![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 3 years ago
Closed 3 years ago
#8339 closed defect (duplicate)
Crash in color chooser
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Platform | 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-12.3-arm64-arm-64bit
ChimeraX Version: 1.5 (2022-11-24 00:03:27 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Aborted
Thread 0x00000002c4807000 (most recent call first):
File "/private/var/folders/ht/62vn9s5906l37_519kbwyf_r0000gn/T/AppTranslocation/2F052660-B889-46C0-B9A0-22CFE4F70BA7/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 316 in wait
File "/private/var/folders/ht/62vn9s5906l37_519kbwyf_r0000gn/T/AppTranslocation/2F052660-B889-46C0-B9A0-22CFE4F70BA7/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 574 in wait
File "/private/var/folders/ht/62vn9s5906l37_519kbwyf_r0000gn/T/AppTranslocation/2F052660-B889-46C0-B9A0-22CFE4F70BA7/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 1297 in run
File "/private/var/folders/ht/62vn9s5906l37_519kbwyf_r0000gn/T/AppTranslocation/2F052660-B889-46C0-B9A0-22CFE4F70BA7/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/private/var/folders/ht/62vn9s5906l37_519kbwyf_r0000gn/T/AppTranslocation/2F052660-B889-46C0-B9A0-22CFE4F70BA7/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Current thread 0x000000010286c580 (most recent call first):
File "/private/var/folders/ht/62vn9s5906l37_519kbwyf_r0000gn/T/AppTranslocation/2F052660-B889-46C0-B9A0-22CFE4F70BA7/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 283 in event_loop
File "/private/var/folders/ht/62vn9s5906l37_519kbwyf_r0000gn/T/AppTranslocation/2F052660-B889-46C0-B9A0-22CFE4F70BA7/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py", line 884 in init
File "/private/var/folders/ht/62vn9s5906l37_519kbwyf_r0000gn/T/AppTranslocation/2F052660-B889-46C0-B9A0-22CFE4F70BA7/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py", line 1035 in
File "/private/var/folders/ht/62vn9s5906l37_519kbwyf_r0000gn/T/AppTranslocation/2F052660-B889-46C0-B9A0-22CFE4F70BA7/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 87 in _run_code
File "/private/var/folders/ht/62vn9s5906l37_519kbwyf_r0000gn/T/AppTranslocation/2F052660-B889-46C0-B9A0-22CFE4F70BA7/d/ChimeraX-1.5.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" : 600000,
"procLaunch" : "2023-01-17 12:21:30.1575 -0500",
"procRole" : "Foreground",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "MacBookPro18,3",
"procStartAbsTime" : 14041987564622,
"coalitionID" : 72614,
"osVersion" : {
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"build" : "21E230",
"releaseType" : "User"
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"captureTime" : "2023-01-20 12:30:21.7092 -0500",
"incident" : "0800AA95-122A-4C65-9339-13EE79A86462",
"bug_type" : "309",
"pid" : 77833,
"procExitAbsTime" : 14617944532960,
"translated" : false,
"cpuType" : "ARM-64",
"procName" : "ChimeraX",
"procPath" : "\/Volumes\/VOLUME\/*\/ChimeraX-1.5.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.5.0","CFBundleVersion":"1.5.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"62284603-9141-55F8-8388-1E1E9043FE0B","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "C833433B-D409-A246-A9D6-E06D6F611475",
"wakeTime" : 500,
"sleepWakeUUID" : "4D1CFA8A-F726-4F99-A040-E457E2F6F3EC",
"sip" : "enabled",
"isCorpse" : 1,
"exception" : {"codes":"0x0000000000000000, 0x0000000000000000","rawCodes":[0,0],"type":"EXC_CRASH","signal":"SIGABRT"},
"ktriageinfo" : "VM - Compressor failed a blocking pager_get\n",
"asi" : {"libsystem_c.dylib":["Assertion failed: (backingScaleFactor > 0.f), function drawnFocusRingBitmapForTime, file NSAutomaticFocusRing.m, line 346."]},
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===== Log before crash start =====
UCSF ChimeraX version: 1.5 (2022-11-24)
© 2016-2022 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open 6CO8 format mmcif fromDatabase pdb
6co8 title:
Structure of Zika virus at a resolution of 3.1 Angstrom [more info...]
