![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 20 months ago
Closed 20 months ago
#14739 closed defect (duplicate)
Crashed in QTabBar::paintEvent(), QPainter::begin: Paint device returned engine == 0
| Reported by: | Owned by: | pett | |
|---|---|---|---|
| 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 0x0000000102ab1600 (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
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{
"uptime" : 100000,
"procLaunch" : "2024-03-05 15:38:58.0928 +0000",
"procRole" : "Background",
"version" : 2,
"userID" : 502,
"deployVersion" : 210,
"modelCode" : "MacBookAir7,2",
"procStartAbsTime" : 61877393134170,
"coalitionID" : 5443,
"osVersion" : {
"train" : "macOS 12.7.2",
"build" : "21G1974",
"releaseType" : "User"
},
"captureTime" : "2024-03-09 22:03:18.3364 +0000",
"incident" : "C2E16338-49F2-4842-A126-4C146EE90DBF",
"bug_type" : "309",
"pid" : 87933,
"procExitAbsTime" : 109673468441966,
"cpuType" : "X86-64",
"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":"6176D895-B3D5-5F14-9A52-D3962DEB645A","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "47F69659-C3E7-90F8-F1AA-AD82CA10C6E5",
"wakeTime" : 23,
"sleepWakeUUID" : "8B0A5001-0410-481F-A86A-95365EEA750F",
"sip" : "enabled",
"vmRegionInfo" : "0x18 is not in any region. Bytes before following region: 140737486647272\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n VM_ALLOCATE 7fffffe5f000-7fffffe60000 [ 4K] r-x\/r-x SM=ALI ",
"isCorpse" : 1,
"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: 140737486647272\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n VM_ALLOCATE 7fffffe5f000-7fffffe60000 [ 4K] r-x\/r-x SM=ALI ",
"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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"path" : "\/Applications\/ChimeraX-1.6.1.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/PyQt6\/Qt6\/lib\/QtWebEngineCore.framework\/Versions\/A\/QtWebEngineCore",
"name" : "QtWebEngineCore"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4406804480,
"size" : 64028672,
"uuid" : "24c9d5c5-4854-3af4-9550-cb0204044dfa",
"path" : "\/Applications\/ChimeraX-1.6.1.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/numpy\/.dylibs\/libopenblas64_.0.dylib",
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},
"vmSummary" : "ReadOnly portion of Libraries: Total=1.5G resident=0K(0%) swapped_out_or_unallocated=1.5G(100%)\nWritable regions: Total=21.7G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=21.7G(100%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 896K 7 \nActivity Tracing 256K 1 \nCG backing stores 9732K 10 \nCG image 232K 44 \nColorSync 240K 28 \nCoreAnimation 876K 59 \nCoreGraphics 16K 3 \nCoreServices 628K 3 \nCoreUI image data 1476K 22 \nFoundation 36K 2 \nIOKit 15.5M 2 \nKernel Alloc Once 8K 1 \nMALLOC 21.2G 2582 \nMALLOC guard page 32K 8 \nMALLOC_LARGE (reserved) 256K 1 reserved VM address space (unallocated)\nMALLOC_NANO (reserved) 256.0M 1 reserved VM address space (unallocated)\nMach message 16K 3 \nOpenGL GLSL 384K 4 \nSTACK GUARD 84K 21 \nStack 146.2M 22 \nStack Guard 56.0M 1 \nVM_ALLOCATE 136.8M 1336 \n__CTF 756 1 \n__DATA 45.2M 688 \n__DATA_CONST 31.5M 348 \n__DATA_DIRTY 1659K 218 \n__FONT_DATA 4K 1 \n__GLSLBUILTINS 5176K 1 \n__LINKEDIT 675.8M 156 \n__OBJC_RO 82.9M 1 \n__OBJC_RW 3200K 2 \n__TEXT 810.8M 688 \n__UNICODE 592K 1 \ndyld private memory 1056K 3 \nmapped file 228.8M 58 \nshared memory 3120K 31 \n=========== ======= ======= \nTOTAL 23.6G 6358 \nTOTAL, minus reserved VM space 23.4G 6358 \n",
"legacyInfo" : {
"threadTriggered" : {
"name" : "CrBrowserMain",
"queue" : "com.apple.main-thread"
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"trialInfo" : {
"rollouts" : [
{
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"factorPackIds" : {
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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
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
> ui tool show Registration
Thank you for registering your copy of ChimeraX. By providing the information
requested you will be helping us document the impact this software is having
in the scientific community. The information you supplied will only be used
for reporting summary usage statistics; no individual data will be released.
