![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 2 years ago
Closed 2 years ago
#10348 closed defect (duplicate)
Crash emitting color_pause signal
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | General Controls | 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: 1.4 (2022-06-03 23:39:42 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault
Thread 0x0000000311e65000 (most recent call first):
File "/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 316 in wait
File "/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 574 in wait
File "/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 1297 in run
File "/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Current thread 0x0000000201245280 (most recent call first):
File "/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/widgets/color_button.py", line 147 in
File "/Applications/ChimeraX-1.4.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-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/ChimeraX_main.py", line 870 in init
File "/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/ChimeraX_main.py", line 1021 in
File "/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 87 in _run_code
File "/Applications/ChimeraX-1.4.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" : 720000,
"procRole" : "Foreground",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "MacBookPro18,3",
"coalitionID" : 2240,
"osVersion" : {
"train" : "macOS 13.5.1",
"build" : "22G90",
"releaseType" : "User"
},
"captureTime" : "2023-12-14 15:54:20.6215 -0800",
"incident" : "66B0DF07-2F01-4613-9D4B-DDB1BC537FF0",
"pid" : 87744,
"translated" : true,
"cpuType" : "X86-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2023-12-14 15:47:24.8998 -0800",
"procStartAbsTime" : 17498601269423,
"procExitAbsTime" : 17508576190052,
"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":"B5236F1B-CB88-5785-A255-50E8FEB952C7","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "56900282-8AB7-46FC-C8C9-A0404C9F72A1",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 0,
"wakeTime" : 27044,
"sleepWakeUUID" : "4321EAA1-BCE1-42D1-97F5-F4BA56DBE3E7",
"sip" : "enabled",
"vmRegionInfo" : "0x7e is not in any region. Bytes before following region: 140722925027202\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n mapped file 7ffc9bf54000-7ffcab0a8000 [241.3M] r-x\/r-x SM=COW ...t_id=72a62aa5",
"exception" : {"codes":"0x0000000000000001, 0x000000000000007e","rawCodes":[1,126],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x000000000000007e"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":87744},
"ktriageinfo" : "VM - (arg = 0x0) pmap_enter retried due to resource shortage\nVM - (arg = 0x0) pmap_enter retried due to resource shortage\nVM - (arg = 0x0) pmap_enter retried due to resource shortage\nVM - (arg = 0x0) pmap_enter retried due to resource shortage\n",
"vmregioninfo" : "0x7e is not in any region. Bytes before following region: 140722925027202\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n mapped file 7ffc9bf54000-7ffcab0a8000 [241.3M] r-x\/r-x SM=COW ...t_id=72a62aa5",
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"faultingThread" : 0,
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"path" : "\/usr\/lib\/system\/libsystem_kernel.dylib",
"name" : "libsystem_kernel.dylib"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 140703374020608,
"size" : 49152,
"uuid" : "3a3fa85c-f1fe-336c-bf68-924fc947ade3",
"path" : "\/usr\/lib\/system\/libsystem_pthread.dylib",
"name" : "libsystem_pthread.dylib"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 140703372632064,
"size" : 557048,
"uuid" : "d5b303ad-54f4-323b-bbe2-2d0f34c45649",
"path" : "\/usr\/lib\/system\/libsystem_c.dylib",