Chain information for 6co8 #1
---
Chain | Description | UniProt
A C E | E protein | POLG_ZIKVF
B D F | M protein | POLG_ZIKVF
Non-standard residues in 6co8 #1
---
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose
6co8 mmCIF Assemblies
---
1| complete icosahedral assembly
2| icosahedral asymmetric unit
3| icosahedral pentamer
4| icosahedral 23 hexamer
5| icosahedral asymmetric unit, std point frame
> nucleotides atoms
> style nucleic stick
Changed 0 atom styles
> style sphere
Changed 13248 atom styles
> style sphere
Changed 13248 atom styles
> style sphere
Changed 13248 atom styles
> style stick
Changed 13248 atom styles
> style stick
Changed 13248 atom styles
> nucleotides atoms
> style nucleic stick
Changed 0 atom styles
> nucleotides atoms
> style nucleic stick
Changed 0 atom styles
> hide surfaces
> select add #1
13248 atoms, 13536 bonds, 1734 residues, 1 model selected
> view clip false
> show sel atoms
> show sel cartoons
> hide sel atoms
> hide #1 models
> show #1 models
> select subtract #1
Nothing selected
> lighting soft
> lighting full
> lighting soft
> lighting simple
> lighting soft
> set bgColor white
> lighting simple
Alignment identifier is 1
Alignment identifier is 2
> select /A,C,E:1-2
57 atoms, 54 bonds, 6 residues, 1 model selected
> select /A,C,E:1-13
312 atoms, 312 bonds, 39 residues, 1 model selected
> select /B,D,F:72-75
91 atoms, 94 bonds, 12 residues, 1 model selected
> select /B,D,F
1800 atoms, 1845 bonds, 225 residues, 1 model selected
> color sel orange
> color sel orange red
> color sel orange
> select /A,C,E:1-2
57 atoms, 54 bonds, 6 residues, 1 model selected
> select /A,C,E:1-4
99 atoms, 96 bonds, 12 residues, 1 model selected
> select /B,D,F:75
19 atoms, 16 bonds, 3 residues, 1 model selected
> select /B,D,F
1800 atoms, 1845 bonds, 225 residues, 1 model selected
> color sel orange red
> select /A,C,E:1
24 atoms, 21 bonds, 3 residues, 1 model selected
> select /A,C,E:1-51
1128 atoms, 1140 bonds, 153 residues, 1 model selected
> color sel red
> select /A,C,E:52
24 atoms, 21 bonds, 3 residues, 1 model selected
> select /A,C,E:52
24 atoms, 21 bonds, 3 residues, 1 model selected
> select /A,C,E:52-53
48 atoms, 45 bonds, 6 residues, 1 model selected
> select /A,C,E:52-135
1908 atoms, 1938 bonds, 252 residues, 1 model selected
> color sel yellow
> select /A,C,E:136-137
63 atoms, 63 bonds, 6 residues, 1 model selected
> select /A,C,E:136-194
1335 atoms, 1356 bonds, 177 residues, 1 model selected
> color sel red
> select /A,C,E:130-132
72 atoms, 72 bonds, 9 residues, 1 model selected
> select /A,C,E:27-132
2370 atoms, 2406 bonds, 318 residues, 1 model selected
> select /A,C,E:190
18 atoms, 15 bonds, 3 residues, 1 model selected
> select /A,C,E:190-191
45 atoms, 42 bonds, 6 residues, 1 model selected
> select /A,C,E:193
33 atoms, 30 bonds, 3 residues, 1 model selected
> select /A,C,E:193
33 atoms, 30 bonds, 3 residues, 1 model selected
> select /A,C,E:194
21 atoms, 18 bonds, 3 residues, 1 model selected
> select /A,C,E:194
21 atoms, 18 bonds, 3 residues, 1 model selected
> select /A,C,E:195
12 atoms, 9 bonds, 3 residues, 1 model selected
> select /A,C,E:195-288
2214 atoms, 2283 bonds, 282 residues, 1 model selected
> select /A,C,E:285
18 atoms, 15 bonds, 3 residues, 1 model selected
> select /A,C,E:195-285
2154 atoms, 2220 bonds, 273 residues, 1 model selected
> color sel yellow
> select /A,C,E:300
24 atoms, 21 bonds, 3 residues, 1 model selected
> select /A,C,E:285-300
387 atoms, 387 bonds, 48 residues, 1 model selected
> select /A,C,E:286-287
30 atoms, 27 bonds, 6 residues, 1 model selected
> select /A,C,E:286-300
369 atoms, 369 bonds, 45 residues, 1 model selected
> color sel red
> select /A,C,E:301-302
39 atoms, 36 bonds, 6 residues, 1 model selected
