id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 9376 Crashed in QTabBar::paintEvent(), QPainter::begin: Paint device returned engine == 0 chimerax-bug-report@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-12.5-arm64-arm-64bit ChimeraX Version: 1.6rc202304072249 (2023-04-07 22:49:08 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 0x0000000102d04580 (most recent call first): File ""/private/var/folders/qn/1085xfxs3g15rmlh3q7t_w8w0000gn/T/AppTranslocation/176412EF-9F6E-400C-B8EB-4832EC1F9ACD/d/ChimeraX-1.6-rc2023.04.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py"", line 275 in event_loop File ""/private/var/folders/qn/1085xfxs3g15rmlh3q7t_w8w0000gn/T/AppTranslocation/176412EF-9F6E-400C-B8EB-4832EC1F9ACD/d/ChimeraX-1.6-rc2023.04.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py"", line 892 in init File ""/private/var/folders/qn/1085xfxs3g15rmlh3q7t_w8w0000gn/T/AppTranslocation/176412EF-9F6E-400C-B8EB-4832EC1F9ACD/d/ChimeraX-1.6-rc2023.04.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py"", line 1043 in File ""/private/var/folders/qn/1085xfxs3g15rmlh3q7t_w8w0000gn/T/AppTranslocation/176412EF-9F6E-400C-B8EB-4832EC1F9ACD/d/ChimeraX-1.6-rc2023.04.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py"", line 87 in _run_code File ""/private/var/folders/qn/1085xfxs3g15rmlh3q7t_w8w0000gn/T/AppTranslocation/176412EF-9F6E-400C-B8EB-4832EC1F9ACD/d/ChimeraX-1.6-rc2023.04.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py"", line 197 in _run_module_as_main {""app_name"":""ChimeraX"",""timestamp"":""2023-07-10 19:16:57.00 +0200"",""app_version"":""1.6.0"",""slice_uuid"":""a5992708-d5b4-36ec-ac0a-e525f6105b56"",""build_version"":""1.6.0.0"",""platform"":1,""bundleID"":""edu.ucsf.cgl.ChimeraX"",""share_with_app_devs"":0,""is_first_party"":0,""bug_type"":""309"",""os_version"":""macOS 12.5 (21G72)"",""incident_id"":""0610B993-6937-45A5-BD42-8AD28197508F"",""name"":""ChimeraX""} { ""uptime"" : 1300000, ""procLaunch"" : ""2023-07-10 11:47:08.5932 +0200"", ""procRole"" : ""Background"", ""version"" : 2, ""userID"" : 501, ""deployVersion"" : 210, ""modelCode"" : ""MacBookPro18,3"", ""procStartAbsTime"" : 33030430072826, ""coalitionID"" : 122451, ""osVersion"" : { ""train"" : ""macOS 12.5"", ""build"" : ""21G72"", ""releaseType"" : ""User"" }, ""captureTime"" : ""2023-07-10 19:16:52.3138 +0200"", ""incident"" : ""0610B993-6937-45A5-BD42-8AD28197508F"", ""bug_type"" : ""309"", ""pid"" : 72129, ""procExitAbsTime"" : 33459909123524, ""translated"" : false, ""cpuType"" : ""ARM-64"", ""procName"" : ""ChimeraX"", ""procPath"" : ""\/Volumes\/VOLUME\/*\/ChimeraX-1.6-rc2023.04.07.app\/Contents\/MacOS\/ChimeraX"", ""bundleInfo"" : {""CFBundleShortVersionString"":""1.6.0"",""CFBundleVersion"":""1.6.0.0"",""CFBundleIdentifier"":""edu.ucsf.cgl.ChimeraX""}, ""storeInfo"" : {""deviceIdentifierForVendor"":""46C5C682-FFA0-5933-99A8-8DEF11668CF7"",""thirdParty"":true}, ""parentProc"" : ""launchd"", ""parentPid"" : 1, ""coalitionName"" : ""edu.ucsf.cgl.ChimeraX"", ""crashReporterKey"" : ""F3322CE2-C3C9-D6D1-944C-287162EF24E9"", ""wakeTime"" : 3, ""sleepWakeUUID"" : ""25CFC518-1A11-4F97-806A-0BA9DF6E74BF"", ""sip"" : ""enabled"", ""vmRegionInfo"" : ""0x18 is not in any region. 