![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 3 years ago
Closed 3 years ago
#8367 closed defect (can't reproduce)
Crash destroying atomic structure
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Core | 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-10.16-x86_64-i386-64bit
ChimeraX Version: 1.4 (2022-06-03 23:39:42 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
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{
"uptime" : 210000,
"procLaunch" : "2023-01-23 14:48:43.5551 +0000",
"procRole" : "Background",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "MacBookPro14,2",
"procStartAbsTime" : 212545960626166,
"coalitionID" : 2352,
"osVersion" : {
"train" : "macOS 12.6.2",
"build" : "21G320",
"releaseType" : "User"
},
"captureTime" : "2023-01-23 15:05:02.3313 +0000",
"incident" : "911F676E-9311-4AD3-9FBE-F859F7B960F7",
"bug_type" : "309",
"pid" : 90982,
"procExitAbsTime" : 213524666448414,
"cpuType" : "X86-64",
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.4.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.4.0","CFBundleVersion":"1.4.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"4D171165-2346-5DCA-BDE1-76C56B4320BA","thirdParty":true},
"parentProc" : "bash",
"parentPid" : 90271,
"coalitionName" : "com.googlecode.iterm2",
"crashReporterKey" : "EF7E5736-BD73-EC8B-9E14-B6797D473A00",
"responsiblePid" : 2231,
"responsibleProc" : "iTerm2",
"wakeTime" : 3035,
"bridgeVersion" : {"build":"14Y910","train":"3.0"},
"sleepWakeUUID" : "EAF39F14-7938-4649-BCA6-6AFF68018EAD",
"sip" : "enabled",
"isCorpse" : 1,
"exception" : {"codes":"0x0000000000000000, 0x0000000000000000","rawCodes":[0,0],"type":"EXC_CRASH","signal":"SIGABRT"},
"ktriageinfo" : "VM - Compressor failed a blocking pager_get\nVM - Compressor failed a blocking pager_get\nVM - Compressor failed a blocking pager_get\nVM - Compressor failed a blocking pager_get\nVM - Compressor failed a blocking pager_get\n",
"asi" : {"libsystem_c.dylib":["abort() called"]},
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"faultingThread" : 0,
"threads" : 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"vmSummary" : "ReadOnly portion of Libraries: Total=1.4G resident=0K(0%) swapped_out_or_unallocated=1.4G(100%)\nWritable regions: Total=47.9G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=47.9G(100%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 384K 3 \nActivity Tracing 256K 1 \nCG backing stores 2160K 4 \nCG image 152K 9 \nColorSync 228K 27 \nCoreAnimation 216K 16 \nCoreGraphics 12K 2 \nCoreServices 204K 1 \nCoreUI image data 3744K 26 \nFoundation 16K 1 \nKernel Alloc Once 8K 1 \nMALLOC 46.4G 9706 \nMALLOC guard page 32K 7 \nMALLOC_LARGE (reserved) 384K 1 reserved VM address space (unallocated)\nMALLOC_NANO (reserved) 128.0M 1 reserved VM address space (unallocated)\nMach message 16K 2 \nObjC additional data 15K 1 \nOpenGL GLSL 384K 4 \nSTACK GUARD 84K 21 \nStack 138.7M 22 \nStack Guard 56.0M 1 \nVM_ALLOCATE 1.2G 5955 \n__CTF 756 1 \n__DATA 44.8M 673 \n__DATA_CONST 32.4M 340 \n__DATA_DIRTY 1641K 213 \n__FONT_DATA 4K 1 \n__GLSLBUILTINS 5176K 1 \n__LINKEDIT 675.8M 148 \n__TEXT 805.3M 672 \n__UNICODE 592K 1 \ndyld private memory 1184K 3 \nmapped file 116.1M 45 \nshared memory 2976K 25 \n=========== ======= ======= \nTOTAL 49.6G 17935 \nTOTAL, minus reserved VM space 49.5G 17935 \n",
"legacyInfo" : {
"threadTriggered" : {
"name" : "CrBrowserMain",
"queue" : "com.apple.main-thread"
}
},
"trialInfo" : {
"rollouts" : [
{
"rolloutId" : "60186475825c62000ccf5450",
"factorPackIds" : {
},
"deploymentId" : 240000026
},
{
"rolloutId" : "5fb4245a1bbfe8005e33a1e1",
"factorPackIds" : {
},
"deploymentId" : 240000021
}
],
"experiments" : [
]
}
}
Log:
UCSF ChimeraX version: 1.4 (2022-06-03)
© 2016-2022 Regents of the University of California. All rights reserved.
