![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 23 months ago
Closed 23 months ago
#10336 closed defect (duplicate)
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 0x00000001188b0600 (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" : 2100000,
"procLaunch" : "2023-12-12 11:14:06.7896 -0800",
"procRole" : "Background",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "MacBookPro16,2",
"procStartAbsTime" : 2121286955782729,
"coalitionID" : 296874,
"osVersion" : {
"train" : "macOS 12.2.1",
"build" : "21D62",
"releaseType" : "User"
},
"captureTime" : "2023-12-12 13:59:15.3463 -0800",
"incident" : "C36E7102-E030-4990-AC82-F865E0C3BA94",
"bug_type" : "309",
"pid" : 93110,
"procExitAbsTime" : 2126966555351931,
"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":"E5C324D9-64F9-5D64-BF03-E50A2944A6D5","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "708048E2-2049-C5D8-7FD8-3A69D0587290",
"wakeTime" : 505,
"bridgeVersion" : {"build":"19P744","train":"6.2"},
"sleepWakeUUID" : "5AB035E0-41FC-45DE-BD6F-CE7EDF4D4041",
"sip" : "enabled",
"vmRegionInfo" : "0x18 is not in any region. Bytes before following region: 4441182184\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 108b71000-108b72000 [ 4K] r-x\/r-x SM=COW ...acOS\/ChimeraX",
"isCorpse" : 1,
"exception" : {"codes":"0x0000000000000001, 0x0000000000000018","rawCodes":[1,24],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000000000000018"},
"ktriageinfo" : "VM - Fault hit memory shortage\n",
"vmregioninfo" : "0x18 is not in any region. Bytes before following region: 4441182184\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 108b71000-108b72000 [ 4K] r-x\/r-x SM=COW ...acOS\/ChimeraX",
"extMods" : {"caller":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"system":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"targeted":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"warnings":0},
"faultingThread" : 0,
"threads" : 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"path" : "\/Applications\/ChimeraX-1.6.1.app\/Contents\/MacOS\/ChimeraX",
"name" : "ChimeraX",
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"path" : "\/usr\/lib\/dyld",
"name" : "dyld"
},
{
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"arch" : "x86_64",
"base" : 5093015552,
"size" : 174571520,
"uuid" : "473ca65c-6149-3bfa-a88b-95ac735bcd3b",
"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"
}
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"sharedCache" : {
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"uuid" : "0939015d-8308-3e69-b095-bd928f835202"
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"vmSummary" : "ReadOnly portion of Libraries: Total=1.4G resident=0K(0%) swapped_out_or_unallocated=1.4G(100%)\nWritable regions: Total=1.0G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=1.0G(100%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 512K 4 \nActivity Tracing 256K 1 \nCG backing stores 6240K 16 \nCG image 72K 5 \nColorSync 232K 26 \nCoreAnimation 144K 11 \nCoreGraphics 16K 3 \nCoreUI image data 2292K 16 \nFoundation 16K 1 \nIOKit 15.5M 2 \nKernel Alloc Once 8K 1 \nMALLOC 377.4M 498 \nMALLOC guard page 32K 8 \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 88K 22 \nStack 154.2M 23 \nStack Guard 56.0M 1 \nVM_ALLOCATE 98.1M 72 \nVM_ALLOCATE (reserved) 32.0M 1 reserved VM address space (unallocated)\n__DATA 44.0M 652 \n__DATA_CONST 31.4M 335 \n__DATA_DIRTY 1621K 213 \n__FONT_DATA 4K 1 \n__GLSLBUILTINS 5176K 1 \n__LINKEDIT 670.4M 142 \n__OBJC_RO 81.8M 1 \n__OBJC_RW 3136K 2 \n__TEXT 796.2M 656 \n__UNICODE 588K 1 \ndyld private memory 1056K 3 \nmapped file 107.2M 42 \nshared memory 3028K 37 \n=========== ======= ======= \nTOTAL 2.8G 2805 \nTOTAL, minus reserved VM space 2.4G 2805 \n",
"legacyInfo" : {
"threadTriggered" : {
"name" : "CrBrowserMain",
"queue" : "com.apple.main-thread"
