id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 17375 Crash moving window between screens chimerax-bug-report@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-14.6.1-arm64-arm-64bit ChimeraX Version: 1.8 (2024-06-10 23:15:52 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 0x0000000203d48f40 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 315 in event_loop File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1003 in init File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1166 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, chimerax.pdb_lib._load_libs, chimerax.surface._surface, 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.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, psutil._psutil_osx, psutil._psutil_posix, PIL._imagingmath, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif (total: 57) {""app_name"":""ChimeraX"",""timestamp"":""2025-04-14 15:28:32.00 -0500"",""app_version"":""1.8.0"",""slice_uuid"":""17982d98-65bc-3327-8526-577ec996453c"",""build_version"":""1.8.0.0"",""platform"":1,""bundleID"":""edu.ucsf.cgl.ChimeraX"",""share_with_app_devs"":0,""is_first_party"":0,""bug_type"":""309"",""os_version"":""macOS 14.6.1 (23G93)"",""roots_installed"":0,""name"":""ChimeraX"",""incident_id"":""CC16A03D-9825-4EA6-978A-76DDBE17BBB8""} { ""uptime"" : 1700000, ""procRole"" : ""Foreground"", ""version"" : 2, ""userID"" : 505, ""deployVersion"" : 210, ""modelCode"" : ""Mac14,7"", ""coalitionID"" : 4691, ""osVersion"" : { ""train"" : ""macOS 14.6.1"", ""build"" : ""23G93"", ""releaseType"" : ""User"" }, ""captureTime"" : ""2025-04-14 15:28:16.4130 -0500"", ""codeSigningMonitor"" : 1, ""incident"" : ""CC16A03D-9825-4EA6-978A-76DDBE17BBB8"", ""pid"" : 40011, ""translated"" : false, ""cpuType"" : ""ARM-64"", ""roots_installed"" : 0, ""bug_type"" : ""309"", ""procLaunch"" : ""2025-04-13 13:38:09.1422 -0500"", ""procStartAbsTime"" : 41842429750593, ""procExitAbsTime"" : 42557754671139, ""procName"" : ""ChimeraX"", ""procPath"" : ""\/Applications\/ChimeraX-1.8.app\/Contents\/MacOS\/ChimeraX"", ""bundleInfo"" : {""CFBundleShortVersionString"":""1.8.0"",""CFBundleVersion"":""1.8.0.0"",""CFBundleIdentifier"":""edu.ucsf.cgl.ChimeraX""}, ""storeInfo"" : {""deviceIdentifierForVendor"":""196C1F65-08EB-5B0B-A775-7FD2C1C1733F"",""thirdParty"":true}, ""parentProc"" : ""launchd"", ""parentPid"" : 1, ""coalitionName"" : ""edu.ucsf.cgl.ChimeraX"", ""crashReporterKey"" : ""69C4FDCB-8FA8-9030-32AB-19B3569E58C9"", ""codeSigningID"" : ""edu.ucsf.cgl.ChimeraX"", ""codeSigningTeamID"" : ""LWV8X224YF"", ""codeSigningFlags"" : 570491649, ""codeSigningValidationCategory"" : 6, ""codeSigningTrustLevel"" : 4294967295, ""instructionByteStream"" : {""beforePC"":""fyMD1f17v6n9AwCRd+D\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A=="",""atPC"":""AwEAVH8jA9X9e7+p\/QMAkWzg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g==""}, ""wakeTime"" : 1532, ""sleepWakeUUID"" : ""994F11C2-A590-4492-BC5D-A29B3769706A"", ""sip"" : ""enabled"", ""vmRegionInfo"" : ""0x4235303f5348 is not in any region. 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""deploymentId"" : 400000008 } ] } } ===== Log before crash start ===== Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 1.8 (2024-06-10) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /Users/Wan01305/Downloads/cryosparc_P73_J458_map_sharp.mrc Opened cryosparc_P73_J458_map_sharp.mrc as #1, grid size 384,384,384, pixel 0.885, shown at level 0.00073, step 2, values float32 > volume #1 step 1 > volume #1 level 0.01 > set bgColor white > surface dust #1 size 8.85 > open ""/Users/Wan01305/Downloads/cryosparc_P73_J455_map_sharp (1).mrc"" Opened cryosparc_P73_J455_map_sharp (1).mrc as #2, grid size 384,384,384, pixel 0.885, shown at level 0.000753, step 2, values float32 > volume #2 step 1 > volume #2 level 0.0001 > volume #2 level 0.01 > surface dust #1 size 8.85 > surface dust #2 size 8.85 > select add #2 2 models selected > ui mousemode right ""rotate selected models"" > view matrix models > #2,0.70936,0.35087,-0.6113,90.297,0.55095,-0.81695,0.17043,196.18,-0.4396,-0.4577,-0.77283,451.82 > view matrix models > #2,0.5227,0.74199,0.4198,-124.52,-0.65331,0.032276,0.7564,138.81,0.54769,-0.66963,0.50162,114.53 > view matrix models > #2,0.23005,0.93489,-0.27029,6.7345,-0.94078,0.28471,0.18404,238.82,0.24901,0.21194,0.94503,-66.021 > view matrix models > #2,0.87166,-0.33999,-0.35302,139.09,-0.45782,-0.82196,-0.3388,442.73,-0.17498,0.45694,-0.87212,270.33 > view matrix models > #2,0.99025,0.1349,-0.034699,-15.671,0.13661,-0.98922,0.052664,310.98,-0.027221,-0.05689,-0.99801,356.95 > view matrix models > #2,0.84297,-0.47635,-0.24998,149.31,0.073736,-0.35798,0.93081,61.777,-0.53288,-0.80308,-0.26664,438.86 > view matrix models > #2,0.8527,-0.44422,-0.27491,136.79,0.062284,-0.43603,0.89777,95.09,-0.51868,-0.78265,-0.34414,461.86 > view matrix models > #2,0.57087,-0.65418,-0.49614,255.02,0.13755,-0.51954,0.8433,106.96,-0.80943,-0.54966,-0.20661,443.89 > view matrix models > #2,0.57087,-0.65418,-0.49614,265.66,0.13755,-0.51954,0.8433,99.219,-0.80943,-0.54966,-0.20661,441.8 > view matrix models > #2,0.57087,-0.65418,-0.49614,245.65,0.13755,-0.51954,0.8433,136.65,-0.80943,-0.54966,-0.20661,414.11 > view matrix models > #2,0.55027,-0.66527,-0.5046,292.81,0.13028,-0.52851,0.83887,192.82,-0.82476,-0.52734,-0.20415,397.13 > view matrix models > #2,0.55027,-0.66527,-0.5046,267.78,0.13028,-0.52851,0.83887,200.91,-0.82476,-0.52734,-0.20415,404.62 > view matrix models > #2,0.55027,-0.66527,-0.5046,278.29,0.13028,-0.52851,0.83887,199.69,-0.82476,-0.52734,-0.20415,401.23 > view matrix models > #2,-0.33767,-0.83308,-0.43813,435.02,0.025889,-0.47351,0.88041,199.51,-0.94091,0.28594,0.18146,213.67 > view matrix models > #2,-0.8951,-0.44585,0.0044625,380.07,0.22582,-0.44468,0.86675,165.53,-0.38446,0.77684,0.49872,-12.364 > view matrix models > #2,-0.24958,-0.89318,-0.37409,420.53,-0.75728,-0.060739,0.65025,291.05,-0.60351,0.44558,-0.66123,277.95 > view matrix models > #2,-0.15051,-0.4976,-0.85425,419.49,-0.8559,0.49802,-0.1393,346.12,0.49475,0.71019,-0.50085,32.661 > view matrix models > #2,0.14353,-0.11029,-0.98348,329.04,-0.88169,0.43709,-0.17769,367.22,0.44947,0.89263,-0.03451,-71.587 > view matrix models > #2,0.14353,-0.11029,-0.98348,356.07,-0.88169,0.43709,-0.17769,380.6,0.44947,0.89263,-0.03451,-74.971 > view matrix models > #2,0.34659,-0.85509,-0.38561,349.44,-0.82833,-0.086098,-0.55359,526.55,0.44017,0.51128,-0.73813,112.71 > view matrix models > #2,0.38003,-0.82585,-0.4166,344.5,-0.69907,0.0385,-0.71402,512.41,0.60571,0.56258,-0.56269,47.817 > view matrix models > #2,0.38003,-0.82585,-0.4166,311.3,-0.69907,0.0385,-0.71402,389.8,0.60571,0.56258,-0.56269,66.946 > view matrix models > #2,0.38003,-0.82585,-0.4166,304.37,-0.69907,0.0385,-0.71402,394.06,0.60571,0.56258,-0.56269,71.172 > view matrix models > #2,0.38003,-0.82585,-0.4166,303.96,-0.69907,0.0385,-0.71402,396.62,0.60571,0.56258,-0.56269,69.22 > view matrix models > #2,0.15658,-0.96276,0.2204,253.2,-0.96851,-0.10593,0.22533,302.48,-0.19359,-0.24874,-0.94903,400.22 > volume flip #1 Opened cryosparc_P73_J458_map_sharp.mrc z flip as #3, grid size 384,384,384, pixel 0.885, shown at step 1, values float32 > surface dust #2 size 8.85 > view matrix models > #2,0.15658,-0.96276,0.2204,181.66,-0.96851,-0.10593,0.22533,230.59,-0.19359,-0.24874,-0.94903,378.15 > view matrix models > #2,0.030336,-0.908,-0.41786,301.61,0.69479,-0.28138,0.66188,-75.224,-0.71857,-0.3104,0.62234,201.43 > view matrix models > #2,0.15771,-0.7329,-0.6618,293.43,0.70001,-0.38973,0.59841,-46.552,-0.6965,-0.55764,0.45157,269.71 > view matrix models > #2,0.88248,-0.20679,-0.42245,48.31,0.46341,0.22866,0.85613,-159.8,-0.080439,-0.95129,0.29762,267.03 > view matrix models > #2,0.87313,-0.27013,-0.4058,65.405,0.46406,0.20562,0.86161,-154.28,-0.14931,-0.94061,0.30489,276.3 > view matrix models > #2,0.87865,0.021139,-0.477,26.764,0.44795,0.30933,0.83884,-165.65,0.16528,-0.95072,0.26232,235.97 > view matrix models > #2,0.85864,0.1206,-0.49819,16.466,0.43477,0.34344,0.83248,-168.35,0.2715,-0.9314,0.24245,219.4 > view matrix models > #2,0.83533,0.19688,-0.51329,9.6231,0.42186,0.36912,0.82812,-169.98,0.35251,-0.90829,0.22528,205.67 > view matrix models > #2,0.88764,-0.13113,-0.44147,45.393,0.46054,0.25582,0.84998,-160.35,0.0014762,-0.95779,0.28747,258.57 > view matrix models > #2,0.88766,-0.1304,-0.44166,45.295,0.4605,0.25608,0.84992,-160.38,0.0022744,-0.95782,0.28736,258.47 > view matrix models > #2,0.88328,-0.19928,-0.42438,54.84,0.46323,0.23137,0.8555,-157.53,-0.072298,-0.95224,0.29668,267.62 > select add #3 4 models selected > view matrix models > #2,0.88328,-0.19928,-0.42438,110.63,0.46323,0.23137,0.8555,-138.84,-0.072298,-0.95224,0.29668,286.3,#3,1,0,0,55.791,0,1,0,18.682,0,0,1,18.678 > select subtract #3 2 models selected > view matrix models > #2,0.88328,-0.19928,-0.42438,110.28,0.46323,0.23137,0.8555,-135.73,-0.072298,-0.95224,0.29668,291.16 > view matrix models > #2,0.60829,-0.66686,-0.43045,234.73,0.76419,0.63859,0.090594,-121.58,0.21447,-0.38405,0.89806,45.416 > view matrix models > #2,0.70366,-0.54547,-0.45532,203.2,0.69077,0.67526,0.25856,-145.18,0.16642,-0.49647,0.85195,80.164 > view matrix models > #2,0.70366,-0.54547,-0.45532,260.37,0.69077,0.67526,0.25856,-124.67,0.16642,-0.49647,0.85195,110.34 > view matrix models > #2,0.70366,-0.54547,-0.45532,283.26,0.69077,0.67526,0.25856,-101.4,0.16642,-0.49647,0.85195,97.412 > fitmap #2 inMap #3 Fit map cryosparc_P73_J455_map_sharp (1).mrc in map cryosparc_P73_J458_map_sharp.mrc z flip using 186728 points correlation = 0.2765, correlation about mean = 0.05929, overlap = 2326 steps = 184, shift = 5.76, angle = 4.98 degrees Position of cryosparc_P73_J455_map_sharp (1).mrc (#2) relative to cryosparc_P73_J458_map_sharp.mrc z flip (#3) coordinates: Matrix rotation and translation 0.65889510 -0.61604357 -0.43167992 243.21845106 0.73973747 0.63480854 0.22317389 -109.89456175 0.13654926 -0.46637799 0.87398275 73.59997307 Axis -0.42467076 -0.34995238 0.83497789 Axis point 270.08616444 242.93288098 0.00000000 Rotation angle (degrees) 54.27869064 Shift along axis -3.37555211 > view matrix models > #2,0.6589,-0.61604,-0.43168,286.42,0.73974,0.63481,0.22317,-86.372,0.13655,-0.46638,0.87398,86.5 > view matrix models > #2,0.6589,-0.61604,-0.43168,281.26,0.73974,0.63481,0.22317,-86.978,0.13655,-0.46638,0.87398,86.985 > view matrix models > #2,0.6589,-0.61604,-0.43168,279.09,0.73974,0.63481,0.22317,-86.032,0.13655,-0.46638,0.87398,88.068 > view matrix models > #2,0.87892,-0.43624,-0.19284,172.71,0.38539,0.88775,-0.25174,7.6624,0.28102,0.14694,0.94839,-52.649 > fitmap #2 inMap #3 Fit map cryosparc_P73_J455_map_sharp (1).mrc in map cryosparc_P73_J458_map_sharp.mrc z flip using 186728 points correlation = 0.9206, correlation about mean = 0.8652, overlap = 1.345e+04 steps = 576, shift = 11, angle = 20.9 degrees Position of cryosparc_P73_J455_map_sharp (1).mrc (#2) relative to cryosparc_P73_J458_map_sharp.mrc z flip (#3) coordinates: Matrix rotation and translation 0.87082828 -0.49130728 -0.01659069 104.13584134 0.49148666 0.86947103 0.04960836 -69.72422264 -0.00994782 -0.05135446 0.99863094 8.77504792 Axis -0.10219026 -0.00672362 0.99474215 Axis point 185.16614551 162.97347251 0.00000000 Rotation angle (degrees) 29.60345660 Shift along axis -1.44395958 > select add #3 4 models selected > view matrix models > #2,0.88995,-0.45595,-0.0099753,149.56,0.42986,0.84593,-0.31563,26.139,0.15235,0.27661,0.94883,-47.065,#3,0.99917,0.040465,0.0046005,48.291,-0.036038,0.93113,-0.36291,97.998,-0.018969,0.36245,0.93181,-27.995 > view matrix models > #2,0.88995,-0.45595,-0.0099753,149.72,0.42986,0.84593,-0.31563,57.234,0.15235,0.27661,0.94883,-74.303,#3,0.99917,0.040465,0.0046005,48.45,-0.036038,0.93113,-0.36291,129.09,-0.018969,0.36245,0.93181,-55.232 > surface dust #2 size 8.85 > surface dust #3 size 8.85 > select subtract #3 2 models selected > select add #3 4 models selected > select subtract #2 2 models selected > select subtract #3 Nothing selected > open /Users/Wan01305/Downloads/cryosparc_P73_J457_map_sharp.mrc