![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 2 years ago
Closed 2 years ago
#9079 closed defect (nonchimerax)
Graphics crash, macOS 13.0.1, Intel Iris Plus Graphics 645
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Graphics | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.5 (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
Current thread 0x00007ff857b8e4c0 (most recent call first):
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/opengl.py", line 235 in swap_buffers
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/opengl.py", line 497 in swap_buffers
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/view.py", line 191 in draw
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/updateloop.py", line 73 in draw_new_frame
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/updateloop.py", line 139 in _redraw_timer_callback
File "/Applications/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 "/Applications/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 "/Applications/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 "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 87 in _run_code
File "/Applications/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" : 14000,
"procRole" : "Background",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "MacBookPro15,4",
"coalitionID" : 1788,
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"build" : "22A400",
"releaseType" : "User"
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"captureTime" : "2023-05-27 16:53:25.0016 -0700",
"incident" : "E9F6DE93-5D47-435A-9134-649217ADEA02",
"pid" : 6699,
"cpuType" : "X86-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2023-05-27 10:26:49.1849 -0700",
"procStartAbsTime" : 8017222156044,
"procExitAbsTime" : 14957709581083,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.5.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.5.0","CFBundleVersion":"1.5.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"3797185F-F589-59D0-BC7C-83B7EE255631","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "442CB65D-A072-19B0-686F-A2ACD0B5B815",
"wakeTime" : 4,
"bridgeVersion" : {"build":"20P420","train":"7.0"},
"sleepWakeUUID" : "E6833F82-781E-4B25-B897-2A484AFC01C7",
"sip" : "enabled",
"exception" : {"codes":"0x0000000000000000, 0x0000000000000000","rawCodes":[0,0],"type":"EXC_CRASH","signal":"SIGABRT"},
"asiSignatures" : ["Graphics hardware encountered an error and was reset: 0x00000002\n"],
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"faultingThread" : 0,
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"path" : "\/Applications\/ChimeraX-1.5.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/PyQt6\/QtGui.abi3.so",
"name" : "QtGui.abi3.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4445007872,
"CFBundleShortVersionString" : "3.9.11, (c) 2001-2021 Python Software Foundation.",
"CFBundleIdentifier" : "org.python.python",
"size" : 2527232,
"uuid" : "ef9cc1f4-5991-3213-9a9e-e68c578b6c1b",
"path" : "\/Applications\/ChimeraX-1.5.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/Python",
"name" : "Python",
"CFBundleVersion" : "3.9.11"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4451790848,
"size" : 1589248,
"uuid" : "2be8100b-aa99-3117-95ff-0200ddc4032f",
"path" : "\/Applications\/ChimeraX-1.5.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/PyQt6\/QtCore.abi3.so",
"name" : "QtCore.abi3.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4545675264,
"size" : 5259264,
"uuid" : "35b47b1c-6952-3d39-a5e7-711f3ca228f2",
"path" : "\/Applications\/ChimeraX-1.5.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/PyQt6\/Qt6\/lib\/QtCore.framework\/Versions\/A\/QtCore",
"name" : "QtCore"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4730617856,
"size" : 4964352,
"uuid" : "f36760e5-d1e7-3a93-ae8c-1c3e55e3fc35",
"path" : "\/Applications\/ChimeraX-1.5.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/PyQt6\/Qt6\/lib\/QtWidgets.framework\/Versions\/A\/QtWidgets",
"name" : "QtWidgets"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4534288384,
"size" : 2801664,
"uuid" : "babd94e3-ec19-3110-ab5b-11c39432d8c5",
"path" : "\/Applications\/ChimeraX-1.5.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/PyQt6\/QtWidgets.abi3.so",
"name" : "QtWidgets.abi3.so"
},
{
"source" : "P",
"arch" : "x86_64h",
"base" : 140703467040768,
"CFBundleShortVersionString" : "6.9",
