![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 9 months ago
Closed 9 months ago
#16618 closed defect (duplicate)
Crash on Mac waking from sleep
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Window Toolkit | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-13.7-x86_64-i386-64bit
ChimeraX Version: 1.8.dev202403210048 (2024-03-21 00:48:29 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault
Current thread 0x00007ff85b574800 (most recent call first):
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 280 in event_loop
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 918 in init
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1069 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.surface._surface, chimerax.pdb_lib._load_libs, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif (total: 52)
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{
"uptime" : 79000,
"procRole" : "Background",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "MacBookPro16,1",
"coalitionID" : 5775,
"osVersion" : {
"train" : "macOS 13.7",
"build" : "22H123",
"releaseType" : "User"
},
"captureTime" : "2025-01-10 09:30:18.5164 -0800",
"incident" : "60995CB0-AA54-44FA-AC1A-11EC4E727AFD",
"pid" : 64270,
"cpuType" : "X86-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-01-09 10:47:40.6371 -0800",
"procStartAbsTime" : 65006010869736,
"procExitAbsTime" : 79429270642941,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX_Daily.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.8.0","CFBundleVersion":"1.8.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"7C6B2945-57E4-54F2-8371-8C23A25F1144","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "4B8C08D7-14BD-7948-C61A-CC411D179A37",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 0,
"wakeTime" : 152,
"bridgeVersion" : {"build":"22P353","train":"9.0"},
"sleepWakeUUID" : "FE7D9422-4417-4407-8128-645D529BFB5E",
"sip" : "enabled",
"vmRegionInfo" : "0 is not in any region. Bytes before following region: 4330123264\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 102187000-10218b000 [ 16K] r-x\/r-x SM=COW ...acOS\/ChimeraX",
"exception" : {"codes":"0x0000000000000001, 0x0000000000000000","rawCodes":[1,0],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000000000000000"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":64270},
"vmregioninfo" : "0 is not in any region. Bytes before following region: 4330123264\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 102187000-10218b000 [ 16K] r-x\/r-x SM=COW ...acOS\/ChimeraX",
"extMods" : {"caller":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"system":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"targeted":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"warnings":0},
"faultingThread" : 0,
"threads" : 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===== Log before crash start =====
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.8.dev202403210048 (2024-03-21)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/Users/yingyingjin/Dropbox/Current Writings/NAC_paper/structure
> PDB/E_NAC_K_1mer/E_NAC_K_1mercluster_s5.pdb"
Summary of feedback from opening /Users/yingyingjin/Dropbox/Current
Writings/NAC_paper/structure PDB/E_NAC_K_1mer/E_NAC_K_1mercluster_s5.pdb
---
warnings | Ignored bad PDB record found on line 1
REMARK GENERATED BY TRJCONV
Ignored bad PDB record found on line 3
REMARK THIS IS A SIMULATION BOX
Ignored bad PDB record found on line 285
REMARK GENERATED BY TRJCONV
Ignored bad PDB record found on line 287
REMARK THIS IS A SIMULATION BOX
Ignored bad PDB record found on line 569
REMARK GENERATED BY TRJCONV
3155 messages similar to the above omitted
E_NAC_K_1mercluster_s5.pdb title:
Protein in water t= 403700.00000 step= 1 [more info...]