> select /A,C,E:301-400
2262 atoms, 2313 bonds, 300 residues, 1 model selected
> color sel blue
> select /A,C,E:401
30 atoms, 30 bonds, 3 residues, 1 model selected
> select /A,C,E:401-402
63 atoms, 63 bonds, 6 residues, 1 model selected
> color sel blue
> select /A,C,E:403
18 atoms, 15 bonds, 3 residues, 1 model selected
> select /A,C,E:403-501
2145 atoms, 2184 bonds, 297 residues, 1 model selected
> color sel cornflower blue
> select /A,C,E:402
33 atoms, 30 bonds, 3 residues, 1 model selected
> select /A,C,E:401-402
63 atoms, 63 bonds, 6 residues, 1 model selected
> select clear
> view
> lighting full
> set bgColor black
> select /E
3790 atoms, 3870 bonds, 501 residues, 1 model selected
> select /E
3790 atoms, 3870 bonds, 501 residues, 1 model selected
> select /A
3787 atoms, 3867 bonds, 501 residues, 1 model selected
> select /C
3787 atoms, 3867 bonds, 501 residues, 1 model selected
> select clear
> select /C
3787 atoms, 3867 bonds, 501 residues, 1 model selected
> hide sel target a
> cartoon hide sel
> select /E
3790 atoms, 3870 bonds, 501 residues, 1 model selected
> cartoon hide sel
> select /D
600 atoms, 615 bonds, 75 residues, 1 model selected
> cartoon hide sel
> select /F
601 atoms, 616 bonds, 75 residues, 1 model selected
> cartoon hide sel
> select /D
600 atoms, 615 bonds, 75 residues, 1 model selected
> cartoon sel
> select /B
599 atoms, 614 bonds, 75 residues, 1 model selected
> cartoon hide sel
> select /F
601 atoms, 616 bonds, 75 residues, 1 model selected
> cartoon sel
> select /A
3787 atoms, 3867 bonds, 501 residues, 1 model selected
> cartoon hide sel
> select /C
3787 atoms, 3867 bonds, 501 residues, 1 model selected
> cartoon sel
> select /B
599 atoms, 614 bonds, 75 residues, 1 model selected
> select /D
600 atoms, 615 bonds, 75 residues, 1 model selected
> select /B
599 atoms, 614 bonds, 75 residues, 1 model selected
> cartoon sel
> select /A
3787 atoms, 3867 bonds, 501 residues, 1 model selected
> select /C
3787 atoms, 3867 bonds, 501 residues, 1 model selected
> select /D
600 atoms, 615 bonds, 75 residues, 1 model selected
> select /A
3787 atoms, 3867 bonds, 501 residues, 1 model selected
> select /C
3787 atoms, 3867 bonds, 501 residues, 1 model selected
> select /B
599 atoms, 614 bonds, 75 residues, 1 model selected
> select /B
599 atoms, 614 bonds, 75 residues, 1 model selected
> select /D
600 atoms, 615 bonds, 75 residues, 1 model selected
> select /D
600 atoms, 615 bonds, 75 residues, 1 model selected
> select /F
601 atoms, 616 bonds, 75 residues, 1 model selected
> select /B
599 atoms, 614 bonds, 75 residues, 1 model selected
> cartoon hide sel
> select /D
600 atoms, 615 bonds, 75 residues, 1 model selected
> cartoon hide sel
> ui mousemode right "move picked models"
> ui mousemode right "translate selected models"
> view sel
> view matrix models #1,1,0,0,-1.4792,0,1,0,6.2175,0,0,1,-2.4054
> set bgColor white
> lighting simple
> view
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting simple
> lighting soft
> lighting shadows true intensity 0.5
> lighting full
> lighting shadows false
> lighting simple
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting soft
> lighting full
> lighting shadows false
> lighting shadows true
> lighting shadows false
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> lighting simple
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting simple
> lighting soft
> lighting full
> lighting simple
> lighting flat
> lighting shadows true intensity 0.5
> lighting flat
> lighting shadows true intensity 0.5
> lighting flat
> lighting shadows true intensity 0.5
> lighting flat
> lighting simple
> graphics silhouettes false
> lighting shadows true
> lighting simple
> lighting shadows true
> graphics silhouettes true
> graphics silhouettes false