> open /Users/ellamarshall/Downloads/5d7y.pdb
5d7y.pdb title:
Crystal structure of hepatitis B virus T=4 capsid In complex with the
allosteric modulator HAP18 [more info...]
Chain information for 5d7y.pdb #1
---
Chain | Description | UniProt
A B C D | capsid protein | CAPSD_HBVD1 1-149
Non-standard residues in 5d7y.pdb #1
---
58H — methyl
(4R)-4-(2-chloro-4-fluorophenyl)-6-{[4-(3-hydroxypenta-1,4-diyn-3-yl)piperidin-1-yl]methyl}-2-(pyridin-2-yl)-1,4-dihydropyrimidine-5-carboxylate
> select /A/B/C/D
4610 atoms, 4756 bonds, 572 residues, 1 model selected
> select ::name="58H"
74 atoms, 80 bonds, 2 residues, 1 model selected
> CLOSE ALL
Unknown command: CLOSE ALL
> close all
> open "/Users/ellamarshall/Downloads/5d7y (1).pdb"
5d7y (1).pdb title:
Crystal structure of hepatitis B virus T=4 capsid In complex with the
allosteric modulator HAP18 [more info...]
Chain information for 5d7y (1).pdb #1
---
Chain | Description | UniProt
A B C D | capsid protein | CAPSD_HBVD1 1-149
Non-standard residues in 5d7y (1).pdb #1
---
58H — methyl
(4R)-4-(2-chloro-4-fluorophenyl)-6-{[4-(3-hydroxypenta-1,4-diyn-3-yl)piperidin-1-yl]methyl}-2-(pyridin-2-yl)-1,4-dihydropyrimidine-5-carboxylate
> view orient
> zoom 1.1
> turn x 180
> surface /a
> select /A/B/C/D
4610 atoms, 4756 bonds, 572 residues, 1 model selected
> show sel cartoons
> show sel surfaces
> hide /a cartoons
> hide /b
> show Ca
> lighting gentle
> set bgColor white
> set bgColor #ffffff00
> set silhouettes true
> set silhouetedepth 0.02
Expected a keyword
> set silhouetteDepthJump 0.02
> size ion atom 1.6
Expected a keyword
> size ions atomRadius 1.6
Changed 0 atom radii
> rainbow palette pubu-5
> save "/Users/ellamarshall/Desktop/ella's test chimeraX from youtube .jpg"
> width 1344 height 903 supersample 3
> save "/Users/ellamarshall/Desktop/ella test from youtube white bg.cxs"
> close all
> open /Users/ellamarshall/Downloads/7OD4.cif format mmcif
Summary of feedback from opening /Users/ellamarshall/Downloads/7OD4.cif
---
warnings | Unable to fetch template for ' MET': might have incorrect bonds
Skipping atom "CA" near line 593: missing coordinates
note | PDBx/mmCIF styling lost near line 593. Rereading mmCIF file from the
beginning.
7OD4.cif title:
Hepatitis B core protein. [more info...]
