The following bug report has been submitted:
Platform: macOS-12.2.1-x86_64-i386-64bit
ChimeraX Version: 1.4.dev202203190100 (2022-03-19 01:00:21 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Illegal instruction
Current thread 0x00000002049cf600 (most recent call first):
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 318 in event_loop
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/ChimeraX_main.py", line 867 in init
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/ChimeraX_main.py", line 1018 in
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 87 in _run_code
File "/Applications/ChimeraX_Daily.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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"procLaunch" : "2022-05-03 16:01:21.0986 -0700",
"procRole" : "Background",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "MacBookPro17,1",
"procStartAbsTime" : 3575037184374,
"coalitionID" : 7771,
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"build" : "21D62",
"releaseType" : "User"
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"captureTime" : "2022-05-04 10:27:18.2003 -0700",
"incident" : "183BF87D-B94E-458D-BB5E-55E054E4D07E",
"bug_type" : "309",
"pid" : 13964,
"procExitAbsTime" : 3731940282678,
"translated" : true,
"cpuType" : "X86-64",
"procName" : "ChimeraX",
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"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "5B058C6F-D5F2-5BED-2820-341606CBA172",
"wakeTime" : 826,
"sleepWakeUUID" : "59C62C91-10A6-4C42-B778-FA1255ABD261",
"sip" : "enabled",
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"uuid" : "07b03f58-60bf-3ed9-96e4-bb6c7813925c",
"path" : "\/System\/Library\/Frameworks\/OpenGL.framework\/Versions\/A\/Resources\/GLEngine.bundle\/GLEngine",
"name" : "GLEngine"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 140712253071360,
"CFBundleShortVersionString" : "19.2.2",
"CFBundleIdentifier" : "com.apple.opengl",
"size" : 65536,
"uuid" : "5dbf3817-d830-3e43-aaf1-4fd8db553a09",
"path" : "\/System\/Library\/Frameworks\/OpenGL.framework\/Versions\/A\/OpenGL",
"name" : "OpenGL",
"CFBundleVersion" : "19.2.2"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 140703300149248,
"CFBundleShortVersionString" : "6.9",
"CFBundleIdentifier" : "com.apple.AppKit",
"size" : 15278080,
"uuid" : "9d3ab204-4858-3120-b002-5c38b02edec4",
"path" : "\/System\/Library\/Frameworks\/AppKit.framework\/Versions\/C\/AppKit",
"name" : "AppKit",
"CFBundleVersion" : "2113.30.116"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4604735488,
"size" : 63488000,
"uuid" : "10431d8f-5e3b-3bbc-abd5-81f6a73a5269",
"path" : "\/Applications\/ChimeraX_Daily.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/numpy\/.dylibs\/libopenblas64_.0.dylib",
"name" : "libopenblas64_.0.dylib"
}
],
"sharedCache" : {
"base" : 140703252987904,
"size" : 15218196480,
"uuid" : "5c9ff5db-8827-329a-8a37-2483935a9ea1"
},
"vmSummary" : "ReadOnly portion of Libraries: Total=1.4G resident=0K(0%) swapped_out_or_unallocated=1.4G(100%)\nWritable regions: Total=3.6G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=3.6G(100%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 768K 6 \nActivity Tracing 256K 1 \nCG backing stores 7552K 16 \nCG image 684K 89 \nColorSync 240K 28 \nCoreAnimation 5996K 113 \nCoreGraphics 36K 8 \nCoreUI image data 5188K 51 \nFoundation 16K 1 \nKernel Alloc Once 8K 1 \nMALLOC 2.1G 478 \nMALLOC guard page 192K 8 \nMALLOC_MEDIUM (reserved) 832.0M 8 reserved VM address space (unallocated)\nMach message 16K 4 \nOpenGL GLSL 384K 5 \nRosetta Arena 4096K 2 \nRosetta Generic 1448K 359 \nRosetta IndirectBranch 2048K 1 \nRosetta JIT 128.0M 1 \nRosetta Return Stack 740K 74 \nRosetta Thread Context 740K 74 \nSTACK GUARD 40K 10 \nStack 161.1M 37 \nStack Guard 56.1M 27 \nVM_ALLOCATE 240.6M 357 \nVM_ALLOCATE (reserved) 128.1M 13 reserved VM address space (unallocated)\n__DATA 43.9M 641 \n__DATA_CONST 29.6M 337 \n__DATA_DIRTY 1619K 212 \n__FONT_DATA 4K 1 \n__GLSLBUILTINS 5176K 1 \n__LINKEDIT 729.2M 134 \n__OBJC_RO 81.8M 1 \n__OBJC_RW 3136K 2 \n__TEXT 755.1M 647 \n__UNICODE 588K 1 \ndyld private memory 1184K 3 \nmapped file 5.2G 1084 \nshared memory 3536K 25 \nunshared pmap 10.8M 9 \n=========== ======= ======= \nTOTAL 10.5G 4870 \nTOTAL, minus reserved VM space 9.5G 4870 \n",
"legacyInfo" : {
"threadTriggered" : {
"name" : "CrBrowserMain",
"queue" : "com.apple.main-thread"
}
},
"trialInfo" : {
"rollouts" : [
{
"rolloutId" : "60da5e84ab0ca017dace9abf",
"factorPackIds" : {
},
"deploymentId" : 240000008
},
{
"rolloutId" : "607844aa04477260f58a8077",
"factorPackIds" : {
"SIRI_MORPHUN_ASSETS" : "6103050cbfe6dc472e1c982a"
},
"deploymentId" : 240000066
},
{
"rolloutId" : "602ad4dac86151000cf27e46",
"factorPackIds" : {
"SIRI_DICTATION_ASSETS" : "61fb0e87c773c43cde3bb80e"
},
"deploymentId" : 240000305
},
{
"rolloutId" : "601d9415f79519000ccd4b69",
"factorPackIds" : {
"SIRI_TEXT_TO_SPEECH" : "622657ce37186c771d5404ad"
},
"deploymentId" : 240000414
},
{
"rolloutId" : "5fb4245a1bbfe8005e33a1e1",
"factorPackIds" : {
},
"deploymentId" : 240000015
},
{
"rolloutId" : "5fc94383418129005b4e9ae0",
"factorPackIds" : {
},
"deploymentId" : 240000359
},
{
"rolloutId" : "5ffde50ce2aacd000d47a95f",
"factorPackIds" : {
},
"deploymentId" : 240000140
}
],
"experiments" : [
]
},
"reportNotes" : [
"thread_get_state(PAGEIN) returned 0x10000003: (ipc\/send) invalid destination port",
"thread_get_state(EXCEPTION) returned 0x10000003: (ipc\/send) invalid destination port",
"thread_get_state(FLAVOR) returned 0x10000003: (ipc\/send) invalid destination port"
]
}
===== Log before crash start =====
UCSF ChimeraX version: 1.4.dev202203190100 (2022-03-19)
© 2016-2022 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/john/Desktop/cryosparc_P454_J149_005_volume_map.mrc
Opened cryosparc_P454_J149_005_volume_map.mrc as #1, grid size 250,250,250,
pixel 0.843, shown at level 0.0626, step 1, values float32
> open /Users/john/Desktop/cryosparc_P454_J149_005_volume_map_sharp.mrc
Opened cryosparc_P454_J149_005_volume_map_sharp.mrc as #2, grid size
250,250,250, pixel 0.843, shown at level 0.0728, step 1, values float32
> surface dust #2 size 8.43
> surface dust #1 size 8.43
> volume #2 level 0.1503
> volume #1 level 0.0953
> set bgColor white
> lighting simple
> lighting soft
> lighting full
> lighting soft
> color #2 #a3ffb2 models transparency 0
> color #2 #a38eb2 models transparency 0
> color #2 #a38e82 models transparency 0
> color #2 #a38ea4 models transparency 0
> color #2 #a36ca4 models transparency 0
> color #2 #7e6ca4 models transparency 0
> color #2 #696ca4 models transparency 0
> color #2 #466ca4 models transparency 0
> color #2 #2e6ca4 models transparency 0
> color #2 #2e9fa4 models transparency 0
> color #2 #2e9f8e models transparency 0
> color #2 #2e5e8e models transparency 0
> color #2 #2e1f8e models transparency 0
> color #2 #2e7e8e models transparency 0
> color #2 #807e8e models transparency 0
> color #2 #807e80 models transparency 0
> color #2 #807ec2 models transparency 0
> color #2 #607ec2 models transparency 0
> open 4R7G
4r7g title:
Determination of the formylglycinamide ribonucleotide amidotransferase ammonia
pathway by combining 3D-RISM theory with experiment [more info...]