}
},
"trialInfo" : {
"rollouts" : [
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{
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"factorPackIds" : {
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],
"experiments" : [
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}
}
===== Log before crash start =====
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
QPainter::begin: Paint device returned engine == 0, type: 3
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "/Users/fli05@amgen.com/Library/CloudStorage/OneDrive-Amgen/General -
> HGSNAT_Data_Share/Paper/Fig2_Mechanism/BindingSite.cxs"
Opened cryosparc_P130_J67_008_volume_map_sharp.mrc as #3, grid size
432,432,432, pixel 0.813, shown at level 0.242, step 1, values float32
Opened cryosparc_P130_J67_008_volume_map.mrc as #4, grid size 432,432,432,
pixel 0.813, shown at level 0.103, step 1, values float32
Opened cryosparc_P129_J167_008_volume_map_sharp.mrc as #6, grid size
432,432,432, pixel 0.813, shown at level 0.169, step 1, values float32
Opened cryosparc_P129_J167_008_volume_map.mrc as #2, grid size 432,432,432,
pixel 0.813, shown at level 0.0795, step 1, values float32
Opened cryosparc_P130_J67_008_volume_map_sharp.mrc 0 as #7.1, grid size
432,432,432, pixel 0.813, shown at level 0.242, step 1, values float32
Opened cryosparc_P130_J67_008_volume_map_sharp.mrc 1 as #7.2, grid size
432,432,432, pixel 0.813, shown at level 0.242, step 1, values float32
Opened cryosparc_P130_J67_008_volume_map_sharp.mrc 2 as #7.3, grid size
432,432,432, pixel 0.813, shown at level 0.242, step 1, values float32
Opened cryosparc_P130_J67_008_volume_map_sharp.mrc 3 as #7.4, grid size
432,432,432, pixel 0.813, shown at level 0.242, step 1, values float32
Opened cryosparc_P130_J67_008_volume_map_sharp.mrc 4 as #7.5, grid size
432,432,432, pixel 0.813, shown at level 0.242, step 1, values float32
Opened cryosparc_P129_J167_008_volume_map_sharp.mrc 0 as #8.1, grid size
432,432,432, pixel 0.813, shown at level 0.169, step 1, values float32
Opened cryosparc_P129_J167_008_volume_map_sharp.mrc 1 as #8.2, grid size
432,432,432, pixel 0.813, shown at level 0.169, step 1, values float32
Opened cryosparc_P129_J167_008_volume_map_sharp.mrc 2 as #8.3, grid size
432,432,432, pixel 0.813, shown at level 0.169, step 1, values float32
Opened cryosparc_P129_J167_008_volume_map_sharp.mrc 3 as #8.4, grid size
432,432,432, pixel 0.813, shown at level 0.169, step 1, values float32
Opened cryosparc_P129_J167_008_volume_map_sharp.mrc 4 as #8.5, grid size
432,432,432, pixel 0.813, shown at level 0.169, step 1, values float32
Log from Tue Dec 12 10:07:44 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "/Users/fli05@amgen.com/Library/CloudStorage/OneDrive-Amgen/General -
> HGSNAT_Data_Share/Paper/Fig1/Overall_CoAProduct_Map.cxs"
Opened cryosparc_P130_J87_map_lp7.mrc as #2, grid size 432,432,432, pixel
0.813, shown at level 0.0461, step 1, values float32
Opened cryosparc_P130_J67_008_volume_map_sharp.mrc as #3, grid size
432,432,432, pixel 0.813, shown at level 0.708, step 1, values float32
Opened cryosparc_P130_J67_008_volume_map.mrc as #4, grid size 432,432,432,
pixel 0.813, shown at level 0.0908, step 1, values float32
Log from Sun Nov 12 13:03:29 2023UCSF 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/fli05@amgen.com/Documents/Phenix/HGSNAT_CoAProduct/RealSpaceRefine_11/CoA_Product_Boyang_real_space_refined_001-coot_CH3Up_real_space_refined_002-coot-7_real_space_refined_011.pdb
Summary of feedback from opening
/Users/fli05@amgen.com/Documents/Phenix/HGSNAT_CoAProduct/RealSpaceRefine_11/CoA_Product_Boyang_real_space_refined_001-coot_CH3Up_real_space_refined_002-coot-7_real_space_refined_011.pdb
---
warnings | Cannot find consistent set of bond orders for ring system
containing atom C07 in residue MUG /A:789