> open /Users/tina/PG/projects/minicell-
> structure/periplasmic_scaffold/lafter/lafter_vs_raw.cxs
Opened scaffold-new-postprocess_imasked as #4, grid size 800,800,800, pixel
2.2, shown at level 0.00631, step 1, values float32
Opened Refine3d_job975_scaffold_LAFTER_filtered_imasked as #3, grid size
800,800,800, pixel 2.2, shown at level 0.126, step 1, values float32
Log from Sun Jan 22 21:45:11 2023UCSF ChimeraX version: 1.4 (2022-06-03)
© 2016-2022 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open Refine3d_job975_scaffold_LAFTER_filtered.mrc
Opened Refine3d_job975_scaffold_LAFTER_filtered.mrc as #1, grid size
800,800,800, pixel 2.2, shown at step 1, values float32
> volume #1 region 0,0,0,799,799,799 step 4
[Repeated 1 time(s)]
> set bgColor white
> lighting soft
> volume #1 change image level -0.007422,0 level 0.1291,0.8 level 1.139,1
> volume #1 level 0.07052
> volume #1 step 1
> volume #1 color #4f4f4f
> volume #1 color #4d4d4d
> volume #1 color #4d4d4d82
> volume #1 color #f4f4f482
> volume #1 color #f4f4f4
> color #1 silver models transparency 0
> color #1 #d6d6d6 models transparency 0
> color #1 silver models transparency 0
> color #1 darkgrey models transparency 0
> color #1 #a9a9a982 models
> color #1 #a9a9a980 models
> color #1 darkgrey models transparency 0
> volume #1 level 0.2472
> view
> lighting soft
> lighting simple
> view orient
> turn x -90
> clip
> zoom 1.5
> volume #1 level 0.05312
> ~clip
> zoom 0.6
> view orient
> turn x -30
[Repeated 1 time(s)]
> volume #1 level 0.04366
> volume #1 level 0.045
> volume #1 level 0.05
> volume #1 level 0.06
> volume #1 level 0.07
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting depthCue false
> lighting soft
[Repeated 1 time(s)]
> lighting shadows true intensity 0.5
> lighting shadows false
> camera ortho
> save lafter_turn60.png format png transparentBackground true
> save lafter_turn-60.png format png transparentBackground true
> view orient
> save lafter.png format png transparentBackground true
> turn x -60
> volume #1 level 0.2736
> save lafter_low_turn-60.png format png transparentBackground true
> view orient
> turn x -60
> turn x -30
> volume #1 level 0.07947
> volume #1 level 0.2641
> volume #1 level 0.2546
> volume #1 level 0.2499
> volume #1 level 0.2452
> volume #1 level 0.2073
> volume #1 level 0.212
> volume #1 level 0.2168
> volume #1 level 0.2262
> volume #1 level 0.1079
> volume #1 level 0.05106
> open /Users/tina/PG/projects/minicell-
> structure/periplasmic_scaffold/scaffold-new-postprocess.mrc
Opened scaffold-new-postprocess.mrc as #2, grid size 800,800,800, pixel 2.2,
shown at step 1, values float32
> volume #2 region 0,0,0,799,799,799 step 4
[Repeated 1 time(s)]
> volume #2 step 1
> volume #2 change image level -0.0001261,0 level 0.006522,0.8 level 0.01695,1
> volume #2 level 0.002151
> volume #2 level 0.002823
> volume #2 color darkgrey
> volume #2 level 0.007591
> view orient
> volume #2 level 0.002285
> volume #2 level 0.002823
> view orient
> turn x -30
[Repeated 1 time(s)]
> volume #2 level 0.002688
> volume #2 level 0.002352
> volume #2 level 0.002151
> volume #2 level 0.001882
> ui tool show "Hide Dust"
> surface dust #2 size 13.2
[Repeated 1 time(s)]
> surface dust #2 size 13.96
> surface dust #2 size 27.61
> surface dust #2 size 28.22
> surface dust #2 size 55.85
> surface dust #2 size 57.06
> surface dust #2 size 160.48
> surface dust #2 size 156.97
> surface dust #2 size 74.34
> volume #2 level 0.001949
> volume #2 level 0.002017
> view orient
> turn x -30
[Repeated 1 time(s)]
> view orient
> turn x -50
> ui tool show "Segment Map"
Segmenting scaffold-new-postprocess.mrc, density threshold 0.002017
Only showing 60 of 552 regions.
