![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 2 years ago
Closed 2 years ago
#9576 closed defect (duplicate)
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-13.4-arm64-arm-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 0x00000001f3925e00 (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" : 140000,
"procRole" : "Background",
"version" : 2,
"userID" : 22932962,
"deployVersion" : 210,
"modelCode" : "MacBookPro18,3",
"coalitionID" : 1853,
"osVersion" : {
"train" : "macOS 13.4",
"build" : "22F66",
"releaseType" : "User"
},
"captureTime" : "2023-08-14 11:28:59.7347 -0400",
"incident" : "5B661780-8568-4398-AFEC-5AC51F480DFB",
"pid" : 22393,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2023-08-10 14:13:18.2352 -0400",
"procStartAbsTime" : 617577234381,
"procExitAbsTime" : 3385459284153,
"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":"768DF056-38AA-5AE7-AEB2-7CB0E4489CB9","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "52E8BCBB-0ECD-E76A-418B-CCE1EDC18AAE",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 0,
"wakeTime" : 2,
"sleepWakeUUID" : "5016101B-C079-4E44-B674-D6EFDEE1A2E1",
"sip" : "enabled",
"vmRegionInfo" : "0x18 is not in any region. Bytes before following region: 105559961370600\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n MALLOC_NANO (reserved) 600198000000-6001a0000000 [128.0M] rw-\/rwx SM=NUL ...(unallocated)",
"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: 105559961370600\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n MALLOC_NANO (reserved) 600198000000-6001a0000000 [128.0M] rw-\/rwx SM=NUL ...(unallocated)",
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"name" : "AppKit",
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"CFBundleIdentifier" : "com.apple.HIToolbox",
"size" : 3358720,
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"path" : "\/System\/Library\/Frameworks\/Carbon.framework\/Versions\/A\/Frameworks\/HIToolbox.framework\/Versions\/A\/HIToolbox",
"name" : "HIToolbox"
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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
> open /Users/rslack/Library/CloudStorage/OneDrive-
> EmoryUniversity/Documents/Data/Structures/A3G/Chimera/ClusPro_Docking_2_5.cxs
> format session
opened ChimeraX session
> close session
> open /Users/rslack/Downloads/RT_Domains_Session.cxs
opened ChimeraX session
> select /A/B
8209 atoms, 8064 bonds, 19 pseudobonds, 1310 residues, 3 models selected
> hide sel surfaces
> select /B
3412 atoms, 3370 bonds, 2 pseudobonds, 529 residues, 2 models selected
> show sel cartoons
> select clear
> ui tool show "Show Sequence Viewer"
> sequence chain /B
Alignment identifier is 1/B
> select /B:233
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /B:233-234
17 atoms, 16 bonds, 2 residues, 1 model selected
> select
> /B:27-44,77-84,97-103,112-118,121-129,134-138,154-175,196-211,235-239,254-268,276-284,296-312,363-384,394-405,420-427
1506 atoms, 1523 bonds, 180 residues, 1 model selected
> select /B:210
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /B:210-240
117 atoms, 121 bonds, 1 pseudobond, 13 residues, 2 models selected
> select /B:210
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /B:210-246
163 atoms, 168 bonds, 1 pseudobond, 19 residues, 2 models selected
> name frozen HDX1 sel
> select
> /B:27-44,77-84,97-103,112-118,121-129,134-138,154-175,196-211,235-239,254-268,276-284,296-312,363-384,394-405,420-427
1506 atoms, 1523 bonds, 180 residues, 1 model selected
> select /B:380
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /B:380-386