Cannot find consistent set of bond orders for ring system containing atom C07
in residue MUG /B:785
Chain information for
CoA_Product_Boyang_real_space_refined_001-coot_CH3Up_real_space_refined_002-coot-7_real_space_refined_011.pdb
#1
---
Chain | Description
A | No description available
B | No description available
> set bgColor white
> open "/Users/fli05@amgen.com/Library/CloudStorage/OneDrive-Amgen/General -
> HGSNAT_Data_Share/StructureData/CoAandProduct/Map/cryosparc_P130_J87_map_lp7.mrc"
Cannot open files: [Errno 60] Operation timed out
> open "/Users/fli05@amgen.com/Library/CloudStorage/OneDrive-Amgen/General -
> HGSNAT_Data_Share/StructureData/CoAandProduct/Map/cryosparc_P130_J87_map_lp7.mrc"
Opened cryosparc_P130_J87_map_lp7.mrc as #2, grid size 432,432,432, pixel
0.813, shown at level 0.0254, step 2, values float32
> volume #2 step 1
> volume #2 level 0.07837
> hide #!2 models
> show #!2 models
> volume #2 level 0.08585
> hide #!2 models
> select /B:198
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
125 atoms, 124 bonds, 25 residues, 1 model selected
> select up
1021 atoms, 1040 bonds, 151 residues, 1 model selected
> select up
4179 atoms, 4301 bonds, 548 residues, 1 model selected
> ui tool show "Color Actions"
> color sel dark orange
> select clear
> select /A:505
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
170 atoms, 171 bonds, 23 residues, 1 model selected
> select up
3127 atoms, 3229 bonds, 399 residues, 1 model selected
> select up
4256 atoms, 4382 bonds, 556 residues, 1 model selected
> select up
8435 atoms, 8683 bonds, 1104 residues, 1 model selected
> select down
4256 atoms, 4382 bonds, 556 residues, 1 model selected
> ui tool show "Color Actions"
> color sel royal blue
> select clear
> select ::name="COA"
96 atoms, 100 bonds, 2 residues, 1 model selected
> ui tool show "Color Actions"
> open "/Users/fli05@amgen.com/Library/CloudStorage/OneDrive-Amgen/General -
> HGSNAT_Data_Share/StructureData/CoAandProduct/Map/cryosparc_P130_J67_008_volume_map_sharp.mrc"
Opened cryosparc_P130_J67_008_volume_map_sharp.mrc as #3, grid size
432,432,432, pixel 0.813, shown at level 0.0404, step 2, values float32
> color sel lime green
[Repeated 1 time(s)]
> hide #!1 models
> volume #3 step 1
> volume #3 level 0.2106
> hide #!3 models
> open "/Users/fli05@amgen.com/Library/CloudStorage/OneDrive-Amgen/General -
> HGSNAT_Data_Share/StructureData/CoAandProduct/Map/cryosparc_P130_J67_008_volume_map.mrc"
Opened cryosparc_P130_J67_008_volume_map.mrc as #4, grid size 432,432,432,
pixel 0.813, shown at level 0.0226, step 2, values float32
> volume #4 step 1
> volume #4 level 0.08856
> volume #4 color #ffff99
> hide #!4 models
> show #!1 models
> select ::name="MUG"
54 atoms, 58 bonds, 2 residues, 1 model selected
> ui tool show "Color Actions"
> color sel deep pink
> ui tool show "Color Zone"
> color zone #4 near #1 distance 4.88
> ui tool show "Hide Dust"
> surface dust #4 size 4.88
> volume #3 level 0.7083
> volume #4 level 0.1048
> color zone #4 near #1 distance 4.98
> color zone #4 near #1 distance 5.08
> color zone #4 near #1 distance 5.18
> color zone #4 near #1 distance 5.28
> color zone #4 near #1 distance 5.38
> color zone #4 near #1 distance 5.48
> color zone #4 near #1 distance 5.58
> color zone #4 near #1 distance 5.68
> color zone #4 near #1 distance 5.78
> color zone #4 near #1 distance 5.88
> color zone #4 near #1 distance 5.98
> color zone #4 near #1 distance 6.08
> color zone #4 near #1 distance 6.18
> color zone #4 near #1 distance 6.28
> color zone #4 near #1 distance 6.38
> color zone #4 near #1 distance 6.48
> color zone #4 near #1 distance 6.58
> color zone #4 near #1 distance 6.68
> color zone #4 near #1 distance 6.78
> color zone #4 near #1 distance 6.88
> color zone #4 near #1 distance 6.98
> color zone #4 near #1 distance 7.08
> color zone #4 near #1 distance 7.18