"name" : "libsystem_c.dylib"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 140703374217216,
"size" : 40944,
"uuid" : "f1798256-c6b5-335c-bbb5-7978acf41deb",
"path" : "\/usr\/lib\/system\/libsystem_platform.dylib",
"name" : "libsystem_platform.dylib"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 140703374434304,
"CFBundleShortVersionString" : "6.9",
"CFBundleIdentifier" : "com.apple.CoreFoundation",
"size" : 4829184,
"uuid" : "478d855c-04f6-3c1e-b658-e34aeb66490a",
"path" : "\/System\/Library\/Frameworks\/CoreFoundation.framework\/Versions\/A\/CoreFoundation",
"name" : "CoreFoundation",
"CFBundleVersion" : "1979"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 140703541772288,
"CFBundleShortVersionString" : "2.1.1",
"CFBundleIdentifier" : "com.apple.HIToolbox",
"size" : 3112954,
"uuid" : "bbbf9caf-5b24-3c4c-b275-e85d272258c9",
"path" : "\/System\/Library\/Frameworks\/Carbon.framework\/Versions\/A\/Frameworks\/HIToolbox.framework\/Versions\/A\/HIToolbox",
"name" : "HIToolbox"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 140703424995328,
"CFBundleShortVersionString" : "6.9",
"CFBundleIdentifier" : "com.apple.AppKit",
"size" : 16809984,
"uuid" : "c5499c27-03c5-3194-815e-94cf6e6b68db",
"path" : "\/System\/Library\/Frameworks\/AppKit.framework\/Versions\/C\/AppKit",
"name" : "AppKit",
"CFBundleVersion" : "2299.70.136"
}
],
"sharedCache" : {
"base" : 140703369887744,
"size" : 21474836480,
"uuid" : "bd5d42c5-887c-35ef-a80f-58bb1f31d586"
},
"vmSummary" : "ReadOnly portion of Libraries: Total=1.1G resident=0K(0%) swapped_out_or_unallocated=1.1G(100%)\nWritable regions: Total=3.7G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=3.7G(100%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 256K 2 \nActivity Tracing 256K 1 \nCG backing stores 8704K 8 \nCG image 2008K 46 \nColorSync 264K 30 \nCoreAnimation 5092K 129 \nCoreGraphics 80K 11 \nCoreImage 36K 3 \nCoreUI image data 5244K 42 \nFoundation 48K 2 \nKernel Alloc Once 8K 1 \nMALLOC 1.7G 316 \nMALLOC guard page 192K 8 \nMALLOC_MEDIUM (reserved) 808.0M 10 reserved VM address space (unallocated)\nMALLOC_NANO (reserved) 384.0M 1 reserved VM address space (unallocated)\nMach message 16K 4 \nOpenGL GLSL 384K 4 \nRosetta Arena 4096K 2 \nRosetta Generic 1648K 409 \nRosetta IndirectBranch 2048K 1 \nRosetta JIT 128.0M 1 \nRosetta Return Stack 816K 80 \nRosetta Thread Context 800K 80 \nSTACK GUARD 48K 12 \nStack 179.2M 42 \nStack Guard 56.1M 30 \nVM_ALLOCATE 205.5M 297 \nVM_ALLOCATE (reserved) 224.1M 13 reserved VM address space (unallocated)\n__CTF 824 1 \n__DATA 45.4M 734 \n__DATA_CONST 39.0M 387 \n__DATA_DIRTY 1807K 225 \n__FONT_DATA 2352 1 \n__GLSLBUILTINS 5174K 1 \n__INFO_FILTER 8 1 \n__LINKEDIT 200.7M 139 \n__OBJC_RO 66.3M 1 \n__OBJC_RW 2011K 2 \n__TEXT 912.5M 741 \ndyld private memory 420K 4 \nmapped file 4.8G 1738 \nshared memory 3016K 22 \nunshared pmap 13.6M 9 \n=========== ======= ======= \nTOTAL 9.8G 5591 \nTOTAL, minus reserved VM space 8.4G 5591 \n",
"legacyInfo" : {
"threadTriggered" : {
"name" : "CrBrowserMain",
"queue" : "com.apple.main-thread"
}
},
"logWritingSignature" : "f2bd7e5945dba35419f797932b1b55eae0370a50",
"trialInfo" : {
"rollouts" : [
{
"rolloutId" : "5ffde50ce2aacd000d47a95f",
"factorPackIds" : {
},
"deploymentId" : 240000352
},
{
"rolloutId" : "63508950b3714d3622fc77f7",
"factorPackIds" : {
"SIRI_MEMORY_SYNC_CONFIG" : "63508beab3714d3622fc7808"
},
"deploymentId" : 240000004
}
],
"experiments" : [
{
"treatmentId" : "a092db1b-c401-44fa-9c54-518b7d69ca61",
"experimentId" : "64a844035c85000c0f42398a",
"deploymentId" : 400000019
}
]
}
}
===== Log before crash start =====
UCSF ChimeraX version: 1.4 (2022-06-03)
© 2016-2022 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/gyungheejo/Downloads/emd_29288.map
Opened emd_29288.map as #1, grid size 340,340,340, pixel 1.08, shown at level