Chain information for 7OD4.cif #1
---
Chain | Description | UniProt
A A_10 A_11 A_12 A_13 A_14 A_15 A_16 A_17 A_18 A_19 A_2 A_20 A_21 A_22 A_23
A_24 A_25 A_26 A_27 A_28 A_29 A_3 A_30 A_31 A_32 A_33 A_34 A_35 A_36 A_37 A_38
A_39 A_4 A_40 A_41 A_42 A_43 A_44 A_45 A_46 A_47 A_48 A_49 A_5 A_50 A_51 A_52
A_53 A_54 A_55 A_56 A_57 A_58 A_59 A_6 A_60 A_7 A_8 A_9 B B_10 B_11 B_12 B_13
B_14 B_15 B_16 B_17 B_18 B_19 B_2 B_20 B_21 B_22 B_23 B_24 B_25 B_26 B_27 B_28
B_29 B_3 B_30 B_31 B_32 B_33 B_34 B_35 B_36 B_37 B_38 B_39 B_4 B_40 B_41 B_42
B_43 B_44 B_45 B_46 B_47 B_48 B_49 B_5 B_50 B_51 B_52 B_53 B_54 B_55 B_56 B_57
B_58 B_59 B_6 B_60 B_7 B_8 B_9 C C_10 C_11 C_12 C_13 C_14 C_15 C_16 C_17 C_18
C_19 C_2 C_20 C_21 C_22 C_23 C_24 C_25 C_26 C_27 C_28 C_29 C_3 C_30 C_31 C_32
C_33 C_34 C_35 C_36 C_37 C_38 C_39 C_4 C_40 C_41 C_42 C_43 C_44 C_45 C_46 C_47
C_48 C_49 C_5 C_50 C_51 C_52 C_53 C_54 C_55 C_56 C_57 C_58 C_59 C_6 C_60 C_7
C_8 C_9 D D_10 D_11 D_12 D_13 D_14 D_15 D_16 D_17 D_18 D_19 D_2 D_20 D_21 D_22
D_23 D_24 D_25 D_26 D_27 D_28 D_29 D_3 D_30 D_31 D_32 D_33 D_34 D_35 D_36 D_37
D_38 D_39 D_4 D_40 D_41 D_42 D_43 D_44 D_45 D_46 D_47 D_48 D_49 D_5 D_50 D_51
D_52 D_53 D_54 D_55 D_56 D_57 D_58 D_59 D_6 D_60 D_7 D_8 D_9 | External core
antigen | W6CP35_HBV 1-183
> show cartoons
> hide atoms
> turn x 90
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/ellamarshall/Desktop/movie1.mp4
Movie saved to /Users/ellamarshall/Desktop/movie1.mp4
> roll
> stop
> movie record
> roll y 2 180
> movie encode
Movie saved to /Users/ellamarshall/Desktop/movie.mp4
> hide atoms
> show surfaces
> hide surfaces
> show atoms
> open /Users/ellamarshall/Downloads/5d7y.pdb format pdb
5d7y.pdb title:
Crystal structure of hepatitis B virus T=4 capsid In complex with the
allosteric modulator HAP18 [more info...]
Chain information for 5d7y.pdb #2
---
Chain | Description | UniProt
A B C D | capsid protein | CAPSD_HBVD1 1-149
Non-standard residues in 5d7y.pdb #2
---
58H — methyl
(4R)-4-(2-chloro-4-fluorophenyl)-6-{[4-(3-hydroxypenta-1,4-diyn-3-yl)piperidin-1-yl]methyl}-2-(pyridin-2-yl)-1,4-dihydropyrimidine-5-carboxylate
> orient
Unknown command: orient
> view orient
> ui mousemode right "move picked models"
> ui mousemode right "translate selected models"
> ui mousemode right zoom
> ui mousemode right "translate selected models"
> ui mousemode right zoom
Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps,
got 2 atomic models, 0 maps.
> select clear
> show cartoons
> select #2/B:126
8 atoms, 7 bonds, 1 residue, 1 model selected
> ui mousemode right "translate selected models"
> ui mousemode right "translate selected atoms"
> undo
> view clip false
> view orient
> ui tool show "Volume Viewer"
> hide #2 models
> show #2 models
> transparency 50
> ui mousemode right "translate selected atoms"
> ui mousemode right select
> clear select
Unknown command: clear select
> clear select
Unknown command: clear select
> select clear
> select #2/A#2/B#2/C#2/D
4610 atoms, 4756 bonds, 572 residues, 1 model selected
> lighting soft
> transparency 0
> material transparentCastShadows true
Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps,
got 2 atomic models, 0 maps.