> color zone #4 near #1 distance 7.28
> color zone #4 near #1 distance 7.38
> color zone #4 near #1 distance 7.48
> color zone #4 near #1 distance 7.58
> color zone #4 near #1 distance 7.68
> color zone #4 near #1 distance 7.78
> color zone #4 near #1 distance 7.88
> color zone #4 near #1 distance 7.98
> color zone #4 near #1 distance 8.08
> color zone #4 near #1 distance 8.18
> color zone #4 near #1 distance 8.28
> color zone #4 near #1 distance 8.38
> color zone #4 near #1 distance 8.48
> color zone #4 near #1 distance 8.58
> color zone #4 near #1 distance 8.68
> color zone #4 near #1 distance 8.78
> color zone #4 near #1 distance 8.88
> color zone #4 near #1 distance 8.98
> color zone #4 near #1 distance 9.08
> color zone #4 near #1 distance 9.18
> color zone #4 near #1 distance 9.28
> color zone #4 near #1 distance 9.38
> color zone #4 near #1 distance 9.48
> color zone #4 near #1 distance 9.58
> color zone #4 near #1 distance 9.68
> color zone #4 near #1 distance 9.78
> color zone #4 near #1 distance 9.88
> color zone #4 near #1 distance 9.98
> color zone #4 near #1 distance 10.08
> color zone #4 near #1 distance 9.98
> color zone #4 near #1 distance 9.88
> color zone #4 near #1 distance 9.78
> color zone #4 near #1 distance 9.68
> color zone #4 near #1 distance 9.58
> color zone #4 near #1 distance 9.48
> color zone #4 near #1 distance 9.38
> color zone #4 near #1 distance 9.28
> color zone #4 near #1 distance 9.18
> color zone #4 near #1 distance 9.08
> color zone #4 near #1 distance 8.98
> color zone #4 near #1 distance 8.88
> color zone #4 near #1 distance 8.78
> color zone #4 near #1 distance 8.68
> color zone #4 near #1 distance 8.58
> color zone #4 near #1 distance 8.48
> color zone #4 near #1 distance 8.38
> color zone #4 near #1 distance 8.48
> volume #4 level 0.09191
> volume #4 level 0.088
> surface dust #4 size 4.84
> surface dust #4 size 65.33
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> volume #4 level 0.08409
> volume #4 level 0.102
> surface dust #4 size 64.92
> surface dust #4 size 3.09
> volume #4 level 0.0908
> volume #4 color white
> color zone #4 near #1 distance 8.48
> volume #2 level 0.04615
> volume #4 color #cccccc
> volume #4 color #cccccc2a
> volume #4 color #cccccc
> volume #2 color #b2b2b21e
> color zone #4 near #1 distance 8.48
> volume #4 color white
> volume #4 color #ffffff00
> color zone #4 near #1 distance 8.48
> surface dust #4 size 3.11
> surface dust #4 size 4.97
> surface dust #4 size 4.94
> surface dust #4 size 6.26
> color zone #4 near #1 distance 8.47
> color zone #4 near #1 distance 7.64
> color zone #4 near #1 distance 7.74
> color zone #4 near #1 distance 1.83
> color zone #4 near #1 distance 5
[Repeated 1 time(s)]
> color zone #4 near #1 distance 7
[Repeated 1 time(s)]
> color zone #4 near #1 distance 8
[Repeated 1 time(s)]
> color zone #4 near #1 distance 1
> color zone #4 near #1 distance 10
[Repeated 1 time(s)]
> surface dust #4 size 6.22
> surface dust #4 size 4.61
> surface dust #4 size 4.52
> surface dust #4 size 4.61
> hide #!1 models
> show #!2 models
> save "/Users/fli05@amgen.com/OneDrive - Amgen/General -
> HGSNAT_Data_Share/Paper/Fig1/Overall_CoAProduct_Map.cxs"
——— End of log from Sun Nov 12 13:03:29 2023 ———
opened ChimeraX session
> open "/Users/fli05@amgen.com/Library/CloudStorage/OneDrive-Amgen/General -
> HGSNAT_Data_Share/StructureData/ActylCoAandSubstrate/Model/RealSpaceRefine_10/ACO_MGN_Dock_J167-coot-24_Hflip_real_space_refined_010.pdb"
Summary of feedback from opening
/Users/fli05@amgen.com/Library/CloudStorage/OneDrive-Amgen/General -
HGSNAT_Data_Share/StructureData/ActylCoAandSubstrate/Model/RealSpaceRefine_10/ACO_MGN_Dock_J167-coot-24_Hflip_real_space_refined_010.pdb
---
warnings | Cannot find consistent set of bond orders for ring system
containing atom C07 in residue MGN /A:788