Chain information for E_NAC_K_1mercluster_s5.pdb
---
Chain | Description
1.1/? 1.2/? 1.3/? 1.4/? 1.5/? 1.6/? 1.7/? 1.8/? 1.9/? 1.10/? 1.11/? 1.12/? 1.13/? 1.14/? 1.15/? 1.16/? 1.17/? 1.18/? 1.19/? 1.20/? 1.21/? 1.22/? 1.23/? 1.24/? 1.25/? 1.26/? 1.27/? 1.28/? 1.29/? 1.30/? 1.31/? 1.32/? 1.33/? 1.34/? 1.35/? 1.36/? 1.37/? 1.38/? 1.39/? 1.40/? 1.41/? 1.42/? 1.43/? 1.44/? 1.45/? 1.46/? 1.47/? 1.48/? 1.49/? 1.50/? 1.51/? 1.52/? 1.53/? 1.54/? 1.55/? 1.56/? 1.57/? 1.58/? 1.59/? 1.60/? 1.61/? 1.62/? 1.63/? 1.64/? 1.65/? 1.66/? 1.67/? 1.68/? 1.69/? 1.70/? 1.71/? 1.72/? 1.73/? 1.74/? 1.75/? 1.76/? 1.77/? 1.78/? 1.79/? 1.80/? 1.81/? 1.82/? 1.83/? 1.84/? 1.85/? 1.86/? 1.87/? 1.88/? 1.89/? 1.90/? 1.91/? 1.92/? 1.93/? 1.94/? 1.95/? 1.96/? 1.97/? 1.98/? 1.99/? 1.100/? 1.101/? 1.102/? 1.103/? 1.104/? 1.105/? 1.106/? 1.107/? 1.108/? 1.109/? 1.110/? 1.111/? 1.112/? 1.113/? 1.114/? 1.115/? 1.116/? 1.117/? 1.118/? 1.119/? 1.120/? 1.121/? 1.122/? 1.123/? 1.124/? 1.125/? 1.126/? 1.127/? 1.128/? 1.129/? 1.130/? 1.131/? 1.132/? 1.133/? 1.134/? 1.135/? 1.136/? 1.137/? 1.138/? 1.139/? 1.140/? 1.141/? 1.142/? 1.143/? 1.144/? 1.145/? 1.146/? 1.147/? 1.148/? 1.149/? 1.150/? 1.151/? 1.152/? 1.153/? 1.154/? 1.155/? 1.156/? 1.157/? 1.158/? 1.159/? 1.160/? 1.161/? 1.162/? 1.163/? 1.164/? 1.165/? 1.166/? 1.167/? 1.168/? 1.169/? 1.170/? 1.171/? 1.172/? 1.173/? 1.174/? 1.175/? 1.176/? 1.177/? 1.178/? 1.179/? 1.180/? 1.181/? 1.182/? 1.183/? 1.184/? 1.185/? 1.186/? 1.187/? 1.188/? 1.189/? 1.190/? 1.191/? 1.192/? 1.193/? 1.194/? 1.195/? 1.196/? 1.197/? 1.198/? 1.199/? 1.200/? 1.201/? 1.202/? 1.203/? 1.204/? 1.205/? 1.206/? 1.207/? 1.208/? 1.209/? 1.210/? 1.211/? 1.212/? 1.213/? 1.214/? 1.215/? 1.216/? 1.217/? 1.218/? 1.219/? 1.220/? 1.221/? 1.222/? 1.223/? 1.224/? 1.225/? 1.226/? 1.227/? 1.228/? 1.229/? 1.230/? 1.231/? 1.232/? 1.233/? 1.234/? 1.235/? 1.236/? 1.237/? 1.238/? 1.239/? 1.240/? 1.241/? 1.242/? 1.243/? 1.244/? 1.245/? 1.246/? 1.247/? 1.248/? 1.249/? 1.250/? 1.251/? 1.252/? 1.253/? 1.254/? 1.255/? 1.256/? 1.257/? 1.258/? 1.259/? 1.260/? 1.261/? 1.262/? 1.263/? 1.264/? 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1.390/? 1.391/? 1.392/? 1.393/? 1.394/? 1.395/? 1.396/? 1.397/? 1.398/? 1.399/? 1.400/? 1.401/? 1.402/? 1.403/? 1.404/? 1.405/? 1.406/? 1.407/? 1.408/? 1.409/? 1.410/? 1.411/? 1.412/? 1.413/? 1.414/? 1.415/? 1.416/? 1.417/? 1.418/? 1.419/? 1.420/? 1.421/? 1.422/? 1.423/? 1.424/? 1.425/? 1.426/? 1.427/? 1.428/? 1.429/? 1.430/? 1.431/? 1.432/? 1.433/? 1.434/? 1.435/? 1.436/? 1.437/? 1.438/? 1.439/? 1.440/? 1.441/? 1.442/? 1.443/? 1.444/? 1.445/? 1.446/? 1.447/? 1.448/? 1.449/? 1.450/? 1.451/? 1.452/? 1.453/? 1.454/? 1.455/? 1.456/? 1.457/? 1.458/? 1.459/? 1.460/? 1.461/? 1.462/? 1.463/? 1.464/? 1.465/? 