Opened cryosparc_P73_J457_map_sharp.mrc as #4, grid size 384,384,384, pixel 0.885, shown at level 0.00081, step 2, values float32 > volume #4 step 1 > volume #4 level 0.001 > volume #4 level 0.01 > surface dust #2 size 8.85 > surface dust #3 size 8.85 > surface dust #4 size 8.85 > select add #4 2 models selected > view matrix models > #4,0.96787,0.25106,0.013809,-40.996,-0.13288,0.55734,-0.81958,239.63,-0.21346,0.79141,0.5728,-30.171 > view matrix models > #4,0.96794,0.25106,0.0081138,-22.861,-0.13697,0.55461,-0.82076,244,-0.21056,0.79333,0.57122,-33.436 > view matrix models > #4,0.064186,-0.98771,0.14253,320.99,0.99716,0.069107,0.02984,-4.4649,-0.039323,0.14021,0.98934,-18.927 > view matrix models > #4,0.069473,-0.98944,0.12717,323.04,0.99601,0.075959,0.04688,-8.3858,-0.056045,0.12341,0.99077,-13.456 > view matrix models > #4,0.069473,-0.98944,0.12717,366.94,0.99601,0.075959,0.04688,16.971,-0.056045,0.12341,0.99077,0.8082 > view matrix models > #4,0.069473,-0.98944,0.12717,361.25,0.99601,0.075959,0.04688,35.442,-0.056045,0.12341,0.99077,-23.101 > view matrix models > #4,0.069473,-0.98944,0.12717,358.19,0.99601,0.075959,0.04688,40.101,-0.056045,0.12341,0.99077,-17.969 > view matrix models > #4,0.085924,-0.9845,0.15288,351.08,0.99227,0.098347,0.075629,24.719,-0.089493,0.1452,0.98535,-13.058 > view matrix models > #4,0.085924,-0.9845,0.15288,351.22,0.99227,0.098347,0.075629,24.688,-0.089493,0.1452,0.98535,-12.885 > view matrix models > #4,0.11538,-0.97522,-0.18879,403.1,0.99331,0.11424,0.016959,31.76,0.0050283,-0.18948,0.98187,30.64 > view matrix models > #4,0.077157,-0.98976,0.12011,359.2,0.99498,0.08414,0.054187,30.392,-0.063738,0.11533,0.99128,-12.939 > view matrix models > #4,0.077157,-0.98976,0.12011,358.99,0.99498,0.08414,0.054187,33.562,-0.063738,0.11533,0.99128,-12.531 > view matrix models > #4,0.077157,-0.98976,0.12011,360.55,0.99498,0.08414,0.054187,30.084,-0.063738,0.11533,0.99128,-12.928 > view matrix models > #4,0.077157,-0.98976,0.12011,360.36,0.99498,0.08414,0.054187,32.499,-0.063738,0.11533,0.99128,-11.639 > view matrix models > #4,0.082938,-0.98835,0.12759,357.88,0.99525,0.088704,0.040184,34.589,-0.051034,0.12365,0.99101,-14.898 Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps, got 0 atomic models, 3 maps. > hide #!2 models > fitmap #4 inMap #3 Fit map cryosparc_P73_J457_map_sharp.mrc in map cryosparc_P73_J458_map_sharp.mrc z flip using 195345 points correlation = 0.889, correlation about mean = 0.8157, overlap = 1.354e+04 steps = 920, shift = 9, angle = 27.9 degrees Position of cryosparc_P73_J457_map_sharp.mrc (#4) relative to cryosparc_P73_J458_map_sharp.mrc z flip (#3) coordinates: Matrix rotation and translation 0.28270281 -0.95781806 -0.05161084 287.19486003 0.95920603 0.28238854 0.01343513 -43.44997686 0.00170590 -0.05330358 0.99857689 7.80750422 Axis -0.03477919 -0.02778467 0.99900872 Axis point 172.80475562 170.39599447 0.00000000 Rotation angle (degrees) 73.63029881 Shift along axis -0.98139789 > select subtract #4 Nothing selected > show #!2 models > hide #!4 models > hide #!3 models > show #!4 models > open /Users/Wan01305/Downloads/cryosparc_P73_J456_map_sharp.mrc Opened cryosparc_P73_J456_map_sharp.mrc as #5, grid size 384,384,384, pixel 0.885, shown at level 0.000712, step 2, values float32 > volume #5 step 1 > volume #5 level 0.01 > surface dust #2 size 8.85 > surface dust #4 size 8.85 > surface dust #5 size 8.85 > select add #5 2 models selected > view matrix models #5,1,0,0,63.483,0,1,0,16.545,0,0,1,3.2683 > view matrix models > #5,0.99972,0.022715,0.0063864,53.895,-0.02279,0.99967,0.011923,36.677,-0.0061134,-0.012066,0.99991,-13.208 > view matrix models > #5,0.90895,-0.3425,-0.23769,173.13,0.36302,0.36993,0.8552,-54.882,-0.20498,-0.86362,0.46058,257.82 > view matrix models > #5,0.9832,-0.18179,0.016279,90.657,0.17729,0.93007,-0.32176,73.905,0.043351,0.31924,0.94668,-70.035 > view matrix models > #5,0.98134,-0.19047,0.026197,86.498,0.18814,0.9233,-0.33483,84.02,0.039587,0.33352,0.94191,-73.146 > view matrix