Chain information for 4r7g #3
---
Chain | Description | UniProt
A | Phosphoribosylformylglycinamidine synthase | PUR4_SALTY
Non-standard residues in 4r7g #3
---
ADP — adenosine-5'-diphosphate
MG — magnesium ion
SO4 — sulfate ion
> ui mousemode right "translate selected models"
> hide #!2 models
> show #!2 models
> select add #3
10182 atoms, 10168 bonds, 11 pseudobonds, 1514 residues, 3 models selected
> view matrix models #3,1,0,0,-5.6207,0,1,0,83.934,0,0,1,126.66
> view matrix models #3,1,0,0,62.685,0,1,0,113.07,0,0,1,123.31
> view matrix models #3,1,0,0,64.905,0,1,0,107.25,0,0,1,112.29
> view matrix models #3,1,0,0,131.87,0,1,0,143.12,0,0,1,112.43
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.155,-0.94414,0.29083,61.93,0.44996,-0.19461,-0.87158,106.05,0.87949,0.26596,0.39466,153.84
> view matrix models
> #3,0.15155,-0.97244,-0.17717,60.578,-0.41676,0.099666,-0.90354,89.606,0.89629,0.21077,-0.39017,152
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.15155,-0.97244,-0.17717,66.602,-0.41676,0.099666,-0.90354,96.358,0.89629,0.21077,-0.39017,151.33
> view matrix models
> #3,0.15155,-0.97244,-0.17717,28.696,-0.41676,0.099666,-0.90354,45.995,0.89629,0.21077,-0.39017,98.907
> view matrix models
> #3,0.15155,-0.97244,-0.17717,58.291,-0.41676,0.099666,-0.90354,49.357,0.89629,0.21077,-0.39017,112.81
> view matrix models
> #3,0.15155,-0.97244,-0.17717,56.58,-0.41676,0.099666,-0.90354,104.77,0.89629,0.21077,-0.39017,139.76
> view matrix models
> #3,0.15155,-0.97244,-0.17717,64.795,-0.41676,0.099666,-0.90354,103.13,0.89629,0.21077,-0.39017,143.64
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.40359,-0.88935,0.21488,76.958,-0.19413,-0.31275,-0.92979,92.602,0.89411,0.33354,-0.29887,148.94
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.40359,-0.88935,0.21488,78.476,-0.19413,-0.31275,-0.92979,83.552,0.89411,0.33354,-0.29887,152.44
> select add #2
10182 atoms, 10168 bonds, 11 pseudobonds, 1514 residues, 5 models selected
> select subtract #2
10182 atoms, 10168 bonds, 11 pseudobonds, 1514 residues, 3 models selected
> view matrix models
> #3,0.40359,-0.88935,0.21488,79.228,-0.19413,-0.31275,-0.92979,80.915,0.89411,0.33354,-0.29887,150.22
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.3383,-0.90332,0.26375,76.406,0.017124,-0.27432,-0.96149,89.746,0.94088,0.32978,-0.077333,151.64
> view matrix models
> #3,0.35158,-0.86595,0.35571,78.491,0.049366,-0.36229,-0.93076,86.985,0.93485,0.3448,-0.084626,152.09
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.35158,-0.86595,0.35571,77.207,0.049366,-0.36229,-0.93076,89.723,0.93485,0.3448,-0.084626,152.07
> ui tool show Matchmaker
> select add #2
10182 atoms, 10168 bonds, 11 pseudobonds, 1514 residues, 5 models selected
> select subtract #2
10182 atoms, 10168 bonds, 11 pseudobonds, 1514 residues, 3 models selected
> ui tool show "Fit in Map"
> fitmap #3 inMap #2
Fit molecule 4r7g (#3) to map cryosparc_P454_J149_005_volume_map_sharp.mrc
(#2) using 10182 atoms
average map value = 0.05325, steps = 92
shifted from previous position = 1.09
rotated from previous position = 6.96 degrees
atoms outside contour = 8598, contour level = 0.15032
Position of 4r7g (#3) relative to cryosparc_P454_J149_005_volume_map_sharp.mrc