> select /A,C,E:1-2
57 atoms, 54 bonds, 6 residues, 1 model selected
> select /A,C,E:1-8
174 atoms, 171 bonds, 24 residues, 1 model selected
> select /B,D,F:1
14 atoms, 11 bonds, 3 residues, 1 model selected
> select /B,D,F:1-7
149 atoms, 152 bonds, 21 residues, 1 model selected
> select /B,D,F:7
30 atoms, 30 bonds, 3 residues, 1 model selected
> graphics silhouettes true
> graphics silhouettes false
> show sel atoms
> select /B
599 atoms, 614 bonds, 75 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select /F
601 atoms, 616 bonds, 75 residues, 1 model selected
> select /D
600 atoms, 615 bonds, 75 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select /F:7
10 atoms, 10 bonds, 1 residue, 1 model selected
> select /F:7
10 atoms, 10 bonds, 1 residue, 1 model selected
> select /F:10
11 atoms, 10 bonds, 1 residue, 1 model selected
> select /F:10
11 atoms, 10 bonds, 1 residue, 1 model selected
> style sel stick
Changed 11 atom styles
> show sel atoms
> select /F:15
11 atoms, 10 bonds, 1 residue, 1 model selected
> select /F:15
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel ball
Changed 11 atom styles
> select /F:10
11 atoms, 10 bonds, 1 residue, 1 model selected
> select /F:10
11 atoms, 10 bonds, 1 residue, 1 model selected
> style sel ball
Changed 11 atom styles
> select /F:7
10 atoms, 10 bonds, 1 residue, 1 model selected
> select /F:7
10 atoms, 10 bonds, 1 residue, 1 model selected
> style sel ball
Changed 10 atom styles
> select /F:19
14 atoms, 15 bonds, 1 residue, 1 model selected
> select /F:19
14 atoms, 15 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel ball
Changed 14 atom styles
> select /F:23
11 atoms, 10 bonds, 1 residue, 1 model selected
> select /F:23
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel ball
Changed 11 atom styles
> select /F:19
14 atoms, 15 bonds, 1 residue, 1 model selected
> select /F:19
14 atoms, 15 bonds, 1 residue, 1 model selected
> select /F:23
11 atoms, 10 bonds, 1 residue, 1 model selected
> select /F:23
11 atoms, 10 bonds, 1 residue, 1 model selected
> select /F:24
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /F:24
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel ball
Changed 9 atom styles
> select /F:25
12 atoms, 12 bonds, 1 residue, 1 model selected
> select /F:25
12 atoms, 12 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel ball
Changed 12 atom styles
> select /F:28
10 atoms, 10 bonds, 1 residue, 1 model selected
> select /F:28
10 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel ball
Changed 10 atom styles
> select /F:35
14 atoms, 15 bonds, 1 residue, 1 model selected
> select /F:35
14 atoms, 15 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel ball
Changed 14 atom styles
> select /F:38
11 atoms, 10 bonds, 1 residue, 1 model selected
> select /F:38
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel ball
Changed 11 atom styles
> select /F:51
14 atoms, 15 bonds, 1 residue, 1 model selected
> select /F:51
14 atoms, 15 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel ball
Changed 14 atom styles
> select /A-E:1
24 atoms, 21 bonds, 3 residues, 1 model selected
> select /A-E:1-26
591 atoms, 597 bonds, 78 residues, 1 model selected
> select /A-E:26-27
57 atoms, 57 bonds, 6 residues, 1 model selected
> select /A-E:26-27
57 atoms, 57 bonds, 6 residues, 1 model selected
> select /A-E:26
27 atoms, 24 bonds, 3 residues, 1 model selected
> select /A-E:26
27 atoms, 24 bonds, 3 residues, 1 model selected
> show sel atoms
> style sel ball
Changed 27 atom styles
> select /A
3787 atoms, 3867 bonds, 501 residues, 1 model selected
> hide sel target a
> select /C
3787 atoms, 3867 bonds, 501 residues, 1 model selected
> select /C
3787 atoms, 3867 bonds, 501 residues, 1 model selected
> select /E
