![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 7 months ago
Closed 7 months ago
#17055 closed defect (duplicate)
Crashed in QTabBar::paintEvent(), QPainter::begin: Paint device returned engine == 0
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Window Toolkit | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault
Thread 0x0000000322b0e000 (most recent call first):
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 576 in _handle_results
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x0000000321b0b000 (most recent call first):
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 528 in _handle_tasks
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x0000000320b08000 (most recent call first):
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/selectors.py", line 416 in select
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/connection.py", line 936 in wait
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 499 in _wait_for_updates
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 519 in _handle_workers
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x000000031fb05000 (most recent call first):
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x000000031eb02000 (most recent call first):
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x000000031daff000 (most recent call first):
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x000000031cafc000 (most recent call first):
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x000000031baf9000 (most recent call first):
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x000000031aaf6000 (most recent call first):
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x0000000319af3000 (most recent call first):
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x0000000318af0000 (most recent call first):
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Current thread 0x00000002042f1200 (most recent call first):
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 275 in event_loop
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py", line 892 in init
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py", line 1043 in
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 87 in _run_code
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 197 in _run_module_as_main
{"app_name":"ChimeraX","timestamp":"2025-03-09 17:54:50.00 +0000","app_version":"1.6.1","slice_uuid":"5df621ee-554e-36a8-b448-93b2334e5480","build_version":"1.6.1.0","platform":1,"bundleID":"edu.ucsf.cgl.ChimeraX","share_with_app_devs":0,"is_first_party":0,"bug_type":"309","os_version":"macOS 15.3.1 (24D70)","roots_installed":0,"name":"ChimeraX","incident_id":"B632C967-EB28-468C-B9A0-339138967314"}
{
"uptime" : 64000,
"procRole" : "Background",
"version" : 2,
"userID" : 504,
"deployVersion" : 210,
"modelCode" : "MacBookPro18,3",
"coalitionID" : 20384,
"osVersion" : {
"train" : "macOS 15.3.1",
"build" : "24D70",
"releaseType" : "User"
},
"captureTime" : "2025-03-09 17:52:23.1023 +0000",
"codeSigningMonitor" : 1,
"incident" : "B632C967-EB28-468C-B9A0-339138967314",
"pid" : 52346,
"translated" : true,
"cpuType" : "X86-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-03-07 19:18:35.0543 +0000",
"procStartAbsTime" : 1275030971062,
"procExitAbsTime" : 1542802984021,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.6.1.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.6.1","CFBundleVersion":"1.6.1.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"BD323E9A-315C-590A-A825-7BA1CF88FD91","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "F5DE670C-99E6-8E0A-332A-34D135B1721D",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"bootSessionUUID" : "FE4EB123-DC9F-449A-9000-61EEBF799100",
"wakeTime" : 4,
"sleepWakeUUID" : "ABF1D899-3F2E-42B6-829D-6E2C1B7551C4",
"sip" : "enabled",
"vmRegionInfo" : "0x18 is not in any region. Bytes before following region: 4362866664\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 1040c1000-1040c2000 [ 4K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.6.1.app\/Contents\/MacOS\/ChimeraX",
"exception" : {"codes":"0x0000000000000001, 0x0000000000000018","rawCodes":[1,24],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000000000000018"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":52346},
"vmregioninfo" : "0x18 is not in any region. Bytes before following region: 4362866664\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 1040c1000-1040c2000 [ 4K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.6.1.app\/Contents\/MacOS\/ChimeraX",
"extMods" : {"caller":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"system":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"targeted":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"warnings":0},
"faultingThread" : 0,
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"reportNotes" : [
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}
===== Log before crash start =====
Startup Messages
---
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle
You can double click a model's Name or ID in the model panel to edit those
fields
UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> /Users/ajackso8/Downloads/fold_pcna3_apex2_exo1/fold_pcna3_apex2_exo1_model_0.cif
Chain information for fold_pcna3_apex2_exo1_model_0.cif #1
---
Chain | Description
A B C | .
D | .
E | .
> open
> /Users/ajackso8/Downloads/fold_pcna3_apex2_exo1/fold_pcna3_apex2_exo1_model_0.cif
Chain information for fold_pcna3_apex2_exo1_model_0.cif #2
---
Chain | Description
A B C | .
D | .
E | .