> CLOSE ALL
Unknown command: CLOSE ALL
> close all
> open /Users/ellamarshall/Downloads/emd_37631.map.gz
File reader requires uncompressed file;
'/Users/ellamarshall/Downloads/emd_37631.map.gz' is compressed
> open "/Users/ellamarshall/Downloads/emd_37631 (1).map"
Opened emd_37631 (1).map as #1, grid size 240,240,240, pixel 1.94, shown at
level 0.0564, step 1, values float32
> open "/Users/ellamarshall/Downloads/emd_37631 (1).map"
Opened emd_37631 (1).map as #2, grid size 240,240,240, pixel 1.94, shown at
level 0.0564, step 1, values float32
> hide #!2 models
> open 5d7y
Summary of feedback from opening 5d7y fetched from pdb
---
note | Fetching compressed mmCIF 5d7y from
http://files.rcsb.org/download/5d7y.cif
5d7y title:
Crystal structure of Hepatitis B virus T=4 capsid in complex with the
allosteric modulator HAP18 [more info...]
Chain information for 5d7y #3
---
Chain | Description | UniProt
A B C D | Capsid protein | CAPSD_HBVD1 1-149
Non-standard residues in 5d7y #3
---
58H — methyl
(4R)-4-(2-chloro-4-fluorophenyl)-6-{[4-(3-hydroxypenta-1,4-diyn-3-yl)piperidin-1-yl]methyl}-2-(pyridin-2-yl)-1,4-dihydropyrimidine-5-carboxylate
5d7y mmCIF Assemblies
---
1| complete icosahedral assembly
2| icosahedral asymmetric unit
3| icosahedral pentamer
4| icosahedral 23 hexamer
5| icosahedral asymmetric unit, std point frame
6| crystal asymmetric unit, crystal frame
> select add #3
4610 atoms, 4756 bonds, 572 residues, 1 model selected
> select subtract #3
Nothing selected
> select /A/B/C/D
4610 atoms, 4756 bonds, 572 residues, 1 model selected
> delete /C,D
> select subtract #3
Nothing selected
> select add #3
2305 atoms, 2378 bonds, 286 residues, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models #3,1,0,0,-22.823,0,1,0,127.18,0,0,1,-0.66826
> view matrix models #3,1,0,0,-29.521,0,1,0,217.97,0,0,1,-13.057
> view matrix models #3,1,0,0,-20.642,0,1,0,242.96,0,0,1,-29.777
> view orient
> view matrix models #3,1,0,0,-14.249,0,1,0,294.26,0,0,1,24.619
> view matrix models #3,1,0,0,-20.6,0,1,0,283.67,0,0,1,3.2271
> view matrix models #3,1,0,0,13.856,0,1,0,339.72,0,0,1,14.614
> view matrix models #3,1,0,0,37.509,0,1,0,364.5,0,0,1,8.0921
> fitmap #3 inMap #1
Fit molecule 5d7y (#3) to map emd_37631 (1).map (#1) using 2305 atoms
average map value = 0.04523, steps = 376
shifted from previous position = 50.7
rotated from previous position = 92.1 degrees
atoms outside contour = 1554, contour level = 0.056403
Position of 5d7y (#3) relative to emd_37631 (1).map (#1) coordinates:
Matrix rotation and translation
0.74712037 0.02287625 -0.66429498 245.32624482
0.65845386 0.11109391 0.74437669 72.75742084
0.09082767 -0.99354659 0.06793756 208.70939275
Axis -0.86955461 -0.37781897 0.31800566
Axis point 0.00000000 129.47994739 145.41823334
Rotation angle (degrees) 92.11607492
Shift along axis -174.44293406
> select clear
> hide atoms
> show cartoons
> select /A/B
2305 atoms, 2378 bonds, 286 residues, 1 model selected
> ui mousemode right zoom
> lighting soft
> transparency #1.1 50
> ui tool show "Side View"
> ui mousemode right zoom
> select ~sel
5 models selected
> transparency sel & #1.1 0
> transparency sel & #1.1 50
> material transparentCastShadows true
> select ~sel
2305 atoms, 2378 bonds, 286 residues, 1 model selected
> view orient
> help sym
> hide #3 models
> show #3 models
> ui tool show Matchmaker
> rainbow polymers palette pubugn
> undo
> select clear
> rainbow polymers palette pubugn
> rainbow
> undo
> select add #3
2305 atoms, 2378 bonds, 286 residues, 1 model selected
> select add #1
2305 atoms, 2378 bonds, 286 residues, 3 models selected
> rainbow sel
> close all
> open /Users/ellamarshall/Downloads/7OD4.cif format mmcif
Summary of feedback from opening /Users/ellamarshall/Downloads/7OD4.cif
---
warnings | Unable to fetch template for ' MET': might have incorrect bonds
Skipping atom "CA" near line 593: missing coordinates
note | PDBx/mmCIF styling lost near line 593. Rereading mmCIF file from the
beginning.
