![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 2 years ago
Closed 2 years ago
#9226 closed defect (can't reproduce)
Crashed in QTabBar::paintEvent(), QPainter::begin: Paint device returned engine == 0
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Window Toolkit | Version: | |
| Keywords: | Cc: | Tom Goddard | |
| 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
Current thread 0x00007ff8519f6640 (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":"2023-06-21 11:26:22.00 -0700","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 13.4 (22F66)","roots_installed":0,"name":"ChimeraX","incident_id":"E212B1DA-AFA1-45A5-8769-8AC74956FEC0"}
{
"uptime" : 35000,
"procRole" : "Foreground",
"version" : 2,
"userID" : 545168783,
"deployVersion" : 210,
"modelCode" : "MacBookPro16,1",
"coalitionID" : 3742,
"osVersion" : {
"train" : "macOS 13.4",
"build" : "22F66",
"releaseType" : "User"
},
"captureTime" : "2023-06-21 11:26:06.7901 -0700",
"incident" : "E212B1DA-AFA1-45A5-8769-8AC74956FEC0",
"pid" : 16821,
"cpuType" : "X86-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2023-06-21 11:13:39.0205 -0700",
"procStartAbsTime" : 34966738231874,
"procExitAbsTime" : 35689965750089,
"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":"38B4B509-A108-52E3-81C7-B2A6BA96518B","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "9B18D030-B306-6304-2536-D0F294D493BC",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 0,
"wakeTime" : 5,
"bridgeVersion" : {"build":"20P5058","train":"7.5"},
"sleepWakeUUID" : "07521564-FA19-446E-BC15-0BB8F857F5F1",
"sip" : "enabled",
"vmRegionInfo" : "0x18 is not in any region. Bytes before following region: 140737487409128\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n shared memory 7ffffff19000-7ffffff1a000 [ 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"},
"vmregioninfo" : "0x18 is not in any region. Bytes before following region: 140737487409128\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n shared memory 7ffffff19000-7ffffff1a000 [ 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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"base" : 140703418327040,
"CFBundleShortVersionString" : "6.9",
"CFBundleIdentifier" : "com.apple.AppKit",
"size" : 16809977,
"uuid" : "935dfca1-61f9-377d-895a-99ef90266c86",
"path" : "\/System\/Library\/Frameworks\/AppKit.framework\/Versions\/C\/AppKit",
"name" : "AppKit",
"CFBundleVersion" : "2299.60.124"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 140703529439232,
"CFBundleShortVersionString" : "2.1.1",
"CFBundleIdentifier" : "com.apple.HIToolbox",
"size" : 3112946,
"uuid" : "c476550b-ba3d-3c03-ba02-b4b3cfa25e68",
"path" : "\/System\/Library\/Frameworks\/Carbon.framework\/Versions\/A\/Frameworks\/HIToolbox.framework\/Versions\/A\/HIToolbox",
"name" : "HIToolbox"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 140703459450880,
"CFBundleShortVersionString" : "1.22",
"CFBundleIdentifier" : "com.apple.HIServices",
"size" : 376825,
"uuid" : "ac6059a2-d71c-3fec-8666-b8097073bd5a",
"path" : "\/System\/Library\/Frameworks\/ApplicationServices.framework\/Versions\/A\/Frameworks\/HIServices.framework\/Versions\/A\/HIServices",
"name" : "HIServices"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 140703446896640,
"CFBundleShortVersionString" : "1.600.0",
"CFBundleIdentifier" : "com.apple.SkyLight",
"size" : 4141042,
"uuid" : "7f8a712a-38b5-366d-b8bd-56d6b7af9347",
"path" : "\/System\/Library\/PrivateFrameworks\/SkyLight.framework\/Versions\/A\/SkyLight",
"name" : "SkyLight"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 140703365029888,
"size" : 294900,
"uuid" : "da743230-0aca-3094-821c-5e1565d8b187",
"path" : "\/usr\/lib\/system\/libdispatch.dylib",
"name" : "libdispatch.dylib"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 140703363211264,
"size" : 624080,
"uuid" : "9e98a840-a3ac-31c1-ab97-829af9bd6864",
"path" : "\/usr\/lib\/dyld",
"name" : "dyld"
}
],
"sharedCache" : {
"base" : 140703362588672,
"size" : 21474836480,
"uuid" : "867bf49e-1375-3009-9693-a1621961928a"
},
