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Opened 20 months ago
Closed 20 months ago
#14669 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: | pett | |
| 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 0x0000700020c97000 (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 0x000070001fc94000 (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 0x000070001ec91000 (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 0x000070001dc8e000 (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 0x000070001cc8b000 (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 0x000070001bc88000 (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 0x000070001ac85000 (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 0x0000700019c82000 (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 0x0000700018c7f000 (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 0x0000700017c7c000 (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 0x0000700016c79000 (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 0x00007ff849954b40 (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":"2024-02-29 18:43:14.00 +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 14.1.2 (23B92)","roots_installed":0,"name":"ChimeraX","incident_id":"DF9094AE-C401-453F-B986-A93AE2C5ACCC"}
{
"uptime" : 54000,
"procRole" : "Background",
"version" : 2,
"userID" : 1516671447,
"deployVersion" : 210,
"modelCode" : "MacBookPro15,2",
"coalitionID" : 1723,
"osVersion" : {
"train" : "macOS 14.1.2",
"build" : "23B92",
"releaseType" : "User"
},
"captureTime" : "2024-02-29 18:42:33.3728 +0000",
"codeSigningMonitor" : 0,
"incident" : "DF9094AE-C401-453F-B986-A93AE2C5ACCC",
"pid" : 3464,
"cpuType" : "X86-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2024-02-27 19:33:51.9976 +0000",
"procStartAbsTime" : 1143471037226,
"procExitAbsTime" : 54600978248677,
"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":"F93EF397-1C3C-5671-9E69-56F084C31F60","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "42AB39BB-59BD-B9BA-94BB-32DCD3A61D5C",
"lowPowerMode" : 1,
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"wakeTime" : 7750,
"bridgeVersion" : {"build":"21P1069","train":"8.1"},
"sleepWakeUUID" : "D707EBE8-384D-4F14-8740-18381F748D23",
"sip" : "enabled",
"vmRegionInfo" : "0x18 is not in any region. Bytes before following region: 140737486393320\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n shared memory 7fffffe21000-7fffffe22000 [ 4K] r-x\/r-x SM=SHM ",
"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":3464},
"vmregioninfo" : "0x18 is not in any region. Bytes before following region: 140737486393320\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n shared memory 7fffffe21000-7fffffe22000 [ 4K] r-x\/r-x SM=SHM ",
"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,
"threads" : 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===== Log before crash start =====
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/cruzmin/Downloads/test_3827a/test_3827a_unrelaxed_rank_001_alphafold2_ptm_model_2_seed_000.pdb
Chain information for
test_3827a_unrelaxed_rank_001_alphafold2_ptm_model_2_seed_000.pdb #1
---
Chain | Description
A | No description available
> open
> /Users/cruzmin/Downloads/test_3827a/test_3827a_unrelaxed_rank_001_alphafold2_ptm_model_2_seed_000.pdb
Chain information for
test_3827a_unrelaxed_rank_001_alphafold2_ptm_model_2_seed_000.pdb #2
---
Chain | Description
A | No description available
> ui tool show "AlphaFold Error Plot"
> hide #2 models
> ui tool show "AlphaFold Error Plot"
> alphafold pae #1 file
> /Users/cruzmin/Downloads/test_3827a/test_3827a_scores_rank_001_alphafold2_ptm_model_2_seed_000.json
> color bfactor #1 palette alphafold
581 atoms, 70 residues, atom bfactor range 53.2 to 98.1
> select add #1
581 atoms, 588 bonds, 70 residues, 1 model selected
> show sel surfaces
> color (#!1 & sel) purple
> transparency (#!1 & sel) 60
> lighting simple
> lighting soft
> lighting full
> lighting flat
> lighting shadows true intensity 0.5
> lighting simple
> ui tool show Matchmaker
> coulombic sel
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for
test_3827a_unrelaxed_rank_001_alphafold2_ptm_model_2_seed_000.pdb_A SES
surface #1.1: minimum, -13.58, mean 0.67, maximum 12.82
To also show corresponding color key, enter the above coulombic command and
add key true
Alignment identifier is 1/A
> select #1/A:24
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/A:24-29
56 atoms, 57 bonds, 6 residues, 1 model selected
> select add #1
581 atoms, 588 bonds, 70 residues, 2 models selected
> select subtract #1
1 model selected
> show #2 models
> hide #!1 models
> show #!1 models
> hide #2 models