1.466/? 1.467/? 1.468/? 1.469/? 1.470/? 1.471/? 1.472/? 1.473/? 1.474/? 1.475/? 1.476/? 1.477/? 1.478/? 1.479/? 1.480/? 1.481/? 1.482/? 1.483/? 1.484/? 1.485/? 1.486/? 1.487/? 1.488/? 1.489/? 1.490/? 1.491/? 1.492/? 1.493/? 1.494/? 1.495/? 1.496/? 1.497/? 1.498/? 1.499/? 1.500/? 1.501/? 1.502/? 1.503/? 1.504/? 1.505/? 1.506/? 1.507/? 1.508/? 1.509/? 1.510/? 1.511/? 1.512/? 1.513/? 1.514/? 1.515/? 1.516/? 1.517/? 1.518/? 1.519/? 1.520/? 1.521/? 1.522/? 1.523/? 1.524/? 1.525/? 1.526/? 1.527/? 1.528/? 1.529/? 1.530/? 1.531/? 1.532/? 1.533/? 1.534/? 1.535/? 1.536/? 1.537/? 1.538/? 1.539/? 1.540/? 1.541/? 1.542/? 1.543/? 1.544/? 1.545/? 1.546/? 1.547/? 1.548/? 1.549/? 1.550/? 1.551/? 1.552/? 1.553/? 1.554/? 1.555/? 1.556/? 1.557/? 1.558/? 1.559/? 1.560/? 1.561/? 1.562/? 1.563/? 1.564/? 1.565/? 1.566/? 1.567/? 1.568/? 1.569/? 1.570/? 1.571/? 1.572/? 1.573/? 1.574/? 1.575/? 1.576/? 1.577/? 1.578/? 1.579/? 1.580/? 1.581/? 1.582/? 1.583/? 1.584/? 1.585/? 1.586/? 1.587/? 1.588/? 1.589/? 1.590/? 1.591/? 1.592/? 1.593/? 1.594/? 1.595/? 1.596/? 1.597/? 1.598/? 1.599/? 1.600/? 1.601/? 1.602/? 1.603/? 1.604/? 1.605/? 1.606/? 1.607/? 1.608/? 1.609/? 1.610/? 1.611/? 1.612/? 1.613/? 1.614/? 1.615/? 1.616/? 1.617/? 1.618/? 1.619/? 1.620/? 1.621/? 1.622/? 1.623/? 1.624/? 1.625/? 1.626/? 1.627/? 1.628/? 1.629/? 1.630/? 1.631/? 1.632/? 1.633/? 1.634/? 1.635/? 1.636/? 1.637/? 1.638/? 1.639/? 1.640/? 1.641/? 1.642/? 1.643/? 1.644/? 1.645/? 1.646/? 1.647/? 1.648/? 1.649/? 1.650/? 1.651/? 1.652/? 1.653/? 1.654/? 1.655/? 1.656/? 1.657/? 1.658/? 1.659/? 1.660/? 1.661/? 1.662/? 1.663/? 1.664/? 1.665/? 1.666/? 1.667/? 1.668/? 1.669/? 1.670/? 1.671/? 1.672/? 1.673/? 1.674/? 1.675/? 1.676/? 1.677/? 1.678/? 1.679/? 1.680/? 1.681/? 1.682/? 1.683/? 1.684/? 1.685/? 1.686/? 1.687/? 1.688/? 1.689/? 1.690/? 1.691/? 1.692/? 1.693/? 1.694/? 1.695/? 1.696/? 1.697/? 1.698/? 1.699/? 1.700/? 1.701/? 1.702/? 1.703/? 1.704/? 1.705/? 1.706/? 1.707/? 1.708/? 1.709/? 1.710/? 1.711/? 1.712/? 1.713/? 1.714/? 1.715/? 1.716/? 1.717/? 1.718/? 1.719/? 1.720/? 1.721/? 1.722/? 1.723/? 1.724/? 1.725/? 1.726/? 1.727/? 1.728/? 1.729/? 1.730/? 1.731/? 1.732/? 1.733/? 1.734/? 1.735/? 1.736/? 1.737/? 1.738/? 1.739/? 1.740/? 1.741/? 1.742/? 1.743/? 1.744/? 1.745/? 1.746/? 1.747/? 1.748/? 1.749/? 1.750/? 1.751/? 1.752/? 1.753/? 1.754/? 1.755/? 1.756/? 1.757/? 1.758/? 1.759/? 1.760/? 1.761/? 1.762/? 1.763/? 1.764/? 1.765/? 1.766/? 1.767/? 1.768/? 1.769/? 1.770/? 1.771/? 1.772/? 1.773/? 1.774/? 1.775/? 1.776/? 1.777/? 1.778/? 1.779/? 1.780/? 1.781/? 1.782/? 1.783/? 1.784/? 1.785/? 1.786/? 1.787/? 1.788/? 1.789/? 1.790/? 1.791/? 1.792/? 1.793/? 1.794/? 1.795/? 1.796/? 1.797/? 1.798/? 1.799/? 1.800/? 1.801/? 1.802/? 1.803/? 1.804/? 1.805/? 1.806/? 1.807/? 