models > #5,0.98134,-0.19047,0.026197,86.462,0.18814,0.9233,-0.33483,86.83,0.039587,0.33352,0.94191,-73.799 > view matrix models > #5,0.97184,0.15578,-0.17679,64.616,-0.22237,0.85447,-0.4695,185.05,0.077922,0.4956,0.86505,-95.626 > view matrix models > #5,0.79823,-0.56187,-0.2171,224.25,0.42565,0.78117,-0.45672,94.907,0.42622,0.27216,0.86271,-110.26 > view matrix models > #5,0.63931,-0.73338,-0.23114,281.37,0.47536,0.61322,-0.63087,149.09,0.60441,0.29345,0.74066,-110.77 > view matrix models > #5,0.17809,-0.97691,-0.11805,381.12,0.32,0.17094,-0.93187,291.07,0.93053,0.12818,0.34305,-82.808 > view matrix models > #5,0.76295,0.6316,-0.13783,11.412,-0.6458,0.75429,-0.11825,202.15,0.029277,0.17923,0.98337,-59.279 > view matrix models > #5,0.82251,0.53391,-0.19598,29.057,-0.56759,0.79251,-0.2231,200.93,0.036203,0.29474,0.95489,-75.815 > view matrix models > #5,0.82251,0.53391,-0.19598,20.133,-0.56759,0.79251,-0.2231,219.2,0.036203,0.29474,0.95489,-51.117 > view matrix models > #5,0.86756,0.46856,-0.16668,19.649,-0.44853,0.59241,-0.66923,310.85,-0.21483,0.65536,0.72412,-36.438 > view matrix models > #5,0.94861,0.30179,0.095173,-1.3951,-0.19514,0.79465,-0.57485,218.76,-0.24912,0.52674,0.8127,-23.158 > view matrix models > #5,0.98221,0.044681,0.1824,23.775,-0.053342,0.99766,0.042855,57.128,-0.18006,-0.051823,0.98229,38.993 > view matrix models > #5,0.98038,-0.02601,0.1954,34.266,0.011375,0.99707,0.075647,41.641,-0.1968,-0.07194,0.9778,45.88 > view matrix models > #5,0.98038,-0.02601,0.1954,33.348,0.011375,0.99707,0.075647,41.117,-0.1968,-0.07194,0.9778,42 > view matrix models > #5,0.98038,-0.02601,0.1954,31.71,0.011375,0.99707,0.075647,40.958,-0.1968,-0.07194,0.9778,41.955 > view matrix models > #5,0.94656,-0.30715,-0.0984,135.72,0.28435,0.93871,-0.19484,54.235,0.15221,0.15645,0.97589,-52.079 > volume flip #5 Opened cryosparc_P73_J456_map_sharp.mrc z flip as #6, grid size 384,384,384, pixel 0.885, shown at step 1, values float32 > select subtract #5 Nothing selected > select add #6 2 models selected > view matrix models > #6,0.94656,-0.30715,-0.0984,134.67,0.28435,0.93871,-0.19484,47.655,0.15221,0.15645,0.97589,-55 > view matrix models > #6,0.97871,-0.028525,-0.20328,100.6,0.06232,-0.90226,0.42666,286.61,-0.19558,-0.43024,-0.88127,417.75 > surface dust #6 size 8.85 > view matrix models > #6,0.99825,-0.0044096,-0.059018,67.241,0.016854,-0.93475,0.35491,311.13,-0.056732,-0.35528,-0.93304,391.69 > hide #!6 models > show #!6 models > hide #!4 models > fitmap #6 inMap #2 Fit map cryosparc_P73_J456_map_sharp.mrc z flip in map cryosparc_P73_J455_map_sharp (1).mrc using 210802 points correlation = 0.9001, correlation about mean = 0.8333, overlap = 1.491e+04 steps = 204, shift = 7.84, angle = 5.25 degrees Position of cryosparc_P73_J456_map_sharp.mrc z flip (#6) relative to cryosparc_P73_J455_map_sharp (1).mrc (#2) coordinates: Matrix rotation and translation 0.88354664 -0.46788619 -0.02068457 103.38279106 -0.46825137 -0.88338594 -0.01923377 402.97632609 -0.00927324 0.02667951 -0.99960103 336.53754490 Axis 0.97044587 -0.24119543 -0.00771854 Axis point 0.00000000 212.28439844 171.13678994 Rotation angle (degrees) 178.64449794 Shift along axis 0.53377508 > show #!3 models > hide #!6 models > hide #!2 models > show #!5 models > hide #!5 models > close #5 > close #1 > show #!4 models > hide #!4 models > show #!4 models > hide #!4 models > show #!4 models > hide #!4 models > show #!6 models > select subtract #6 Nothing selected > hide #!3 models > show #!4 models > hide #!4 models > show #!3 models > hide #!3 models > hide #!6 models > show #!3 models > show #!4 models > hide #!4 models > show #!6 models > hide #!6 models > show #!4 models > hide #!4 models > hide #!3 models > show #!4 models > show #!6 models > hide #!4 models > hide #!6 models > show #!4 models > hide #!4 models > show #!2 models > show #!4 models > save ""/Users/Wan01305/Documents/CCHFV paper/PITC and EC map from > deepenhancer combine.cxs"" includeMaps true > hide #!4 models > hide #!2 models > show #!3 models > open ""/Users/Wan01305/Documents/CCHFV paper/apo model build files/apo map > and model/output_J364-coot-2b_real_space_refined_028.pdb"" Chain information for output_J364-coot-2b_real_space_refined_028.pdb #1 --- Chain | Description A | No description available > select add #1 12013 atoms, 12209 bonds, 12 pseudobonds, 1504 residues, 2 models selected > view matrix models > #1,-0.33616,0.74737,-0.57309,196.73,-0.74829,0.15755,0.64439,168.69,0.57189,0.64546,0.50629,-128.99 > view matrix models > #1,-0.60537,0.60747,-0.5143,258.04,-0.61803,0.04841,0.78466,141.55,0.50156,0.79286,0.34613,-115.6 > view matrix models > #1,-0.60537,0.60747,-0.5143,318.05,-0.61803,0.04841,0.78466,183.39,0.50156,0.79286,0.34613,-116.98 > view matrix models > #1,-0.60537,0.60747,-0.5143,305.08,-0.61803,0.04841,0.78466,190.83,0.50156,0.79286,0.34613,-122.81 > view matrix models > #1,-0.47609,0.64356,-0.5993,290.17,-0.68227,0.15965,0.71345,191.19,0.55483,0.74856,0.36308,-127.67 > view matrix models > #1,-0.66111,0.40865,-0.62924,368.82,-0.73694,-0.51121,0.44226,365.44,-0.14095,0.75609,0.63911,-55.609 > view matrix models > #1,-0.51309,0.62446,-0.58889,298.18,-0.85574,-0.42543,0.29447,396.01,-0.066647,0.65503,0.75266,-69.942 > view matrix models > #1,-0.58618,0.81014,0.007948,176.34,-0.75689,-0.55109,0.35131,391.44,0.28899,0.19991,0.93623,-82.295 > view matrix models > #1,-0.99822,-0.045046,-0.038987,418.45,0.028278,-0.93427,0.35544,324.23,-0.052436,0.3537,0.93389,-53.399 > view matrix models > #1,-0.98858,-0.14594,-0.037566,434.55,0.11953,-0.91119,0.39427,297.78,-0.091768,0.38528,0.91823,-49.53 > view matrix models > #1,-0.98858,-0.14594,-0.037566,421.03,0.11953,-0.91119,0.39427,294.41,-0.091768,0.38528,0.91823,-49.568 > view matrix models > #1,-0.98858,-0.14594,-0.037566,420.33,0.11953,-0.91119,0.39427,303.42,-0.091768,0.38528,0.91823,-45.007 > view matrix models > #1,-0.73746,0.64568,0.19812,196.77,-0.5364,-0.73818,0.40911,383.82,0.4104,0.19543,0.89072,-93.665 > view matrix models > #1,-0.7031,0.67246,0.23122,180.45,-0.58408,-0.73159,0.3516,400.7,0.40559,0.11216,0.90715,-80.908 > view matrix models > #1,-0.7031,0.67246,0.23122,182.37,-0.58408,-0.73159,0.3516,394.7,0.40559,0.11216,0.90715,-76.933 > view matrix models > #1,-0.93823,-0.33322,0.093163,424.38,0.28729,-0.90032,-0.32694,389.3,0.19282,-0.27999,0.94044,23.548 > fitmap #1 inMap #3 Fit molecule output_J364-coot-2b_real_space_refined_028.pdb (#1) to map cryosparc_P73_J458_map_sharp.mrc z flip (#3) using 12013 atoms average map value = 0.3737, steps = 128 shifted from previous position = 12.6 rotated from previous position = 11 degrees atoms outside contour = 959, contour level = 0.01 Position of output_J364-coot-2b_real_space_refined_028.pdb (#1) relative to cryosparc_P73_J458_map_sharp.mrc z flip (#3) coordinates: Matrix rotation and translation -0.99144059 -0.12970459 0.01490905 358.36278272 0.12967569 -0.99155224 -0.00289349 316.84840913 0.01515840 -0.00093539 0.99988467 -3.18134889 Axis 0.00754895 -0.00096131 0.99997104 Axis point 168.87623126 170.09184783 0.00000000 Rotation angle (degrees) 172.54809584 Shift along axis -0.78058089 > select subtract #1 Nothing selected > ui mousemode right ""translate selected models"" > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!2 models > hide #!2 models > color #1 #db4423ff > show #!2 models > transparency #1-2 50 > ui tool show ""Side View"" > select add #1 12013 atoms, 12209 bonds, 12 pseudobonds, 1504 residues, 2 models selected > color zone #2 near sel & #1 distance 5.31 > color zone #2 near sel & #1 distance 2 > select subtract #1 Nothing selected > hide #!2 models > show #!4 models > select add #4 2 models selected > color zone #4 near sel & #1 distance 2 color zone: No atoms specified. > select subtract #4 Nothing selected > select add #4 2 models selected > select add #1 12013 atoms, 12209 bonds, 12 pseudobonds, 1504 residues, 4 models selected > color zone #4 near sel & #1 distance 2 > select add #4 12013 atoms, 12209 bonds, 12 pseudobonds, 1504 residues, 5 models selected > select