"CFBundleIdentifier" : "com.apple.CoreFoundation",
"size" : 4820992,
"uuid" : "dbc459f3-81bb-398a-8f74-3f7392392bb7",
"path" : "\/System\/Library\/Frameworks\/CoreFoundation.framework\/Versions\/A\/CoreFoundation",
"name" : "CoreFoundation",
"CFBundleVersion" : "1953.1"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 140703627665408,
"CFBundleShortVersionString" : "2.1.1",
"CFBundleIdentifier" : "com.apple.HIToolbox",
"size" : 3112947,
"uuid" : "ff73b93b-3c5b-3f73-948f-0a35a80f7fad",
"path" : "\/System\/Library\/Frameworks\/Carbon.framework\/Versions\/A\/Frameworks\/HIToolbox.framework\/Versions\/A\/HIToolbox",
"name" : "HIToolbox"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4436905984,
"CFBundleShortVersionString" : "1.5.0",
"CFBundleIdentifier" : "edu.ucsf.cgl.ChimeraX",
"size" : 4096,
"uuid" : "5df621ee-554e-36a8-b448-93b2334e5480",
"path" : "\/Applications\/ChimeraX-1.5.app\/Contents\/MacOS\/ChimeraX",
"name" : "ChimeraX",
"CFBundleVersion" : "1.5.0.0"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 140703463292928,
"size" : 607568,
"uuid" : "28fd2071-57f3-3873-87bf-e4f674a82de6",
"path" : "\/usr\/lib\/dyld",
"name" : "dyld"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4553867264,
"size" : 64028672,
"uuid" : "24c9d5c5-4854-3af4-9550-cb0204044dfa",
"path" : "\/Applications\/ChimeraX-1.5.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/numpy\/.dylibs\/libopenblas64_.0.dylib",
"name" : "libopenblas64_.0.dylib"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5066297344,
"size" : 165052416,
"uuid" : "4aa1de3e-464c-340c-ab61-bcd39bfc7658",
"path" : "\/Applications\/ChimeraX-1.5.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/PyQt6\/Qt6\/lib\/QtWebEngineCore.framework\/Versions\/A\/QtWebEngineCore",
"name" : "QtWebEngineCore"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5441134592,
"size" : 63373312,
"uuid" : "ccf8b470-9ccf-3558-9748-04374e88d1ea",
"path" : "\/Applications\/ChimeraX-1.5.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/scipy\/.dylibs\/libopenblas.0.dylib",
"name" : "libopenblas.0.dylib"
}
],
"vmSummary" : "ReadOnly portion of Libraries: Total=1.2G resident=0K(0%) swapped_out_or_unallocated=1.2G(100%)\nWritable regions: Total=1.2G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=1.2G(100%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 1792K 14 \nActivity Tracing 256K 1 \nCG backing stores 5760K 16 \nCG image 412K 58 \nColorSync 248K 29 \nCoreAnimation 224K 33 \nCoreGraphics 20K 4 \nCoreServices 624K 2 \nCoreUI image data 4972K 51 \nFoundation 40K 2 \nKernel Alloc Once 8K 1 \nMALLOC 647.4M 716 \nMALLOC guard page 32K 8 \nMALLOC_LARGE (reserved) 384K 1 reserved VM address space (unallocated)\nMALLOC_NANO (reserved) 128.0M 1 reserved VM address space (unallocated)\nMach message 16K 3 \nOpenGL GLSL 384K 4 \nSTACK GUARD 112K 28 \nStack 149.7M 29 \nStack Guard 56.0M 1 \nVM_ALLOCATE 141.5M 169 \nVM_ALLOCATE (reserved) 128.0M 3 reserved VM address space (unallocated)\n__CTF 756 1 \n__DATA 48.5M 803 \n__DATA_CONST 41.0M 388 \n__DATA_DIRTY 1823K 226 \n__FONT_DATA 2352 1 \n__GLSLBUILTINS 5174K 1 \n__LINKEDIT 222.6M 198 \n__OBJC_RO 65.1M 1 \n__OBJC_RW 1982K 2 \n__TEXT 977.0M 806 \ndyld private memory 512K 3 \nmapped file 213.7M 59 \nshared memory 3036K 36 \n=========== ======= ======= \nTOTAL 2.8G 3699 \nTOTAL, minus reserved VM space 2.5G 3699 \n",
"legacyInfo" : {
"threadTriggered" : {
"name" : "CrBrowserMain",
"queue" : "com.apple.main-thread"
}
},
"trialInfo" : {
"rollouts" : [
{
"rolloutId" : "5ffde50ce2aacd000d47a95f",
"factorPackIds" : {
},
"deploymentId" : 240000271
},
{
"rolloutId" : "63582c5f8a53461413999550",
"factorPackIds" : {
"PROACTIVE_MAIL_INTELLIGENCE_SALIENCY" : "636525247ea6e25a76dc2008"
},
"deploymentId" : 240000002
}
],
"experiments" : [
{
"treatmentId" : "6dd670af-0633-45e4-ae5f-122ae4df02be",
"experimentId" : "64406ba83deb637ac8a04419",
"deploymentId" : 900000005
},
{
"treatmentId" : "c28e4ee6-1b08-4f90-8e05-2809e78310a3",
"experimentId" : "6317d2003d24842ff850182a",
"deploymentId" : 400000013
}
]
},
"reportNotes" : [
"dyld_process_snapshot_create_for_process failed with 5"
]
}
===== 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 5vms
Summary of feedback from opening 5vms fetched from pdb
---
note | Fetching compressed mmCIF 5vms from
http://files.rcsb.org/download/5vms.cif
5vms title:
CryoEM structure of Xenopus KCNQ1 channel [more info...]