1.808/? 1.809/? 1.810/? 1.811/? 1.812/? 1.813/? 1.814/? 1.815/? 1.816/? 1.817/? 1.818/? 1.819/? 1.820/? 1.821/? 1.822/? 1.823/? 1.824/? 1.825/? 1.826/? 1.827/? 1.828/? 1.829/? 1.830/? 1.831/? 1.832/? 1.833/? 1.834/? 1.835/? 1.836/? 1.837/? 1.838/? 1.839/? 1.840/? 1.841/? 1.842/? 1.843/? 1.844/? 1.845/? 1.846/? 1.847/? 1.848/? 1.849/? 1.850/? 1.851/? 1.852/? 1.853/? 1.854/? 1.855/? 1.856/? 1.857/? 1.858/? 1.859/? 1.860/? 1.861/? 1.862/? 1.863/? 1.864/? 1.865/? 1.866/? 1.867/? 1.868/? 1.869/? 1.870/? 1.871/? 1.872/? 1.873/? 1.874/? 1.875/? 1.876/? 1.877/? 1.878/? 1.879/? 1.880/? 1.881/? 1.882/? 1.883/? 1.884/? 1.885/? 1.886/? 1.887/? 1.888/? 1.889/? 1.890/? 1.891/? 1.892/? 1.893/? 1.894/? 1.895/? 1.896/? 1.897/? 1.898/? 1.899/? 1.900/? 1.901/? 1.902/? 1.903/? 1.904/? 1.905/? 1.906/? 1.907/? 1.908/? 1.909/? 1.910/? 1.911/? 1.912/? 1.913/? 1.914/? 1.915/? 1.916/? 1.917/? 1.918/? 1.919/? 1.920/? 1.921/? 1.922/? 1.923/? 1.924/? 1.925/? 1.926/? 1.927/? 1.928/? 1.929/? 1.930/? 1.931/? 1.932/? 1.933/? 1.934/? 1.935/? 1.936/? 1.937/? 1.938/? 1.939/? 1.940/? 1.941/? 1.942/? 1.943/? 1.944/? 1.945/? 1.946/? 1.947/? 1.948/? 1.949/? 1.950/? 1.951/? 1.952/? 1.953/? 1.954/? 1.955/? 1.956/? 1.957/? 1.958/? 1.959/? 1.960/? 1.961/? 1.962/? 1.963/? 1.964/? 1.965/? 1.966/? 1.967/? 1.968/? 1.969/? 1.970/? 1.971/? 1.972/? 1.973/? 1.974/? 1.975/? 1.976/? 1.977/? 1.978/? 1.979/? 1.980/? 1.981/? 1.982/? 1.983/? 1.984/? 1.985/? 1.986/? 1.987/? 1.988/? 1.989/? 1.990/? 1.991/? 1.992/? 1.993/? 1.994/? 1.995/? 1.996/? 1.997/? 1.998/? 1.999/? 1.1000/? 1.1001/? 1.1002/? 1.1003/? 1.1004/? 1.1005/? 1.1006/? 1.1007/? 1.1008/? 1.1009/? 1.1010/? 1.1011/? 1.1012/? 1.1013/? 1.1014/? 1.1015/? 1.1016/? 1.1017/? 1.1018/? 1.1019/? 1.1020/? 1.1021/? 1.1022/? 1.1023/? 1.1024/? 1.1025/? 1.1026/? 1.1027/? 1.1028/? 1.1029/? 1.1030/? 1.1031/? 1.1032/? 1.1033/? 1.1034/? 1.1035/? 1.1036/? 1.1037/? 1.1038/? 1.1039/? 1.1040/? 1.1041/? 1.1042/? 1.1043/? 1.1044/? 1.1045/? 1.1046/? 1.1047/? 1.1048/? 1.1049/? 1.1050/? 1.1051/? 1.1052/? 1.1053/? 1.1054/? 1.1055/? 1.1056/? 1.1057/? 1.1058/? 1.1059/? 1.1060/? 1.1061/? 1.1062/? 1.1063/? 1.1064/? 1.1065/? 1.1066/? 1.1067/? 1.1068/? 1.1069/? 1.1070/? 1.1071/? 1.1072/? 1.1073/? 1.1074/? 1.1075/? 1.1076/? 1.1077/? 1.1078/? 1.1079/? 1.1080/? 1.1081/? 1.1082/? 1.1083/? 1.1084/? 1.1085/? 1.1086/? 1.1087/? 1.1088/? 1.1089/? 1.1090/? 1.1091/? 1.1092/? 1.1093/? 1.1094/? 1.1095/? 1.1096/? 1.1097/? 1.1098/? 1.1099/? 1.1100/? 1.1101/? 1.1102/? 1.1103/? 1.1104/? 1.1105/? 1.1106/? 1.1107/? 1.1108/? 1.1109/? 1.1110/? 1.1111/? 1.1112/? 1.1113/? 1.1114/? 1.1115/? 1.1116/? 1.1117/? 1.1118/? 1.1119/? 1.1120/? 1.1121/? 1.1122/? 1.1123/? 1.1124/? 1.1125/? 1.1126/? 1.1127/? 1.1128/? 1.1129/? 1.1130/? 1.1131/? 1.1132/? 1.1133/? 