> ui tool show "AlphaFold Error Plot"
> alphafold pae #1 file
> /Users/ajackso8/Downloads/fold_pcna3_apex2_exo1/fold_pcna3_apex2_exo1_summary_confidences_0.json
JSON file
"/Users/ajackso8/Downloads/fold_pcna3_apex2_exo1/fold_pcna3_apex2_exo1_summary_confidences_0.json"
is not AlphaFold predicted aligned error data, expected a top level list
> alphafold pae #1 file
> /Users/ajackso8/Downloads/fold_pcna3_apex2_exo1/fold_pcna3_apex2_exo1_full_data_0.json
> select #2/E:1-846
6607 atoms, 6730 bonds, 846 residues, 1 model selected
> hide sel cartoons
> hide sel atoms
> select #2/E:1-846
6607 atoms, 6730 bonds, 846 residues, 1 model selected
> surface hidePatches sel
> cartoon hide sel
> hide sel target a
> select #2/E:1-846
6607 atoms, 6730 bonds, 846 residues, 1 model selected
> select #2/E:1-846
6607 atoms, 6730 bonds, 846 residues, 1 model selected
> select #2/D:1-518
4029 atoms, 4123 bonds, 518 residues, 1 model selected
> select /E:1-846
13214 atoms, 13460 bonds, 1692 residues, 2 models selected
> hide sel atoms
> open
> /Users/ajackso8/Downloads/fold_pcna3_apex2_exo1_dna_with_ssdna/fold_pcna3_apex2_exo1_dna_with_ssdna_model_0.cif
Chain information for fold_pcna3_apex2_exo1_dna_with_ssdna_model_0.cif #3
---
Chain | Description
A B C | .
D | .
E | .
F | .
G | .
> close session
> open
> /Users/ajackso8/Downloads/fold_pcna3_apex2_exo1_dna_with_ssdna/fold_pcna3_apex2_exo1_dna_with_ssdna_model_1.cif
Chain information for fold_pcna3_apex2_exo1_dna_with_ssdna_model_1.cif #1
---
Chain | Description
A B C | .
D | .
E | .
F | .
G | .
> ui tool show "AlphaFold Error Plot"
> alphafold pae #1 file
> /Users/ajackso8/Downloads/fold_pcna3_apex2_exo1_dna_with_ssdna/fold_pcna3_apex2_exo1_dna_with_ssdna_full_data_1.json
> select #3/D:1-518
Nothing selected
> select /D:1-518
4029 atoms, 4123 bonds, 518 residues, 1 model selected
> select /D:1-518
4029 atoms, 4123 bonds, 518 residues, 1 model selected
> show sel atoms
> show sel cartoons
> style sel sphere
Changed 4029 atom styles
> style sel sphere
Changed 4029 atom styles
> style sel stick
Changed 4029 atom styles
> style sel stick
Changed 4029 atom styles
> style sel stick
Changed 4029 atom styles
> style sel sphere
Changed 4029 atom styles
Alignment identifier is 1/D
> select /D:456
14 atoms, 15 bonds, 1 residue, 1 model selected
> select /D:456-457
23 atoms, 24 bonds, 2 residues, 1 model selected
> select /D:466
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /D:466-468
22 atoms, 22 bonds, 3 residues, 1 model selected
> select /D:469
6 atoms, 5 bonds, 1 residue, 1 model selected
> select /D:469-518
398 atoms, 412 bonds, 50 residues, 1 model selected
> color sel light gray
> select /D:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /D:1-345
2683 atoms, 2743 bonds, 345 residues, 1 model selected
> select /D:8
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /D:8
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel red
> select /D:10
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /D:10
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel red
> save "/Users/ajackso8/Downloads/fold_pcna3_apex2_exo1_dna_with_ssdna/session
> apex2 cat residues red znf grey.cxs"
> close session
> open
> /Users/ajackso8/Downloads/fold_pcna3_apex2_exo1_dna_with_3prime_resection/fold_pcna3_apex2_exo1_dna_with_3prime_resection_model_0.cif
Chain information for
fold_pcna3_apex2_exo1_dna_with_3prime_resection_model_0.cif #1
---
Chain | Description
A B C | .
D | .
E | .
F | .
G | .
> open
> /Users/ajackso8/Downloads/fold_pcna3_apex2_exo1_dna_with_3prime_resection/fold_pcna3_apex2_exo1_dna_with_3prime_resection_model_0.cif
Chain information for
fold_pcna3_apex2_exo1_dna_with_3prime_resection_model_0.cif #2
---
Chain | Description
A B C | .
D | .
E | .
F | .
G | .