"vmSummary" : "ReadOnly portion of Libraries: Total=1.1G resident=0K(0%) swapped_out_or_unallocated=1.1G(100%)\nWritable regions: Total=2.0G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=2.0G(100%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 384K 3 \nActivity Tracing 256K 1 \nCG backing stores 2688K 4 \nCG image 100K 12 \nColorSync 252K 27 \nCoreAnimation 112K 15 \nCoreGraphics 16K 3 \nCoreUI image data 3072K 34 \nFoundation 16K 1 \nIOKit 23.3M 3 \nKernel Alloc Once 8K 1 \nMALLOC 1.2G 877 \nMALLOC guard page 32K 7 \nMALLOC_LARGE (reserved) 384K 1 reserved VM address space (unallocated)\nMALLOC_NANO (reserved) 384.0M 1 reserved VM address space (unallocated)\nMach message 16K 2 \nOpenGL GLSL 384K 4 \nSTACK GUARD 116K 29 \nStack 157.7M 30 \nStack Guard 56.0M 1 \nVM_ALLOCATE 226.9M 157 \nVM_ALLOCATE (reserved) 64.0M 1 reserved VM address space (unallocated)\n__CTF 824 1 \n__DATA 47.1M 752 \n__DATA_CONST 52.2M 382 \n__DATA_DIRTY 1785K 220 \n__FONT_DATA 2352 1 \n__GLSLBUILTINS 5174K 1 \n__INFO_FILTER 8 1 \n__LINKEDIT 202.5M 149 \n__OBJC_RO 66.3M 1 \n__OBJC_RW 2013K 2 \n__TEXT 953.8M 753 \ndyld private memory 292K 3 \nmapped file 116.7M 51 \nshared memory 3000K 30 \n=========== ======= ======= \nTOTAL 3.5G 3561 \nTOTAL, minus reserved VM space 3.1G 3561 \n",
"legacyInfo" : {
"threadTriggered" : {
"name" : "CrBrowserMain",
"queue" : "com.apple.main-thread"
}
},
"logWritingSignature" : "441ead0f185532c52392b81fbbfa815460f3ff57",
"trialInfo" : {
"rollouts" : [
{
"rolloutId" : "62c73fd17cce0d1b0bcb8a02",
"factorPackIds" : {
"SIRI_DIALOG_ASSETS" : "645e39c59e69a025b0a37ea1"
},
"deploymentId" : 240000119
},
{
"rolloutId" : "6425c75e4327780c10cc4252",
"factorPackIds" : {
"SIRI_HOME_AUTOMATION_INTENT_SELECTION_CACHE" : "642600a457e7664b1698eb32"
},
"deploymentId" : 240000004
}
],
"experiments" : [
{
"treatmentId" : "c28e4ee6-1b08-4f90-8e05-2809e78310a3",
"experimentId" : "6317d2003d24842ff850182a",
"deploymentId" : 400000013
}
]
}
}
===== Log before crash start =====
UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open /Users/haoyangli/Desktop/GPC_DHT01.cxs
Log from Fri May 12 15:04:25 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open /Users/haoyangli/Desktop/123.cxs
Log from Mon May 1 17:48:59 2023UCSF ChimeraX version: 1.5 (2022-11-24)
© 2016-2022 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/haoyangli/Downloads/7puy.cif format mmcif
7puy.cif title:
Structure of the membrane soluble spike complex from the Lassa virus in a
C3-symmetric map [more info...]
Chain information for 7puy.cif #1
---
Chain | Description | UniProt
A B C | Pre-glycoprotein polyprotein GP complex | GLYC_LASSJ
a b c | Glycoprotein G2 | GLYC_LASSJ
Non-standard residues in 7puy.cif #1
---
BDP — beta-D-glucopyranuronic acid (beta-D-glucuronic acid; D-glucuronic acid;
glucuronic acid)
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)
XYS — alpha-D-xylopyranose (alpha-D-xylose; D-xylose; xylose; XYLOPYRANOSE)
> hide atoms
> show cartoons
> lighting soft
> set bgColor white
> graphics silhouettes true
> sequence chain #1/a#1/b#1/c
Alignment identifier is 1
> atggagagacagggaaagacaccattgggtctagttgac
Unknown command: atggagagacagggaaagacaccattgggtctagttgac
> hide atoms
> show cartoons
> select /a-c:384
27 atoms, 24 bonds, 3 residues, 1 model selected
> select /a-c:384
27 atoms, 24 bonds, 3 residues, 1 model selected
> select /a-c:425
27 atoms, 24 bonds, 3 residues, 1 model selected
> select /a-c:425-426
48 atoms, 45 bonds, 6 residues, 1 model selected
> select /a-c:431
21 atoms, 18 bonds, 3 residues, 1 model selected
> select /a-c:431-433
69 atoms, 66 bonds, 9 residues, 1 model selected
> select /a-c:433
24 atoms, 21 bonds, 3 residues, 1 model selected
> select /a-c:433
24 atoms, 21 bonds, 3 residues, 1 model selected
> show sel atoms
> select /a-c:448
30 atoms, 30 bonds, 3 residues, 1 model selected
> select /a-c:447-448
54 atoms, 54 bonds, 6 residues, 1 model selected
> open /Users/haoyangli/Downloads/7sgd.pdb
7sgd.pdb title:
Lassa virus glycoprotein construct(josiah GPCYSR4) recovered from GPC- I53-50
nanoparticle by localized reconstruction [more info...]