57 atoms, 58 bonds, 7 residues, 1 model selected
> select /B:381
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /B:381-382
15 atoms, 14 bonds, 2 residues, 1 model selected
> select /B:380
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /B:380-394
125 atoms, 129 bonds, 15 residues, 1 model selected
> name frozen HDX2 sel
> select /B:410
14 atoms, 15 bonds, 1 residue, 1 model selected
> select /B:410-414
52 atoms, 56 bonds, 5 residues, 1 model selected
> select /B:409
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /B:409-414
59 atoms, 63 bonds, 6 residues, 1 model selected
> name frozen HDX3 sel
> lighting soft
> lighting full
> lighting soft
> show sel surfaces
> hide sel surfaces
> select /A:61
11 atoms, 11 bonds, 1 residue, 1 model selected
> select /A:61-65
42 atoms, 42 bonds, 5 residues, 1 model selected
> select /A:63
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /A:63-64
17 atoms, 16 bonds, 2 residues, 1 model selected
> select /A:62
5 atoms, 4 bonds, 1 residue, 1 model selected
> select /A:62-72
95 atoms, 96 bonds, 11 residues, 1 model selected
> name frozen HDX4 sel
> select /A:534
5 atoms, 4 bonds, 1 residue, 1 model selected
> select /A:534-555
157 atoms, 160 bonds, 22 residues, 1 model selected
> name frozen HDX5 sel
> select HDX1, HDX2, HDX3, HDX4, HDX5
Expected an objects specifier or a keyword
> select HDX1
3281 atoms, 168 bonds, 1 pseudobond, 398 residues, 2 models selected
> select HDX1
3281 atoms, 168 bonds, 1 pseudobond, 398 residues, 2 models selected
> select /B:327
5 atoms, 4 bonds, 1 residue, 1 model selected
> select /B:325-327
21 atoms, 20 bonds, 3 residues, 1 model selected
> select /B:210
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /B:210-247
170 atoms, 176 bonds, 1 pseudobond, 20 residues, 2 models selected
> name frozen HDX1 sel
> select HDX1
3281 atoms, 176 bonds, 1 pseudobond, 398 residues, 2 models selected
> select /B:394
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /B:394
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/B:210-247,380-394
295 atoms, 305 bonds, 1 pseudobond, 35 residues, 2 models selected
> select #1/B:210-247,380-394,409-415
363 atoms, 377 bonds, 1 pseudobond, 42 residues, 2 models selected
> ui tool show "Volume Viewer"
> ui tool show "Measure Volume and Area"
> ui tool show "Measure and Color Blobs"
> ui tool show "Surface Zone"
No surface chosen for zoning
> molmap #1/B:210-247,380-394,409-415
Missing or invalid "resolution" argument: Expected a number
> molmap #1 3.5
Opened 5J2M.pdb map 3.5 as #2, grid size 84,115,91, pixel 1.17, shown at level
0.103, step 1, values float32
> hide #!2 models
> select #2/B:210-247,380-394,409-415
Nothing selected
> show surfaces
> show #!2 models
> hide #!2 models
> hide surfaces
> show #!2 models
> select /A
4797 atoms, 4694 bonds, 17 pseudobonds, 781 residues, 2 models selected
> close #2
> molmap #2/B:210-247,380-394,409-415 3.5
No atoms specified
> molmap #1/B:210-247,380-394,409-415 3.5
Opened 5J2M.pdb map 3.5 as #2, grid size 42,63,63, pixel 1.17, shown at level
0.0798, step 1, values float32
> select clear
> select add #2
2 models selected
> transparency #2.1 50
No visible atoms or bonds selected
> select /B:61
11 atoms, 11 bonds, 1 residue, 1 model selected
> select /B:61-76
138 atoms, 140 bonds, 16 residues, 1 model selected
> select /A:61-62
16 atoms, 16 bonds, 2 residues, 1 model selected
> select /A:61-76
138 atoms, 140 bonds, 16 residues, 1 model selected
> select /A:535-536
21 atoms, 22 bonds, 2 residues, 1 model selected
> select /A:535-555