subtract #4 12013 atoms, 12209 bonds, 12 pseudobonds, 1504 residues, 2 models selected > hide #!4 models > show #!6 models > color zone #6 near sel & #1 distance 2 > select subtract #1 Nothing selected > show #!4 models > hide #!4 models > show #!4 models > hide #!4 models > show #!4 models > hide #!6 models > hide #!4 models > show #!4 models > hide #!4 models > show #!4 models > hide #!4 models > show #!4 models > hide #!4 models > show #!6 models > volume #6 level 0.005 > volume #6 level 0.0005 > volume #6 level 0.0007 > volume #6 level 0.001 > hide #!6 models > show #!4 models > hide #!4 models > show #!4 models > volume #4 level 0.001 > hide #!4 models > show #!4 models > hide #!4 models > show #!4 models > hide #!4 models > show #!4 models > volume #4 level 0.01 > hide #!4 models > show #!4 models > volume #4 level 0.02 > volume #4 level 0.04 > hide #!4 models > show #!6 models > volume #6 level 0.01 > hide #!6 models > show #!6 models > volume #6 level 0.005 > volume #6 level 0.001 > volume #6 level 0.002 > hide #!6 models > show #!6 models > volume #6 level 0.01 > volume #4 level 0.01 > show #!4 models > hide #!6 models > hide #!4 models > show #!2 models > hide #!2 models > show #!4 models > hide #!4 models > show #!6 models > show #!4 models > hide #!6 models > show #!6 models > hide #!4 models > hide #!6 models > show #!4 models > show #!6 models > hide #!4 models > show #!4 models > hide #!4 models > show #!4 models > hide #!6 models > show #!6 models > hide #!4 models > show #!4 models > hide #!6 models > show #!6 models > hide #!4 models > show #!4 models > hide #!6 models > show #!6 models > hide #!4 models > hide #!6 models > show #!6 models > show #!4 models > hide #!6 models > show #!6 models > hide #!4 models > show #!4 models > hide #!4 models > show #!4 models > hide #!6 models > hide #!4 models > show #!4 models > hide #!4 models > show #!2 models > show #!4 models > hide #!1 models > transparency #2,4 0 > hide #!4 models > show #!4 models > hide #!4 models > show #!4 models > hide #!4 models > show #!4 models > hide #!4 models > show #!4 models > hide #!4 models > show #!4 models > hide #!4 models > show #!4 models > hide #!4 models > show #!4 models > hide #!4 models > show #!4 models > show #!1 models > hide #!2 models > hide #!4 models > show surfaces > show #!4 models > hide #!4 models > show #!4 models > hide #!4 models > show #!6 models > hide #!6 models > show #!6 models > hide #!6 models > show #!6 models > hide #!6 models > show #!6 models > hide #!6 models > show #!4 models > hide #!4 models > show #!3 models > hide #!3 models > show #!2 models > hide #!2 models > show #!4 models > show #!2 models > hide #!1 models > hide #!4 models > show #!4 models > hide #!2 models > hide #!4 models > show #!1 models > hide surfaces > show #!4 models > show #!2 models > hide #!2 models > hide #!4 models > show #!4 models > hide #!4 models > show #!4 models > hide #!4 models > show #!4 models > show #!2 models > hide #!4 models > show #!4 models > hide #!4 models > show #!4 models > hide #!2 models > hide #!4 models > show surfaces > show #!4 models ===== Log before crash end ===== Log: Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 1.8 (2024-06-10) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 Metal - 88.1 OpenGL renderer: Apple M2 OpenGL vendor: Apple Python: 3.11.4 Locale: UTF-8 Qt version: PyQt6 6.6.1, Qt 6.6.1 Qt runtime version: 6.6.3 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: Mac14,7 Model Number: Z16S0005DLL/A Chip: Apple M2 Total Number of Cores: 8 (4 performance and 4 efficiency) Memory: 16 GB System Firmware Version: 10151.140.19 OS Loader Version: 10151.140.19 Software: System Software Overview: System Version: macOS 14.6.1 (23G93) Kernel Version: Darwin 23.6.0 Time since boot: 68 days, 3 hours, 54 minutes Graphics/Displays: Apple M2: Chipset Model: Apple M2 Type: GPU Bus: Built-In Total Number of Cores: 10 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: PHL 272P7VU: Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition) UI