Cannot find consistent set of bond orders for ring system containing atom C07
in residue MGN /B:784
Chain information for
ACO_MGN_Dock_J167-coot-24_Hflip_real_space_refined_010.pdb #5
---
Chain | Description
A | No description available
B | No description available
> open "/Users/fli05@amgen.com/Library/CloudStorage/OneDrive-Amgen/General -
> HGSNAT_Data_Share/StructureData/ActylCoAandSubstrate/Map/cryosparc_P129_J167_008_volume_map_sharp.mrc"
Opened cryosparc_P129_J167_008_volume_map_sharp.mrc as #6, grid size
432,432,432, pixel 0.813, shown at level 0.0397, step 2, values float32
> volume #6 step 1
> volume #6 level 0.15
> hide #!2 models
> close #2
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> save "/Users/fli05@amgen.com/OneDrive - Amgen/General -
> HGSNAT_Data_Share/Paper/Fig2_Mechanism/BindingSite.cxs"
> hide #!6 models
> hide #!5 models
> hide #!4 models
> show #!1 models
> select clear
> show #!3 models
> volume #3 level 0.2914
> volume #3 color #ffffb277
> volume #3 color #ffffb263
> volume #3 level 0.364
> volume #3 level 0.3156
> show #!4 models
> color #4 #ffffff62 models
> color #4 #ffffff2e models
> color #4 #ffffff6a models
> volume #4 level 0.1009
> volume #4 level 0.1073
> volume #4 level 0.1035
> hide #!3 models
> open "/Users/fli05@amgen.com/Library/CloudStorage/OneDrive-Amgen/General -
> HGSNAT_Data_Share/StructureData/ActylCoAandSubstrate/Map/cryosparc_P129_J167_008_volume_map.mrc"
Opened cryosparc_P129_J167_008_volume_map.mrc as #2, grid size 432,432,432,
pixel 0.813, shown at level 0.0235, step 2, values float32
> volume #2 step 1
> volume #2 level 0.1075
> volume #2 color #ffffb289
> hide #!4 models
> hide #!2 models
> hide #!1 models
> show #!5 models
> show #!2 models
> volume #2 level 0.09946
> volume #2 level 0.07946
[Repeated 1 time(s)]
> hide #!5 models
> show #!6 models
> show #!5 models
> hide #!2 models
> volume #6 color #b2b2b26a
> volume #6 color #b2b2b250
> volume #6 level 0.1913
> volume #6 level 0.2372
> volume #6 level 0.2143
> volume #6 level 0.1821
> volume #6 level 0.2143
> hide #!6 models
> hide #!5 models
> show #!3 models
> show #!1 models
> save "/Users/fli05@amgen.com/OneDrive - Amgen/General -
> HGSNAT_Data_Share/Paper/Fig2_Mechanism/BindingSite.cxs"
> hide #!3 models
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
27 atoms, 29 bonds, 1 residue, 1 model selected
> select add #1/B:785@C18
28 atoms, 29 bonds, 2 residues, 1 model selected
> select up
54 atoms, 58 bonds, 2 residues, 1 model selected
> select up
8435 atoms, 8683 bonds, 1104 residues, 1 model selected
> select down
54 atoms, 58 bonds, 2 residues, 1 model selected
> select add #1/A:788@C2P
55 atoms, 58 bonds, 3 residues, 1 model selected
> select up
57 atoms, 59 bonds, 4 residues, 1 model selected
> select up
150 atoms, 158 bonds, 4 residues, 1 model selected
> select up
8435 atoms, 8683 bonds, 1104 residues, 1 model selected
> select down
150 atoms, 158 bonds, 4 residues, 1 model selected
> color sel lime
> show #!3 models
> ui tool show "Color Zone"
> color zone #3 near #1 distance 4.88
> color zone #3 near #1 distance 4.76
> color zone #3 near #1 distance 3.62
> color zone #3 near #1 distance 3.67
> color zone #3 near #1 distance 2.19
> volume #3 level 0.3309
> volume #3 level 0.3563
> volume #3 level 0.2418
> color zone #3 near #1 distance 2.15
> color zone #3 near #1 distance 2.37
> color zone #3 near #1 distance 2.26
> color zone #3 near #1 distance 2.72
> volume splitbyzone #3
Opened cryosparc_P130_J67_008_volume_map_sharp.mrc 0 as #7.1, grid size
432,432,432, pixel 0.813, shown at level 0.242, step 1, values float32
Opened cryosparc_P130_J67_008_volume_map_sharp.mrc 1 as #7.2, grid size
432,432,432, pixel 0.813, shown at level 0.242, step 1, values float32
Opened cryosparc_P130_J67_008_volume_map_sharp.mrc 2 as #7.3, grid size
432,432,432, pixel 0.813, shown at level 0.242, step 1, values float32