0.136, step 2, values float32
> set bgColor white
> lighting full
> lighting soft
> preset "overall look" "publication 1 (silhouettes)"
Using preset: Overall Look / Publication 1 (Silhouettes)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes t
lighting depthCue f
> volume #1 level 0.3543
> volume #1 step 1
> volume #1 level 0.6793
> volume #1 level 0.4471
> volume #1 level 0.3914
> open "/Users/gyungheejo/Desktop/HIV nanoparticles/gp41-free
> Env/38G-dn5_VRC01_PGT145_model_building/cryosparc_P383_J375_004_volume_map_sharp.mrc"
Opened cryosparc_P383_J375_004_volume_map_sharp.mrc as #2, grid size
360,360,360, pixel 0.725, shown at level 0.042, step 2, values float32
> open "/Users/gyungheejo/Desktop/HIV nanoparticles/gp41-free
> Env/38G-dn5_VRC01_PGT145_model_building/38G-dn5_VRC01_PGT145_model-
> coot-0-1.pdb"
Chain information for 38G-dn5_VRC01_PGT145_model-coot-0-1.pdb #3
---
Chain | Description
A B C | No description available
D F G | No description available
E H I | No description available
J | No description available
N | No description available
> style stick
Changed 19532 atom styles
> hide atoms
> show cartoons
> select add #3
19532 atoms, 20027 bonds, 15 pseudobonds, 2431 residues, 2 models selected
> select add #2
19532 atoms, 20027 bonds, 15 pseudobonds, 2431 residues, 4 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #2,1,0,0,29.297,0,1,0,-66.735,0,0,1,77.656,#3,1,0,0,29.297,0,1,0,-66.735,0,0,1,77.656
> ui mousemode right "rotate selected models"
> view matrix models
> #2,-0.71824,-0.68856,0.10014,330.29,0.667,-0.72232,-0.18268,72.226,0.19812,-0.06442,0.97806,61.44,#3,-0.71824,-0.68856,0.10014,330.29,0.667,-0.72232,-0.18268,72.226,0.19812,-0.06442,0.97806,61.44
> view matrix models
> #2,-0.86827,0.48718,0.093568,209.66,-0.49139,-0.87051,-0.027405,227.09,0.068101,-0.069773,0.99524,77.494,#3,-0.86827,0.48718,0.093568,209.66,-0.49139,-0.87051,-0.027405,227.09,0.068101,-0.069773,0.99524,77.494
> view matrix models
> #2,-0.80574,0.56733,0.17008,182.9,-0.57806,-0.81581,-0.017227,230.92,0.12898,-0.11219,0.98528,75.601,#3,-0.80574,0.56733,0.17008,182.9,-0.57806,-0.81581,-0.017227,230.92,0.12898,-0.11219,0.98528,75.601
> ui mousemode right "translate selected models"
> view matrix models
> #2,-0.80574,0.56733,0.17008,219.77,-0.57806,-0.81581,-0.017227,354.22,0.12898,-0.11219,0.98528,70.411,#3,-0.80574,0.56733,0.17008,219.77,-0.57806,-0.81581,-0.017227,354.22,0.12898,-0.11219,0.98528,70.411
> ui mousemode right "rotate selected models"
> view matrix models
> #2,-0.81797,0.57473,-0.024518,242.79,-0.57441,-0.81373,0.088867,341.34,0.031123,0.086774,0.99574,58.356,#3,-0.81797,0.57473,-0.024518,242.79,-0.57441,-0.81373,0.088867,341.34,0.031123,0.086774,0.99574,58.356
> ui mousemode right "translate selected models"
> view matrix models
> #2,-0.81797,0.57473,-0.024518,212.57,-0.57441,-0.81373,0.088867,353.4,0.031123,0.086774,0.99574,62.299,#3,-0.81797,0.57473,-0.024518,212.57,-0.57441,-0.81373,0.088867,353.4,0.031123,0.086774,0.99574,62.299
> view matrix models
> #2,-0.81797,0.57473,-0.024518,217.49,-0.57441,-0.81373,0.088867,356.46,0.031123,0.086774,0.99574,60.422,#3,-0.81797,0.57473,-0.024518,217.49,-0.57441,-0.81373,0.088867,356.46,0.031123,0.086774,0.99574,60.422
> view matrix models
> #2,-0.81797,0.57473,-0.024518,217.85,-0.57441,-0.81373,0.088867,354.9,0.031123,0.086774,0.99574,59.68,#3,-0.81797,0.57473,-0.024518,217.85,-0.57441,-0.81373,0.088867,354.9,0.031123,0.086774,0.99574,59.68
> view matrix models
> #2,-0.81797,0.57473,-0.024518,217.88,-0.57441,-0.81373,0.088867,359.24,0.031123,0.086774,0.99574,59.344,#3,-0.81797,0.57473,-0.024518,217.88,-0.57441,-0.81373,0.088867,359.24,0.031123,0.086774,0.99574,59.344
> ui mousemode right "rotate selected models"
> view matrix models
