![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
#15381 closed defect (duplicate)
Crash changing Mac display configuration
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Window Toolkit | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-14.5-x86_64-i386-64bit
ChimeraX Version: 1.8rc202405202242 (2024-05-20 22:42:21 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 0x00007ff84577efc0 (most recent call first):
File "/Applications/ChimeraX-1.8-rc2024.05.20.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 285 in event_loop
File "/Applications/ChimeraX-1.8-rc2024.05.20.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1006 in init
File "/Applications/ChimeraX-1.8-rc2024.05.20.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1169 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, chimerax.surface._surface, lxml._elementpath, lxml.etree, openmm._openmm, openmm.app.internal.compiled, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.pdb_lib._load_libs, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, PIL._imagingmath, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw (total: 64)
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{
"uptime" : 170000,
"procRole" : "Foreground",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "MacBookPro16,1",
"coalitionID" : 2203,
"osVersion" : {
"train" : "macOS 14.5",
"build" : "23F79",
"releaseType" : "User"
},
"captureTime" : "2024-06-05 17:29:33.0714 +0200",
"codeSigningMonitor" : 0,
"incident" : "793CE7A5-9E1E-4480-8E75-BA56D14D618B",
"pid" : 63675,
"cpuType" : "X86-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2024-06-05 12:28:26.0142 +0200",
"procStartAbsTime" : 156890247566369,
"procExitAbsTime" : 174957186112661,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.8-rc2024.05.20.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.8.0","CFBundleVersion":"1.8.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"4C566CA2-7029-58F4-BB6C-330D5EB4C521","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "1E417656-A8B0-359C-066A-118A8C09BB7C",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"wakeTime" : 26340,
"bridgeVersion" : {"build":"21P5077","train":"8.5"},
"sleepWakeUUID" : "3BE4AABB-0D42-4A4C-9CFB-768BC79385A6",
"sip" : "enabled",
"vmRegionInfo" : "0 is not in any region. Bytes before following region: 4301340672\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 100614000-100618000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.8-rc2024.05.20.app\/Contents\/MacOS\/ChimeraX",
"exception" : {"codes":"0x0000000000000001, 0x0000000000000000","rawCodes":[1,0],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000000000000000"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":63675},
"vmregioninfo" : "0 is not in any region. Bytes before following region: 4301340672\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 100614000-100618000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.8-rc2024.05.20.app\/Contents\/MacOS\/ChimeraX",
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"faultingThread" : 0,
"threads" : 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===== Log before crash start =====
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.8rc202405202242 (2024-05-20)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> /Users/wxg622/Desktop/T4_final/T4/Contracted/Tip/PDB/fulltip_0_isolde-0.pdb
> format pdb
Chain information for fulltip_0_isolde-0.pdb #1
---
Chain | Description
C D E F G H | No description available
I J K L M S | No description available
IA IB IC ID IE IK | No description available
IM IN IO IP IQ IR | No description available
N O P Q R Z | No description available
> close
> open /Users/wxg622/Desktop/T4_final/Figures/precontracted_composite.cxs
> format session
Opened B_NU3_P48_J2508_007_volume_map_sharp.mrc as #1, grid size 750,750,750,
pixel 1.08, shown at level 0.425, step 1, values float32
Opened NC_P1_NU_P48_J2372_108Apx.mrc as #2, grid size 750,750,750, pixel 1.08,
shown at level 0.42, step 1, values float32
Opened cryosparc_P48_cryosparc_P48_J1925_004_volume_map.mrc as #3, grid size
768,768,768, pixel 1.08, shown at level 0.265, step 1, values float32
Opened cryosparc_P48_cryosparc_P48_J1933_003_volume_map.mrc as #5, grid size
540,540,540, pixel 1.08, shown at level 0.321, step 1, values float32
opened ChimeraX session
> lighting simple
> hide #!1 models
> show #!1 models
> open
> /Users/wxg622/Desktop/T4_final/T4/Extended/Baseplate/maps/J2604_005_volume_map.mrc
Opened J2604_005_volume_map.mrc as #4, grid size 750,750,750, pixel 1.08,
shown at step 1, values float32
> hide #!1 models
> show #!1 models
> close #4
> close #1
> open
> /Users/wxg622/Desktop/T4_final/T4/Extended/Baseplate/maps/J2604_005_volume_map.mrc
Opened J2604_005_volume_map.mrc as #1, grid size 750,750,750, pixel 1.08,
shown at step 1, values float32
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> volume #1 region 0,0,0,749,749,749 step 4
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> volume #1 step 1
> select add #1
3 models selected
> ui mousemode right "translate selected models"
> view matrix models #1,1,0,0,-41.966,0,1,0,27.559,0,0,1,615.97
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> view matrix models
> #1,0.86109,0.50841,0.0068025,-193.44,-0.50706,0.85964,-0.062546,307.37,-0.037646,0.050408,0.99802,611.36
> view matrix models
> #1,0.86109,0.50841,0.0068025,-193.38,-0.50706,0.85964,-0.062546,297.67,-0.037646,0.050408,0.99802,585.37
> view matrix models
> #1,0.86109,0.50841,0.0068025,-148.58,-0.50706,0.85964,-0.062546,270.08,-0.037646,0.050408,0.99802,584.91
Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps,
got 0 atomic models, 4 maps.