(#2) coordinates:
Matrix rotation and translation
0.29354056 -0.91896834 0.26330806 73.50726886
0.01445247 -0.27114452 -0.96243014 93.15339612
0.95583737 0.28631773 -0.06631056 150.97051629
Axis 0.73199847 -0.40595096 0.54715817
Axis point 0.00000000 29.81745961 98.99558773
Rotation angle (degrees) 121.46363240
Shift along axis 98.59624960
> hide #!3 models
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.29354,-0.91897,0.26331,73.507,0.014452,-0.27114,-0.96243,93.153,0.95584,0.28632,-0.066311,150.97
> select add #2
10182 atoms, 10168 bonds, 11 pseudobonds, 1514 residues, 5 models selected
> view matrix models
> #2,0.97546,0.0042171,0.22013,-20.606,0.071462,0.93962,-0.33467,33.482,-0.20825,0.34219,0.91626,-5.8811,#3,0.49681,-0.83453,0.23819,84.723,-0.28533,-0.41627,-0.86331,75.739,0.81961,0.36094,-0.44492,149.02
> view matrix models
> #2,0.95056,-0.30677,0.048237,32.508,0.30964,0.92452,-0.22223,-1.2017,0.023577,0.22618,0.9738,-23.6,#3,0.3207,-0.77655,0.54233,81.087,-0.10816,-0.59886,-0.79352,74.131,0.94098,0.19582,-0.27605,146.22
> view matrix models
> #2,0.95341,-0.29636,0.056353,30.278,0.30117,0.92439,-0.23409,0.91218,0.017282,0.24015,0.97058,-24.09,#3,0.32945,-0.77967,0.53253,81.261,-0.12198,-0.59444,-0.79484,73.82,0.93626,0.1969,-0.29094,146.08
> view matrix models
> #2,0.57606,0.79563,-0.18745,-20.666,-0.80943,0.52326,-0.26651,161.65,-0.11395,0.30526,0.94543,-14.764,#3,0.0014183,-0.79878,-0.60162,67.493,-0.48478,0.52565,-0.69906,110.66,0.87464,0.29265,-0.38648,148.03
> view matrix models
> #2,0.57033,0.78007,-0.25731,-11.227,-0.82137,0.5381,-0.18923,153.35,-0.0091533,0.31927,0.94762,-27.328,#3,-0.06726,-0.8093,-0.58353,64.516,-0.4142,0.55473,-0.72161,114.53,0.9077,0.19316,-0.37252,144.8
> view matrix models
> #2,0.61764,0.76096,-0.19865,-20.164,-0.7839,0.5753,-0.23353,150.11,-0.063422,0.29995,0.95184,-20.103,#3,0.0024276,-0.8308,-0.55657,66.133,-0.445,0.49752,-0.74461,110.83,0.89553,0.24948,-0.3685,146.88
> open /Users/john/Desktop/cryosparc_P454_J155_006_volume_map_sharp.mrc
Opened cryosparc_P454_J155_006_volume_map_sharp.mrc as #4, grid size
250,250,250, pixel 0.843, shown at level 0.0684, step 1, values float32
> select subtract #2
10182 atoms, 10168 bonds, 11 pseudobonds, 1514 residues, 3 models selected
> select subtract #3
Nothing selected
> hide #!2 models
> show #!2 models
> hide #!4 models
> show #!4 models
> select add #4
2 models selected
> view matrix models
> #4,0.95838,0.27697,-0.069247,-17.39,-0.27328,0.96017,0.05826,26.932,0.082625,-0.036911,0.9959,-4.4257
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.95838,0.27697,-0.069247,51.959,-0.27328,0.96017,0.05826,62.395,0.082625,-0.036911,0.9959,-14.959
> surface dust #4 size 8.43
> volume #4 level 0.1408
> view matrix models
> #4,0.95838,0.27697,-0.069247,62.488,-0.27328,0.96017,0.05826,75.909,0.082625,-0.036911,0.9959,-7.376
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.95851,0.27709,-0.066859,62.216,-0.2731,0.95992,0.063062,75.423,0.081653,-0.042187,0.99577,-6.6983
> view matrix models
> #4,0.95764,0.27614,-0.081709,63.934,-0.2743,0.96107,0.033155,78.498,0.087683,-0.0093375,0.9961,-10.868
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.95764,0.27614,-0.081709,1.1078,-0.2743,0.96107,0.033155,-48.622,0.087683,-0.0093375,0.9961,-15.723