Chain information for 7sgd.pdb #2
---
Chain | Description | UniProt
A B C a b c | josiah GPCYSR4 I53-50A | Q6GWS0_9VIRU
Non-standard residues in 7sgd.pdb #2
---
BMA — β-D-mannopyranose (β-D-mannose; D-mannose; mannose)
FUC — α-L-fucopyranose (α-L-fucose; 6-deoxy-α-L-galactopyranose; L-fucose;
fucose)
MAN — α-D-mannopyranose (α-D-mannose; D-mannose; mannose)
NAG — 2-acetamido-2-deoxy-β-D-glucopyranose (N-acetyl-β-D-glucosamine;
2-acetamido-2-deoxy-β-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-acetyl-D-glucosamine)
> hide sel atoms
> show sel cartoons
> select add #2
9174 atoms, 9444 bonds, 9 pseudobonds, 1095 residues, 3 models selected
> show sel atoms
> hide sel atoms
> show sel cartoons
> sequence chain #2/A#2/B#2/C#2/a#2/b#2/c
Alignment identifier is 2
> mmaker #2/A to #1/A showAlignment true
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 7puy.cif, chain A (#1) with 7sgd.pdb, chain A (#2), sequence
alignment score = 1149.4
Alignment identifier is 3
Showing conservation header ("seq_conservation" residue attribute) for
alignment 3
Hiding conservation header for alignment 3
Chains used in RMSD evaluation for alignment 3: 7puy.cif #1/A, 7sgd.pdb #2/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 3
RMSD between 133 pruned atom pairs is 1.045 angstroms; (across all 169 pairs:
2.141)
> open "/Users/haoyangli/Downloads/7uot (1).pdb"
7uot (1).pdb title:
Native lassa glycoprotein In complex with neutralizing antibodies 8.9F and
37.2D [more info...]
Chain information for 7uot (1).pdb #3
---
Chain | Description | UniProt
A B C | glycoprotein G1 | GLYC_LASSJ
H | 8.9F heavy chain (variable domain) |
L | 8.9F light chain (variable domain) |
O Q S | 37.2D heavy chain (variable domain) |
P R T | 37.2D light chain (variable domain) |
a b c | GP2 | GLYC_LASSJ
Non-standard residues in 7uot (1).pdb #3
---
BMA — β-D-mannopyranose (β-D-mannose; D-mannose; mannose)
FUC — α-L-fucopyranose (α-L-fucose; 6-deoxy-α-L-galactopyranose; L-fucose;
fucose)
MAN — α-D-mannopyranose (α-D-mannose; D-mannose; mannose)
NAG — 2-acetamido-2-deoxy-β-D-glucopyranose (N-acetyl-β-D-glucosamine;
2-acetamido-2-deoxy-β-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-acetyl-D-glucosamine)
> select add #3
26008 atoms, 26764 bonds, 15 pseudobonds, 3167 residues, 5 models selected
> select subtract #2
16888 atoms, 17374 bonds, 6 pseudobonds, 2078 residues, 3 models selected
> select add #1
27229 atoms, 27979 bonds, 15 pseudobonds, 3338 residues, 4 models selected
> hide sel atoms
> show sel cartoons
> mmaker #3/A to #1/A showAlignment true
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 7puy.cif, chain A (#1) with 7uot (1).pdb, chain A (#3), sequence
alignment score = 1198.8
Alignment identifier is 3
Showing conservation header ("seq_conservation" residue attribute) for
alignment 3
Hiding conservation header for alignment 3
Chains used in RMSD evaluation for alignment 3: 7puy.cif #1/A, 7uot (1).pdb
#3/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 3
RMSD between 160 pruned atom pairs is 0.747 angstroms; (across all 183 pairs:
1.431)
> hide #!2 models
> color #3 #9437ffff
> show #!2 models
> hide #!3 models
> hide #!1 models
> select #2/b:423
9 atoms, 8 bonds, 1 residue, 1 model selected
> open /Users/haoyangli/Downloads/7sge.pdb
7sge.pdb title:
I53-50 nanoparticle core reconstructed from GPC-I53-50NP by focused refinement
[more info...]