> #2,-0.74184,0.67006,-0.026283,196.44,-0.66911,-0.73706,0.095028,361.97,0.044302,0.088082,0.99513,57.496,#3,-0.74184,0.67006,-0.026283,196.44,-0.66911,-0.73706,0.095028,361.97,0.044302,0.088082,0.99513,57.496
> ui mousemode right "translate selected models"
> view matrix models
> #2,-0.74184,0.67006,-0.026283,197.72,-0.66911,-0.73706,0.095028,360.04,0.044302,0.088082,0.99513,57.582,#3,-0.74184,0.67006,-0.026283,197.72,-0.66911,-0.73706,0.095028,360.04,0.044302,0.088082,0.99513,57.582
> ui tool show "Fit in Map"
> fitmap #2 inMap #1
Fit map cryosparc_P383_J375_004_volume_map_sharp.mrc in map emd_29288.map
using 58286 points
correlation = 0.4844, correlation about mean = 0.07395, overlap = 875.4
steps = 88, shift = 3.06, angle = 4.68 degrees
Position of cryosparc_P383_J375_004_volume_map_sharp.mrc (#2) relative to
emd_29288.map (#1) coordinates:
Matrix rotation and translation
-0.75480538 0.65385965 0.05231059 191.93418708
-0.64889717 -0.75597487 0.08622336 362.51896301
0.09592347 0.03113766 0.99490157 55.80431271
Axis -0.04222259 -0.03342879 -0.99854883
Axis point 161.67393247 145.25858697 0.00000000
Rotation angle (degrees) 139.28286957
Shift along axis -75.94586023
> fitmap #3 inMap #2
Fit molecule 38G-dn5_VRC01_PGT145_model-coot-0-1.pdb (#3) to map
cryosparc_P383_J375_004_volume_map_sharp.mrc (#2) using 19532 atoms
average map value = 0.06954, steps = 76
shifted from previous position = 3.12
rotated from previous position = 4.67 degrees
atoms outside contour = 5924, contour level = 0.041973
Position of 38G-dn5_VRC01_PGT145_model-coot-0-1.pdb (#3) relative to
cryosparc_P383_J375_004_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
0.99999908 -0.00135638 -0.00005054 0.18486232
0.00135638 0.99999908 -0.00001292 -0.19293427
0.00005055 0.00001285 1.00000000 0.03504937
Axis 0.00949144 -0.03723800 0.99926135
Axis point 141.12764839 135.88777824 0.00000000
Rotation angle (degrees) 0.07777213
Shift along axis 0.04396258
> select subtract #3
2 models selected
> select add #3
19532 atoms, 20027 bonds, 15 pseudobonds, 2431 residues, 4 models selected
> select subtract #2
19532 atoms, 20027 bonds, 15 pseudobonds, 2431 residues, 2 models selected
> select subtract #3
Nothing selected
> hide #!3 models
> ui mousemode right zoom
> select add #2
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #2,-0.92684,0.3753,0.010926,253.17,-0.37387,-0.9252,0.065013,348.55,0.034508,0.056172,0.99782,60.666
> ui mousemode right "translate selected models"
> view matrix models
> #2,-0.92684,0.3753,0.010926,254.86,-0.37387,-0.9252,0.065013,346.74,0.034508,0.056172,0.99782,61.089
> ui tool show "Fit in Map"
> fitmap #2 inMap #1
Fit map cryosparc_P383_J375_004_volume_map_sharp.mrc in map emd_29288.map
using 58286 points
correlation = 0.6501, correlation about mean = 0.3589, overlap = 1628
steps = 80, shift = 0.854, angle = 5.02 degrees
Position of cryosparc_P383_J375_004_volume_map_sharp.mrc (#2) relative to
emd_29288.map (#1) coordinates:
Matrix rotation and translation
-0.91777319 0.39632317 0.02490618 249.73582404
-0.39679330 -0.91773184 -0.01798187 358.27689390
0.01573057 -0.02638589 0.99952806 74.87375333
Axis -0.01059489 0.01156764 -0.99987696
Axis point 161.60628792 153.82821933 0.00000000
Rotation angle (degrees) 156.63376174
Shift along axis -73.36604503
> select subtract #2
Nothing selected
> show #!3 models
> hide #!1 models
> fitmap #3 inMap #2
Fit molecule 38G-dn5_VRC01_PGT145_model-coot-0-1.pdb (#3) to map
cryosparc_P383_J375_004_volume_map_sharp.mrc (#2) using 19532 atoms
average map value = 0.06955, steps = 180
shifted from previous position = 4.38
rotated from previous position = 18.4 degrees
atoms outside contour = 5926, contour level = 0.041973
Position of 38G-dn5_VRC01_PGT145_model-coot-0-1.pdb (#3) relative to