> view matrix models
> #4,0.95764,0.27614,-0.081709,-44.432,-0.2743,0.96107,0.033155,-30.67,0.087683,-0.0093375,0.9961,-20.46
> view matrix models
> #4,0.95764,0.27614,-0.081709,-21.051,-0.2743,0.96107,0.033155,30.333,0.087683,-0.0093375,0.9961,-7.8644
> view matrix models
> #4,0.95764,0.27614,-0.081709,-64.138,-0.2743,0.96107,0.033155,66.328,0.087683,-0.0093375,0.9961,-6.577
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.95901,0.27503,-0.068281,-65.544,-0.27402,0.96143,0.023887,67.212,0.072217,-0.0041967,0.99738,-5.6141
> view matrix models
> #4,-0.42906,0.76201,-0.48502,72.669,0.62858,0.6375,0.4455,-37.35,0.64868,-0.11373,-0.75251,124.49
> view matrix models
> #4,-0.13687,0.67529,-0.72474,75.504,0.40923,0.70482,0.57944,-34.991,0.90211,-0.21728,-0.37282,69.656
> view matrix models
> #4,-0.1605,0.68266,-0.71289,76.009,0.42629,0.69936,0.57373,-35.633,0.89023,-0.21182,-0.40326,73.459
> view matrix models
> #4,0.22664,0.91958,-0.32094,-30.496,0.43296,0.20005,0.87894,-14.542,0.87246,-0.33816,-0.3528,83.607
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.22664,0.91958,-0.32094,105.31,0.43296,0.20005,0.87894,-22.134,0.87246,-0.33816,-0.3528,75.094
> view matrix models
> #4,0.22664,0.91958,-0.32094,95.058,0.43296,0.20005,0.87894,-72.547,0.87246,-0.33816,-0.3528,-2.5726
> view matrix models
> #4,0.22664,0.91958,-0.32094,36.92,0.43296,0.20005,0.87894,-58.367,0.87246,-0.33816,-0.3528,-2.8852
> view matrix models
> #4,0.22664,0.91958,-0.32094,10.326,0.43296,0.20005,0.87894,-54.572,0.87246,-0.33816,-0.3528,1.3824
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.15668,0.85132,-0.5007,43.46,0.97244,-0.22159,-0.072451,30.707,-0.17263,-0.47555,-0.86258,179.19
> view matrix models
> #4,0.13261,0.86736,-0.4797,42.152,0.95839,-0.23563,-0.16112,42.792,-0.25278,-0.43837,-0.86252,183.73
> view matrix models
> #4,-0.61551,0.78678,-0.046099,85.584,0.64778,0.47172,-0.59821,45.348,-0.44892,-0.39807,-0.80001,193.83
> ui mousemode right "translate selected models"
> view matrix models
> #4,-0.61551,0.78678,-0.046099,118.18,0.64778,0.47172,-0.59821,111.03,-0.44892,-0.39807,-0.80001,222.99
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> select subtract #4
Nothing selected
> select add #4
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #4,-0.8707,0.16892,-0.46189,253.67,-0.25058,-0.96049,0.12108,284.88,-0.42319,0.22117,0.87863,-17.919
> view matrix models
> #4,-0.98292,-0.038412,-0.17998,258.7,-0.12186,-0.597,0.79293,163.59,-0.13791,0.80132,0.58212,-79.474
> view matrix models
> #4,-0.97221,0.14718,-0.18208,238.03,-0.19996,-0.92651,0.31874,255.61,-0.12178,0.34629,0.93019,-68.497
> ui mousemode right "translate selected models"
> view matrix models
> #4,-0.97221,0.14718,-0.18208,205.81,-0.19996,-0.92651,0.31874,191.76,-0.12178,0.34629,0.93019,-19.097
> view matrix models
> #4,-0.97221,0.14718,-0.18208,211.53,-0.19996,-0.92651,0.31874,189.56,-0.12178,0.34629,0.93019,-14.471
> ui mousemode right "rotate selected models"
> view matrix models
> #4,-0.96645,0.072918,0.24631,174.85,-0.05167,-0.99445,0.09166,204.37,0.25162,0.075857,0.96485,-28.867
> view matrix models
> #4,-0.88091,0.3382,0.33107,128.85,-0.3353,-0.93967,0.067743,231.08,0.33401,-0.051334,0.94117,-21.644