Chain information for 7sge.pdb #4
---
Chain | Description
A | josiah GPCYSR4-I53-50A - nanoparticle component
B | I53-50B component
> hide #!2 models
> select add #2
9120 atoms, 9390 bonds, 9 pseudobonds, 1089 residues, 2 models selected
> select subtract #2
Nothing selected
> sequence chain #4/A
Alignment identifier is 4/A
> select #4/A:1
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #4/A:1-53
407 atoms, 412 bonds, 53 residues, 1 model selected
> select clear
> select #4/A:1
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #4/A:1
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #4/A:1
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #4/A:1-4
30 atoms, 29 bonds, 4 residues, 1 model selected
> select clear
> color #4 bychain
> show #!1 models
> hide #!1 models
> show #!2 models
> hide #4 models
> select #2/a-c:423
27 atoms, 24 bonds, 3 residues, 1 model selected
> select #2/a-c:423
27 atoms, 24 bonds, 3 residues, 1 model selected
> open /Users/haoyangli/Downloads/6p6f.cif
6p6f.cif title:
BG505 sosip-I53-50NP [more info...]
Chain information for 6p6f.cif #5
---
Chain | Description
A | I53-50A.1NT1
B | I53-50B.4PT1
6p6f.cif mmCIF Assemblies
---
1| complete icosahedral assembly
2| icosahedral asymmetric unit
3| icosahedral pentamer
4| icosahedral 23 hexamer
5| icosahedral asymmetric unit, std point frame
> close #5
> select #4/A:6
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #4/A:6-206
1520 atoms, 1549 bonds, 201 residues, 1 model selected
> show #!1 models
> hide #!2 models
> select #1/a-c:432
24 atoms, 21 bonds, 3 residues, 1 model selected
> select #1/a-c:432
24 atoms, 21 bonds, 3 residues, 1 model selected
> show sel atoms
> select #1/a-c:427
21 atoms, 21 bonds, 3 residues, 1 model selected
> select #1/a-c:427
21 atoms, 21 bonds, 3 residues, 1 model selected
> show sel atoms
> select #1/a-c:428-429
36 atoms, 33 bonds, 6 residues, 1 model selected
> select #1/a-c:428-431
81 atoms, 78 bonds, 12 residues, 1 model selected
> select #1/a-c:423-424
39 atoms, 36 bonds, 6 residues, 1 model selected
> select #1/a-c:417-424
213 atoms, 213 bonds, 24 residues, 1 model selected
> select #1/a-c:424
12 atoms, 9 bonds, 3 residues, 1 model selected
> select #1/a-c:422-424
72 atoms, 69 bonds, 9 residues, 1 model selected
> show #!3 models
> hide #!1 models
> show #!2 models
> show #!1 models
> hide #!3 models
> hide #!1 models
> select #2/c:422
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #2/a-c:423
27 atoms, 24 bonds, 3 residues, 1 model selected
> select #2/a-c:423
27 atoms, 24 bonds, 3 residues, 1 model selected
> show #4 models
> hide #4 models
> show #!3 models
> hide #!2 models
> show #!2 models
> hide #!3 models
> hide #!2 models
> show #!3 models
> color #!3 bychain
> interfaces #!3 & ~solvent
24 buried areas: B b 2272, A a 2260, C c 2224, A B 1223, A C 1187, B C 1171, H
L 822, Q R 799, O P 794, S T 793, c S 766, b Q 763, a O 745, b c 704, a c 687,
a b 687, A b 615, B c 615, C a 580, L q 368, C H 326, B g 321, A M 310, C r
302
> hbonds #!3 reveal true
3334 hydrogen bonds found
> hide #!3 atoms
> show #!3 atoms
> hide #!3 atoms
> interfaces #!3 & ~solvent
24 buried areas: B b 2272, A a 2260, C c 2224, A B 1223, A C 1187, B C 1171, H
L 822, Q R 799, O P 794, S T 793, c S 766, b Q 763, a O 745, b c 704, a c 687,
a b 687, A b 615, B c 615, C a 580, L q 368, C H 326, B g 321, A M 310, C r
302
> select add #3
16861 atoms, 17344 bonds, 1539 pseudobonds, 2075 residues, 4 models selected
> select add #2
25954 atoms, 26710 bonds, 1548 pseudobonds, 3161 residues, 5 models selected
> interfaces select & #!3 & ~solvent