> view matrix models
> #1,0.86109,0.50841,0.0068025,-137.19,-0.50706,0.85964,-0.062546,274.98,-0.037646,0.050408,0.99802,568.86
Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps,
got 0 atomic models, 4 maps.
> close
> open
> /Users/wxg622/Desktop/T4_final/T4/Extended/Neck/PDB/LR_neck_portal_wacs_tail_renamed.cif
> format mmcif
Summary of feedback from opening
/Users/wxg622/Desktop/T4_final/T4/Extended/Neck/PDB/LR_neck_portal_wacs_tail_renamed.cif
---
warnings | Missing entity information. Treating each chain as a separate entity.
Atom H1 is not in the residue template for ASN /BK:21
Atom H1 is not in the residue template for ASN /BL:21
Atom H is not in the residue template for THR /AA:2
Atom H is not in the residue template for THR /AB:2
Atom H is not in the residue template for VAL /BW:5
Atom H is not in the residue template for THR /AC:2
Atom H is not in the residue template for THR /AD:2
2 messages similar to the above omitted
Too many hydrogens missing from residue template(s) to warn about
Missing or incomplete sequence information. Inferred polymer connectivity.
Chain information for LR_neck_portal_wacs_tail_renamed.cif #1
---
Chain | Description
AA AB AC AD AE AF AG AH AI AJ AK AL AM AN AO AP AQ AR | No description available
AS AT AU AV AW AX AY AZ BA BB BC BD BE BF BG BH BI BJ | No description available
BK BL BM BN BO BP BQ BR BS BT BU BV | No description available
BW BX BY BZ CA CB CC CD CE CF CG CH | No description available
CI CJ CK CL CM CN CO CP CQ CR CS CT | No description available
CU CV CW CX CY CZ | No description available
DA DB DC DD DE DF | No description available
DG DH DI DJ DK DL | No description available
DM DN DO DP DQ DR | No description available
156 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> lighting simple
> hide atoms
> show cartoons
> color /DG,DH,DI,DJ,DK,DL #D8BFD8
> color /CU,CV,CW,CX,CY,CZ #DDA0DD
> color /DA,DB,DC,DD,DE,DF #BA55D3
> color /CI,CJ,CK,CL,CM,CN,CO,CP,CQ,CR,CS,CT #9932CC
> color /BW,BX,BY,BZ,CA,CB,CC,CD,CE,CF,CG,CH #800080
> color
> /AA,AB,AC,AD,AE,AF,AG,AH,AI,AJ,AK,AL,AM,AN,AO,AP,AQ,AR,AS,AT,AU,AV,AW,AX,AY,AZ,BA,BB,BC,BD,BE,BF,BG,BH,BI,BJ
> #800000
> color /BK,BL,BM,BN,BO,BP,BQ,BR,BS,BT,BU,BV #87CEFA
> color /DM,DN,DO,DP,DQ,DR #1E90FF
> select /BN:627
20 atoms, 20 bonds, 1 residue, 1 model selected
> select add /BU:425
34 atoms, 33 bonds, 2 residues, 1 model selected
Alignment identifier is 1
> select /BN:625
10 atoms, 9 bonds, 1 residue, 1 model selected
> select /BN,BU:656
14 atoms, 12 bonds, 2 residues, 1 model selected
> select /BN,BU:598-656
1800 atoms, 1818 bonds, 118 residues, 1 model selected
> color sel bychain
> select /BN:640
19 atoms, 18 bonds, 1 residue, 1 model selected
> select clear
> select /BN:641
14 atoms, 13 bonds, 1 residue, 1 model selected
> select /BN,BU:492-493
34 atoms, 32 bonds, 4 residues, 1 model selected
> select /BN,BU:492-493
34 atoms, 32 bonds, 4 residues, 1 model selected
> select clear
> select /BN:640
19 atoms, 18 bonds, 1 residue, 1 model selected
> select /BN,BU:656
14 atoms, 12 bonds, 2 residues, 1 model selected
> select /BO:10
19 atoms, 18 bonds, 1 residue, 1 model selected
> select /BN:625
10 atoms, 9 bonds, 1 residue, 1 model selected
> select /BN:607
16 atoms, 15 bonds, 1 residue, 1 model selected
> select /BU:628
21 atoms, 21 bonds, 1 residue, 1 model selected
> select /BU:640
19 atoms, 18 bonds, 1 residue, 1 model selected
> select /CW:234
12 atoms, 11 bonds, 1 residue, 1 model selected
> select up
116 atoms, 116 bonds, 8 residues, 1 model selected
> select up
4381 atoms, 4441 bonds, 272 residues, 1 model selected
> select up
383010 atoms, 386766 bonds, 24480 residues, 1 model selected
> select down
4381 atoms, 4441 bonds, 272 residues, 1 model selected
> save /Users/wxg622/Desktop/T4_final/T4/monomers/gp15.pdb selectedOnly true
> relModel #1
> open 8HDR
Summary of feedback from opening 8HDR fetched from pdb
---
note | Fetching compressed mmCIF 8hdr from http://files.rcsb.org/download/8hdr.cif
8hdr title:
Cyanophage Pam3 neck [more info...]