152 atoms, 155 bonds, 21 residues, 1 model selected
> molmap #1/A:61-76,535-555
Missing or invalid "resolution" argument: Expected a number
> molmap #1/A:61-76,535-555 3.5
Opened 5J2M.pdb map 3.5 as #3, grid size 62,87,44, pixel 1.17, shown at level
0.0857, step 1, values float32
> volume #3 level 0.1343
> volume #3 level 0.07757
> volume #3 style image
> volume #3 colorMode opaque8 showOutlineBox true orthoplanes xyz
> positionPlanes 30,43,21 imageMode orthoplanes
> volume #3 style mesh
> volume #3 style image maximumIntensityProjection true colorMode auto8
> imageMode "full region"
> volume #3 style surface maximumIntensityProjection false
> hide #!3 models
> show #!3 models
> set bgColor black
> hide #!3 models
> show #!3 models
> hide #3.1 models
> show #3.1 models
> show #3.2 models
> hide #3.2 models
> show #3.2 models
> hide #3.2 models
> show #3.2 models
> hide #3.2 models
> show #3.2 models
> hide #3.2 models
> volume #3 step 4
> volume #3 step 2
> volume #3 step 1
> volume #3 change image level 0,0 level 0.09808,0.8 level 1.504,1
> volume #3 level 0.07757
> volume #3 style image colorMode opaque8 imageMode "box faces"
> volume #3 style surface
> close #3
> molmap #1/A:61-76,535-555 3.5
Opened 5J2M.pdb map 3.5 as #3, grid size 62,87,44, pixel 1.17, shown at level
0.0857, step 1, values float32
> hide #!2 models
> show #!2 models
> set bgColor white
> volume #3 region 0,0,4,61,86,43
> color #3 #531b93ff models
> color #3 #531b9380 models
> volume #3 region 0,0,1,61,86,43
> volume #3 level 0.0798
> color #3 #fffb00ff models
> color #3 #fffb0075 models
> color #3 #fffb007d models
> color #3 #fffb0080 models
> color #3 #9437ffff models
> color #3 #9437ff7d models
> color #3 #9437ff80 models
> color #2 #9437ffff models
> color #2 #9437ff80 models
> select clear
> lighting soft
> open /Users/rslack/Downloads/5J2M_8CX2_docked_prot-prot-
> docking_3_pose_1_-_prepared.pdb
5J2M_8CX2_docked_prot-prot-docking_3_pose_1_-_prepared.pdb title:
prot-prot-docking_3_pose_1 - prepared [more info...]
Chain information for 5J2M_8CX2_docked_prot-prot-
docking_3_pose_1_-_prepared.pdb #4
---
Chain | Description
A | No description available
B | No description available
F G | No description available
K | No description available
L | No description available
P | No description available
T | No description available
Non-standard residues in 5J2M_8CX2_docked_prot-prot-
docking_3_pose_1_-_prepared.pdb #4
---
MG — (MG)
ZN — (ZN)
> hide #!1 models
> hide #!2 models
> hide #!3 models
> select add #4
30265 atoms, 30826 bonds, 19 pseudobonds, 1774 residues, 3 models selected
> hide sel atoms
> show sel cartoons
> select #4/A
9147 atoms, 9261 bonds, 10 pseudobonds, 561 residues, 2 models selected
> select #4/A:427-560
2072 atoms, 2084 bonds, 132 residues, 1 model selected
> color sel orange
> select #4/A:319-426
1829 atoms, 1862 bonds, 108 residues, 1 model selected
> color sel yellow
> select #4/A:1-85,118-155
2035 atoms, 2060 bonds, 123 residues, 1 model selected
> color sel blue
> select #4/A:86-117,156-236
1862 atoms, 1890 bonds, 113 residues, 1 model selected
> color sel red
> select #4/A:237-318
1346 atoms, 1359 bonds, 82 residues, 1 model selected
> color sel lime
> select #4/B
6628 atoms, 6718 bonds, 2 pseudobonds, 398 residues, 2 models selected
> color (#!4 & sel) white
> ui tool show Matchmaker
> matchmaker #!4 to #1 cutoffDistance 1.5 bring #1.3
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 | 1.5
Matchmaker 5J2M.pdb, chain A (#1) with 5J2M_8CX2_docked_prot-prot-
docking_3_pose_1_-_prepared.pdb, chain A (#4), sequence alignment score =