Chain information for 5vms #1
---
Chain | Description | UniProt
A | Potassium voltage-gated channel subfamily KQT member 1 | KCNQ1_XENLA
B | Calmodulin | CALM_HUMAN
Non-standard residues in 5vms #1
---
CA — calcium ion
5vms mmCIF Assemblies
---
1| complete point assembly
2| point asymmetric unit
3| point asymmetric unit, std point frame
> sym #1 assembly 1 copies true
> close #1
> view orient
> zoom 1.1
> turn x 180
> surface /a
> hide /a cartoons
> hide /b
> show Ca
> hide pbonds
> cartoon style modeHelix tube
> lighting gentle
> set bgColor white
> set silhouettes true
> set sihuettedepth 0.02
Expected a keyword
> set silhouetteDepthJump 0.02
> set silhouetteDepthJump 0.03
> size ions atomRadius 1.6
Changed 12 atom radii
> color modify ions hue +45
> rainbow palette pubu-5
> help palette
> raibow polymers palette PuBu-5
Unknown command: raibow polymers palette PuBu-5
> rainbow polymers palette pubu-5
> save "/Users/mildredkissai/Desktop/tutorial from youtube.cxs"
> save /Users/mildredkissai/Desktop/image1.png supersample 3
> save /Users/mildredkissai/Desktop/test_image.png width 1344 height 903
> supersample 3
> close
> open 4eiy
Summary of feedback from opening 4eiy fetched from pdb
---
notes | Fetching compressed mmCIF 4eiy from
http://files.rcsb.org/download/4eiy.cif
Fetching CCD ZMA from http://ligand-expo.rcsb.org/reports/Z/ZMA/ZMA.cif
Fetching CCD NA from http://ligand-expo.rcsb.org/reports/N/NA/NA.cif
Fetching CCD CLR from http://ligand-expo.rcsb.org/reports/C/CLR/CLR.cif
Fetching CCD OLA from http://ligand-expo.rcsb.org/reports/O/OLA/OLA.cif
Fetching CCD OLC from http://ligand-expo.rcsb.org/reports/O/OLC/OLC.cif
Fetching CCD OLB from http://ligand-expo.rcsb.org/reports/O/OLB/OLB.cif
Fetching CCD PEG from http://ligand-expo.rcsb.org/reports/P/PEG/PEG.cif
4eiy title:
Crystal structure of the chimeric protein of A2aAR-BRIL in complex with
ZM241385 at 1.8A resolution [more info...]
Chain information for 4eiy #1
---
Chain | Description | UniProt
A | Adenosine receptor A2a/Soluble cytochrome b562 chimera | AA2AR_HUMAN
Non-standard residues in 4eiy #1
---
CLR — cholesterol
NA — sodium ion
OLA — oleic acid
OLB — (2S)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate
OLC — (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate (1-Oleoyl-R-glycerol)
PEG — di(hydroxyethyl)ether
ZMA —
4-{2-[(7-amino-2-furan-2-yl[1,2,4]triazolo[1,5-a][1,3,5]triazin-5-yl)amino]ethyl}phenol
> set bgColor black
> set silhouettes false
> select /A:-1-307
2308 atoms, 2370 bonds, 299 residues, 1 model selected
> select clear
> select :ZMA
25 atoms, 28 bonds, 1 residue, 1 model selected
> view sel
> view
> view sel
> view orient
> view sel
> view
> view sel
> view
> color grey
> view sel
> color sel lime
> color sel byhetero
> select sel @ show sel atoms
> color sel byhetero
> label sel text "{0.name} {0.number}{0.insertion_code}"
> select solvent
177 atoms, 177 residues, 1 model selected
> ~label sel residues
> select clear
> ui tool show "Side View"
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
25 atoms, 28 bonds, 1 residue, 1 model selected