> select #2/G:1-120
2453 atoms, 2750 bonds, 120 residues, 1 model selected
> select #2/F:1-40
832 atoms, 934 bonds, 40 residues, 1 model selected
> select #2/G:1-120
2453 atoms, 2750 bonds, 120 residues, 1 model selected
> select #2/D:1-518
4029 atoms, 4123 bonds, 518 residues, 1 model selected
> close session
> open
> /Users/ajackso8/Downloads/fold_pcna3_apex2_exo1_3prime_ttttt/fold_pcna3_apex2_exo1_3prime_ttttt_model_0.cif
Chain information for fold_pcna3_apex2_exo1_3prime_ttttt_model_0.cif #1
---
Chain | Description
A B C | .
D | .
E | .
F | .
G | .
> close session
> open
> /Users/ajackso8/Downloads/fold_pcna3_apex2_dsdna_with_resection/fold_pcna3_apex2_dsdna_with_resection_model_0.cif
Chain information for fold_pcna3_apex2_dsdna_with_resection_model_0.cif #1
---
Chain | Description
A B C | .
D | .
E | .
F | .
> color bychain
> select /D:1-518
4029 atoms, 4123 bonds, 518 residues, 1 model selected
Alignment identifier is 1/D
> select /D:488
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /D:488-490
23 atoms, 22 bonds, 3 residues, 1 model selected
> select /D:477
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /D:477-483
58 atoms, 57 bonds, 7 residues, 1 model selected
> select /D:468
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /D:468-518
406 atoms, 420 bonds, 51 residues, 1 model selected
> color sel yellow
> select
> /D:2-8,43-47,66-71,82-87,94-97,133-142,147-156,191-197,243-245,277-282,290-295,307-311,313-316,477-480,491-494,512-514
734 atoms, 736 bonds, 90 residues, 1 model selected
> select /D:10
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /D:10
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel red
> select
> /D:2-8,43-47,66-71,82-87,94-97,133-142,147-156,191-197,243-245,277-282,290-295,307-311,313-316,477-480,491-494,512-514
734 atoms, 736 bonds, 90 residues, 1 model selected
> select /D:8
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /D:8
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel red
> select
13428 atoms, 13962 bonds, 1468 residues, 1 model selected
> style sel stick
Changed 13428 atom styles
> style sel stick
Changed 13428 atom styles
> hide sel atoms
> show sel surfaces
> hide sel surfaces
> show sel cartoons
> select /D:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /D:1-8
69 atoms, 70 bonds, 8 residues, 1 model selected
> alphafold contacts /A toResidues /D distance 5 outputFile z.txt
Structure fold_pcna3_apex2_dsdna_with_resection_model_0.cif #1 does not have
PAE data opened
> alphafold contacts /A toResidues /D distance 8 outputFile z.txt
Structure fold_pcna3_apex2_dsdna_with_resection_model_0.cif #1 does not have
PAE data opened
> ui tool show "AlphaFold Error Plot"
> alphafold pae #1 file
> /Users/ajackso8/Downloads/fold_pcna3_apex2_dsdna_with_resection/fold_pcna3_apex2_dsdna_with_resection_full_data_0.json
> alphafold contacts /A toResidues /D distance 5 outputFile z.txt
> alphafold contacts /A toResidues /D distance 3 outputFile z.txt
> save
> /Users/ajackso8/Downloads/fold_pcna3_apex2_dsdna_with_resection/session.cxs
Unsupported scale factor (0.000000) detected on Display0
QPainter::begin: Paint device returned engine == 0, type: 3
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open
> /Users/ajackso8/Downloads/fold_pcna3_apex2_dsdna_with_resection/session.cxs
Log from Fri Mar 7 21:39:53 2025 Startup Messages
---
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle
You can double click a model's Name or ID in the model panel to edit those
fields
UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> /Users/ajackso8/Downloads/fold_pcna3_apex2_exo1/fold_pcna3_apex2_exo1_model_0.cif
Chain information for fold_pcna3_apex2_exo1_model_0.cif #1
---
Chain | Description
A B C | .
D | .
E | .
> open
> /Users/ajackso8/Downloads/fold_pcna3_apex2_exo1/fold_pcna3_apex2_exo1_model_0.cif
Chain information for fold_pcna3_apex2_exo1_model_0.cif #2
---
Chain | Description
A B C | .
D | .
E | .