1.1134/? 1.1135/? 1.1136/? 1.1137/? 1.1138/? 1.1139/? 1.1140/? 1.1141/? 1.1142/? 1.1143/? 1.1144/? 1.1145/? 1.1146/? 1.1147/? 1.1148/? 1.1149/? 1.1150/? 1.1151/? 1.1152/? 1.1153/? 1.1154/? 1.1155/? 1.1156/? 1.1157/? 1.1158/? 1.1159/? 1.1160/? 1.1161/? 1.1162/? 1.1163/? 1.1164/? 1.1165/? 1.1166/? 1.1167/? 1.1168/? 1.1169/? 1.1170/? 1.1171/? 1.1172/? 1.1173/? 1.1174/? 1.1175/? 1.1176/? 1.1177/? 1.1178/? 1.1179/? 1.1180/? 1.1181/? 1.1182/? 1.1183/? 1.1184/? 1.1185/? 1.1186/? 1.1187/? 1.1188/? 1.1189/? 1.1190/? 1.1191/? 1.1192/? 1.1193/? 1.1194/? 1.1195/? 1.1196/? 1.1197/? 1.1198/? 1.1199/? 1.1200/? 1.1201/? 1.1202/? 1.1203/? 1.1204/? 1.1205/? 1.1206/? 1.1207/? 1.1208/? 1.1209/? 1.1210/? 1.1211/? 1.1212/? 1.1213/? 1.1214/? 1.1215/? 1.1216/? 1.1217/? 1.1218/? 1.1219/? 1.1220/? 1.1221/? 1.1222/? 1.1223/? 1.1224/? 1.1225/? 1.1226/? 1.1227/? 1.1228/? 1.1229/? 1.1230/? 1.1231/? 1.1232/? 1.1233/? 1.1234/? 1.1235/? 1.1236/? 1.1237/? 1.1238/? 1.1239/? 1.1240/? 1.1241/? 1.1242/? 1.1243/? 1.1244/? 1.1245/? 1.1246/? 1.1247/? 1.1248/? 1.1249/? 1.1250/? 1.1251/? 1.1252/? 1.1253/? 1.1254/? 1.1255/? 1.1256/? 1.1257/? 1.1258/? 1.1259/? 1.1260/? 1.1261/? 1.1262/? 1.1263/? 1.1264/? 1.1265/? 1.1266/? 1.1267/? 1.1268/? 1.1269/? 1.1270/? 1.1271/? 1.1272/? 1.1273/? 1.1274/? 1.1275/? 1.1276/? 1.1277/? 1.1278/? 1.1279/? 1.1280/? 1.1281/? 1.1282/? 1.1283/? 1.1284/? 1.1285/? 1.1286/? 1.1287/? 1.1288/? 1.1289/? 1.1290/? 1.1291/? 1.1292/? 1.1293/? 1.1294/? 1.1295/? 1.1296/? 1.1297/? 1.1298/? 1.1299/? 1.1300/? 1.1301/? 1.1302/? 1.1303/? 1.1304/? 1.1305/? 1.1306/? 1.1307/? 1.1308/? 1.1309/? 1.1310/? 1.1311/? 1.1312/? 1.1313/? 1.1314/? 1.1315/? 1.1316/? 1.1317/? 1.1318/? 1.1319/? 1.1320/? 1.1321/? 1.1322/? 1.1323/? 1.1324/? 1.1325/? 1.1326/? 1.1327/? 1.1328/? 1.1329/? 1.1330/? 1.1331/? 1.1332/? 1.1333/? 1.1334/? 1.1335/? 1.1336/? 1.1337/? 1.1338/? 1.1339/? 1.1340/? 1.1341/? 1.1342/? 1.1343/? 1.1344/? 1.1345/? 1.1346/? 1.1347/? 1.1348/? 1.1349/? 1.1350/? 1.1351/? 1.1352/? 1.1353/? 1.1354/? 1.1355/? 1.1356/? 1.1357/? 1.1358/? 1.1359/? 1.1360/? 1.1361/? 1.1362/? 1.1363/? 1.1364/? 1.1365/? 1.1366/? 1.1367/? 1.1368/? 1.1369/? 1.1370/? 1.1371/? 1.1372/? 1.1373/? 1.1374/? 1.1375/? 1.1376/? 1.1377/? 1.1378/? 1.1379/? 1.1380/? 1.1381/? 1.1382/? 1.1383/? 1.1384/? 1.1385/? 1.1386/? 1.1387/? 1.1388/? 1.1389/? 1.1390/? 1.1391/? 1.1392/? 1.1393/? 1.1394/? 1.1395/? 1.1396/? 1.1397/? 1.1398/? 1.1399/? 1.1400/? 1.1401/? 1.1402/? 1.1403/? 1.1404/? 1.1405/? 1.1406/? 1.1407/? 1.1408/? 1.1409/? 1.1410/? 1.1411/? 1.1412/? 1.1413/? 1.1414/? 1.1415/? 1.1416/? 1.1417/? 1.1418/? 1.1419/? 1.1420/? 1.1421/? 1.1422/? 1.1423/? 1.1424/? 1.1425/? 1.1426/? 1.1427/? 1.1428/? 1.1429/? 1.1430/? 1.1431/? 1.1432/? 1.1433/? 1.1434/? 1.1435/? 1.1436/? 1.1437/? 