Showing 60 of 552 region surfaces
5661 watershed regions, grouped to 552 regions
Showing scaffold-new-postprocess.seg - 552 regions, 60 surfaces
> hide #!2 models
Showing 552 region surfaces
Opened scaffold-new-postprocess_imasked as #4, grid size 800,800,800, pixel
2.2, shown at step 1, values float32
> hide #!3 models
> close #2
> show #!1 models
> hide #!4 models
> volume #1 level 0.008091
> volume #1 level 0.01239
> volume #1 level 0.01669
Segmenting Refine3d_job975_scaffold_LAFTER_filtered.mrc, density threshold
0.016685
Showing 593 region surfaces
8935 watershed regions, grouped to 593 regions
Showing Refine3d_job975_scaffold_LAFTER_filtered.seg - 593 regions, 593
surfaces
> hide #!1 models
Ungrouped to 64 regions
Ungrouped to 3 regions
Ungrouped to 4 regions
Ungrouped to 3 regions
Ungrouped to 4 regions
Ungrouped to 2 regions
Ungrouped to 10 regions
Ungrouped to 3 regions
Ungrouped to 43 regions
Ungrouped to 4 regions
Ungrouped to 3 regions
[Repeated 5 time(s)]Ungrouped to 4 regions
Ungrouped to 3 regions
[Repeated 2 time(s)]Ungrouped to 4 regions
Ungrouped to 2 regions
Ungrouped to 3 regions
[Repeated 1 time(s)]Ungrouped to 2 regions
Ungrouped to 20 regions
> select clear
Drag select of 13248, 13264, 13268, 13263, 13299, 13258, 13265, 13257, 13262,
13267, 12609, 12418, 12401, 12425, 12649, 12383, 12407, 13308, 13311, 13260,
13199, 13309, 13110, 13307, 12688, 12331, 12697, 12816, 12479, 12902, 12920,
12412, 12904, 12414, 12813, 12918, 12486, 12687, 13208, 13286, 13280, 13285,
13226, 13152, 13291, 13181, 13259, 12815, 13290, 12703, 13225, 13287, 13278,
13241, 13060, 13224, 13180, 12689, 13298, 13134, 13115, 13057, 13059, 13127,
13072, 13243, 13132, 13054, 13098, 13099, 13083, 13055, 13074, 13131, 13201,
13223, 12345, 12347, 12444, 12437, 12485, 12712, 12411, 12597, 12738, 12921,
12560, 13202, 12478, 12343, 12441, 12443, 12882, 12473, 12540, 12644, 12474,
12346, 13332, 12521, 12690, 12409, 12923, 12919, 12449, 12456, 12641, 12774,
12580, 12730, 12737, 12595, 13028, 12557, 12525, 12445, 13013, 12599, 12733,
12448, 13014, 12598, 12576, 12739, 12968, 12735, 12442, 13221, 12578, 13173,
12562, 12572, 12453, 12575, 12458, 12577, 13245, 13270, 13313, 13266, 13327,
13126, 13312, 13342, 13319, 13252, 13251, 13061, 13081, 13116, 13320, 13317,
13091, 13318, 13092, 13094, 13084, 13177, 13114, 13206, 13247, 13249, 13242,
13276, 13153, 13237, 13236, 13141, 13123, 13073, 13179, 13168, 13163, 13340,
13275, 13143, 13066, 13146, 13086, 13246, 13080, 13335, 13269, 13065, 13129,
13274, 13164, 13250, 13079, 13144, 13314, 13064, 13339, 13149, 13322, 13111,
13106, 13078, 13156, 13101, 13088, 13056, 13097, 13137, 13159, 12715, 13316,
12373, 12875, 12995, 12978, 12695, 12376, 12996, 13067, 12694, 12926, 12402,
12405, 13261, 12924, 13169, 13063, 13128, 13176, 13109, 13166, 13139, 13171,
13162, 13334, 13336, 13121, 13058, 13172, 13167, 13087, 13089, 13107, 13130,