7OD4.cif title:
Hepatitis B core protein. [more info...]
Chain information for 7OD4.cif #1
---
Chain | Description | UniProt
A A_10 A_11 A_12 A_13 A_14 A_15 A_16 A_17 A_18 A_19 A_2 A_20 A_21 A_22 A_23
A_24 A_25 A_26 A_27 A_28 A_29 A_3 A_30 A_31 A_32 A_33 A_34 A_35 A_36 A_37 A_38
A_39 A_4 A_40 A_41 A_42 A_43 A_44 A_45 A_46 A_47 A_48 A_49 A_5 A_50 A_51 A_52
A_53 A_54 A_55 A_56 A_57 A_58 A_59 A_6 A_60 A_7 A_8 A_9 B B_10 B_11 B_12 B_13
B_14 B_15 B_16 B_17 B_18 B_19 B_2 B_20 B_21 B_22 B_23 B_24 B_25 B_26 B_27 B_28
B_29 B_3 B_30 B_31 B_32 B_33 B_34 B_35 B_36 B_37 B_38 B_39 B_4 B_40 B_41 B_42
B_43 B_44 B_45 B_46 B_47 B_48 B_49 B_5 B_50 B_51 B_52 B_53 B_54 B_55 B_56 B_57
B_58 B_59 B_6 B_60 B_7 B_8 B_9 C C_10 C_11 C_12 C_13 C_14 C_15 C_16 C_17 C_18
C_19 C_2 C_20 C_21 C_22 C_23 C_24 C_25 C_26 C_27 C_28 C_29 C_3 C_30 C_31 C_32
C_33 C_34 C_35 C_36 C_37 C_38 C_39 C_4 C_40 C_41 C_42 C_43 C_44 C_45 C_46 C_47
C_48 C_49 C_5 C_50 C_51 C_52 C_53 C_54 C_55 C_56 C_57 C_58 C_59 C_6 C_60 C_7
C_8 C_9 D D_10 D_11 D_12 D_13 D_14 D_15 D_16 D_17 D_18 D_19 D_2 D_20 D_21 D_22
D_23 D_24 D_25 D_26 D_27 D_28 D_29 D_3 D_30 D_31 D_32 D_33 D_34 D_35 D_36 D_37
D_38 D_39 D_4 D_40 D_41 D_42 D_43 D_44 D_45 D_46 D_47 D_48 D_49 D_5 D_50 D_51
D_52 D_53 D_54 D_55 D_56 D_57 D_58 D_59 D_6 D_60 D_7 D_8 D_9 | External core
antigen | W6CP35_HBV 1-183
> rainbow polymers palette pubugn
> undo
> view name p1
> select /A
1144 atoms, 1179 bonds, 143 residues, 1 model selected
> show target m
> log metadata #1
Metadata for 7OD4.cif #1
---
Title | Hepatitis B core protein.