Chain information for 8hdr #2
---
Chain | Description
1 2 Y Z m n o p q r s t u v w x y z | pam3 tube protein
A B C D E F | Pam3 connector protein
G H I J K L | Pam3 terminator protein
M N O P Q R S T U V W X | Pam3 sheath protein
a b c d e f g h i j k l | Pam3 adaptor protein
> ui tool show Matchmaker
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> matchmaker #2 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker LR_neck_portal_wacs_tail_renamed.cif, chain BK (#1) with 8hdr,
chain T (#2), sequence alignment score = 145
RMSD between 35 pruned atom pairs is 0.991 angstroms; (across all 310 pairs:
17.689)
> matchmaker #2 to #1/BN pairing bs ssFraction 0.754
Parameters
---
Chain pairing | bs
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.754
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker LR_neck_portal_wacs_tail_renamed.cif, chain BN (#1) with 8hdr,
chain T (#2), sequence alignment score = 730.416
RMSD between 21 pruned atom pairs is 1.298 angstroms; (across all 331 pairs:
27.320)
> select clear
> ui tool show Matchmaker
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> matchmaker #2/G to #1/BN pairing ss ssFraction 0.754
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.754
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker LR_neck_portal_wacs_tail_renamed.cif, chain BN (#1) with 8hdr,
chain G (#2), sequence alignment score = 244.71
RMSD between 4 pruned atom pairs is 1.190 angstroms; (across all 127 pairs:
26.998)
> ui tool show Matchmaker
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> matchmaker #2/G to #1/CW pairing ss ssFraction 0.754
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.754
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker LR_neck_portal_wacs_tail_renamed.cif, chain CW (#1) with 8hdr,
chain G (#2), sequence alignment score = 372.372
RMSD between 21 pruned atom pairs is 0.703 angstroms; (across all 137 pairs:
15.066)
> select clear
> hide atoms
> show cartoons
> select #2/G:44
9 atoms, 8 bonds, 1 residue, 1 model selected
> select add #1/CW:255
29 atoms, 28 bonds, 2 residues, 2 models selected
> select up
168 atoms, 169 bonds, 13 residues, 2 models selected
> select up
5628 atoms, 5714 bonds, 428 residues, 2 models selected
> select up
461718 atoms, 467076 bonds, 34776 residues, 2 models selected
> select down
5628 atoms, 5714 bonds, 428 residues, 2 models selected
> select ~sel
456090 atoms, 461362 bonds, 60 pseudobonds, 34348 residues, 3 models selected
> hide sel cartoons
> select clear
> select #1/CW:150
21 atoms, 21 bonds, 1 residue, 1 model selected
Alignment identifier is 1/CW
> select #1/CW:231
15 atoms, 14 bonds, 1 residue, 1 model selected
> select clear
> select add #1
383010 atoms, 386766 bonds, 60 pseudobonds, 24480 residues, 2 models selected
> select clear
> show cartoons
> hide #2 models
> select #1/DE:150
14 atoms, 13 bonds, 1 residue, 1 model selected
Alignment identifier is 1/DE
> select #1/DE:178
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #1/DE:174
20 atoms, 20 bonds, 1 residue, 1 model selected
> select #1/DE:174-196
366 atoms, 370 bonds, 23 residues, 1 model selected
> select #1/DE:76
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #1/DE:62
14 atoms, 14 bonds, 1 residue, 1 model selected
> select #1/DE:62-83
362 atoms, 366 bonds, 22 residues, 1 model selected
> select clear
Drag select of 326 residues
Drag select of 511 residues
Alignment identifier is 1
Alignment identifier is 2
> select clear
> select #1/DA-DF:62
84 atoms, 84 bonds, 6 residues, 1 model selected
> select #1/DA-DF:62-83
2172 atoms, 2196 bonds, 132 residues, 1 model selected
> select clear
> color #1 #ebebebff
> select #1/DA-DF:62-63
228 atoms, 228 bonds, 12 residues, 1 model selected
> select #1/DA-DF:62-82
2112 atoms, 2136 bonds, 126 residues, 1 model selected
> color sel purple
> select #1/DD:178
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #1/DA-DF:174-175
234 atoms, 234 bonds, 12 residues, 1 model selected
> select #1/DA-DF:175-196
2076 atoms, 2094 bonds, 132 residues, 1 model selected
> color sel purple
> select #1/DD:222
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #1/DA-DF:217-246