> hide #!1 models
> show #!1 models
> show #2 models
> select #1/A:6-13,16-21,27-32,35-41,46-64
393 atoms, 396 bonds, 46 residues, 1 model selected
> select #1/A:24-29
56 atoms, 57 bonds, 6 residues, 1 model selected
> select #1/A:6-13,16-21,27-32,35-41,46-64
393 atoms, 396 bonds, 46 residues, 1 model selected
> select add #1
581 atoms, 588 bonds, 70 residues, 2 models selected
> hide #2 models
> hide #!1 models
> show #!1 models
> show #2 models
> select subtract #1
1 model selected
> open "/Users/cruzmin/Library/CloudStorage/OneDrive-
> NorwichBioScienceInstitutes/Vts1 paper 2023/SAM domain structures
> Magnaporthe/SAM_Mst50_dd8af/SAM_Mst50_dd8af_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb"
Chain information for
SAM_Mst50_dd8af_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb #3
---
Chain | Description
A | No description available
> hide #!1 models
> hide #2 models
> hide #3 models
> show #3 models
> show #2 models
> show #!1 models
> hide #2 models
> hide #!1 models
> coulombic #3
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for
SAM_Mst50_dd8af_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb_A SES
surface #3.1: minimum, -14.72, mean -2.18, maximum 9.67
To also show corresponding color key, enter the above coulombic command and
add key true
> rainbow #!3
> hide #!3 surfaces
> color #3 cyan
> show #2 models
> ui tool show Matchmaker
> matchmaker #!3 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker test_3827a_unrelaxed_rank_001_alphafold2_ptm_model_2_seed_000.pdb,
chain A (#1) with
SAM_Mst50_dd8af_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb, chain
A (#3), sequence alignment score = 105.1
RMSD between 50 pruned atom pairs is 1.013 angstroms; (across all 62 pairs:
2.480)
> close #1
> select add #2
581 atoms, 588 bonds, 70 residues, 1 model selected
> select add #3
1083 atoms, 1098 bonds, 134 residues, 2 models selected
Alignment identifier is 2/A
Alignment identifier is 3/A
> hide #2 models
> hide #!3 models
> show #!3 models
> show #2 models
> select subtract #2
502 atoms, 510 bonds, 64 residues, 2 models selected
> select subtract #3
1 model selected
> ui tool show Matchmaker
> select add #2
581 atoms, 588 bonds, 70 residues, 1 model selected
> select add #3
1083 atoms, 1098 bonds, 134 residues, 2 models selected
> select #2/A:20
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/A:20
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel orange
> hide sel atoms
> color sel cyan
> undo
Unsupported scale factor (0.000000) detected on Display1
> select add #2
581 atoms, 588 bonds, 70 residues, 1 model selected
> select subtract #2
Nothing selected
> open "/Users/cruzmin/Library/CloudStorage/OneDrive-
> NorwichBioScienceInstitutes/Vts1 paper 2023/SAM domain structures
> Magnaporthe/DmSmaug_SAM_67437/DmSmaug_SAM_67437_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb"
Chain information for
DmSmaug_SAM_67437_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb #1
---
Chain | Description
A | No description available
> open "/Users/cruzmin/Library/CloudStorage/OneDrive-
> NorwichBioScienceInstitutes/Vts1 paper 2023/SAM domain structures
> Magnaporthe/SAM_ScVts1_d2fe7/SAM_ScVts1_d2fe7_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb"
Chain information for
SAM_ScVts1_d2fe7_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb #4
---
Chain | Description
A | No description available
> open "/Users/cruzmin/Library/CloudStorage/OneDrive-
> NorwichBioScienceInstitutes/Vts1 paper 2023/SAM domain structures
> Magnaporthe/SAM_Mst11_9b88c/SAM_Mst11_9b88c_unrelaxed_rank_001_alphafold2_ptm_model_5_seed_000.pdb"
Chain information for
SAM_Mst11_9b88c_unrelaxed_rank_001_alphafold2_ptm_model_5_seed_000.pdb #5
---
Chain | Description
A | No description available
> open "/Users/cruzmin/Library/CloudStorage/OneDrive-
> NorwichBioScienceInstitutes/Vts1 paper 2023/SAM domain structures
> Magnaporthe/SAM_MGG_07310_216b4/SAM_MGG_07310_216b4_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb"
Chain information for
SAM_MGG_07310_216b4_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb #6
---
Chain | Description
A | No description available
> open "/Users/cruzmin/Library/CloudStorage/OneDrive-
> NorwichBioScienceInstitutes/Vts1 paper 2023/SAM domain structures
> Magnaporthe/SAM_MGG_00492_746d4/SAM_MGG_00492_746d4_unrelaxed_rank_001_alphafold2_ptm_model_1_seed_000.pdb"
Chain information for
SAM_MGG_00492_746d4_unrelaxed_rank_001_alphafold2_ptm_model_1_seed_000.pdb #7
---
Chain | Description
A | No description available
> open "/Users/cruzmin/Library/CloudStorage/OneDrive-
> NorwichBioScienceInstitutes/Vts1 paper 2023/SAM domain structures