Opened cryosparc_P130_J67_008_volume_map_sharp.mrc 3 as #7.4, grid size
432,432,432, pixel 0.813, shown at level 0.242, step 1, values float32
> hide #!7.2 models
> hide #!7.4 models
> hide #!7.1 models
> save "/Users/fli05@amgen.com/OneDrive - Amgen/General -
> HGSNAT_Data_Share/Paper/Fig2_Mechanism/BindingSite.cxs"
> hide #!7 models
> hide #!7.3 models
> hide #!1 models
> show #!5 models
> show #!6 models
> hide #!6 models
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
24 atoms, 26 bonds, 1 residue, 1 model selected
> select add #5/B:781@P3B
25 atoms, 28 bonds, 2 residues, 1 model selected
> select up
29 atoms, 28 bonds, 4 residues, 1 model selected
> select up
150 atoms, 158 bonds, 4 residues, 1 model selected
> color sel yellow
> show #!6 models
> color zone #6 near #5 distance 4.88
> color zone #6 near #5 distance 4.93
> color zone #6 near #5 distance 4.75
> color zone #6 near #5 distance 4.9
> color zone #6 near #5 distance 3.89
> color zone #6 near #5 distance 3.92
> color zone #6 near #5 distance 2.11
> color zone #6 near #5 distance 1.43
> color single #6
> select clear
> select #5/B:75
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
43 atoms, 42 bonds, 6 residues, 1 model selected
> select up
996 atoms, 1014 bonds, 150 residues, 1 model selected
> select up
4122 atoms, 4242 bonds, 544 residues, 1 model selected
> select up
8312 atoms, 8558 bonds, 1097 residues, 1 model selected
> select up
16747 atoms, 17241 bonds, 2201 residues, 11 models selected
> select up
16747 atoms, 17241 bonds, 2201 residues, 11 models selected
> hide #!6 models
> select up
16747 atoms, 17241 bonds, 2201 residues, 11 models selected
> color (#!5 & sel) hot pink
> select clear
> select add #5/A:275
11 atoms, 13 bonds, 1 residue, 1 model selected
> select subtract #5/A:275
3 bonds, 1 model selected
> select up
8 atoms, 4 bonds, 4 residues, 1 model selected
> select up
150 atoms, 158 bonds, 4 residues, 1 model selected
> color sel blue
> select clear
> show #!6 models
> color zone #6 near #5 distance 1.43
> color zone #6 near #5 distance 1.44
> color zone #6 near #5 distance 1.67
> color zone #6 near #5 distance 2.08
> color zone #6 near #5 distance 2.07
> color zone #6 near #5 distance 2.24
> hide #!6 models
> select #5/B:781@C2B
1 atom, 1 residue, 1 model selected
> select #5/A:784@O3B
1 atom, 1 residue, 1 model selected
> select add #5/A:788@C04
2 atoms, 1 bond, 2 residues, 1 model selected
> select up
6 atoms, 2 bonds, 4 residues, 1 model selected
> select up
150 atoms, 158 bonds, 4 residues, 1 model selected
> show #!6 models
> color zone #6 near #5 distance 2.31
> color zone #6 near #5 distance 2.29
> color zone #6 near #5 distance 2.72
> color zone #6 near #5 distance 2.7
> color zone #6 near #5 distance 3
> volume #6 level 0.1967
> volume #6 level 0.1694
> color zone #6 near #5 distance 2.95
> color zone #6 near #5 distance 2.6
> volume splitbyzone #6
Opened cryosparc_P129_J167_008_volume_map_sharp.mrc 0 as #8.1, grid size
432,432,432, pixel 0.813, shown at level 0.169, step 1, values float32
Opened cryosparc_P129_J167_008_volume_map_sharp.mrc 1 as #8.2, grid size
432,432,432, pixel 0.813, shown at level 0.169, step 1, values float32
Opened cryosparc_P129_J167_008_volume_map_sharp.mrc 2 as #8.3, grid size
432,432,432, pixel 0.813, shown at level 0.169, step 1, values float32
> hide #!5 models
> select add #5
8312 atoms, 8558 bonds, 5 pseudobonds, 1097 residues, 2 models selected
> select subtract #5
Nothing selected
> hide #!8 models
> hide #!8.3 models
> show #!1 models
> select clear
> select #1/B:784@P1A
1 atom, 1 residue, 1 model selected
> select subtract #1/B:784@P1A
Nothing selected
> select #1/A:788@N8P
1 atom, 1 residue, 1 model selected
> select add #1/B:784@CBP
2 atoms, 2 residues, 1 model selected
> select subtract #1/B:784@CBP
1 atom, 1 residue, 1 model selected