Citation | Makbul, C., Khayenko, V., Maric, H.M., Bottcher, B. (2021).
Conformational Plasticity of Hepatitis B Core Protein Spikes Promotes Peptide
Binding Independent of the Secretion Phenotype. Microorganisms, 9. PMID:
33946808. DOI: 10.3390/microorganisms9050956
Gene source | Hepatitis B virus
Experimental method | Electron microscopy
Resolution | 2.8000000000000003Å
> log chains #1
Chain information for 7OD4.cif #1
---
Chain | Description | UniProt
A A_10 A_11 A_12 A_13 A_14 A_15 A_16 A_17 A_18 A_19 A_2 A_20 A_21 A_22 A_23
A_24 A_25 A_26 A_27 A_28 A_29 A_3 A_30 A_31 A_32 A_33 A_34 A_35 A_36 A_37 A_38
A_39 A_4 A_40 A_41 A_42 A_43 A_44 A_45 A_46 A_47 A_48 A_49 A_5 A_50 A_51 A_52
A_53 A_54 A_55 A_56 A_57 A_58 A_59 A_6 A_60 A_7 A_8 A_9 B B_10 B_11 B_12 B_13
B_14 B_15 B_16 B_17 B_18 B_19 B_2 B_20 B_21 B_22 B_23 B_24 B_25 B_26 B_27 B_28
B_29 B_3 B_30 B_31 B_32 B_33 B_34 B_35 B_36 B_37 B_38 B_39 B_4 B_40 B_41 B_42
B_43 B_44 B_45 B_46 B_47 B_48 B_49 B_5 B_50 B_51 B_52 B_53 B_54 B_55 B_56 B_57
B_58 B_59 B_6 B_60 B_7 B_8 B_9 C C_10 C_11 C_12 C_13 C_14 C_15 C_16 C_17 C_18
C_19 C_2 C_20 C_21 C_22 C_23 C_24 C_25 C_26 C_27 C_28 C_29 C_3 C_30 C_31 C_32
C_33 C_34 C_35 C_36 C_37 C_38 C_39 C_4 C_40 C_41 C_42 C_43 C_44 C_45 C_46 C_47
C_48 C_49 C_5 C_50 C_51 C_52 C_53 C_54 C_55 C_56 C_57 C_58 C_59 C_6 C_60 C_7
C_8 C_9 D D_10 D_11 D_12 D_13 D_14 D_15 D_16 D_17 D_18 D_19 D_2 D_20 D_21 D_22
D_23 D_24 D_25 D_26 D_27 D_28 D_29 D_3 D_30 D_31 D_32 D_33 D_34 D_35 D_36 D_37
D_38 D_39 D_4 D_40 D_41 D_42 D_43 D_44 D_45 D_46 D_47 D_48 D_49 D_5 D_50 D_51
D_52 D_53 D_54 D_55 D_56 D_57 D_58 D_59 D_6 D_60 D_7 D_8 D_9 | External core
antigen | W6CP35_HBV 1-183
> select /A
1144 atoms, 1179 bonds, 143 residues, 1 model selected
> hide ~Aa
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide ~/Aa
> undo
> hide ~/A
> view
> view name p2
> view orient
> show all
> move y-90
Missing or invalid "axis" argument: Expected 3 floats or "x", or "y", or "z"
or two atoms
> move Y-90
Missing or invalid "axis" argument: Expected 3 floats or "x", or "y", or "z"
or two atoms
> move y -90
> move y -200
> zoom 0.75
> move y -120
> view orient
> view name p2
> turn x 90
> zoom 0.6
> turn x 90
> zoom 0.2
> turn x 90
> zoom 2
> undo
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/ellamarshall/Desktop/movie2.mp4
Movie saved to /Users/ellamarshall/Desktop/movie2.mp4
> fly p1 p2
> crossfade
> hide ~/A
> roll y 4 90 center £2
Invalid "center" argument: Expected 3 floats or object specifier
> roll y 4 90 centre #2
Expected a keyword
> roll "y" 4 90 centre #2
Expected a keyword
> roll "y" 4 90 center #2
Invalid "center" argument: Center argument no objects specified
> roll "y" 4 90
> crossfade
> show ~/A
> fly p2 60
> roll z 3 120
> stop
> split
Split 7OD4.cif (#1) into 240 models
Chain information for 7OD4.cif A #1.1
---
Chain | Description
A | No description available
Chain information for 7OD4.cif A_10 #1.2
---
Chain | Description
A_10 | No description available
Chain information for 7OD4.cif A_11 #1.3
---
Chain | Description
A_11 | No description available
Chain information for 7OD4.cif A_12 #1.4
---
Chain | Description
A_12 | No description available
Chain information for 7OD4.cif A_13 #1.5
---
Chain | Description
A_13 | No description available