Looks like: 1920 x 1080 @ 60.00Hz Main Display: Yes Mirror: Off Online: Yes Rotation: Supported Color LCD: Display Type: Built-In Retina LCD Resolution: 2560 x 1600 Retina 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: 2.15.0 beautifulsoup4: 4.12.3 blockdiag: 3.0.0 blosc2: 2.0.0 build: 1.2.1 certifi: 2023.11.17 cftime: 1.6.4 charset-normalizer: 3.3.2 ChimeraX-AddCharge: 1.5.17 ChimeraX-AddH: 2.2.6 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.5 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.12.7 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.1.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.57.1 ChimeraX-AtomicLibrary: 14.0.6 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.4.6 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.12.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2.7 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: 1.0.5 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.6 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.8 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: 1.2.4 ChimeraX-DiffPlot: 1.0 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: 1.1.10 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.1.6 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 ChimeraX-Map: 1.2 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: 2.7.1 ChimeraX-MedicalToolbar: 1.0.3 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.14.1 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.17 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: 1.2 ChimeraX-NMRSTAR: 1.0.2 ChimeraX-NRRD: 1.2 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.13.5 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: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.4.1 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: 3.0.15 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-StdCommands: 1.16.5 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.2.1 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: 1.39.1 ChimeraX-uniprot: 2.3 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.4.3 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: 1.1.4 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.2.2 contourpy: 1.2.1 cxservices: 1.2.2 cycler: 0.12.1 Cython: 3.0.10 debugpy: 1.8.1 decorator: 5.1.1 docutils: 0.20.1 executing: 2.0.1 filelock: 3.13.4 fonttools: 4.53.0 funcparserlib: 2.0.0a0 glfw: 2.7.0 grako: 3.16.5 h5py: 3.11.0 html2text: 2024.2.26 idna: 3.7 ihm: 1.0 imagecodecs: 2024.1.1 imagesize: 1.4.1 ipykernel: 6.29.2 ipython: 8.21.0 ipywidgets: 8.1.3 jedi: 0.19.1 jinja2: 3.1.4 jupyter-client: 8.6.0 jupyter-core: 5.7.2 jupyterlab-widgets: 3.0.11 kiwisolver: 1.4.5 line-profiler: 4.1.2 lxml: 5.2.1 lz4: 4.3.3 MarkupSafe: 2.1.5 matplotlib: 3.8.4 matplotlib-inline: 0.1.7 msgpack: 1.0.8 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.10.0 numpy: 1.26.4 openvr: 1.26.701 packaging: 23.2 ParmEd: 4.2.2 parso: 0.8.4 pep517: 0.13.1 pexpect: 4.9.0 pillow: 10.3.0 pip: 24.0 pkginfo: 1.10.0 platformdirs: 4.2.2 prompt-toolkit: 3.0.47 psutil: 5.9.8 ptyprocess: 0.7.0 pure-eval: 0.2.2 py-cpuinfo: 9.0.0 pycollada: 0.8 pydicom: 2.4.4 pygments: 2.17.2 pynmrstar: 3.3.4 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.3401 pyparsing: 3.1.2 pyproject-hooks: 1.1.0 PyQt6-commercial: 6.6.1 PyQt6-Qt6: 6.6.3 PyQt6-sip: 13.6.0 PyQt6-WebEngine-commercial: 6.6.0 PyQt6-WebEngine-Qt6: 6.6.3 python-dateutil: 2.9.0.post0 pytz: 2024.1 pyzmq: 26.0.3 qtconsole: 5.5.1 QtPy: 2.4.1 RandomWords: 0.4.0 requests: 2.31.0 scipy: 1.13.0 setuptools: 69.5.1 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: 2.0.1 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: 0.6.3 tables: 3.8.0 tcia-utils: 1.5.1 tifffile: 2024.1.30 tinyarray: 1.2.4 tornado: 6.4.1 traitlets: 5.14.2 typing-extensions: 4.12.2 tzdata: 2024.1 urllib3: 2.2.1 wcwidth: 0.2.13 webcolors: 1.13 wheel: 0.43.0 wheel-filename: 1.4.1 widgetsnbextension: 4.0.11 }}} " defect closed normal Window Toolkit duplicate all ChimeraX