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\n=========== ======= ======= \nTOTAL 6.9G 4964 \nTOTAL, minus reserved VM space 6.1G 4964 \n"", ""legacyInfo"" : { ""threadTriggered"" : { ""name"" : ""CrBrowserMain"", ""queue"" : ""com.apple.main-thread"" } }, ""trialInfo"" : { ""rollouts"" : [ { ""rolloutId"" : ""6112e14f37f5d11121dcd519"", ""factorPackIds"" : { ""SIRI_TEXT_TO_SPEECH"" : ""634710168e8be655c1316aaa"" }, ""deploymentId"" : 240000231 }, { ""rolloutId"" : ""60f8ddccefea4203d95cbeef"", ""factorPackIds"" : { ""NETWORK_SERVICE_PROXY_CONFIG_UPDATE"" : ""6401414cc679dd6bc5828183"" }, ""deploymentId"" : 240000025 } ], ""experiments"" : [ { ""treatmentId"" : ""c28e4ee6-1b08-4f90-8e05-2809e78310a3"", ""experimentId"" : ""6317d2003d24842ff850182a"", ""deploymentId"" : 400000013 } ] } } ===== Log before crash start ===== UCSF ChimeraX version: 1.6rc202304072249 (2023-04-07) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open > /Users/karlaivettedelaobecerra/Downloads/cryosparc_P25_J586_005_volume_map_sharp(1).mrc > /Users/karlaivettedelaobecerra/Downloads/cryosparc_P25_J607_006_volume_map_sharp.mrc.download Unrecognized file suffix '.download' > open > /Users/karlaivettedelaobecerra/Downloads/cryosparc_P25_J586_005_volume_map_sharp(1).mrc Opened cryosparc_P25_J586_005_volume_map_sharp(1).mrc as #1, grid size 420,420,420, pixel 1.04, shown at level 0.0438, step 2, values float32 > volume #1 level 0.08587 > volume #1 step 1 > surface dust #1 size 5 > volume flip #1 Opened cryosparc_P25_J586_005_volume_map_sharp(1).mrc z flip as #2, grid size 420,420,420, pixel 1.04, shown at step 1, values float32 > surface dust #2 size 5 > volume #2 level 0.1023 > open > /Users/karlaivettedelaobecerra/Downloads/cryosparc_P25_J607_006_volume_map_sharp.mrc Opened cryosparc_P25_J607_006_volume_map_sharp.mrc as #3, grid size 420,420,420, pixel 1.04, shown at level 0.0456, step 2, values float32 > volume #3 level 0.1089 > surface dust #3 size 5 > volume flip #3 Opened cryosparc_P25_J607_006_volume_map_sharp.mrc z flip as #4, grid size 420,420,420, pixel 1.04, shown at step 1, values float32 > surface dust #4 size 5 > volume #4 level 0.1492 > open > /Users/karlaivettedelaobecerra/Downloads/cryosparc_P3_J115_map_sharp.mrc Opened cryosparc_P3_J115_map_sharp.mrc as #5, grid size 380,380,380, pixel 1.04, shown at level 0.133, step 2, values float32 > surface dust #5 size 5 > volume #5 level 0.282 > ui mousemode right ""translate selected models"" > volume #5 step 1 > ui mousemode right ""translate selected models"" > select #5 2 models selected > view matrix models > #5,0.2991,-0.065605,0.95196,-48.688,0.40309,0.91294,-0.063733,-47.382,-0.8649,0.40279,0.29951,232.13 > view matrix models > #5,-0.3825,0.62041,0.68468,4.6574,0.34925,0.78313,-0.51452,80.628,-0.85541,0.04232,-0.51622,467.49 > view matrix models > #5,-0.99734,0.0093992,-0.072245,395.9,0.041266,0.89011,-0.45387,106.57,0.06004,-0.45564,-0.88814,464.46 > view matrix models > #5,-0.47163,0.87735,-0.088502,131.15,0.51322,0.19149,-0.83662,229.47,-0.71706,-0.44,-0.54058,538.96 > view matrix models > #5,-0.93123,-0.22113,0.28968,353.27,-0.35582,0.72355,-0.5915,243.09,-0.0788,-0.6539,-0.75247,501.41 > view matrix models > #5,-0.80524,-0.3737,-0.46037,512.72,-0.02971,0.80086,-0.59812,167.04,0.59221,-0.46795,-0.65598,317.1 > view matrix models > #5,-0.99925,0.033332,-0.019663,380.84,0.038058,0.75423,-0.65551,174.83,-0.0070189,-0.65577,-0.75493,488.51 > view matrix models > #5,-0.6376,0.63727,-0.43284,280.03,0.75453,0.40327,-0.51774,76.832,-0.15538,-0.6567,-0.73797,513.65 > view matrix models > #5,-0.8623,-0.14318,0.48573,284.73,-0.30347,0.91399,-0.26932,130.12,-0.40539,-0.37964,-0.83159,527.4 > view matrix models > #5,-0.48783,0.6642,-0.56645,273.59,0.86715,0.29411,-0.40194,52.486,-0.10037,-0.68727,-0.71943,505.18 > view matrix models > #5,0.89708,-0.28861,-0.33459,144.15,-0.22788,-0.95093,0.20928,376.77,-0.37858,-0.11149,-0.91883,488.5 > view matrix models > #5,-0.12665,-0.83944,-0.52848,486.43,-0.94793,-0.05452,0.31377,320.5,-0.2922,0.5407,-0.78883,319.49 > view matrix models > #5,-0.88694,0.42698,0.17617,243.17,0.43983,0.66427,0.6044,-143.83,0.14104,0.61355,-0.77696,219.96 > view matrix models > #5,0.056283,0.94728,-0.31542,63.116,0.76482,0.16216,0.6235,-113.25,0.64178,-0.27633,-0.71538,282.87 > view matrix models > #5,0.98385,0.16329,-0.073334,-13.309,0.15622,-0.58326,0.79712,111.42,0.087388,-0.7957,-0.59935,465.41 > view matrix models > #5,0.98776,0.02599,-0.15382,28.957,0.13223,-0.66265,0.73716,143.65,-0.082772,-0.74848,-0.65798,500.98 > view matrix models > #5,0.32525,-0.94319,0.067862,297.22,-0.27806,-0.026802,0.96019,53.87,-0.90382,-0.33117,-0.27098,498.36 > view matrix models > #5,-0.92874,0.020253,0.37017,289.71,0.23995,0.79398,0.55858,-121.1,-0.2826,0.6076,-0.74226,295.18 > view matrix models > #5,-0.9185,0.026763,-0.39452,443.69,-0.27629,0.67032,0.68872,-25.057,0.28288,0.74159,-0.60829,133.41 > view matrix models > #5,-0.83302,0.55324,0.0021968,244.26,0.35875,0.53714,0.7634,-136.46,0.42116,0.63671,-0.64593,134.86 > view matrix models > #5,0.46816,0.20301,0.86001,-113.98,0.68567,0.53045,-0.49848,61.555,-0.55739,0.82305,0.10913,131.3 > view matrix models > #5,0.98549,-0.15218,-0.075228,47.583,0.0605,0.7289,-0.68194,180.85,0.15861,0.66749,0.72753,-103.07 > view matrix models > #5,0.98714,0.0035167,0.15979,-31.061,0.095907,0.78674,-0.60979,148.08,-0.12786,0.61728,0.77629,-48.504 > hide #!5 models > show #!5 models > select add #4 4 models selected > select subtract #5 2 models selected > view matrix models > #4,0.76169,0.42371,0.4902,-140.96,-0.47062,0.88179,-0.03092,138.13,-0.44535,-0.20715,0.87106,172.27 > view matrix models > #4,0.13043,-0.76151,0.6349,220.51,0.48894,0.60649,0.62698,-162.93,-0.86251,0.22865,0.45144,265.35 > view matrix models > #4,-0.52894,-0.78135,0.33124,439.43,0.47828,0.047968,0.8769,-96.693,-0.70105,0.62225,0.34833,168.08 > view matrix models > #4,-0.8715,-0.22865,0.43383,378.43,0.44676,-0.0054201,0.89463,-82.132,-0.2022,0.97349,0.10687,33.159 > view matrix models > #4,0.42826,-0.69943,0.57217,153.51,0.66958,0.67082,0.31885,-150.97,-0.60684,0.24657,0.75561,138.12 > view matrix models > #4,0.95381,-0.12881,0.27138,-20.889,0.0848,0.98211,0.16813,-51.667,-0.28818,-0.13735,0.94767,105.47 > view matrix models > #4,0.95381,-0.12881,0.27138,-23.666,0.0848,0.98211,0.16813,-82.732,-0.28818,-0.13735,0.94767,102.27 > view matrix models > #4,0.82953,-0.36219,0.42509,20.522,0.31012,0.93177,0.18874,-127.59,-0.46444,-0.024738,0.88526,131.91 > ui tool show ""Fit in Map"" > fitmap #4 inMap #5 Fit map cryosparc_P25_J607_006_volume_map_sharp.mrc z flip in map cryosparc_P3_J115_map_sharp.mrc using 134794 points correlation = 0.2702, correlation about mean = 0.03503, overlap = 3168 steps = 200, shift = 15.2, angle = 18.4 degrees Position of cryosparc_P25_J607_006_volume_map_sharp.mrc