13326, 12748, 12997, 12372, 13192, 12940, 13108, 12483, 12983, 12692, 12476,
12750, 12980, 12753, 12480, 12982, 12922, 12404, 12817, 12700, 12611, 12482,
12403, 12976, 13341, 12561, 13119, 13211, 13151, 12714, 13117, 13120, 13209,
13205, 13178, 12830, 12550, 13329, 13118, 13210, 12464, 12770, 12891, 12591,
12604, 13069, 12552, 12603, 13207, 13271, 13138, 13315, 13273, 13331, 12672,
13142, 12760, 12772, 12320, 13321, 13147, 13289, 13170, 13272, 13277, 13070,
13232, 12861, 13148, 13112, 13160, 12844, 13090, 12605, 12512, 13155, 13191,
13095, 13227, 12802, 13068, 13165, 12333, 13154, 13150, 12909, 13145, 12505,
12836, 12640, 12860, 12837, 12856, 12868, 13037, 13093, 13255, 12857, 13113,
13024, 12664, 13253, 12931, 12494, 13293, 12910, 12653, 12884, 12936, 12881,
12887, 12354, 12803, 12790, 12869, 12786, 12797, 12801, 12509, 12349, 12906,
12933, 12805, 12928, 12855, 12500, 12870, 12811, 12806, 12851, 12911, 13161,
12930, 13294, 12666, 12885, 12934, 12659, 12886, 12636, 13254, 13231, 12546,
13125, 12519, 13295, 13292, 12800, 12513, 12501, 12356, 12352, 13002, 12510,
12847, 12709, 12496, 12927, 12665, 12645, 12788, 12607, 10705, 12633, 13026,
12862, 12780, 13001, 12932, 12716, 12663, 13000, 12925, 12756, 12895, 13071,
12455, 12988, 13075, 12796, 13005, 12631, 12507, 12839, 12514, 12504, 12710,
13122, 12718, 13102, 12515, 12520, 12502, 12792, 12994, 12495, 12794, 12508,
10051, 10062, 10056, 11876, 10061, 10054, 10052, 9944, 9950, 9943, 10049,
10069, 10059, 10063, 9942, 10070, 11855, 12434, 868, 887, 899, 828, 835, 841,
894, 904, 843, 854, 859, 881, 909, 834, 906, 831, 871, 13193, 12524, 13196,
12431, 13195, 7872, 7882, 7824, 7880, 7865, 7838, 7812, 7806, 7883, 7816,
11251, 8472, 11763, 12958, 12682, 10642, 12211, 13045, 12547, 12907, 12523,
12543, 12318, 12545, 12742, 12551, 12614, 12522, 12544, 12746, 12554, 12616,
12717, 12582, 12548, 13011, 12602, 11493, 10621, 12859, 12542, 12680, 11762,
11233, 11497, 8955, 8468, 8731, 8723, 8465, 8545, 12194, 10637, 8712, 11508,
11239, 8699, 8453, 8695, 8522, 8708, 8540, 12555, 12617, 12766, 12359, 12549,
12357, 12619, 12773, 11766, 10643, 12620, 12588, 12618, 12671, 12587, 12899,
12556, 12769, 10967, 12228, 8924, 8467, 8728, 11498, 11857, 8471, 8733, 11499,
12197, 8476, 8738, 11510, 10679, 8583, 8748, 8603, 11757, 7442, 8774, 8601,
8772, 11260, 11765, 8753, 8586, 11496, 11787, 10641, 11741, 11201, 10638,
13044, 12553, 12615, 12771, 12765, 12484, 12754, 12757, 12763, 12764, 12858
> select clear
Drag select of 13248, 13264, 13268, 13263, 13299, 13258, 13265, 13257, 13262,
13267, 12609, 12418, 12401, 12425, 12649, 12383, 12407, 13308, 13311, 13260,
13199, 13309, 13110, 13307, 12688, 12331, 12697, 12816, 12479, 12902, 12920,
12412, 12904, 12414, 12813, 12918, 12486, 12687, 13208, 13286, 13280, 13285,
13226, 13152, 13291, 13181, 13259, 12815, 13290, 12703, 13225, 13287, 13278,
13241, 13060, 13224, 13180, 12689, 13298, 13134, 13115, 13057, 13059, 13127,