> ui tool show "AlphaFold Error Plot"
> alphafold pae #1 file
> /Users/ajackso8/Downloads/fold_pcna3_apex2_exo1/fold_pcna3_apex2_exo1_summary_confidences_0.json
JSON file
"/Users/ajackso8/Downloads/fold_pcna3_apex2_exo1/fold_pcna3_apex2_exo1_summary_confidences_0.json"
is not AlphaFold predicted aligned error data, expected a top level list
> alphafold pae #1 file
> /Users/ajackso8/Downloads/fold_pcna3_apex2_exo1/fold_pcna3_apex2_exo1_full_data_0.json
> select #2/E:1-846
6607 atoms, 6730 bonds, 846 residues, 1 model selected
> hide sel cartoons
> hide sel atoms
[Repeated 1 time(s)]
> select #2/E:1-846
6607 atoms, 6730 bonds, 846 residues, 1 model selected
> surface hidePatches sel
> cartoon hide sel
> hide sel target a
> select #2/E:1-846
6607 atoms, 6730 bonds, 846 residues, 1 model selected
> select #2/E:1-846
6607 atoms, 6730 bonds, 846 residues, 1 model selected
> select #2/D:1-518
4029 atoms, 4123 bonds, 518 residues, 1 model selected
> select /E:1-846
13214 atoms, 13460 bonds, 1692 residues, 2 models selected
> hide sel atoms
> open
> /Users/ajackso8/Downloads/fold_pcna3_apex2_exo1_dna_with_ssdna/fold_pcna3_apex2_exo1_dna_with_ssdna_model_0.cif
Chain information for fold_pcna3_apex2_exo1_dna_with_ssdna_model_0.cif #3
---
Chain | Description
A B C | .
D | .
E | .
F | .
G | .
> close session
[Repeated 2 time(s)]
> open
> /Users/ajackso8/Downloads/fold_pcna3_apex2_exo1_dna_with_ssdna/fold_pcna3_apex2_exo1_dna_with_ssdna_model_1.cif
Chain information for fold_pcna3_apex2_exo1_dna_with_ssdna_model_1.cif #1
---
Chain | Description
A B C | .
D | .
E | .
F | .
G | .
> ui tool show "AlphaFold Error Plot"
> alphafold pae #1 file
> /Users/ajackso8/Downloads/fold_pcna3_apex2_exo1_dna_with_ssdna/fold_pcna3_apex2_exo1_dna_with_ssdna_full_data_1.json
> select #3/D:1-518
Nothing selected
> select /D:1-518
4029 atoms, 4123 bonds, 518 residues, 1 model selected
> select /D:1-518
4029 atoms, 4123 bonds, 518 residues, 1 model selected
> show sel atoms
[Repeated 1 time(s)]
> show sel cartoons
[Repeated 1 time(s)]
> style sel sphere
Changed 4029 atom styles
> style sel sphere
Changed 4029 atom styles
> style sel stick
Changed 4029 atom styles
> style sel stick
Changed 4029 atom styles
> style sel stick
Changed 4029 atom styles
> style sel sphere
Changed 4029 atom styles
Alignment identifier is 1/D
> select /D:456
14 atoms, 15 bonds, 1 residue, 1 model selected
> select /D:456-457
23 atoms, 24 bonds, 2 residues, 1 model selected
> select /D:466
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /D:466-468
22 atoms, 22 bonds, 3 residues, 1 model selected
> select /D:469
6 atoms, 5 bonds, 1 residue, 1 model selected
> select /D:469-518
398 atoms, 412 bonds, 50 residues, 1 model selected
> color sel light gray
> select /D:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /D:1-345
2683 atoms, 2743 bonds, 345 residues, 1 model selected
> select /D:8
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /D:8
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel red
> select /D:10
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /D:10
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel red
> save "/Users/ajackso8/Downloads/fold_pcna3_apex2_exo1_dna_with_ssdna/session
> apex2 cat residues red znf grey.cxs"
> close session
> open
> /Users/ajackso8/Downloads/fold_pcna3_apex2_exo1_dna_with_3prime_resection/fold_pcna3_apex2_exo1_dna_with_3prime_resection_model_0.cif
Chain information for
fold_pcna3_apex2_exo1_dna_with_3prime_resection_model_0.cif #1
---
Chain | Description
A B C | .
D | .
E | .
F | .
G | .