> hbonds sel reveal true
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /A ARG 293 NE
10 hydrogen bonds found
> ~hbonds
> ui tool show H-Bonds
> hbonds sel reveal true log true
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /A ARG 293 NE
Finding intermodel H-bonds
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
1 4eiy
10 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
/A ASN 253 ND2 /A ZMA 2401 N17 no hydrogen 3.168 N/A
/A ASN 253 ND2 /A ZMA 2401 O25 no hydrogen 3.011 N/A
/A ZMA 2401 N10 /A HOH 2524 O no hydrogen 2.820 N/A
/A ZMA 2401 N15 /A GLU 169 OE2 no hydrogen 2.790 N/A
/A ZMA 2401 N15 /A ASN 253 OD1 no hydrogen 2.793 N/A
/A ZMA 2401 O4 /A HOH 2668 O no hydrogen 2.900 N/A
/A HOH 2521 O /A ZMA 2401 N19 no hydrogen 2.810 N/A
/A HOH 2583 O /A ZMA 2401 O4 no hydrogen 3.533 N/A
/A HOH 2585 O /A ZMA 2401 N12 no hydrogen 2.730 N/A
/A HOH 2668 O /A ZMA 2401 O4 no hydrogen 2.900 N/A
10 hydrogen bonds found
> ~hbonds
> ui tool show Contacts
> contacts ignoreHiddenModels true reveal true
2930 contacts
> contacts hide
Expected a keyword
> contacts deletee
Expected a keyword
> contacts delete
> ui tool show Contacts
> contacts sel ignoreHiddenModels true reveal true
66 contacts
> contacts delete
> ui tool show Contacts
> contacts sel ignoreHiddenModels true reveal true log true
Allowed overlap: -0.4
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Detect intra-residue contacts: False
Detect intra-molecule contacts: True
66 contacts
atom1 atom2 overlap distance
/A ZMA 2401 C24 /A MET 177 CE 0.288 3.352
/A ZMA 2401 C24 /A HIS 250 CE1 0.180 3.340
/A ZMA 2401 N10 /A PHE 168 CB 0.105 3.415
/A ZMA 2401 O25 /A MET 177 CE 0.095 3.205
/A ZMA 2401 C9 /A HOH 2524 O 0.078 3.262
/A ZMA 2401 C23 /A LEU 85 CD2 0.052 3.588
/A ZMA 2401 N15 /A MET 270 CE 0.050 3.470
/A ZMA 2401 C11 /A PHE 168 CB 0.024 3.466
/A ZMA 2401 C21 /A MET 177 CE -0.021 3.511
/A ZMA 2401 N12 /A HOH 2585 O -0.030 2.730
/A ZMA 2401 C23 /A TRP 246 CZ3 -0.030 3.550
/A ZMA 2401 C6 /A GLU 169 CD -0.052 3.692
/A ZMA 2401 N16 /A PHE 168 CE2 -0.056 3.456
/A ZMA 2401 C1 /A LEU 267 CD1 -0.064 3.704
/A ZMA 2401 C14 /A PHE 168 CD2 -0.080 3.450
/A ZMA 2401 N15 /A GLU 169 CD -0.093 3.613
/A ZMA 2401 N16 /A PHE 168 CD2 -0.100 3.500
/A ZMA 2401 N19 /A HOH 2521 O -0.110 2.810
/A ZMA 2401 C8 /A MET 270 CB -0.111 3.871
/A ZMA 2401 N10 /A HOH 2524 O -0.120 2.820
/A ZMA 2401 C22 /A LEU 85 CD2 -0.122 3.762
/A ZMA 2401 N15 /A GLU 169 CG -0.124 3.644
/A ZMA 2401 N15 /A GLU 169 OE2 -0.130 2.790
/A ZMA 2401 N13 /A PHE 168 CD2 -0.131 3.531
/A ZMA 2401 N15 /A ASN 253 OD1 -0.133 2.793
/A ZMA 2401 C21 /A LEU 249 CD2 -0.135 3.625
/A ZMA 2401 C23 /A MET 177 CE -0.144 3.784
/A ZMA 2401 C9 /A HOH 2541 O -0.146 3.486
/A ZMA 2401 C9 /A PHE 168 CB -0.152 3.912
/A ZMA 2401 N12 /A ILE 274 CD1 -0.191 3.711
/A ZMA 2401 N17 /A PHE 168 CE2 -0.191 3.591
/A ZMA 2401 C20 /A LEU 249 CG -0.203 3.693
/A ZMA 2401 C22 /A LEU 249 CD2 -0.207 3.847
/A ZMA 2401 C21 /A LEU 249 CG -0.211 3.701
/A ZMA 2401 C2 /A LEU 267 CD1 -0.227 3.867
/A ZMA 2401 C24 /A HIS 250 ND1 -0.231 3.631
/A ZMA 2401 N10 /A ILE 274 CD1 -0.247 3.767