cryosparc_P383_J375_004_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
0.99999939 -0.00110263 -0.00008114 0.15545980
0.00110263 0.99999939 0.00000998 -0.16212437
0.00008113 -0.00001007 1.00000000 0.02010091
Axis -0.00906331 -0.07337904 0.99726294
Axis point 145.07979836 141.16036299 0.00000000
Rotation angle (degrees) 0.06334956
Shift along axis 0.03053344
> hide #!3 models
> show #!3 models
> color #2 #ffffb287 models
> color #2 #929292 models transparency 0
> color #2 #929292c2 models
> color #2 #929292a4 models
> color #2 silver models transparency 0
> color #2 #c0c0c0ab models
> ui mousemode right "translate selected models"
> ui mousemode right zoom
> ui tool show "Side View"
> volume #2 step 1
> volume #2 level 0.03549
> show #!1 models
> hide #!2 models
> color #1 #b2b2b2a7 models
> color #1 #b2b2b2a8 models
> hide #!3 models
> show #!3 models
> show #!2 models
> hide #!3 models
> hide #!2 models
> open /Users/gyungheejo/Downloads/8flw.pdb
8flw.pdb title:
Cryo-em structure of PGT145 DU303 fab In complex with BG505 Ds- sosip.664
[more info...]
Chain information for 8flw.pdb #4
---
Chain | Description | UniProt
A B F | ENV polyprotein | Q2N0S6_9HIV1
C G I | ENV polyprotein | Q2N0S6_9HIV1
H | PGT145 DU303 heavy |
L | PGT145 DU303 light |
Non-standard residues in 8flw.pdb #4
---
BMA — β-D-mannopyranose (β-D-mannose; D-mannose; mannose)
MAN — α-D-mannopyranose (α-D-mannose; D-mannose; mannose)
NAG — 2-acetamido-2-deoxy-β-D-glucopyranose (N-acetyl-β-D-glucosamine;
2-acetamido-2-deoxy-β-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-acetyl-D-glucosamine)
TYS — O-sulfo-L-tyrosine
> hide #!1 models
> select add #4
16868 atoms, 17327 bonds, 9 pseudobonds, 2073 residues, 2 models selected
> style sel stick
Changed 16868 atom styles
> hide sel atoms
> show sel cartoons
> show #!1 models
> select subtract #4
Nothing selected
> show #!4 atoms
> show #!4 cartoons
> hide #!4 atoms
> show #!2 models
> hide #!1 models
> show #!1 models
> show #!3 models
> hide #!2 models
> hide #!1 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!3 models
> show #!1 models
> show #!4 atoms
> show #!2 models
> hide #!1 models
> color #2 #ffd479 models transparency 0
> color #2 #ffd479bf models
> color #2 #008f00 models transparency 0
> color #2 #009051 models transparency 0
> color #2 #0090517c models
> color #2 #ff2600 models transparency 0
> color #2 #ffd479 models transparency 0
> color #2 #ffd4799d models
> show #!1 models
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.4 (2022-06-03)
© 2016-2022 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 Metal - 83.1
OpenGL renderer: Apple M1 Pro
OpenGL vendor: Apple
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: MacBookPro18,3
Model Number: MKGQ3KH/A
Chip: Unknown
Total Number of Cores: 10 (8 performance and 2 efficiency)
Memory: 16 GB
System Firmware Version: 8422.141.2
OS Loader Version: 8422.141.2
Software:
System Software Overview:
System Version: macOS 13.5.1 (22G90)
Kernel Version: Darwin 22.6.0
Time since boot: 19일 23시간
Graphics/Displays:
Apple M1 Pro:
Chipset Model: Apple M1 Pro
Type: GPU
Bus: Built-In
Total Number of Cores: 16
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3024 x 1964 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: No
Connection Type: Internal
LG Ultra HD:
Resolution: 5120 x 2880 (5K/UHD+ - Ultra High Definition Plus)
UI Looks like: 2560 x 1440 @ 60.00Hz
Mirror: Off
Online: Yes
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 , 2 years ago
| Component: | Unassigned → General Controls |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash emitting color_pause signal |
comment:2 by , 2 years ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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Duplicate of #8783