> open
> /Users/ajackso8/Downloads/fold_pcna3_apex2_exo1_dna_with_3prime_resection/fold_pcna3_apex2_exo1_dna_with_3prime_resection_model_0.cif
Chain information for
fold_pcna3_apex2_exo1_dna_with_3prime_resection_model_0.cif #2
---
Chain | Description
A B C | .
D | .
E | .
F | .
G | .
> select #2/G:1-120
2453 atoms, 2750 bonds, 120 residues, 1 model selected
> select #2/F:1-40
832 atoms, 934 bonds, 40 residues, 1 model selected
> select #2/G:1-120
2453 atoms, 2750 bonds, 120 residues, 1 model selected
> select #2/D:1-518
4029 atoms, 4123 bonds, 518 residues, 1 model selected
> close session
> open
> /Users/ajackso8/Downloads/fold_pcna3_apex2_exo1_3prime_ttttt/fold_pcna3_apex2_exo1_3prime_ttttt_model_0.cif
Chain information for fold_pcna3_apex2_exo1_3prime_ttttt_model_0.cif #1
---
Chain | Description
A B C | .
D | .
E | .
F | .
G | .
> close session
> open
> /Users/ajackso8/Downloads/fold_pcna3_apex2_dsdna_with_resection/fold_pcna3_apex2_dsdna_with_resection_model_0.cif
Chain information for fold_pcna3_apex2_dsdna_with_resection_model_0.cif #1
---
Chain | Description
A B C | .
D | .
E | .
F | .
> color bychain
> select /D:1-518
4029 atoms, 4123 bonds, 518 residues, 1 model selected
Alignment identifier is 1/D
> select /D:488
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /D:488-490
23 atoms, 22 bonds, 3 residues, 1 model selected
> select /D:477
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /D:477-483
58 atoms, 57 bonds, 7 residues, 1 model selected
> select /D:468
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /D:468-518
406 atoms, 420 bonds, 51 residues, 1 model selected
> color sel yellow
> select
> /D:2-8,43-47,66-71,82-87,94-97,133-142,147-156,191-197,243-245,277-282,290-295,307-311,313-316,477-480,491-494,512-514
734 atoms, 736 bonds, 90 residues, 1 model selected
> select /D:10
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /D:10
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel red
> select
> /D:2-8,43-47,66-71,82-87,94-97,133-142,147-156,191-197,243-245,277-282,290-295,307-311,313-316,477-480,491-494,512-514
734 atoms, 736 bonds, 90 residues, 1 model selected
> select /D:8
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /D:8
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel red
> select
13428 atoms, 13962 bonds, 1468 residues, 1 model selected
> style sel stick
Changed 13428 atom styles
> style sel stick
Changed 13428 atom styles
> hide sel atoms
> show sel surfaces
> hide sel surfaces
> show sel cartoons
> select /D:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /D:1-8
69 atoms, 70 bonds, 8 residues, 1 model selected
> alphafold contacts /A toResidues /D distance 5 outputFile z.txt
Structure fold_pcna3_apex2_dsdna_with_resection_model_0.cif #1 does not have
PAE data opened
> alphafold contacts /A toResidues /D distance 8 outputFile z.txt
Structure fold_pcna3_apex2_dsdna_with_resection_model_0.cif #1 does not have
PAE data opened
> ui tool show "AlphaFold Error Plot"
> alphafold pae #1 file
> /Users/ajackso8/Downloads/fold_pcna3_apex2_dsdna_with_resection/fold_pcna3_apex2_dsdna_with_resection_full_data_0.json
> alphafold contacts /A toResidues /D distance 5 outputFile z.txt
> alphafold contacts /A toResidues /D distance 3 outputFile z.txt
> save
> /Users/ajackso8/Downloads/fold_pcna3_apex2_dsdna_with_resection/session.cxs
——— End of log from Fri Mar 7 21:39:53 2025 ———
opened ChimeraX session
OpenGL version: 4.1 Metal - 89.3
OpenGL renderer: Apple M1 Pro
OpenGL vendor: Apple
Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro18,3
Model Number: Z15J0026PB/A
Chip: Unknown
Total Number of Cores: 8 (6 performance and 2 efficiency)
Memory: 32 GB
System Firmware Version: 11881.81.4
OS Loader Version: 11881.81.4
Software:
System Software Overview:
System Version: macOS 15.3.1 (24D70)
Kernel Version: Darwin 24.3.0
Time since boot: 4 days, 22 hours, 45 minutes
Graphics/Displays:
Apple M1 Pro:
Chipset Model: Apple M1 Pro
Type: GPU
Bus: Built-In
Total Number of Cores: 14
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
HP E273:
Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
UI Looks like: 1920 x 1080 @ 60.00Hz
Main Display: Yes
Mirror: Off
Online: Yes
HU282PPS:
Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition)
UI Looks like: 1920 x 1080 @ 60.00Hz
Mirror: Off
Online: Yes
Installed Packages:
alabaster: 0.7.13
appdirs: 1.4.4
appnope: 0.1.3
asttokens: 2.2.1
Babel: 2.12.1
backcall: 0.2.0
beautifulsoup4: 4.11.2
blockdiag: 3.0.0
build: 0.10.0