> ui mousemode right "translate selected models"
> view matrix models
> #4,-0.88091,0.3382,0.33107,128.39,-0.3353,-0.93967,0.067743,230.66,0.33401,-0.051334,0.94117,-23.16
> view matrix models
> #4,-0.88091,0.3382,0.33107,130.63,-0.3353,-0.93967,0.067743,229.19,0.33401,-0.051334,0.94117,-24.359
> select subtract #4
Nothing selected
> hide #!4 models
> volume #2 level 0.174
> volume #2 level 0.07915
> volume #2 level 0.118
> volume #2 level 0.1395
> open /Users/john/Desktop/cryosparc_P454_J149_005_volume_map.mrc
Opened cryosparc_P454_J149_005_volume_map.mrc as #5, grid size 250,250,250,
pixel 0.843, shown at level 0.0626, step 1, values float32
> volume #5 level 0.08249
> hide #!2 models
> volume #5 level 0.08172
> show #!2 models
> hide #!5 models
> open 4R7G
4r7g title:
Determination of the formylglycinamide ribonucleotide amidotransferase ammonia
pathway by combining 3D-RISM theory with experiment [more info...]
Chain information for 4r7g #6
---
Chain | Description | UniProt
A | Phosphoribosylformylglycinamidine synthase | PUR4_SALTY
Non-standard residues in 4r7g #6
---
ADP — adenosine-5'-diphosphate
MG — magnesium ion
SO4 — sulfate ion
> show #!3 models
> hide #!6 models
> close #6
> close #1
> select add #3
10182 atoms, 10168 bonds, 11 pseudobonds, 1514 residues, 3 models selected
> select subtract #3
Nothing selected
> hide #!3 models
> save /Users/john/Desktop/image1.png supersample 3
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/john/Desktop/movie1.mp4
Movie saved to /Users/john/Desktop/movie1.mp4
> select add #4
2 models selected
> show #!4 models
> select subtract #4
Nothing selected
> hide #!4 models
> show #!3 models
> hide #!3 models
> open /Users/john/Desktop/cryosparc_P454_J95_003_volume_map.mrc
Opened cryosparc_P454_J95_003_volume_map.mrc as #1, grid size 250,250,250,
pixel 0.843, shown at level 0.0498, step 1, values float32
> select add #1
2 models selected
> select subtract #1
Nothing selected
> hide #!2 models
> surface dust #1 size 8.43
> volume #1 level 0.05447
> hide #!1 models
> show #!2 models
QOpenGLFramebufferObject: Framebuffer incomplete attachment.
QOpenGLFramebufferObject: Framebuffer incomplete, missing attachment.
QQuickRenderTarget: textureId is invalid
QQuickWindow: No render target (neither swapchain nor custom target was
provided)
QOpenGLFramebufferObject: Framebuffer incomplete attachment.
QOpenGLFramebufferObject: Framebuffer incomplete, missing attachment.
QQuickRenderTarget: textureId is invalid
QQuickWindow: No render target (neither swapchain nor custom target was
provided)
Traceback (most recent call last):
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/gui.py", line 873, in moveEvent
r.set_default_framebuffer_size(gw.width(), gw.height())
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/graphics/opengl.py", line 582, in
set_default_framebuffer_size
w, h = int(s*width), int(s*height)
ValueError: cannot convert float NaN to integer
Window position QRect(-2147483648,-2147483648 -2147483648x-2147483648) outside
any known screen, using primary screen
Populating font family aliases took 418 ms. Replace uses of missing font
family ".AppleSystemUIFont" with one that exists to avoid this cost.