Missing or invalid "atoms" argument: invalid atoms specifier
> select subtract #2
16834 atoms, 17320 bonds, 1539 pseudobonds, 2072 residues, 3 models selected
> interfaces select & ~solvent
Missing or invalid "atoms" argument: invalid atoms specifier
> select subtract #3
Nothing selected
> interfaces #!3 & ~solvent
24 buried areas: B b 2272, A a 2260, C c 2224, A B 1223, A C 1187, B C 1171, H
L 822, Q R 799, O P 794, S T 793, c S 766, b Q 763, a O 745, b c 704, a c 687,
a b 687, A b 615, B c 615, C a 580, L q 368, C H 326, B g 321, A M 310, C r
302
> select clear
> select #3/C:257
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> style #!3 stick
Changed 16834 atom styles
> select #3/C:258
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #3/C:259
16 atoms, 14 bonds, 2 residues, 1 model selected
> show sel atoms
> select #3/A:150
12 atoms, 12 bonds, 1 residue, 1 model selected
Drag select of 4 atoms, 111 residues, 3 bonds, 40 pseudobonds
> show sel atoms
> select clear
> hide #!3 atoms
> select #3/B:125
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> color #!3 byhetero
> select #3/A:151
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> hide #5 models
> close #5
> hide #!3 models
> show #!1 models
> save /Users/haoyangli/Desktop/123.cxs
——— End of log from Mon May 1 17:48:59 2023 ———
opened ChimeraX session
> hide #!1 atoms
Drag select of 1224 residues, 9 pseudobonds
> select #1/a#1/b#1/c
4731 atoms, 4851 bonds, 576 residues, 1 model selected
> select #3/A#3/B#3/C
4563 atoms, 4668 bonds, 3 pseudobonds, 573 residues, 2 models selected
> select #1/A#1/B#1/C
5319 atoms, 5439 bonds, 9 pseudobonds, 663 residues, 2 models selected
Alignment identifier is 2
> select #1/A-C:2-63
909 atoms, 918 bonds, 3 pseudobonds, 117 residues, 2 models selected
> hide sel cartoons
> select #1/a-c:433
24 atoms, 21 bonds, 3 residues, 1 model selected
> select #1/a-c:433-434
57 atoms, 57 bonds, 6 residues, 1 model selected
> select #1/a-c:433
24 atoms, 21 bonds, 3 residues, 1 model selected
> select #1/a-c:433-448
414 atoms, 429 bonds, 48 residues, 1 model selected
> hide sel cartoons
Drag select of 1059 residues, 6 pseudobonds
> show sel surfaces
> select clear
> select #1/A-C:59
21 atoms, 18 bonds, 3 residues, 1 model selected
> select #1/A-C:59-64
138 atoms, 138 bonds, 18 residues, 1 model selected
> show sel surfaces
> show sel cartoons
> select clear
> open "/Users/haoyangli/Downloads/source_data/pdbs/AF-Multimer for
> base_pdbs/DHT01/DHT01_AF-Mult_model1.pdb" format pdb
Chain information for DHT01_AF-Mult_model1.pdb #5
---
Chain | Description
B | No description available
C | No description available
D | No description available
> select add #5
1705 atoms, 1711 bonds, 190 residues, 1 model selected
> color sel bychain
> view matrix models #5,1,0,0,51.082,0,1,0,79.311,0,0,1,103.53
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.46043,0.6006,0.65367,48.592,0.38905,0.52535,-0.75673,81.386,-0.7979,0.60273,0.0082198,101.76
> ui mousemode right "translate selected models"
> view matrix models
> #5,0.46043,0.6006,0.65367,112.86,0.38905,0.52535,-0.75673,143.64,-0.7979,0.60273,0.0082198,30.688
> view matrix models
> #5,0.46043,0.6006,0.65367,119.01,0.38905,0.52535,-0.75673,128.43,-0.7979,0.60273,0.0082198,33.781
> view matrix models
> #5,0.46043,0.6006,0.65367,124.51,0.38905,0.52535,-0.75673,133.21,-0.7979,0.60273,0.0082198,34.857
> save /Users/haoyangli/Desktop/GPC_DHT01.cxs
> select clear
> select add #5
1705 atoms, 1711 bonds, 190 residues, 1 model selected
> view matrix models