certifi: 2021.10.8
cftime: 1.6.2
charset-normalizer: 3.1.0
ChimeraX-AddCharge: 1.5.9.1
ChimeraX-AddH: 2.2.5
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.3.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.9.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.3
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.43.10
ChimeraX-AtomicLibrary: 10.0.6
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3.2
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.1
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.8
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.2
ChimeraX-ChangeChains: 1.0.2
ChimeraX-CheckWaters: 1.3.1
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.3
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.6.1
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.4.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2
ChimeraX-DistMonitor: 1.4
ChimeraX-DockPrep: 1.1.1
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.1
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-Label: 1.1.7
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.5
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.2
ChimeraX-Map: 1.1.4
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.0.12
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.12
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.9
ChimeraX-ModelPanel: 1.3.7
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.0
ChimeraX-NRRD: 1.0
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.10.1
ChimeraX-PDB: 2.7.2
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 3.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.1
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.8.3
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.1
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.10.3
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1.2
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.2.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Topography: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.28.4
ChimeraX-uniprot: 2.2.2
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.1
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.1.3
contourpy: 1.0.7
cxservices: 1.2.2
cycler: 0.11.0
Cython: 0.29.33
debugpy: 1.6.7
decorator: 5.1.1
docutils: 0.19
executing: 1.2.0
filelock: 3.9.0
fonttools: 4.39.3
funcparserlib: 1.0.1
grako: 3.16.5
h5py: 3.8.0
html2text: 2020.1.16
idna: 3.4
ihm: 0.35
imagecodecs: 2022.9.26
imagesize: 1.4.1
importlib-metadata: 6.6.0
ipykernel: 6.21.1
ipython: 8.10.0
ipython-genutils: 0.2.0
ipywidgets: 8.0.6
jedi: 0.18.2
Jinja2: 3.1.2
jupyter-client: 8.0.2
jupyter-core: 5.3.0
jupyterlab-widgets: 3.0.7
kiwisolver: 1.4.4
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.2
matplotlib: 3.6.3
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.5.6
netCDF4: 1.6.2
networkx: 2.8.8
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.8.4
numpy: 1.23.5
openvr: 1.23.701
packaging: 21.3
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 9.3.0
pip: 23.0
pkginfo: 1.9.6
platformdirs: 3.5.0
prompt-toolkit: 3.0.38
psutil: 5.9.4
ptyprocess: 0.7.0
pure-eval: 0.2.2
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.14.0
pynrrd: 1.0.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.9
pyproject-hooks: 1.0.0
PyQt6-commercial: 6.4.2
PyQt6-Qt6: 6.4.3
PyQt6-sip: 13.4.1
PyQt6-WebEngine-commercial: 6.4.0
PyQt6-WebEngine-Qt6: 6.4.3
python-dateutil: 2.8.2
pytz: 2023.3
pyzmq: 25.0.2
qtconsole: 5.4.0
QtPy: 2.3.1
RandomWords: 0.4.0
requests: 2.28.2
scipy: 1.9.3
setuptools: 67.4.0
setuptools-scm: 7.0.5
sfftk-rw: 0.7.3
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.4.1
sphinx: 6.1.3
sphinx-autodoc-typehints: 1.22
sphinxcontrib-applehelp: 1.0.4
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.1
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
stack-data: 0.6.2
tables: 3.7.0
tcia-utils: 1.2.0
tifffile: 2022.10.10
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.3.1
traitlets: 5.9.0
typing-extensions: 4.5.0
tzdata: 2023.3
urllib3: 1.26.15
wcwidth: 0.2.6
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.7
zipp: 3.15.0
Change History (2)
comment:1 by , 7 months ago
| Component: | Unassigned → Window Toolkit |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crashed in QTabBar::paintEvent(), QPainter::begin: Paint device returned engine == 0 |
comment:2 by , 7 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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