Error in sys.excepthook:
Traceback (most recent call last):
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/graphics.py", line 51, in event
if self.handle_drag_and_drop(event):
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/graphics.py", line 51, in event
if self.handle_drag_and_drop(event):
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/statusbar.py", line 78, in _resize_event
r.set_default_framebuffer_size(w, h)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/graphics/opengl.py", line 582, in
set_default_framebuffer_size
w, h = int(s*width), int(s*height)
ValueError: cannot convert float NaN to integer
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/logger.py", line 300, in ehook
self.session.ui.thread_safe(self.report_exception, exc_info=exc_info)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/gui.py", line 399, in thread_safe
func(*args, **kw)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/logger.py", line 450, in report_exception
self.bug(err_msg.replace("\n", "
"), is_html=True)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/logger.py", line 354, in bug
self._log(Log.LEVEL_BUG, msg, add_newline, image, is_html,
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/logger.py", line 499, in _log
if log.log(*args):
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/log/tool.py", line 328, in log
self.session.ui.thread_safe(f)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/gui.py", line 399, in thread_safe
func(*args, **kw)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/log/tool.py", line 324, in
dlg.showMessage(msg))
SystemError: returned a result with an error set
Original exception was:
Traceback (most recent call last):
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/gui.py", line 873, in moveEvent
r.set_default_framebuffer_size(gw.width(), gw.height())
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/graphics/opengl.py", line 582, in
set_default_framebuffer_size
w, h = int(s*width), int(s*height)
ValueError: cannot convert float NaN to integer
QOpenGLFramebufferObject: Framebuffer incomplete attachment.
QOpenGLFramebufferObject: Framebuffer incomplete, missing attachment.
QQuickRenderTarget: textureId is invalid
QQuickWindow: No render target (neither swapchain nor custom target was
provided)
QOpenGLFramebufferObject: Framebuffer incomplete attachment.
QOpenGLFramebufferObject: Framebuffer incomplete, missing attachment.
QQuickRenderTarget: textureId is invalid
QQuickWindow: No render target (neither swapchain nor custom target was
provided)
Failed to lock QIOSurfaceGraphicsBuffer(0x600003209320, surface=0x0,
size=QSize(-2147483648, -2147483648), isLocked=false, isInUse=false)
-536870206
===== Log before crash end =====
Log:
Startup Messages
---
warning | QMainWidget::resizeDocks: all sizes need to be larger than 0
UCSF ChimeraX version: 1.4.dev202203190100 (2022-03-19)
© 2016-2022 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/john/Desktop/cryosparc_P454_J143_class_00_final_volume.mrc
Opened cryosparc_P454_J143_class_00_final_volume.mrc as #1, grid size
128,128,128, pixel 1.65, shown at level 0.126, step 1, values float32
OpenGL version: 4.1 Metal - 76.3
OpenGL renderer: Apple M1
OpenGL vendor: Apple
Locale: UTF-8
Qt version: PyQt6 6.2.3, Qt 6.2.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro17,1
Processor Name: Unknown
Processor Speed: 2.4 GHz
Number of Processors: 1
Total Number of Cores: 8
L2 Cache: 8 MB
Memory: 16 GB
Software:
System Software Overview:
System Version: macOS 12.2.1 (21D62)
Kernel Version: Darwin 21.3.0
Time since boot: 8 days 23:44
Graphics/Displays:
Apple M1:
Chipset Model: Apple M1
Type: GPU
Bus: Built-In
Total Number of Cores: 8
Vendor: Apple (0x106b)
Metal Family: Supported, Metal GPUFamily Apple 7
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2560 x 1600 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: No
Connection Type: Internal
DELL S2421HS:
Resolution: 3520 x 1980
UI Looks like: 1760 x 990 @ 60.00Hz
Mirror: On
Mirror Status: Hardware Mirror
Online: Yes
Automatically Adjust Brightness: Yes
Dummy 16:9:
Resolution: 3520 x 1980
UI Looks like: 1760 x 990 @ 60.00Hz
Mirror: On
Mirror Status: Master Mirror
Online: Yes
Automatically Adjust Brightness: Yes
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
appnope: 0.1.2
Babel: 2.9.1
backcall: 0.2.0
blockdiag: 3.0.0