Chain information for 7OD4.cif A_14 #1.6
---
Chain | Description
A_14 | No description available
Chain information for 7OD4.cif A_15 #1.7
---
Chain | Description
A_15 | No description available
Chain information for 7OD4.cif A_16 #1.8
---
Chain | Description
A_16 | No description available
Chain information for 7OD4.cif A_17 #1.9
---
Chain | Description
A_17 | No description available
Chain information for 7OD4.cif A_18 #1.10
---
Chain | Description
A_18 | No description available
Chain information for 7OD4.cif A_19 #1.11
---
Chain | Description
A_19 | No description available
Chain information for 7OD4.cif A_2 #1.12
---
Chain | Description
A_2 | No description available
Chain information for 7OD4.cif A_20 #1.13
---
Chain | Description
A_20 | No description available
Chain information for 7OD4.cif A_21 #1.14
---
Chain | Description
A_21 | No description available
Chain information for 7OD4.cif A_22 #1.15
---
Chain | Description
A_22 | No description available
Chain information for 7OD4.cif A_23 #1.16
---
Chain | Description
A_23 | No description available
Chain information for 7OD4.cif A_24 #1.17
---
Chain | Description
A_24 | No description available
Chain information for 7OD4.cif A_25 #1.18
---
Chain | Description
A_25 | No description available
Chain information for 7OD4.cif A_26 #1.19
---
Chain | Description
A_26 | No description available
Chain information for 7OD4.cif A_27 #1.20
---
Chain | Description
A_27 | No description available
Chain information for 7OD4.cif A_28 #1.21
---
Chain | Description
A_28 | No description available
Chain information for 7OD4.cif A_29 #1.22
---
Chain | Description
A_29 | No description available
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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-18.8.6
OpenGL renderer: Intel(R) HD Graphics 6000
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 Air
Model Identifier: MacBookAir7,2
Processor Name: Dual-Core Intel Core i7
Processor Speed: 2.2 GHz
Number of Processors: 1
Total Number of Cores: 2
L2 Cache (per Core): 256 KB
L3 Cache: 4 MB
Hyper-Threading Technology: Enabled
Memory: 8 GB
System Firmware Version: 486.0.0.0.0
OS Loader Version: 540.120.3~37
SMC Version (system): 2.27f2
Software:
System Software Overview:
System Version: macOS 12.7.2 (21G1974)
Kernel Version: Darwin 21.6.0
Time since boot: 9 days 20:16
Graphics/Displays:
Intel HD Graphics 6000:
Chipset Model: Intel HD Graphics 6000
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x1626
Revision ID: 0x0009
Metal Family: Supported, Metal GPUFamily macOS 1
Displays:
Color LCD:
Display Type: LCD
Resolution: 1440 x 900 (Widescreen eXtended Graphics Array Plus)
UI Looks like: 1440 x 900
Framebuffer Depth: 24-Bit Color (ARGB8888)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
HP E223:
Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
UI Looks like: 1920 x 1080 @ 60.00Hz
Framebuffer Depth: 24-Bit Color (ARGB8888)
Display Serial Number: CNC7491755
Mirror: Off
Online: Yes
Rotation: Supported
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 , 20 months 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 , 20 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | accepted → closed |
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