2862.7
RMSD between 558 pruned atom pairs is 0.207 angstroms; (across all 558 pairs:
0.207)
> show #!1 models
> hide #!1 models
> show #!1 models
> show #!2 models
> show #!3 models
> hide #!3 models
> hide #!2 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> select #4/P
556 atoms, 594 bonds, 1 pseudobond, 17 residues, 2 models selected
> show #!1 models
> hide #!1 models
> color (#!4 & sel) cyan
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> select #4/T
786 atoms, 847 bonds, 24 residues, 1 model selected
> show #!1 models
> hide #!1 models
> color sel magenta
> show #!1 models
> hide #!1 models
> show #!1 models
> color sel hot pink
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!2 models
> show #!3 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> select #4/P:816
35 atoms, 37 bonds, 1 residue, 1 model selected
> select #4/P:816
35 atoms, 37 bonds, 1 residue, 1 model selected
> select #4/P:816
35 atoms, 37 bonds, 1 residue, 1 model selected
> select #4/T:709
31 atoms, 32 bonds, 1 residue, 1 model selected
> select clear
> select #4/P:818
32 atoms, 33 bonds, 1 residue, 1 model selected
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!4 models
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/rslack/Desktop/movie1.mp4
Movie saved to /Users/rslack/Desktop/movie1.mp4
> volume #3 region 0,0,1,61,86,43
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/rslack/Desktop/movie1.mp4
Movie saved to /Users/rslack/Desktop/movie1.mp4
> lighting soft
> set bgColor black
> set bgColor white
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/rslack/Desktop/movie1.mp4
Movie saved to /Users/rslack/Desktop/movie1.mp4
> open /Users/rslack/Downloads/8cx0.pdb
8cx0.pdb title:
Cryo-em structure of human APOBEC3G/hiv-1 vif/cbfbeta/elob/eloc monomeric
complex [more info...]
Chain information for 8cx0.pdb #5
---
Chain | Description | UniProt
A | DNA DC->du-editing enzyme apobec-3G | ABC3G_HUMAN 1-384
B | virion infectivity factor | Q77YG0_9HIV1 1-192
C | core-binding factor subunit β | PEBB_HUMAN 1-182
D | elongin-B | ELOB_HUMAN 1-118
E | elongin-C | ELOC_HUMAN 1-112
K | RNA (5'-R(P*ap*ap*ap*ap*ap*ap*ap*A)-3') |
Non-standard residues in 8cx0.pdb #5
---
ZN — zinc ion
> hide #!1 models
> hide #!2 models
> hide #!3 models
> select add #4
30265 atoms, 30826 bonds, 19 pseudobonds, 1774 residues, 3 models selected
> select subtract #4
Nothing selected
> select add #5
7575 atoms, 7802 bonds, 12 pseudobonds, 900 residues, 3 models selected
> hide sel atoms
> show sel cartoons
> hide sel cartoons
> select #5/A
3202 atoms, 3307 bonds, 6 pseudobonds, 378 residues, 2 models selected
> show sel cartoons
> ui tool show "Show Sequence Viewer"
> sequence chain #5/A
Alignment identifier is 5/A
> select #5/A:7-13
62 atoms, 62 bonds, 7 residues, 1 model selected
> select #5/A:21
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #5/A:21-27
65 atoms, 67 bonds, 7 residues, 1 model selected
> select #5/A:7-13
62 atoms, 62 bonds, 7 residues, 1 model selected
> select #5/A:21-27
65 atoms, 67 bonds, 7 residues, 1 model selected
> molmap #5/A:1-13, 21-27, 86-91, 108-119, 124-135, 165-181, 235-260, 264-276,
> 282-289, 340-373 3.5
Opened 8cx0.pdb map 3.5 as #6, grid size 67,58,79, pixel 1.17, shown at level
0.0875, step 1, values float32
> volume #6 level 0.0798
> volume #6 color #9437ff
> volume #6 color #9437ff81
> volume #6 color #9437ff80
> select clear
> volume #6 region 0,0,0,66,57,78
> volume #6 level 0.05
> volume #6 level 0.0798
> volume #6 level 0.1
> volume #6 level 0.0798