3790 atoms, 3870 bonds, 501 residues, 1 model selected
> hide sel target a
> select /A-E:73
33 atoms, 30 bonds, 3 residues, 1 model selected
> select /A-E:73
33 atoms, 30 bonds, 3 residues, 1 model selected
> show sel atoms
> style sel ball
Changed 33 atom styles
> select /A
3787 atoms, 3867 bonds, 501 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select /C
3787 atoms, 3867 bonds, 501 residues, 1 model selected
> select /E
3790 atoms, 3870 bonds, 501 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select /C:93
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /C:93
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel ball
Changed 9 atom styles
> select /C:203
12 atoms, 12 bonds, 1 residue, 1 model selected
> select /C:203
12 atoms, 12 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel ball
Changed 12 atom styles
> select /C:210
10 atoms, 10 bonds, 1 residue, 1 model selected
> select /C:210
10 atoms, 10 bonds, 1 residue, 1 model selected
> style sel ball
Changed 10 atom styles
> show sel atoms
> style sel ball
Changed 10 atom styles
> select /C:212
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /C:211-212
22 atoms, 23 bonds, 2 residues, 1 model selected
> select /C:211
14 atoms, 15 bonds, 1 residue, 1 model selected
> select /C:211
14 atoms, 15 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel ball
Changed 14 atom styles
> select /C:214
10 atoms, 10 bonds, 1 residue, 1 model selected
> select /C:214
10 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel ball
Changed 10 atom styles
> select /C:216-217
23 atoms, 24 bonds, 2 residues, 1 model selected
> select /C:216-217
23 atoms, 24 bonds, 2 residues, 1 model selected
> select /C:216
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /C:216
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel ball
Changed 9 atom styles
> select /C:219
10 atoms, 10 bonds, 1 residue, 1 model selected
> select /C:219
10 atoms, 10 bonds, 1 residue, 1 model selected
> select /C:220
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /C:220
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel ball
Changed 8 atom styles
> select /C:244
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /C:244
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel ball
Changed 9 atom styles
> select /C:249
10 atoms, 10 bonds, 1 residue, 1 model selected
> select /C:249
10 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel ball
Changed 10 atom styles
> select /C:266
10 atoms, 10 bonds, 1 residue, 1 model selected
> select /C:266
10 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel ball
Changed 10 atom styles
> select /C:269
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /C:269
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel ball
Changed 8 atom styles
> select /C:274
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /C:274
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel ball
Changed 9 atom styles
> select /C:420-421
19 atoms, 18 bonds, 2 residues, 1 model selected
> select /C:420-421
19 atoms, 18 bonds, 2 residues, 1 model selected
> select /C:420
11 atoms, 10 bonds, 1 residue, 1 model selected
> select /C:420
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel ball
Changed 11 atom styles
> select /C:449
11 atoms, 11 bonds, 1 residue, 1 model selected
> select /C:449
11 atoms, 11 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel ball
Changed 11 atom styles
> select
> /C:131-133,148-152,197-200,214-219,238-241,261-270,391-395,405-424,426-431,441-455,461-466,469-475,481-496
822 atoms, 830 bonds, 107 residues, 1 model selected
> select /C:462
14 atoms, 15 bonds, 1 residue, 1 model selected
> select /C:462
14 atoms, 15 bonds, 1 residue, 1 model selected
> select /C:462