z flip (#4) relative to cryosparc_P3_J115_map_sharp.mrc (#5) coordinates: Matrix rotation and translation 0.76602184 -0.48904106 0.41719225 45.70939273 0.13578071 0.75746359 0.63860200 -142.47683111 -0.62831054 -0.43253642 0.64663599 313.23586998 Axis -0.66038982 0.64458467 0.38522186 Axis point 0.00000000 415.36758302 379.48917222 Rotation angle (degrees) 54.19272103 Shift along axis -1.35909320 > select subtract #4 Nothing selected > select add #4 2 models selected > view matrix models > #4,0.56762,-0.64628,0.51003,105.72,0.62968,0.7399,0.23677,-169.39,-0.53039,0.18676,0.82693,112.34 > view matrix models > #4,0.56762,-0.64628,0.51003,103.38,0.62968,0.7399,0.23677,-170.18,-0.53039,0.18676,0.82693,116.99 > view matrix models > #4,0.55411,-0.63064,0.54338,95.958,0.60341,0.75396,0.25971,-172.14,-0.57347,0.18397,0.7983,133.5 > select subtract #4 Nothing selected > select add #4 2 models selected > view matrix models > #4,0.5615,-0.62216,0.54556,92.03,0.63846,0.74515,0.19267,-163.77,-0.5264,0.24013,0.81563,107.27 > fitmap #4 inMap #5 Fit map cryosparc_P25_J607_006_volume_map_sharp.mrc z flip in map cryosparc_P3_J115_map_sharp.mrc using 134794 points correlation = 0.6551, correlation about mean = 0.5075, overlap = 1.064e+04 steps = 116, shift = 2.96, angle = 10.6 degrees Position of cryosparc_P25_J607_006_volume_map_sharp.mrc z flip (#4) relative to cryosparc_P3_J115_map_sharp.mrc (#5) coordinates: Matrix rotation and translation 0.55139264 -0.69251920 0.46517020 124.95715885 0.28478213 0.68034856 0.67529621 -165.29879559 -0.78413347 -0.23988120 0.57235628 328.89157802 Axis -0.49975926 0.68221862 0.53368383 Axis point 370.85389861 0.00000000 88.69409980 Rotation angle (degrees) 66.29368234 Shift along axis 0.30570367 > select subtract #4 Nothing selected > volume #4 level 0.198 > volume #4 level 0.138 > ui mousemode right ""translate selected models"" > select add #2 2 models selected > view matrix models > #2,0.98473,-0.061847,0.16271,-18.435,0.019394,0.96791,0.25054,-51.253,-0.17298,-0.24356,0.95434,99.66 > view matrix models > #2,0.57855,-0.64207,0.50302,121.6,0.70143,0.70639,0.094918,-117.13,-0.41627,0.29792,0.85905,61.772 > view matrix models > #2,0.57855,-0.64207,0.50302,120.05,0.70143,0.70639,0.094918,-130.58,-0.41627,0.29792,0.85905,47.487 > view matrix models > #2,0.57855,-0.64207,0.50302,113.38,0.70143,0.70639,0.094918,-154.71,-0.41627,0.29792,0.85905,66.249 > fitmap #2 inMap #4 Fit map cryosparc_P25_J586_005_volume_map_sharp(1).mrc z flip in map cryosparc_P25_J607_006_volume_map_sharp.mrc z flip using 220423 points correlation = 0.9863, correlation about mean = 0.9347, overlap = 1.102e+04 steps = 184, shift = 11.6, angle = 11.1 degrees Position of cryosparc_P25_J586_005_volume_map_sharp(1).mrc z flip (#2) relative to cryosparc_P25_J607_006_volume_map_sharp.mrc z flip (#4) coordinates: Matrix rotation and translation 0.99999654 -0.00239110 0.00110154 0.25185571 0.00239181 0.99999693 -0.00064576 -0.39536263 -0.00109999 0.00064839 0.99999919 0.15020937 Axis 0.23868688 0.40603898 0.88213430 Axis point 170.87602222 101.87971456 0.00000000 Rotation angle (degrees) 0.15532857 Shift along axis 0.03208685 > volume #2 level 0.1174 > select subtract #2 Nothing selected > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > volume #5 level 0.1754 > show #!2 models > hide #!2 models > volume #5 level 