected  

> select add #2/A:566

21 atoms, 22 bonds, 2 residues, 1 model selected  

> select add #2/A:565

32 atoms, 33 bonds, 3 residues, 1 model selected  

> select add #2/A:564

36 atoms, 36 bonds, 4 residues, 1 model selected  

> select add #2/A:563

44 atoms, 43 bonds, 5 residues, 1 model selected  

> select add #2/A:548

48 atoms, 46 bonds, 1 pseudobond, 6 residues, 2 models selected  

> select add #2/A:547

56 atoms, 53 bonds, 1 pseudobond, 7 residues, 2 models selected  

> hide sel cartoons

> select add #2/A:296

68 atoms, 65 bonds, 1 pseudobond, 8 residues, 2 models selected  

> select add #2/A:297

76 atoms, 72 bonds, 1 pseudobond, 9 residues, 2 models selected  

> hide sel cartoons

> select add #2/A:423

80 atoms, 75 bonds, 1 pseudobond, 10 residues, 2 models selected  

> hide sel cartoons

> select add #2/A:424

91 atoms, 86 bonds, 2 pseudobonds, 11 residues, 2 models selected  

> hide sel cartoons

> save C:\Users\L\Desktop\image6.png supersample 3

> select #2

3001 atoms, 3062 bonds, 6 pseudobonds, 392 residues, 2 models selected  

> ~select #2

Nothing selected  

> select #1/A:423-465 #2/A:423-465

392 atoms, 197 bonds, 72 pseudobonds, 48 residues, 4 models selected  
Seqview [ID: 1] region 2 chains [396-465] RMSD: 0.000  
  

> hide sel & #!2 cartoons

> select #2

3001 atoms, 3062 bonds, 6 pseudobonds, 392 residues, 2 models selected  

> ~select #2

Nothing selected  

> select
> #1/A:16-49,134-159,161-182,184-214,216-249,252-272,297-314,321-328,330-371,385-394,424-433,454-494,497-519,524-547,567-584
> #2/A:16-49,134-159,161-182,184-214,216-249,252-272,297-314,321-328,330-371,385-394,424-433,454-494,497-519,524-547,567-584

5550 atoms, 2821 bonds, 1071 pseudobonds, 724 residues, 3 models selected  

> select #2

3001 atoms, 3062 bonds, 6 pseudobonds, 392 residues, 2 models selected  

> ~select #2

Nothing selected  

> select #1/A:359-360 #2/A:359-360

26 atoms, 12 bonds, 5 pseudobonds, 4 residues, 3 models selected  

> select #1/A:359-387 #2/A:359-387

282 atoms, 141 bonds, 51 pseudobonds, 34 residues, 4 models selected  
Seqview [ID: 1] region 2 chains [359-387] RMSD: 0.000  
  

> select #2

3001 atoms, 3062 bonds, 6 pseudobonds, 392 residues, 2 models selected  

> ~select #2

Nothing selected  

> select #1/A:360 #2/A:360

10 atoms, 4 bonds, 2 pseudobonds, 2 residues, 3 models selected  

> select #1/A:360-394 #2/A:360-394

372 atoms, 186 bonds, 69 pseudobonds, 46 residues, 4 models selected  
Seqview [ID: 1] region 2 chains [360-394] RMSD: 0.000  
  

> hide sel & #!2 cartoons


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

Log:
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 555.97
OpenGL renderer: NVIDIA GeForce GTX 1660 Ti/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: ASUSTeK COMPUTER INC.
Model: ASUS TUF Gaming A15 FA506IU_FA506IU
OS: Microsoft Windows 11 家庭中文版 (Build 26100)
Memory: 16,556,658,688
MaxProcessMemory: 137,438,953,344
CPU: 16 AMD Ryzen 7 4800H with Radeon Graphics         
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 (5)

comment:1 by Eric Pettersen, 6 months ago

Cc: Tom Goddard added
Component: Unassigned → UI
Owner: set to Eric Pettersen
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → Crash using open/save dialog

comment:2 by Eric Pettersen, 6 months ago

My dim recollection is that there is frequently something selected or the selection is changing when this crash happens. Perhaps the redraw timer has some kind of negative interaction with the open/save dialog? Anyway, something to keep an eye on.

comment:3 by Tom Goddard, 6 months ago

The last access violation traceback in this report is

File "C:\Program Files (x86)\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\updateloop.py", line 141 in _redraw_timer_callback

Windows fatal exception: access violation

which (looking back at v1.3 github source) code is this line

self._last_timer_finish_time = time.perf_counter()

I don't think perf_counter() caused the crash. I'd guess garbage collection was triggered. This was the last line of the redraw routine and maybe garbage collection was triggered as it exited the routine.

comment:4 by Tom Goddard, 6 months ago

How about this for a theory. The show_open_file_dialog() suggests the we were showing the open file dialog. That is modal. But the redraw timer may be able to fire during a modal dialog. Yes, a test on Mac current ChimeraX doing a roll on a molecule then showing the open dialog, the model continues to roll showing redraw is firing. Maybe if the redraw timer triggers garbage collection and we are in a Qt sub-event-loop from the modal dialog, things sometimes go haywire causing the crash (only on Windows I guess otherwise we would see Mac reports with C stack traces).

Maybe a way to test is to start ChimeraX on Windows, roll, then show the open dialog and leave it up for hours and see if it crashes. If the redraw creates some objects that have circular references then eventually garbage collection will be needed. I'll give that a try today.

comment:5 by Tom Goddard, 6 months ago

I tried opening a model using command "rock" and showing the modal open file dialog and leaving it in that state for about 3 hours. Was still working fine when I logged back in. Not sure if the rock continued when the display and computer slept.

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