14 atoms, 15 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel ball
Changed 14 atom styles
> select /C:474
14 atoms, 15 bonds, 1 residue, 1 model selected
> select /C:474
14 atoms, 15 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel ball
Changed 14 atom styles
> view matrix models #1,1,0,0,0.75112,0,1,0,-18.316,0,0,1,-5.5584
> select clear
> show cartoons
> hide cartoons
> show cartoons
> set bgColor white
> lighting simple
> lighting soft
> lighting full
> lighting simple
> lighting soft
> lighting full
> lighting shadows false
> lighting shadows true
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> lighting simple
> save "/Users/sydney/Desktop/ZIKV Publication Fall 2022 updated
> 10.05.22/mature chimera C6O8.cxs"
> save "/Users/sydney/Desktop/ZIKV Publication Fall 2022 updated
> 10.05.22/mature chimera C6O8.jpg" width 1288 height 903 supersample 3
> lighting simple
> lighting soft
> lighting full
> lighting flat
> lighting shadows true intensity 0.5
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> lighting simple
> graphics silhouettes false
> lighting shadows true
> select /C:52
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /C:52-91
312 atoms, 316 bonds, 40 residues, 1 model selected
> select /C:52
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /C:52-128
581 atoms, 590 bonds, 77 residues, 1 model selected
> select
> /C:9-12,20-23,30-33,41-50,58-65,69-73,90-95,98-99,109-110,112-124,128-129,135-143,164-169,175-180,184-189,202-205,210-211,225-226,243-247,253-257,282-283,291-294,312-314,319-320,326-327,329-333,339-340,344-345,364-365,371-375,384-388,397-401
1171 atoms, 1166 bonds, 144 residues, 1 model selected
> select /C:135
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /C:52-135
636 atoms, 646 bonds, 84 residues, 1 model selected
> color sel #f6fff1ff
> color sel #f6fff0ff
> color sel #f5ffeeff
> color sel #f6ffeaff
> color sel #f7ffe6ff
> color sel #f8ffe1ff
> color sel #f8ffdcff
> color sel #f9ffd8ff
> color sel #f9ffd5ff
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> color sel #f9ffcaff
> color sel #faffc5ff
> color sel #faffbfff
> color sel #fbffb9ff
> color sel #fbffb3ff
> color sel #fbffacff
> color sel #fbffa5ff
> color sel #fbff9fff
> color sel #fcff98ff
> color sel #fcff96ff
> color sel #feff8fff
> color sel #ffff8cff
> color sel #fffc84ff
> color sel #fff97dff
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> color sel #fff164ff
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> color sel #ffed59ff
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> color sel #ffe43eff
> color sel #ffe439ff
> color sel #ffe432ff
> color sel #ffe430ff
> color sel #ffe52bff
> color sel #ffe624ff
> color sel #ffe621ff
> color sel #ffe71eff
> color sel #ffe71aff
> color sel #ffe717ff
> color sel #ffe712ff
> color sel #ffe70eff
> color sel #ffe709ff
> color sel #ffe606ff
> color sel #ffe500ff
> color sel #ffe200ff
> color sel #ffe101ff
> color sel #ffde00ff
> color sel #ffda00ff
> color sel #ffd700ff
> color sel #ffd500ff
> color sel #ffd300ff
> color sel #ffd100ff
> color sel #ffcf00ff
> color sel #ffcd00ff
> color sel #ffca00ff
> color sel #ffca02ff
> color sel #ffcc04ff
> color sel #ffcf07ff
> color sel #ffd50dff
> color sel #ffd80fff
> color sel #ffe015ff
> color sel #ffe91cff
> color sel #ffef1fff
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> color sel #fff821ff
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> color sel #fffa22ff
> color sel #fffb22ff
> color sel #fffb21ff
> color sel #fffa21ff
> color sel #fff920ff
> color sel #fff019ff
> color sel #ffea14ff
> color sel #ffe711ff
> color sel #ffde09ff
> color sel #ffd905ff
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> color sel #ffd100ff
> color sel #ffcf00ff