/A ZMA 2401 C20 /A LEU 249 CD2 -0.262 3.752
/A ZMA 2401 N12 /A PHE 168 CG -0.263 3.513
/A ZMA 2401 C1 /A HOH 2541 O -0.263 3.483
/A ZMA 2401 C14 /A MET 270 CE -0.264 3.754
/A ZMA 2401 C5 /A GLU 169 CD -0.269 3.909
/A ZMA 2401 N12 /A PHE 168 CB -0.272 3.792
/A ZMA 2401 N13 /A MET 270 CE -0.279 3.799
/A ZMA 2401 C18 /A PHE 168 CD2 -0.286 3.656
/A ZMA 2401 N17 /A ASN 253 ND2 -0.288 3.168
/A ZMA 2401 C5 /A HIS 264 CE1 -0.295 3.815
/A ZMA 2401 C22 /A MET 177 CE -0.297 3.937
/A ZMA 2401 C22 /A HOH 2521 O -0.308 3.528
/A ZMA 2401 C2 /A HOH 2541 O -0.315 3.535
/A ZMA 2401 O25 /A LEU 249 CG -0.344 3.644
/A ZMA 2401 C11 /A PHE 168 CD2 -0.347 3.717
/A ZMA 2401 C11 /A PHE 168 CG -0.348 3.568
/A ZMA 2401 N13 /A GLU 169 CG -0.351 3.871
/A ZMA 2401 O25 /A ASN 253 ND2 -0.351 3.011
/A ZMA 2401 C8 /A MET 270 CG -0.365 4.125
/A ZMA 2401 N19 /A LEU 249 CD2 -0.371 3.891
/A ZMA 2401 N17 /A LEU 249 CG -0.374 3.894
/A ZMA 2401 C5 /A HOH 2668 O -0.375 3.595
/A ZMA 2401 C22 /A TRP 246 CZ3 -0.380 3.900
/A ZMA 2401 O4 /A HOH 2668 O -0.380 2.900
/A ZMA 2401 C18 /A PHE 168 CE2 -0.386 3.756
/A ZMA 2401 C6 /A MET 270 CG -0.386 4.026
/A ZMA 2401 C9 /A HOH 2525 O -0.388 3.728
/A ZMA 2401 C14 /A PHE 168 CE2 -0.392 3.762
/A ZMA 2401 C6 /A GLU 169 OE2 -0.399 3.579
66 contacts
> save "/Users/mildredkissai/Desktop/tutorial from youtube 2.cxs"
> contacts delete
===== 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 INTEL-20.2.44
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 645
OpenGL vendor: Intel Inc.
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: MacBookPro15,4
Processor Name: Quad-Core Intel Core i5
Processor Speed: 1.4 GHz
Number of Processors: 1
Total Number of Cores: 4
L2 Cache (per Core): 256 KB
L3 Cache: 6 MB
Hyper-Threading Technology: Enabled
Memory: 16 GB
System Firmware Version: 1916.40.8.0.0 (iBridge: 20.16.420.0.0,0)
OS Loader Version: 564.40.4~27
Software:
System Software Overview:
System Version: macOS 13.0.1 (22A400)
Kernel Version: Darwin 22.1.0
Time since boot: 23 hours, 20 minutes
Graphics/Displays:
Intel Iris Plus Graphics 645:
Chipset Model: Intel Iris Plus Graphics 645
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x3ea6
Revision ID: 0x0001
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2560 x 1600 Retina
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
LG IPS FULLHD:
Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
UI Looks like: 1920 x 1080 @ 60.00Hz
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Display Serial Number:
Mirror: Off
Online: Yes
Rotation: Supported
Connection Type: Thunderbolt/DisplayPort
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-Clipper: 0.19.0
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 , 2 years ago
| Component: | Unassigned → Graphics |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash in swap_buffers |
comment:2 by , 2 years ago
| Resolution: | → nonchimerax |
|---|---|
| Status: | assigned → closed |
| Summary: | Crash in swap_buffers → Graphics crash, macOS 13.0.1, Intel Iris Plus Graphics 645 |
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Apple Intel graphics driver crash.