> select #5/A:7
8 atoms, 7 bonds, 1 residue, 1 model selected
> select clear
> volume #6 region 0,0,0,66,57,78
> select Zn
5 atoms, 5 residues, 2 models selected
> show sel & #!5 atoms
> color (#!5 & sel) black
> select clear
> select #5/B:201@ZN
1 atom, 1 residue, 1 model selected
> hide sel target a
> save /Users/rslack/Downloads/A3G_HDX.tif width 687 height 581 supersample 4
> hide #!6 models
> molmap #5/A:1-13, 21-27, 235-260, 340-373 3.5
Opened 8cx0.pdb map 3.5 as #7, grid size 46,57,75, pixel 1.17, shown at level
0.0885, step 1, values float32
> volume #7 color #d783ff
> volume #7 color #d783ff80
> color #7 #d783ffff models
> color #7 #d783ff80 models
> color #7 #7a81ffff models
> color #7 #7a81ff80 models
> save /Users/rslack/Downloads/A3G_HDX2.tif width 687 height 581 supersample 4
> select #5/A:180,270
18 atoms, 16 bonds, 2 residues, 1 model selected
> show sel atoms
> color sel byhetero
> style sel stick
Changed 18 atom styles
> style sel sphere
Changed 18 atom styles
> style sel ball
Changed 18 atom styles
> style sel sphere
Changed 18 atom styles
> color sel dark gray
> color sel lime
> color sel cyan
> color sel byhetero
> label sel text "{0.label_one_letter_code} {0.number}{0.insertion_code}"
> label height 2
> save /Users/rslack/Downloads/A3G_Xlink.tif width 687 height 581 supersample
> 3
> hide #!7 models
> hide #!5 models
> show #!7 models
> show #!5 models
> hide #!5 models
> hide #!7 models
> show #!1 models
> show #!2 models
> show #!3 models
> select #1/B:154,201,275
27 atoms, 24 bonds, 3 residues, 1 model selected
> select #1/B:154,201,275
27 atoms, 24 bonds, 3 residues, 1 model selected
> show sel atoms
> style sel sphere
Changed 27 atom styles
> color (#!1 & sel) cyan
> color (#!1 & sel) byhetero
> label (#!1 & sel) attribute label_one_letter_code
> label (#!1 & sel) text "{0.label_one_letter_code}
> {0.number}{0.insertion_code}"
> label height 2
> label height 3
> save /Users/rslack/Downloads/RT_Xlink.tif width 687 height 581 supersample 3
> save /Users/rslack/Downloads/RT_Xlink.tif width 687 height 581 supersample 4
> label height 5
> select clear
> save /Users/rslack/Downloads/RT_Xlink.tif width 687 height 581 supersample 4
> hide #!1 models
> hide #!2 models
> hide #!3 models
> show #!4 models
> show #!2 models
> show #!3 models
> volume #3 region 0,0,1,56,86,43
> select #4/B:154,201,275
66 atoms, 63 bonds, 3 residues, 1 model selected
> style sel sphere
Changed 66 atom styles
> style sel sphere
Changed 66 atom styles
> show sel atoms
> color sel cyan
> color sel byhetero
> label sel text "{0.label_one_letter_code} {0.number}{0.insertion_code}"
> label height 5
> select #4/F:180,270
44 atoms, 42 bonds, 2 residues, 1 model selected
> show sel cartoons
> show sel atoms
> color sel cyan
> color sel byhetero
> select #4/G:180,270
44 atoms, 42 bonds, 2 residues, 1 model selected
> show sel atoms
> color sel cyan
> color sel byhetero
> select #4/F
6274 atoms, 6379 bonds, 6 pseudobonds, 379 residues, 2 models selected
> color (#!4 & sel) hot pink
> select #4/G
6276 atoms, 6383 bonds, 377 residues, 1 model selected
> color sel hot pink
> select #4/G:180,270
44 atoms, 42 bonds, 2 residues, 1 model selected
> color sel cyan
> color sel byhetero
> select #4/F:180,270
44 atoms, 42 bonds, 2 residues, 1 model selected
> color sel cyan
> color sel byhetero
> label sel text "{0.label_one_letter_code} {0.number}{0.insertion_code}"
> label height 5
> select #4/G:180,270
44 atoms, 42 bonds, 2 residues, 1 model selected
> label sel text "{0.label_one_letter_code} {0.number}{0.insertion_code}"
> label height 5