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> color sel #ffc801ff
> color sel #ffc600ff
> color sel #ffc100ff
> color sel #ffbf01ff
> color sel #ffbd00ff
> color sel #ffbf01ff
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> color sel #ffc401ff
> color sel #ffc600ff
> color sel #ffc801ff
> color sel #ffca00ff
> color sel #ffcd00ff
> color sel #ffcf00ff
> color sel #ffd100ff
> color sel #ffd300ff
> color sel #ffd100ff
> color sel #ffcf00ff
> color sel #ffcd00ff
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> color sel #ffc801ff
> color sel #ffca00ff
> color sel #ffcd00ff
> color sel #ffcf00ff
> color sel #ffcd00ff
> color sel #ffcf00ff
> color sel #ffd100ff
> color sel #ffcf00ff
> color sel #ffcd00ff
> color sel #ffca00ff
> color sel #ffcd00ff
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> color sel #ffd100ff
> color sel #ffd300ff
> color sel #ffd500ff
> color sel #ffd700ff
> color sel #ffda00ff
> color sel #ffde00ff
> color sel #ffe105ff
> color sel #ffe60bff
> color sel #ffe80eff
> color sel #ffec13ff
> color sel #fff11bff
> color sel #fff522ff
> color sel #fff829ff
> color sel #fffa2eff
> color sel #fffa30ff
> color sel #fffb32ff
> color sel #fffb34ff
> color sel #fffc36ff
> color sel #fffc38ff
> color sel #fffc3aff
> color sel #fffc3bff
> color sel #fffc3cff
> color sel #fffd3dff
> color sel #fffc3eff
> color sel #fffd3fff
> color sel #fffc3fff
> color sel #fffd3fff
> color sel #fffd3eff
> color sel #fffd39ff
> color sel #fffb33ff
> color sel #fff92bff
> color sel #fff827ff
> color sel #fff61fff
> color sel #fff419ff
> color sel #fff211ff
> color sel #fff10dff
> color sel #ffee05ff
> color sel #ffee00ff
> color sel #ffec01ff
> color sel #ffe900ff
> color sel #ffec01ff
> color sel #ffee00ff
> color sel #fff000ff
> color sel #ffee00ff
> color sel #fff000ff
> color sel #fff200ff
> color sel #fff400ff
> color sel #fff900ff
> color sel #fffb00ff
> color sel #fffd00ff
> color sel #feff00ff
> color sel #fcff00ff
> color sel #faff00ff
> color sel #f7ff00ff
> color sel #faff00ff
> color sel #fcff00ff
> color sel #feff00ff
> color sel #fffd00ff
> color sel #fffb00ff
> color sel #fff400ff
> color sel #fff200ff
> color sel #fff000ff
> color sel #ffee00ff
> color sel #ffe900ff
> color sel #ffe700ff
> color sel #ffe500ff
> color sel #ffe200ff
> color sel #ffe101ff
> color sel #ffde00ff
> color sel #ffda00ff
> color sel #ffd500ff
> color sel #ffd300ff
> color sel #ffd100ff
> color sel #ffcf00ff
> color sel #ffcd00ff
> color sel #ffca00ff
> color sel #ffc801ff
> color sel #ffc600ff
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.5 (2022-11-24)
© 2016-2022 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 Metal - 76.3
OpenGL renderer: Apple M1 Pro
OpenGL vendor: Apple
Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro18,3
Chip: Apple M1 Pro
Total Number of Cores: 10 (8 performance and 2 efficiency)
Memory: 16 GB
System Firmware Version: 7459.101.2
OS Loader Version: 7459.101.2
Software:
System Software Overview:
System Version: macOS 12.3 (21E230)
Kernel Version: Darwin 21.4.0
Time since boot: 103 days 16:19
Graphics/Displays:
Apple M1 Pro:
Chipset Model: Apple M1 Pro
Type: GPU
Bus: Built-In
Total Number of Cores: 16
Vendor: Apple (0x106b)
Metal Family: Supported, Metal GPUFamily Apple 7
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
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
appnope: 0.1.3
asttokens: 2.1.0
Babel: 2.11.0
backcall: 0.2.0
blockdiag: 3.0.0
build: 0.8.0
certifi: 2021.10.8
cftime: 1.6.2
charset-normalizer: 2.1.1
ChimeraX-AddCharge: 1.4
ChimeraX-AddH: 2.2.1
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2.1
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.6
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.3
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.41.5