> Magnaporthe/MoMGG_01641/test_55176_unrelaxed_rank_001_alphafold2_ptm_model_2_seed_000.pdb"
Chain information for
test_55176_unrelaxed_rank_001_alphafold2_ptm_model_2_seed_000.pdb #8
---
Chain | Description
A | No description available
> ui tool show Matchmaker
> matchmaker #2,4-8#!3 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker
DmSmaug_SAM_67437_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb,
chain A (#1) with
test_3827a_unrelaxed_rank_001_alphafold2_ptm_model_2_seed_000.pdb, chain A
(#2), sequence alignment score = 142
RMSD between 47 pruned atom pairs is 1.101 angstroms; (across all 61 pairs:
1.980)
Matchmaker
DmSmaug_SAM_67437_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb,
chain A (#1) with
SAM_ScVts1_d2fe7_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb, chain
A (#4), sequence alignment score = 126.9
RMSD between 46 pruned atom pairs is 1.052 angstroms; (across all 62 pairs:
6.312)
Matchmaker
DmSmaug_SAM_67437_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb,
chain A (#1) with
SAM_Mst11_9b88c_unrelaxed_rank_001_alphafold2_ptm_model_5_seed_000.pdb, chain
A (#5), sequence alignment score = 118.4
RMSD between 46 pruned atom pairs is 0.972 angstroms; (across all 62 pairs:
2.005)
Matchmaker
DmSmaug_SAM_67437_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb,
chain A (#1) with
SAM_MGG_07310_216b4_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb,
chain A (#6), sequence alignment score = 68.4
RMSD between 30 pruned atom pairs is 1.062 angstroms; (across all 61 pairs:
3.343)
Matchmaker
DmSmaug_SAM_67437_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb,
chain A (#1) with
SAM_MGG_00492_746d4_unrelaxed_rank_001_alphafold2_ptm_model_1_seed_000.pdb,
chain A (#7), sequence alignment score = 62.3
RMSD between 33 pruned atom pairs is 1.032 angstroms; (across all 60 pairs:
2.673)
Matchmaker
DmSmaug_SAM_67437_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb,
chain A (#1) with
test_55176_unrelaxed_rank_001_alphafold2_ptm_model_2_seed_000.pdb, chain A
(#8), sequence alignment score = 97.5
RMSD between 39 pruned atom pairs is 0.999 angstroms; (across all 57 pairs:
2.506)
Matchmaker
DmSmaug_SAM_67437_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb,
chain A (#1) with
SAM_Mst50_dd8af_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb, chain
A (#3), sequence alignment score = 88.6
RMSD between 40 pruned atom pairs is 0.952 angstroms; (across all 58 pairs:
2.318)
> hide #!3 models
> hide #5 models
> hide #6 models
> hide #7 models
> hide #8 models
> hide #4 models
> hide #2 models
> coulombic #1
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for
DmSmaug_SAM_67437_unrelaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb_A SES
surface #1.1: minimum, -12.37, mean 0.71, maximum 12.25
To also show corresponding color key, enter the above coulombic command and
add key true
Unsupported scale factor (0.000000) detected on Display0
QPainter::begin: Paint device returned engine == 0, type: 3
===== Log before crash end =====
Log:
Startup Messages
---
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle
UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 INTEL-22.1.28
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 655
OpenGL vendor: Intel Inc.
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: MacBookPro15,2
Processor Name: Quad-Core Intel Core i5
Processor Speed: 2.3 GHz
Number of Processors: 1
Total Number of Cores: 4
L2 Cache (per Core): 256 KB
L3 Cache: 6 MB
Hyper-Threading Technology: Enabled
Memory: 8 GB
System Firmware Version: 2020.41.1.0.0 (iBridge: 21.16.1069.0.0,0)
OS Loader Version: 580~743
Software:
System Software Overview:
System Version: macOS 14.1.2 (23B92)
Kernel Version: Darwin 23.1.0
Time since boot: 2 days, 1 hour, 57 minutes
Graphics/Displays:
Intel Iris Plus Graphics 655:
Chipset Model: Intel Iris Plus Graphics 655
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x3ea5
Revision ID: 0x0001
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2560 x 1600 Retina
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
DELL S2721HN:
Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
UI Looks like: 1920 x 1080 @ 60.00Hz
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Display Serial Number: BWCYC23
Mirror: Off
Online: Yes
Rotation: Supported
Connection Type: DVI or HDMI
Adapter Firmware Version: 7.55
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: 2022.2.22
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 , 20 months ago
| Cc: | added |
|---|---|
| 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 , 20 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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