> #5,0.46043,0.6006,0.65367,131.09,0.38905,0.52535,-0.75673,132.76,-0.7979,0.60273,0.0082198,35.893
> view matrix models
> #5,0.46043,0.6006,0.65367,131.04,0.38905,0.52535,-0.75673,131.97,-0.7979,0.60273,0.0082198,33.243
> select clear
> save /Users/haoyangli/Desktop/GPC_DHT01.cxs
> select #1/a-c:426-427
42 atoms, 42 bonds, 6 residues, 1 model selected
> select #1/a-c:426-427
42 atoms, 42 bonds, 6 residues, 1 model selected
> select #1/a-c:427
21 atoms, 21 bonds, 3 residues, 1 model selected
> select #1/a-c:427
21 atoms, 21 bonds, 3 residues, 1 model selected
> select clear
> select #1/A-C:2-259
5235 atoms, 5349 bonds, 9 pseudobonds, 657 residues, 2 models selected
> color (#!1 & sel) cornflower blue
> select #1/a-c:260-261
33 atoms, 30 bonds, 6 residues, 1 model selected
> select #1/a-c:260-448
4605 atoms, 4716 bonds, 567 residues, 1 model selected
> color (#!1 & sel) hot pink
> select clear
> select #1/a-c:260
12 atoms, 9 bonds, 3 residues, 1 model selected
> select #1/a-c:260-448
4605 atoms, 4716 bonds, 567 residues, 1 model selected
> ui tool show "Color Actions"
> color sel pale violet red
> color sel light coral
> color sel thistle
> color sel light pink
> select #1/A-C:2-259
5235 atoms, 5349 bonds, 9 pseudobonds, 657 residues, 2 models selected
> ui tool show "Color Actions"
> color sel light sky blue
> color sel light blue
> select clear
> save /Users/haoyangli/Desktop/GPC_DHT01.cxs
[Repeated 1 time(s)]
——— End of log from Fri May 12 15:04:25 2023 ———
opened ChimeraX session
> hide #5 models
> color #!1 bypolymer
> color #!1 bychain
> undo
> select add #1
10395 atoms, 10659 bonds, 9 pseudobonds, 1266 residues, 2 models selected
> show sel cartoons
> select clear
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.
How to cite UCSF ChimeraX
OpenGL version: 4.1 ATI-4.12.7
OpenGL renderer: AMD Radeon Pro 5300M OpenGL Engine
OpenGL vendor: ATI Technologies 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: MacBookPro16,1
Processor Name: 6-Core Intel Core i7
Processor Speed: 2.6 GHz
Number of Processors: 1
Total Number of Cores: 6
L2 Cache (per Core): 256 KB
L3 Cache: 12 MB
Hyper-Threading Technology: Enabled
Memory: 16 GB
System Firmware Version: 1968.120.12.0.0 (iBridge: 20.16.5058.0.0,0)
OS Loader Version: 577~170
Software:
System Software Overview:
System Version: macOS 13.4 (22F66)
Kernel Version: Darwin 22.5.0
Time since boot: 1 day, 2 hours, 9 minutes
Graphics/Displays:
Intel UHD Graphics 630:
Chipset Model: Intel UHD Graphics 630
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x3e9b
Revision ID: 0x0000
Automatic Graphics Switching: Supported
gMux Version: 5.0.0
Metal Support: Metal 3
AMD Radeon Pro 5300M:
Chipset Model: AMD Radeon Pro 5300M
Type: GPU
Bus: PCIe
PCIe Lane Width: x16
VRAM (Total): 4 GB
Vendor: AMD (0x1002)
Device ID: 0x7340
Revision ID: 0x0043
ROM Revision: 113-D3220E-190
VBIOS Version: 113-D32207P1-020
Option ROM Version: 113-D32207P1-020
EFI Driver Version: 01.A1.190
Automatic Graphics Switching: Supported
gMux Version: 5.0.0
Metal Support: Metal 3
Displays:
ASUS VE278:
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: E4LMTF043857
Main Display: Yes
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: 2022.9.26
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 , 2 years ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Window Toolkit |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Crashed in QTabBar::paintEvent(), QPainter::begin: Paint device returned engine == 0 |
comment:2 by , 2 years ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | accepted → closed |
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