2856 atoms, 2880 bonds, 180 residues, 1 model selected
> select #1/DA-DF:208-246
3654 atoms, 3684 bonds, 234 residues, 1 model selected
> ]
Unknown command: ]
> color sel purple
> select clear
> select #1/DD:106
20 atoms, 20 bonds, 1 residue, 1 model selected
> select #1/DA-DF:100
132 atoms, 126 bonds, 6 residues, 1 model selected
> select #1/DA-DF:100-111
1152 atoms, 1164 bonds, 72 residues, 1 model selected
> color sel purple
> select #1/CY:184
24 atoms, 23 bonds, 1 residue, 1 model selected
> select #1/CU-CZ:176
114 atoms, 108 bonds, 6 residues, 1 model selected
> select #1/CU-CZ:176-184
852 atoms, 846 bonds, 54 residues, 1 model selected
> color sel green
> select #1/CY:72
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #1/CU-CZ:51
102 atoms, 96 bonds, 6 residues, 1 model selected
> select #1/CU-CZ:51-73
2256 atoms, 2268 bonds, 138 residues, 1 model selected
> color sel green
> select #1/CY:50
17 atoms, 16 bonds, 1 residue, 1 model selected
> select #1/CU-CZ:50
102 atoms, 96 bonds, 6 residues, 1 model selected
> select #1/CU-CZ:44-50
684 atoms, 690 bonds, 42 residues, 1 model selected
> color sel green
> select clear
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
Unsupported scale factor (0.000000) detected on Display0
===== Log before crash end =====
Log:
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.8rc202405202242 (2024-05-20)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 ATI-5.5.17
OpenGL renderer: AMD Radeon Pro 5500M OpenGL Engine
OpenGL vendor: ATI Technologies Inc.
Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro16,1
Processor Name: 8-Core Intel Core i9
Processor Speed: 2.3 GHz
Number of Processors: 1
Total Number of Cores: 8
L2 Cache (per Core): 256 KB
L3 Cache: 16 MB
Hyper-Threading Technology: Enabled
Memory: 64 GB
System Firmware Version: 2022.100.22.0.0 (iBridge: 21.16.5077.0.0,0)
OS Loader Version: 580~2215
Software:
System Software Overview:
System Version: macOS 14.5 (23F79)
Kernel Version: Darwin 23.5.0
Time since boot: 5 days, 6 hours, 53 minutes
Graphics/Displays:
Intel UHD Graphics 630:
Chipset Model: Intel UHD Graphics 630
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x3e9b
Revision ID: 0x0002
Automatic Graphics Switching: Supported
gMux Version: 5.0.0
Metal Support: Metal 3
AMD Radeon Pro 5500M:
Chipset Model: AMD Radeon Pro 5500M
Type: GPU
Bus: PCIe
PCIe Lane Width: x16
VRAM (Total): 8 GB
Vendor: AMD (0x1002)
Device ID: 0x7340
Revision ID: 0x0040
ROM Revision: 113-D3220E-190
VBIOS Version: 113-D32206U1-020
Option ROM Version: 113-D32206U1-020
EFI Driver Version: 01.A1.190
Automatic Graphics Switching: Supported
gMux Version: 5.0.0
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 3072 x 1920 Retina
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: No
Connection Type: Internal
PHL 240B7QPJ:
Resolution: 1920 x 1200 (WUXGA - Widescreen Ultra eXtended Graphics Array)
UI Looks like: 1920 x 1200 @ 60.00Hz
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Display Serial Number: AU11810007035
Mirror: Off
Online: Yes
Rotation: Supported
Connection Type: DVI or HDMI
Adapter Firmware Version: 7.55
Installed Packages:
alabaster: 0.7.16
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 2.4.1
Babel: 2.15.0
beautifulsoup4: 4.12.3
biopython: 1.83
blockdiag: 3.0.0
blosc2: 2.0.0
build: 1.2.1
certifi: 2023.11.17
cftime: 1.6.3
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.17
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.7
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.57
ChimeraX-AtomicLibrary: 14.0.5
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.4.6
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.12.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.4
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-Clipper: 0.23.0
ChimeraX-clix: 0.1.5
ChimeraX-ColorActions: 1.0.4
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.6
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.8rc202405202242
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.3
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.3
ChimeraX-DiffPlot: 1.0