> select up
48 atoms, 50 bonds, 1 residue, 1 model selected
> select up
4256 atoms, 4382 bonds, 556 residues, 1 model selected
> select clear
> select add #1/B:784@CCP
1 atom, 1 bond, 1 residue, 1 model selected
> select up
3 atoms, 1 bond, 2 residues, 1 model selected
> select up
96 atoms, 100 bonds, 2 residues, 1 model selected
> ui tool show "Color Actions"
> select clear
[Repeated 1 time(s)]
> select add #1/A:369
5 atoms, 4 bonds, 1 residue, 1 model selected
> select clear
> select #1/A:631
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
142 atoms, 148 bonds, 16 residues, 1 model selected
> select up
3127 atoms, 3229 bonds, 399 residues, 1 model selected
> select up
4256 atoms, 4382 bonds, 556 residues, 1 model selected
> select down
3127 atoms, 3229 bonds, 399 residues, 1 model selected
> ui tool show "Color Actions"
> color sel light goldenrod yellow
> color sel pale goldenrod
> select clear
[Repeated 1 time(s)]
> select add #1/B:85
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
64 atoms, 64 bonds, 8 residues, 1 model selected
> select up
1021 atoms, 1040 bonds, 151 residues, 1 model selected
> select up
4179 atoms, 4301 bonds, 548 residues, 1 model selected
> select up
8435 atoms, 8683 bonds, 1104 residues, 1 model selected
> select down
4179 atoms, 4301 bonds, 548 residues, 1 model selected
> ui tool show "Color Actions"
> color sel orange
> select #1/A:157
11 atoms, 11 bonds, 1 residue, 1 model selected
> select up
50 atoms, 51 bonds, 6 residues, 1 model selected
> select up
1054 atoms, 1074 bonds, 155 residues, 1 model selected
> ui tool show "Color Actions"
> color sel pale goldenrod
> select clear
[Repeated 1 time(s)]
> select up
4 atoms, 2 bonds, 2 residues, 1 model selected
> select up
96 atoms, 100 bonds, 2 residues, 1 model selected
> select ::name="NAG"
182 atoms, 184 bonds, 13 residues, 2 models selected
> hide sel & #!1 atoms
> select ::name="COA"
96 atoms, 100 bonds, 2 residues, 1 model selected
> ui tool show "Color Actions"
> color sel royal blue
> select clear
> select add #1/A:789@C18
1 atom, 1 bond, 1 residue, 1 model selected
> select up
4 atoms, 2 bonds, 2 residues, 1 model selected
> select up
54 atoms, 58 bonds, 2 residues, 1 model selected
> ui tool show "Color Actions"
> color sel medium spring green
> show #!3 models
> close #7
> close #8
> color zone #3 near #5 distance 2.72
> color zone #3 near #1 distance 2.72
> hide #!3 models
> show #!3 models
> volume splitbyzone #3
Opened cryosparc_P130_J67_008_volume_map_sharp.mrc 0 as #7.1, grid size
432,432,432, pixel 0.813, shown at level 0.242, step 1, values float32
Opened cryosparc_P130_J67_008_volume_map_sharp.mrc 1 as #7.2, grid size
432,432,432, pixel 0.813, shown at level 0.242, step 1, values float32
Opened cryosparc_P130_J67_008_volume_map_sharp.mrc 2 as #7.3, grid size
432,432,432, pixel 0.813, shown at level 0.242, step 1, values float32
Opened cryosparc_P130_J67_008_volume_map_sharp.mrc 3 as #7.4, grid size
432,432,432, pixel 0.813, shown at level 0.242, step 1, values float32
Opened cryosparc_P130_J67_008_volume_map_sharp.mrc 4 as #7.5, grid size
432,432,432, pixel 0.813, shown at level 0.242, step 1, values float32
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!3 models
> hide #!3 models
> show #!7 models
> hide #!7.1 models
> hide #!7.2 models
> hide #!7.5 models
> save "/Users/fli05@amgen.com/OneDrive - Amgen/General -
> HGSNAT_Data_Share/Paper/Fig2_Mechanism/BindingSite.cxs"
> hide #!1 models
> show #!1 models
> show #!5 models
> hide #!1 models
> hide #!7.4 models
> hide #!7.3 models
> hide #!7 models
> show #!7.4 models
> show #!7.3 models
> hide #!7 models
> show #!6 models
> hide #!6 models
> show #!1 models
> hide #!1 models
> select #5/A:570
12 atoms, 12 bonds, 1 residue, 1 model selected
> select up
192 atoms, 197 bonds, 24 residues, 1 model selected