ChimeraX-AtomicLibrary: 8.0.3
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3
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: 2.7.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.1
ChimeraX-ChangeChains: 1.0.2
ChimeraX-CheckWaters: 1.3
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.2
ChimeraX-CommandLine: 1.2.4
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.5
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.3.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.2
ChimeraX-Dicom: 1.1
ChimeraX-DistMonitor: 1.3
ChimeraX-DockPrep: 1.0
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.2
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 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: 1.1.2
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.1
ChimeraX-MatchMaker: 2.0.9
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.8
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.6
ChimeraX-ModelPanel: 1.3.6
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.1
ChimeraX-MouseModes: 1.1.1
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.9.1
ChimeraX-PDB: 2.6.8
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-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0.1
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
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.7.2
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
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.1.3
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.24.3
ChimeraX-uniprot: 2.2.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.1.4
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.1
ChimeraX-WebServices: 1.1.0
ChimeraX-Zone: 1.0.1
colorama: 0.4.5
cxservices: 1.2
cycler: 0.11.0
Cython: 0.29.32
debugpy: 1.6.4
decorator: 5.1.1
docutils: 0.19
entrypoints: 0.4
executing: 1.2.0
filelock: 3.7.1
fonttools: 4.38.0
funcparserlib: 1.0.1
grako: 3.16.5
h5py: 3.7.0
html2text: 2020.1.16
idna: 3.4
ihm: 0.33
imagecodecs: 2022.7.31
imagesize: 1.4.1
importlib-metadata: 5.1.0
ipykernel: 6.15.3
ipython: 8.4.0
ipython-genutils: 0.2.0
jedi: 0.18.1
Jinja2: 3.1.2
jupyter-client: 7.3.4
jupyter-core: 5.1.0
kiwisolver: 1.4.4
line-profiler: 3.5.1
lxml: 4.9.1
lz4: 4.0.2
MarkupSafe: 2.1.1
matplotlib: 3.5.2
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.5.6
netCDF4: 1.6.0
networkx: 2.8.5
numexpr: 2.8.4
numpy: 1.23.1
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: 9.2.0
pip: 22.2.2
pkginfo: 1.8.3
platformdirs: 2.5.4
prompt-toolkit: 3.0.33
psutil: 5.9.1
ptyprocess: 0.7.0
pure-eval: 0.2.2
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.12.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.9
PyQt6-commercial: 6.3.1
PyQt6-Qt6: 6.3.2
PyQt6-sip: 13.4.0
PyQt6-WebEngine-commercial: 6.3.1
PyQt6-WebEngine-Qt6: 6.3.2
python-dateutil: 2.8.2
pytz: 2022.6
pyzmq: 24.0.1
qtconsole: 5.3.1
QtPy: 2.3.0
RandomWords: 0.4.0
requests: 2.28.1
scipy: 1.9.0
setuptools: 65.1.1
setuptools-scm: 7.0.5
sfftk-rw: 0.7.2
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
Sphinx: 5.1.1
sphinx-autodoc-typehints: 1.19.1
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
stack-data: 0.6.2
tables: 3.7.0
tifffile: 2022.7.31
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.2
traitlets: 5.3.0
typing-extensions: 4.4.0
urllib3: 1.26.13
wcwidth: 0.2.5
webcolors: 1.12
wheel: 0.37.1
wheel-filename: 1.4.1
zipp: 3.11.0
Change History (2)
comment:1 by , 3 years ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Platform |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Crash in color chooser |
comment:2 by , 3 years ago
| Resolution: | → duplicate |
|---|---|
| Status: | accepted → closed |
Note:
See TracTickets
for help on using tickets.
duplicate of #7995