1.1438/? 1.1439/? 1.1440/? 1.1441/? 1.1442/? 1.1443/? 1.1444/? 1.1445/? 1.1446/? 1.1447/? 1.1448/? 1.1449/? 1.1450/? 1.1451/? 1.1452/? 1.1453/? 1.1454/? 1.1455/? 1.1456/? 1.1457/? 1.1458/? 1.1459/? 1.1460/? 1.1461/? 1.1462/? 1.1463/? 1.1464/? 1.1465/? 1.1466/? 1.1467/? 1.1468/? 1.1469/? 1.1470/? 1.1471/? 1.1472/? 1.1473/? 1.1474/? 1.1475/? 1.1476/? 1.1477/? 1.1478/? 1.1479/? 1.1480/? 1.1481/? 1.1482/? 1.1483/? 1.1484/? 1.1485/? 1.1486/? 1.1487/? 1.1488/? 1.1489/? 1.1490/? 1.1491/? 1.1492/? 1.1493/? 1.1494/? 1.1495/? 1.1496/? 1.1497/? 1.1498/? 1.1499/? 1.1500/? 1.1501/? 1.1502/? 1.1503/? 1.1504/? 1.1505/? 1.1506/? 1.1507/? 1.1508/? 1.1509/? 1.1510/? 1.1511/? 1.1512/? 1.1513/? 1.1514/? 1.1515/? 1.1516/? 1.1517/? 1.1518/? 1.1519/? 1.1520/? 1.1521/? 1.1522/? 1.1523/? 1.1524/? 1.1525/? 1.1526/? 1.1527/? 1.1528/? 1.1529/? 1.1530/? 1.1531/? 1.1532/? 1.1533/? 1.1534/? 1.1535/? 1.1536/? 1.1537/? 1.1538/? 1.1539/? 1.1540/? 1.1541/? 1.1542/? 1.1543/? 1.1544/? 1.1545/? 1.1546/? 1.1547/? 1.1548/? 1.1549/? 1.1550/? 1.1551/? 1.1552/? 1.1553/? 1.1554/? 1.1555/? 1.1556/? 1.1557/? 1.1558/? 1.1559/? 1.1560/? 1.1561/? 1.1562/? 1.1563/? 1.1564/? 1.1565/? 1.1566/? 1.1567/? 1.1568/? 1.1569/? 1.1570/? 1.1571/? 1.1572/? 1.1573/? 1.1574/? 1.1575/? 1.1576/? 1.1577/? 1.1578/? 1.1579/? 1.1580/? | No description available
> hide #1.2-1580 target m
> show #1.2 models
> show #1.1-2 atoms
> hide #1.1 models
> show #1.1 models
> color #1.1 #a7d8a7ff
> color #1.2 #de604eff
> show #1.1-2 atoms
> set bgColor white
> lighting full
> lighting soft
> graphics silhouettes true
> hide #1.2 models
> show #1.3 models
> hide #1.3 models
> show #1.3 models
> show #1.2 models
> hide #1.2 models
> hide #1.3 models
> show #1.2 models
> hide #1.2 models
> hide #1.1 models
> show #1.3 models
> show #1.3 atoms
> hide #1.3 atoms
===== Log before crash end =====
Log:
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.8.dev202403210048 (2024-03-21)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/Users/yingyingjin/Dropbox/Current Writings/NAC_paper/structure
> PDB/nac_6merC/nac_6merC_md_0_5_ccsView_s5.pdb"
Summary of feedback from opening /Users/yingyingjin/Dropbox/Current
Writings/NAC_paper/structure PDB/nac_6merC/nac_6merC_md_0_5_ccsView_s5.pdb
---
warnings | Ignored bad PDB record found on line 1
REMARK GENERATED BY TRJCONV
Ignored bad PDB record found on line 3
REMARK THIS IS A SIMULATION BOX
Ignored bad PDB record found on line 842
REMARK GENERATED BY TRJCONV
Ignored bad PDB record found on line 844
REMARK THIS IS A SIMULATION BOX
Ignored bad PDB record found on line 1683
REMARK GENERATED BY TRJCONV
17 messages similar to the above omitted
nac_6merC_md_0_5_ccsView_s5.pdb title:
Protein in water t= 0.00000 step= 0 [more info...]