> select #4/K,L
598 atoms, 644 bonds, 18 residues, 1 model selected
> color sel blue
> color sel cornflower blue
> select clear
> save /Users/rslack/Downloads/A3G_RT_Dock.tif width 921 height 685
> supersample 4
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/rslack/Desktop/movie2.mp4
Movie saved to /Users/rslack/Desktop/movie2.mp4
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/rslack/Desktop/movie2.mp4
Movie saved to /Users/rslack/Desktop/movie2.mp4
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/rslack/Desktop/movie1.mp4
Movie saved to /Users/rslack/Desktop/movie1.mp4
> hide #!2 models
> hide #!3 models
> hide #!4 models
> show #!6 models
> hide #!6 models
> show #!7 models
> show #!5 models
> select #5/A:180,270
18 atoms, 16 bonds, 2 residues, 1 model selected
> hide sel atoms
> color sel hot pink
> ui tool show "Color Actions"
> color sel salmon
> ~label sel residues
> select clear
> volume #7 region 0,0,0,45,56,74
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/rslack/Desktop/movie1.mp4
Movie saved to /Users/rslack/Desktop/movie1.mp4
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 Metal - 83.1
OpenGL renderer: Apple M1 Pro
OpenGL vendor: Apple
Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro18,3
Model Number: MKGQ3LL/A
Chip: Apple M1 Pro
Total Number of Cores: 10 (8 performance and 2 efficiency)
Memory: 16 GB
System Firmware Version: 8422.121.1
OS Loader Version: 8422.121.1
Software:
System Software Overview:
System Version: macOS 13.4 (22F66)
Kernel Version: Darwin 22.5.0
Time since boot: 4 days, 23 hours, 8 minutes
Graphics/Displays:
Apple M1 Pro:
Chipset Model: Apple M1 Pro
Type: GPU
Bus: Built-In
Total Number of Cores: 16
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3024 x 1964 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
C32F391:
Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
UI Looks like: 1920 x 1080 @ 60.00Hz
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-OpenCommands: 1.1
ChimeraX-PDB: 2.7.2
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 3.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.1
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.8.3
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.1
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.10.3
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1.2
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.2.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Topography: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.28.4
ChimeraX-uniprot: 2.2.2
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.1
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.1.3
contourpy: 1.0.7
cxservices: 1.2.2
cycler: 0.11.0
Cython: 0.29.33
debugpy: 1.6.7
decorator: 5.1.1
docutils: 0.19
executing: 1.2.0
filelock: 3.9.0
fonttools: 4.39.3
funcparserlib: 1.0.1
grako: 3.16.5
h5py: 3.8.0
html2text: 2020.1.16
idna: 3.4
ihm: 0.35
imagecodecs: 2022.2.22
imagesize: 1.4.1
importlib-metadata: 6.6.0
ipykernel: 6.21.1
ipython: 8.10.0
ipython-genutils: 0.2.0
ipywidgets: 8.0.6
jedi: 0.18.2
Jinja2: 3.1.2
jupyter-client: 8.0.2
jupyter-core: 5.3.0
jupyterlab-widgets: 3.0.7
kiwisolver: 1.4.4
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.2
matplotlib: 3.6.3
matplotlib-inline: 0.1.6
MolecularDynamicsViewer: 1.4
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 → QPainter::begin: Paint device returned engine == 0 |
comment:2 by , 2 years ago
| Resolution: | → duplicate |
|---|---|
| Status: | accepted → closed |
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