certifi: 2021.5.30
cftime: 1.6.0
charset-normalizer: 2.0.12
ChimeraX-AddCharge: 1.2.3
ChimeraX-AddH: 2.1.11
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2.1
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.36.2
ChimeraX-AtomicLibrary: 6.1.1
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.1
ChimeraX-BasicActions: 1.1
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.0
ChimeraX-BondRot: 2.0
ChimeraX-BugReporter: 1.0
ChimeraX-BuildStructure: 2.6.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.1
ChimeraX-ButtonPanel: 1.0
ChimeraX-CageBuilder: 1.0
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.2
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.2.2
ChimeraX-ColorActions: 1.0
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.1
ChimeraX-CommandLine: 1.2.2
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0
ChimeraX-Core: 1.4.dev202203190100
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.3.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0
ChimeraX-DataFormats: 1.2.2
ChimeraX-Dicom: 1.0
ChimeraX-DistMonitor: 1.1.5
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0
ChimeraX-FunctionKey: 1.0
ChimeraX-Geometry: 1.1
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1
ChimeraX-Hbonds: 2.1.2
ChimeraX-Help: 1.2
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
ChimeraX-Label: 1.1
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.5
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.1
ChimeraX-Map: 1.1
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1
ChimeraX-Markers: 1.0
ChimeraX-Mask: 1.0
ChimeraX-MatchMaker: 2.0.6
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.1
ChimeraX-Meeting: 1.0
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.7
ChimeraX-MMTF: 2.1
ChimeraX-Modeller: 1.5.5
ChimeraX-ModelPanel: 1.3.2
ChimeraX-ModelSeries: 1.0
ChimeraX-Mol2: 2.0
ChimeraX-Morph: 1.0
ChimeraX-MouseModes: 1.1
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0.2
ChimeraX-OpenCommand: 1.8
ChimeraX-PDB: 2.6.6
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-ResidueFit: 1.0
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
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.5
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0
ChimeraX-Shortcuts: 1.1
ChimeraX-ShowAttr: 1.0
ChimeraX-ShowSequences: 1.0
ChimeraX-SideView: 1.0
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.8
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.0.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0
ChimeraX-SwapRes: 2.1.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Tug: 1.0
ChimeraX-UI: 1.16.3
ChimeraX-uniprot: 2.2
ChimeraX-UnitCell: 1.0
ChimeraX-ViewDockX: 1.1.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0
ChimeraX-WebServices: 1.0
ChimeraX-Zone: 1.0
colorama: 0.4.4
cxservices: 1.1
cycler: 0.11.0
Cython: 0.29.26
debugpy: 1.5.1
decorator: 5.1.1
docutils: 0.17.1
entrypoints: 0.4
filelock: 3.4.2
fonttools: 4.31.1
funcparserlib: 1.0.0a0
grako: 3.16.5
h5py: 3.6.0
html2text: 2020.1.16
idna: 3.3
ihm: 0.27
imagecodecs: 2021.11.20
imagesize: 1.3.0
ipykernel: 6.6.1
ipython: 7.31.1
ipython-genutils: 0.2.0
jedi: 0.18.1
Jinja2: 3.0.3
jupyter-client: 7.1.0
jupyter-core: 4.9.2
kiwisolver: 1.4.0
line-profiler: 3.4.0
lxml: 4.7.1
lz4: 3.1.10
MarkupSafe: 2.1.1
matplotlib: 3.5.1
matplotlib-inline: 0.1.3
msgpack: 1.0.3
nest-asyncio: 1.5.4
netCDF4: 1.5.8
networkx: 2.6.3
numexpr: 2.8.1
numpy: 1.22.1
openvr: 1.16.802
packaging: 21.0
ParmEd: 3.4.3
parso: 0.8.3
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 9.0.1
pip: 21.3.1
pkginfo: 1.8.2
prompt-toolkit: 3.0.28
psutil: 5.9.0
ptyprocess: 0.7.0
pycollada: 0.7.2
pydicom: 2.2.2
Pygments: 2.11.2
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.7
PyQt6-commercial: 6.2.3
PyQt6-sip: 13.2.0
PyQt6-WebEngine-commercial: 6.2.1
python-dateutil: 2.8.2
pytz: 2022.1
pyzmq: 22.3.0
qtconsole: 5.2.2
QtPy: 2.0.1
RandomWords: 0.3.0
requests: 2.27.1
scipy: 1.7.3
setuptools: 59.8.0
sfftk-rw: 0.7.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
Sphinx: 4.3.2
sphinx-autodoc-typehints: 1.15.2
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
suds-community: 1.0.0
tables: 3.7.0
tifffile: 2021.11.2
tinyarray: 1.2.4
tornado: 6.1
traitlets: 5.1.1
urllib3: 1.26.9
wcwidth: 0.2.5
webcolors: 1.11.1
wheel: 0.37.1
wheel-filename: 1.3.0
![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Same bug and same reporter as #6768