Chain information for nac_6merC_md_0_5_ccsView_s5.pdb
---
Chain | Description
1.1/A 1.2/A 1.3/A 1.4/A 1.5/A 1.6/A 1.7/A 1.8/A 1.9/A 1.10/A 1.11/A 1.1/B 1.2/B 1.3/B 1.4/B 1.5/B 1.6/B 1.7/B 1.8/B 1.9/B 1.10/B 1.11/B 1.1/C 1.2/C 1.3/C 1.4/C 1.5/C 1.6/C 1.7/C 1.8/C 1.9/C 1.10/C 1.11/C 1.1/D 1.2/D 1.3/D 1.4/D 1.5/D 1.6/D 1.7/D 1.8/D 1.9/D 1.10/D 1.11/D 1.1/E 1.2/E 1.3/E 1.4/E 1.5/E 1.6/E 1.7/E 1.8/E 1.9/E 1.10/E 1.11/E 1.1/F 1.2/F 1.3/F 1.4/F 1.5/F 1.6/F 1.7/F 1.8/F 1.9/F 1.10/F 1.11/F | No description available
> show atoms
> hide atoms
> show cartoons
> show atoms
> show cartoons
> style stick
Changed 9174 atom styles
> hide atoms
> hide #1.2-11 target m
> show #1.2 models
> hide #1.2 models
> show #1.3 models
> hide #1.3 models
> show #1.4 models
> hide #1.4 models
> show #1.5 models
> hide #1.5 models
> hide #1.1 models
> show #1.2 models
> show #1.3 models
> hide #1.3 models
> hide #1.2 models
> show #1.2 models
> hide #1.2 models
> show #1.1 models
> show #1.11 models
> hide #1.11 models
> show #1.2 models
> select add #1.2
834 atoms, 828 bonds, 66 residues, 1 model selected
> select clear
> select add #1.2
834 atoms, 828 bonds, 66 residues, 1 model selected
> ui mousemode right rotate
> ui mousemode right "rotate selected models"
> view matrix models
> #1.2,0.15824,-0.31994,0.93413,33.263,0.43908,0.87017,0.22365,-19.277,-0.8844,0.37477,0.27817,39.562
> view matrix models
> #1.2,-0.14017,-0.41093,0.90083,52.18,0.79359,0.49743,0.35039,-20.953,-0.59209,0.764,0.25638,8.0515
> select subtract #1.2
Nothing selected
> color #1.1 #d1ad7fff
> color #1.2 #de604eff
> lighting soft
> set bgColor white
> graphics silhouettes true
OpenGL version: 4.1 ATI-4.14.1
OpenGL renderer: AMD Radeon Pro 5300M OpenGL Engine
OpenGL vendor: ATI Technologies Inc.
Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro16,1
Processor Name: 6-Core Intel Core i7
Processor Speed: 2.6 GHz
Number of Processors: 1
Total Number of Cores: 6
L2 Cache (per Core): 256 KB
L3 Cache: 12 MB
Hyper-Threading Technology: Enabled
Memory: 16 GB
System Firmware Version: 2069.0.0.0.0 (iBridge: 22.16.10353.0.0,0)
OS Loader Version: 577.140.2~30
Software:
System Software Overview:
System Version: macOS 13.7 (22H123)
Kernel Version: Darwin 22.6.0
Time since boot: 2 days, 3 hours, 50 minutes
Graphics/Displays:
Intel UHD Graphics 630:
Chipset Model: Intel UHD Graphics 630
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x3e9b
Revision ID: 0x0000
Automatic Graphics Switching: Supported
gMux Version: 5.0.0
Metal Support: Metal 3
AMD Radeon Pro 5300M:
Chipset Model: AMD Radeon Pro 5300M
Type: GPU
Bus: PCIe
PCIe Lane Width: x16
VRAM (Total): 4 GB
Vendor: AMD (0x1002)
Device ID: 0x7340
Revision ID: 0x0043
ROM Revision: 113-D3220E-190
VBIOS Version: 113-D32207P1-019
Option ROM Version: 113-D32207P1-019
EFI Driver Version: 01.A1.190
Automatic Graphics Switching: Supported
gMux Version: 5.0.0
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 3072 x 1920 Retina
Framebuffer Depth: 24-Bit Color (ARGB8888)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
alabaster: 0.7.16
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 2.4.1
Babel: 2.14.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 2.0.0
build: 1.1.1
certifi: 2023.11.17
cftime: 1.6.3
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.16
ChimeraX-AddH: 2.2.5
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.4.3
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.5
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.56
ChimeraX-AtomicLibrary: 14.0.2
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.12.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.5
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.8.dev202403210048
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.3
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-Label: 1.1.9
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.1.4
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.1.3
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.15
ChimeraX-ModelPanel: 1.5
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.1
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.1
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.3
ChimeraX-PDB: 2.7.5
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.1
ChimeraX-PubChem: 2.1
ChimeraX-QScore: 1.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.3
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.2
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 1.0
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.11.2
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StarMap: 1.2.15
ChimeraX-StdCommands: 1.16.3
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.37.1
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.3.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.3
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.2.0
cxservices: 1.2.2
cycler: 0.12.1
Cython: 3.0.9
debugpy: 1.8.1
decorator: 5.1.1
docutils: 0.20.1
executing: 2.0.1
filelock: 3.13.1
fonttools: 4.50.0
funcparserlib: 2.0.0a0
glfw: 2.7.0
grako: 3.16.5
h5py: 3.10.0
html2text: 2024.2.26
idna: 3.6
ihm: 0.43
imagecodecs: 2024.1.1
imagesize: 1.4.1
ipykernel: 6.29.2
ipython: 8.21.0
ipywidgets: 8.1.2
jedi: 0.19.1
Jinja2: 3.1.3
jupyter-client: 8.6.0
jupyter-core: 5.7.2
jupyterlab-widgets: 3.0.10
kiwisolver: 1.4.5
line-profiler: 4.1.2
lxml: 5.1.0
lz4: 4.3.3
MarkupSafe: 2.1.5
matplotlib: 3.8.3
matplotlib-inline: 0.1.6
MolecularDynamicsViewer: 1.4
msgpack: 1.0.8
ndindex: 1.8
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.2.1
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.9.0
numpy: 1.26.4
openvr: 1.26.701
packaging: 23.2
ParmEd: 4.2.2
parso: 0.8.3
pep517: 0.13.1
pexpect: 4.9.0
pillow: 10.2.0
pip: 24.0
pkginfo: 1.10.0
platformdirs: 4.2.0
prompt-toolkit: 3.0.43
psutil: 5.9.8
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.3.0
pygments: 2.17.2
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3302
pyparsing: 3.1.2
pyproject-hooks: 1.0.0
PyQt6-commercial: 6.6.1
PyQt6-Qt6: 6.6.2
PyQt6-sip: 13.6.0
PyQt6-WebEngine-commercial: 6.6.0
PyQt6-WebEngine-Qt6: 6.6.2
pyqtgraph: 0.13.6
python-dateutil: 2.9.0.post0
pytz: 2024.1
pyzmq: 25.1.2
qtconsole: 5.5.1
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.12.0
setuptools: 69.2.0
setuptools-scm: 8.0.4
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 7.2.6
sphinx-autodoc-typehints: 2.0.0
sphinxcontrib-applehelp: 1.0.8
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.6
sphinxcontrib-htmlhelp: 2.0.5
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.7
sphinxcontrib-serializinghtml: 1.1.10
stack-data: 0.6.3
superqt: 0.6.1
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2024.1.30
tinyarray: 1.2.4
tornado: 6.4
traitlets: 5.14.1
typing-extensions: 4.10.0
tzdata: 2024.1
urllib3: 2.2.1
wcwidth: 0.2.13
webcolors: 1.13
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.10
Change History (2)
comment:1 by , 9 months ago
| Component: | Unassigned → Window Toolkit |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash on Mac waking from sleep |
comment:2 by , 9 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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