13072, 13243, 13132, 13054, 13098, 13099, 13083, 13055, 13074, 13131, 13201,
13223, 12345, 12347, 12444, 12437, 12485, 12712, 12411, 12597, 12738, 12921,
12560, 13202, 12478, 12343, 12441, 12443, 12882, 12473, 12540, 12644, 12474,
12346, 13332, 12521, 12690, 12409, 12923, 12919, 12449, 12456, 12641, 12774,
12580, 12730, 12737, 12595, 13028, 12557, 12525, 12445, 13013, 12599, 12733,
12448, 13014, 12598, 12576, 12739, 12968, 12735, 12442, 13221, 12578, 13173,
12562, 12572, 12453, 12575, 12458, 12577, 13245, 13270, 13313, 13266, 13327,
13126, 13312, 13342, 13319, 13252, 13251, 13061, 13081, 13116, 13320, 13317,
13091, 13318, 13092, 13094, 13084, 13177, 13114, 13206, 13247, 13249, 13242,
13276, 13153, 13237, 13236, 13141, 13123, 13073, 13179, 13168, 13163, 13340,
13275, 13143, 13066, 13146, 13086, 13246, 13080, 13335, 13269, 13065, 13129,
13274, 13164, 13250, 13079, 13144, 13314, 13064, 13339, 13149, 13322, 13111,
13106, 13078, 13156, 13101, 13088, 13056, 13097, 13137, 13159, 12715, 13316,
12373, 12875, 12995, 12978, 12695, 12376, 12996, 13067, 12694, 12926, 12402,
12405, 13261, 12924, 13169, 13063, 13128, 13176, 13109, 13166, 13139, 13171,
13162, 13334, 13336, 13121, 13058, 13172, 13167, 13087, 13089, 13107, 13130,
13326, 12748, 12997, 12372, 13192, 12940, 13108, 12483, 12983, 12692, 12476,
12750, 12980, 12753, 12480, 12982, 12922, 12404, 12817, 12700, 12611, 12482,
12403, 12976, 13341, 12561, 13119, 13211, 13151, 12714, 13117, 13120, 13209,
13205, 13178, 12830, 12550, 13329, 13118, 13210, 12464, 12770, 12891, 12591,
12604, 13069, 12552, 12603, 13207, 13271, 13138, 13315, 13273, 13331, 12672,
13142, 12760, 12772, 12320, 13321, 13147, 13289, 13170, 13272, 13277, 13070,
13232, 12861, 13148, 13112, 13160, 12844, 13090, 12605, 12512, 13155, 13191,
13095, 13227, 12802, 13068, 13165, 12333, 13154, 13150, 12909, 13145, 12505,
12836, 12640, 12860, 12837, 12856, 12868, 13037, 13093, 13255, 12857, 13113,
13024, 12664, 13253, 12931, 12494, 13293, 12910, 12653, 12884, 12936, 12881,
12887, 12354, 12803, 12790, 12869, 12786, 12797, 12801, 12509, 12349, 12906,
12933, 12805, 12928, 12855, 12500, 12870, 12811, 12806, 12851, 12911, 13161,
12930, 13294, 12666, 12885, 12934, 12659, 12886, 12636, 13254, 13231, 12546,
13125, 12519, 13295, 13292, 12800, 12513, 12501, 12356, 12352, 13002, 12510,
12847, 12709, 12496, 12927, 12665, 12645, 12788, 12607, 10705, 12633, 13026,
12862, 12780, 13001, 12932, 12716, 12663, 13000, 12925, 12756, 12895, 13071,
12455, 12988, 13075, 12796, 13005, 12631, 12507, 12839, 12514, 12504, 12710,
13122, 12718, 13102, 12515, 12520, 12502, 12792, 12994, 12495, 12794, 12508,
10051, 10062, 10056, 11876, 10061, 10054, 10052, 9944, 9950, 9943, 10049,
10069, 10059, 10063, 9942, 10070, 11855, 12434, 868, 887, 899, 828, 835, 841,
894, 904, 843, 854, 859, 881, 909, 834, 906, 831, 871, 13193, 12524, 13196,
12431, 13195, 7872, 7882, 7824, 7880, 7865, 7838, 7812, 7806, 7883, 7816,