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.3
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: 1.2.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ISOLDE: 1.8.dev0
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-Label: 1.1.10
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.2
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: 2.1.3
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.16
ChimeraX-ModelPanel: 1.5
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.4
ChimeraX-PDB: 2.7.5
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.1
ChimeraX-PubChem: 2.2
ChimeraX-QScore: 1.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.4.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.2
ChimeraX-RIBFIND: 0.2
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.0.4
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.11.2
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.16.4
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.39
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.1
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.4
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.2.1
cxservices: 1.2.2
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.1
decorator: 5.1.1
docutils: 0.20.1
executing: 2.0.1
filelock: 3.13.4
fonttools: 4.51.0
funcparserlib: 2.0.0a0
glfw: 2.7.0
grako: 3.16.5
h5py: 3.11.0
html2text: 2024.2.26
idna: 3.7
ihm: 1.0
imagecodecs: 2024.1.1
imagesize: 1.4.1
ipykernel: 6.29.2
ipython: 8.21.0
ipywidgets: 8.1.2
jedi: 0.19.1
jinja2: 3.1.4
jupyter-client: 8.6.0
jupyter-core: 5.7.2
jupyterlab-widgets: 3.0.10
kiwisolver: 1.4.5
line-profiler: 4.1.2
lxml: 5.2.1
lz4: 4.3.3
MarkupSafe: 2.1.5
matplotlib: 3.8.4
matplotlib-inline: 0.1.7
msgpack: 1.0.8
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.0
numpy: 1.26.4
openvr: 1.26.701
packaging: 23.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pillow: 10.3.0
pip: 24.0
pkginfo: 1.10.0
platformdirs: 4.2.2
prompt-toolkit: 3.0.43
psutil: 5.9.8
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pygments: 2.17.2
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.1.2
pyproject-hooks: 1.1.0
PyQt6-commercial: 6.6.1
PyQt6-Qt6: 6.6.3
PyQt6-sip: 13.6.0
PyQt6-WebEngine-commercial: 6.6.0
PyQt6-WebEngine-Qt6: 6.6.3
python-dateutil: 2.9.0.post0
pytz: 2024.1
pyzmq: 26.0.3
qtconsole: 5.5.1
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
ribfind: 2.0.2
scipy: 1.13.0
setuptools: 69.5.1
setuptools-scm: 8.0.4
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 7.2.6
sphinx-autodoc-typehints: 2.0.1
sphinxcontrib-applehelp: 1.0.8
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.6
sphinxcontrib-htmlhelp: 2.0.5
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.7
sphinxcontrib-serializinghtml: 1.1.10
stack-data: 0.6.3
superqt: 0.6.3
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2024.1.30
tinyarray: 1.2.4
tornado: 6.4
traitlets: 5.14.2
typing-extensions: 4.11.0
tzdata: 2024.1
urllib3: 2.2.1
wcwidth: 0.2.13
webcolors: 1.13
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.10
Change History (3)
comment:1 by , 17 months ago
| Component: | Unassigned → Window Toolkit |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash changing Mac display configuration |
comment:2 by , 17 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
This crash happens on old Intel Macs with AMD graphics when unplugging or plugging in an external display while ChimeraX is running. It is a Qt 6.6 window toolkit bug. I put a work-around into ChimeraX 1.8 release candidates on May 22 two days newer than the release you are using that may help. But I am still getting reports after that work-around so I am currently working on improving the fix. Ultimately the Qt window project has to fix it.
More details in ticket #15277.
I think if you iconify ChimeraX when plugging or unplugging a display it does not crash if that helps you.
comment:3 by , 17 months ago
I put an improved fix into the June 5 ChimeraX builds now on the download page for crashes related to connecting or disconnecting an external display.
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Reported by Artiz