> select up
3079 atoms, 3180 bonds, 399 residues, 1 model selected
> select up
4190 atoms, 4316 bonds, 553 residues, 1 model selected
> ui tool show "Color Actions"
> color sel light pink
> select clear
> select #5/B:430
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
212 atoms, 219 bonds, 26 residues, 1 model selected
> select up
2004 atoms, 2070 bonds, 257 residues, 1 model selected
> select up
2035 atoms, 2102 bonds, 262 residues, 1 model selected
> select up
3051 atoms, 3149 bonds, 392 residues, 1 model selected
> select up
4122 atoms, 4242 bonds, 544 residues, 1 model selected
> color sel violet
> select clear
> select ::name="NAG"
182 atoms, 184 bonds, 13 residues, 2 models selected
> hide sel & #!5 cartoons
> hide sel & #!5 atoms
> select clear
> hide #!5 atoms
> select ::name="ACO"
102 atoms, 106 bonds, 2 residues, 1 model selected
> show sel atoms
> select ::name="MGN"
48 atoms, 52 bonds, 2 residues, 1 model selected
> show sel atoms
> ui tool show "Color Actions"
> color sel pale green
> select ::name="ACO"
102 atoms, 106 bonds, 2 residues, 1 model selected
> color sel cyan
> select clear
> show #!6 models
> color zone #6 near #5 distance 2.6
> volume splitbyzone #6
Opened cryosparc_P129_J167_008_volume_map_sharp.mrc 0 as #8.1, grid size
432,432,432, pixel 0.813, shown at level 0.169, step 1, values float32
Opened cryosparc_P129_J167_008_volume_map_sharp.mrc 1 as #8.2, grid size
432,432,432, pixel 0.813, shown at level 0.169, step 1, values float32
Opened cryosparc_P129_J167_008_volume_map_sharp.mrc 2 as #8.3, grid size
432,432,432, pixel 0.813, shown at level 0.169, step 1, values float32
Opened cryosparc_P129_J167_008_volume_map_sharp.mrc 3 as #8.4, grid size
432,432,432, pixel 0.813, shown at level 0.169, step 1, values float32
Opened cryosparc_P129_J167_008_volume_map_sharp.mrc 4 as #8.5, grid size
432,432,432, pixel 0.813, shown at level 0.169, step 1, values float32
> hide #!8.5 models
> hide #!8.2 models
> hide #!8.1 models
> save "/Users/fli05@amgen.com/OneDrive - Amgen/General -
> HGSNAT_Data_Share/Paper/Fig2_Mechanism/BindingSite.cxs"
> dssp
> ui tool show "Hide Dust"
> surface dust #8.4 size 4.88
> save "/Users/fli05@amgen.com/OneDrive - Amgen/General -
> HGSNAT_Data_Share/Paper/Fig2_Mechanism/BindingSite.cxs"
——— End of log from Tue Dec 12 10:07:44 2023 ———
opened ChimeraX session
OpenGL version: 4.1 INTEL-18.4.6
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics OpenGL Engine
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: MacBookPro16,2
Processor Name: Quad-Core Intel Core i7
Processor Speed: 2.3 GHz
Number of Processors: 1
Total Number of Cores: 4
L2 Cache (per Core): 512 KB
L3 Cache: 8 MB
Hyper-Threading Technology: Enabled
Memory: 16 GB
System Firmware Version: 1715.81.2.0.0 (iBridge: 19.16.10744.0.0,0)
OS Loader Version: 540.80.2~11
Software:
System Software Overview:
System Version: macOS 12.2.1 (21D62)
Kernel Version: Darwin 21.3.0
Time since boot: 30 days 23:34
Graphics/Displays:
Intel Iris Plus Graphics:
Chipset Model: Intel Iris Plus Graphics
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x8a53
Revision ID: 0x0007
Metal Family: Supported, Metal GPUFamily macOS 2
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
P27h-20:
Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition)
UI Looks like: 2560 x 1440 @ 59.00Hz
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Display Serial Number: V908KKL1
Mirror: Off
Online: Yes
Rotation: Supported
Automatically Adjust Brightness: Yes
Connection Type: Thunderbolt/DisplayPort
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-PDBImages: 1.2
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 , 23 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 , 23 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | accepted → closed |
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