11251, 8472, 11763, 12958, 12682, 10642, 12211, 13045, 12547, 12907, 12523,
12543, 12318, 12545, 12742, 12551, 12614, 12522, 12544, 12746, 12554, 12616,
12717, 12582, 12548, 13011, 12602, 11493, 10621, 12859, 12542, 12680, 11762,
11233, 11497, 8955, 8468, 8731, 8723, 8465, 8545, 12194, 10637, 8712, 11508,
11239, 8699, 8453, 8695, 8522, 8708, 8540, 12555, 12617, 12766, 12359, 12549,
12357, 12619, 12773, 11766, 10643, 12620, 12588, 12618, 12671, 12587, 12899,
12556, 12769, 10967, 12228, 8924, 8467, 8728, 11498, 11857, 8471, 8733, 11499,
12197, 8476, 8738, 11510, 10679, 8583, 8748, 8603, 11757, 7442, 8774, 8601,
8772, 11260, 11765, 8753, 8586, 11496, 11787, 10641, 11741, 11201, 10638,
13044, 12553, 12615, 12771, 12765, 12484, 12754, 12757, 12763, 12764, 12858
Opened Refine3d_job975_scaffold_LAFTER_filtered_imasked as #3, grid size
800,800,800, pixel 2.2, shown at step 1, values float32
> hide #!2 models
> surface dust #3 size 13.2
> surface dust #3 size 13.45
> surface dust #3 size 8.13
> view orient
> turn x -60
> volume #3 level 0.02072
> save maps_postprocess1.png format png transparentBackground true
> save maps_lafter1.png format png transparentBackground true
> camera ortho
> turn x -30
> turn x 90
> turn x -30
> volume #3 level 0.1216
> volume #3 level 0.1862
> volume #3 level 0.1781
> volume #4 level 0.005524
> volume #4 level 0.007338
> volume #4 level 0.007459
> surface dust #3 size 8.13
> surface dust #3 size 7.87
> surface dust #3 size 10.46
> surface dust #3 size 10.82
> surface dust #3 size 17.6
> surface dust #3 size 17.89
> surface dust #3 size 33.27
> surface dust #3 size 35.57
> surface dust #3 size 33.82
> surface dust #4 size 13.2
> surface undust #4
[Repeated 2 time(s)]
> volume #3 level 0.166
> surface undust #3
> volume #3 level 0.1297
> volume #3 level 0.1256
> surface dust #3 size 4.68
> surface dust #3 size 4.84
> surface dust #3 size 6.01
> surface dust #3 size 6.22
> surface dust #3 size 10.12
> surface dust #3 size 10.46
> surface dust #3 size 11.57
> surface dust #3 size 11.76
> surface dust #3 size 11
> volume #4 level 0.00631
> volume #4 level 0.006008
> volume #4 level 0.00631
> volume #4 level 0.006855
> volume #4 level 0.006008
> volume #4 level 0.006734
> zoom 0.8
> volume #4 level 0.00631
> save maps_lafter2.png format png transparentBackground true
> save maps_postprocess2.png format png transparentBackground true
> zoom 0.9
[Repeated 1 time(s)]
> save maps_postprocess3.png format png transparentBackground true
> save maps_lafter3.png format png transparentBackground true
> close #2
> close #1
> save /Users/tina/PG/projects/minicell-
> structure/periplasmic_scaffold/lafter/lafter_vs_raw.cxs includeMaps true
——— End of log from Sun Jan 22 21:45:11 2023 ———
opened ChimeraX session
OpenGL version: 4.1 INTEL-18.8.5
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 650
OpenGL vendor: Intel Inc.
Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.3.0, Qt 6.3.0
Qt runtime version: 6.3.0
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro14,2
Processor Name: Dual-Core Intel Core i5
Processor Speed: 3.1 GHz
Number of Processors: 1
Total Number of Cores: 2
L2 Cache (per Core): 256 KB
L3 Cache: 4 MB
Hyper-Threading Technology: Enabled
Memory: 8 GB
System Firmware Version: 499.40.2.0.0
OS Loader Version: 540.120.3~22
SMC Version (system): 2.44f6
Software:
System Software Overview:
System Version: macOS 12.6.2 (21G320)
Kernel Version: Darwin 21.6.0
Time since boot: 6 days 20:49
Graphics/Displays:
Intel Iris Plus Graphics 650:
Chipset Model: Intel Iris Plus Graphics 650
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x5927
Revision ID: 0x0006
Metal Family: Supported, Metal GPUFamily macOS 2
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: No
Connection Type: Internal
HP E272q:
Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition)
UI Looks like: 2560 x 1440 @ 60.00Hz
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Display Serial Number: CNK7101NF8
Mirror: Off
Online: Yes
Rotation: Supported
Connection Type: DVI or HDMI
Adapter Firmware Version: 0.00
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
appnope: 0.1.3
Babel: 2.10.1
backcall: 0.2.0
blockdiag: 3.0.0
certifi: 2021.10.8
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: 2.4.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.39.1
ChimeraX-AtomicLibrary: 7.0
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.1
ChimeraX-BasicActions: 1.1
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.1
ChimeraX-BondRot: 2.0
ChimeraX-BugReporter: 1.0
ChimeraX-BuildStructure: 2.7
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: 2.2.4
ChimeraX-ColorActions: 1.0
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.1
ChimeraX-CommandLine: 1.2.3
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0
ChimeraX-Core: 1.4
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: 1.1
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: 1.2
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: 1.1.1
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: 1.9
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: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.6
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: 1.1.1
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Tug: 1.0
ChimeraX-UI: 1.18.3
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: 1.1.0
ChimeraX-Zone: 1.0
colorama: 0.4.4
cxservices: 1.2
cycler: 0.11.0
Cython: 0.29.26
debugpy: 1.6.0
decorator: 5.1.1
docutils: 0.17.1
entrypoints: 0.4
filelock: 3.4.2
fonttools: 4.33.3
funcparserlib: 1.0.0
grako: 3.16.5
h5py: 3.7.0
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: 4.10.0
kiwisolver: 1.4.2
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: 1.5.5
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: 3.0.29
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: 3.0.9
PyQt6-commercial: 6.3.0
PyQt6-Qt6: 6.3.0
PyQt6-sip: 13.3.1
PyQt6-WebEngine-commercial: 6.3.0
PyQt6-WebEngine-Qt6: 6.3.0
python-dateutil: 2.8.2
pytz: 2022.1
pyzmq: 23.1.0
qtconsole: 5.3.0
QtPy: 2.1.0
RandomWords: 0.3.0
requests: 2.27.1
scipy: 1.7.3
setuptools: 59.8.0
sfftk-rw: 0.7.2
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
Change History (2)
comment:1 by , 3 years ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Core |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Crash destroying atomic structure |
comment:2 by , 3 years ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | accepted → closed |
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