0.282 > volume #5 level 0.1691 > volume #5 level 0.2381 Unsupported scale factor (0.000000) detected on Display1 > open /Users/karlaivettedelaobecerra/Desktop/20230306-c3convREF22.pdb Chain information for 20230306-c3convREF22.pdb #6 --- Chain | Description A | No description available B | No description available C | No description available D | No description available F | No description available G | No description available H | No description available > hide #5-6 target a > cartoon #5-6 > select /F:287 6 atoms, 5 bonds, 1 residue, 1 model selected > view matrix models #6,1,0,0,-8.6116,0,1,0,-24.381,0,0,1,-70.507 Drag select of 74 residues Drag select of 125 residues > view matrix models > #6,-0.85259,-0.20941,-0.47879,529.5,0.52258,-0.34347,-0.78035,328.03,-0.001041,-0.91552,0.40227,258.87 > view matrix models > #6,0.89711,-0.43385,0.083524,92.81,-0.40366,-0.728,0.55415,332.19,-0.17961,-0.53085,-0.82822,466.6 > view matrix models > #6,0.89711,-0.43385,0.083524,97.105,-0.40366,-0.728,0.55415,324.17,-0.17961,-0.53085,-0.82822,540.06 > view matrix models > #6,0.90776,-0.3963,0.13755,75.254,-0.40868,-0.76151,0.50308,343.61,-0.094627,-0.51288,-0.85323,523.34 > view matrix models > #6,0.90776,-0.3963,0.13755,73.653,-0.40868,-0.76151,0.50308,333.63,-0.094627,-0.51288,-0.85323,520.58 > fitmap #6 inMap #4 Fit molecule 20230306-c3convREF22.pdb (#6) to map cryosparc_P25_J607_006_volume_map_sharp.mrc z flip (#4) using 30024 atoms average map value = 0.1077, steps = 344 shifted from previous position = 24.2 rotated from previous position = 29.3 degrees atoms outside contour = 19640, contour level = 0.13798 Position of 20230306-c3convREF22.pdb (#6) relative to cryosparc_P25_J607_006_volume_map_sharp.mrc z flip (#4) coordinates: Matrix rotation and translation 0.55627597 -0.34166344 0.75751115 34.47320150 -0.70314512 -0.67934549 0.20994439 483.78617896 0.44288146 -0.64942729 -0.61814255 382.83538934 Axis -0.87337924 0.31975808 -0.36737375 Axis point 0.00000000 304.95827689 110.55152651 Rotation angle (degrees) 150.52914123 Shift along axis -16.05730889 > fitmap #6 inMap #5 Fit molecule 20230306-c3convREF22.pdb (#6) to map cryosparc_P3_J115_map_sharp.mrc (#5) using 30024 atoms average map value = 0.559, steps = 40 shifted from previous position = 0.107 rotated from previous position = 0.0971 degrees atoms outside contour = 7346, contour level = 0.2381 Position of 20230306-c3convREF22.pdb (#6) relative to cryosparc_P3_J115_map_sharp.mrc (#5) coordinates: Matrix rotation and translation 0.99971508 -0.01901478 -0.01442887 -13.41554518 -0.01981887 -0.99813151 -0.05779888 431.83887957 -0.01330288 0.05806838 -0.99822397 404.99304006 Axis 0.99992871 -0.00971726 -0.00693926 Axis point 0.00000000 209.98486155 208.70774124 Rotation angle (degrees) 176.67855101 Shift along axis -20.42123163 > volume #5 color #ffb2ff80 > view matrix models > #6,0.98467,-0.013002,-0.17396,21.463,0.088399,-0.8225,0.56185,241.81,-0.15038,-0.56862,-0.80874,533.85 > fitmap #6 inMap #5 Fit molecule 20230306-c3convREF22.pdb (#6) to map cryosparc_P3_J115_map_sharp.mrc (#5) using 30024 atoms average map value = 0.5591, steps = 56 shifted from previous position = 2.3 rotated from previous position = 0.00992 degrees atoms outside contour = 7351, contour level = 0.2381 Position of 20230306-c3convREF22.pdb (#6) relative to cryosparc_P3_J115_map_sharp.mrc (#5) coordinates: Matrix rotation and translation 0.99971339 -0.01914430 -0.01437507 -13.39873883 -0.01994638 -0.99812319 -0.05789853 431.88948106 -0.01323967 0.05816867 -0.99821897 404.94860164 Axis 0.99992828 -0.00978161 -0.00691000 Axis point 0.00000000 210.00029855 208.69731479 Rotation angle (degrees) 176.67281133 Shift along axis -20.42054848 > select add #6 30024 atoms, 30641 bonds, 9 pseudobonds, 3812 residues, 2 models selected > select subtract #6 Nothing selected > show #5-6 target ab > style #5-6 stick Changed 30024 atom styles > volume #5 level 0.2882 > color #5-6 byhetero > open > ""/Users/karlaivettedelaobecerra/Library/Containers/com.apple.mail/Data/Library/Mail > Downloads/31DF5541-D7BD-4B9C-99D6-9B5197D0A987/2023C3convModelAngfittedP3J115-coot-0.pdb"" Summary of feedback from opening /Users/karlaivettedelaobecerra/Library/Containers/com.apple.mail/Data/Library/Mail Downloads/31DF5541-D7BD-4B9C-99D6-9B5197D0A987/2023C3convModelAngfittedP3J115-coot-0.pdb --- warning | PDB SEQRES record for chain E is incomplete. Ignoring input sequence records as basis for sequence. Chain information for 2023C3convModelAngfittedP3J115-coot-0.pdb #7 --- Chain | Description A | No description available B | No description available C | No description available D | No description available E | No description available F | No description available G | No description available > open /Users/karlaivettedelaobecerra/Desktop/20230306-c3convREF22.pdb Chain information for 20230306-c3convREF22.pdb #8 --- Chain | Description A | No description available B | No description available C | No description available D | No description available F | No description available G | No description available H | No description available > hide #!8 models > hide #!6 models > hide #!5 models > hide #7 target a > cartoon #7 > coulombic #!7 The following heavy (non-hydrogen) atoms are missing, which may result in inaccurate electrostatics: 2023C3convModelAngfittedP3J115-coot-0.pdb #7/F PRO 508 OXT 2023C3convModelAngfittedP3J115-coot-0.pdb #7/B THR 654 OXT 2023C3convModelAngfittedP3J115-coot-0.pdb #7/C LEU 250 OXT Traceback (most recent call last): File ""/private/var/folders/qn/1085xfxs3g15rmlh3q7t_w8w0000gn/T/AppTranslocation/176412EF-9F6E-400C-B8EB-4832EC1F9ACD/d/ChimeraX-1.6-rc2023.04.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/toolbar/tool.py"", line 205, in callback bundle_info.run_provider(session, name, session.toolbar, display_name=display_name) File ""/private/var/folders/qn/1085xfxs3g15rmlh3q7t_w8w0000gn/T/AppTranslocation/176412EF-9F6E-400C-B8EB-4832EC1F9ACD/d/ChimeraX-1.6-rc2023.04.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/toolshed/info.py"", line 386, in run_provider return api._api_caller.run_provider(api, session, name, mgr, **kw) File ""/private/var/folders/qn/1085xfxs3g15rmlh3q7t_w8w0000gn/T/AppTranslocation/176412EF-9F6E-400C-B8EB-4832EC1F9ACD/d/ChimeraX-1.6-rc2023.04.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/toolshed/__init__.py"", line 1289, in run_provider return cls._get_func(api, ""run_provider"")(session, name, mgr, **kw) File ""/private/var/folders/qn/1085xfxs3g15rmlh3q7t_w8w0000gn/T/AppTranslocation/176412EF-9F6E-400C-B8EB-4832EC1F9ACD/d/ChimeraX-1.6-rc2023.04.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/shortcuts/__init__.py"", line 52, in run_provider shortcuts.run_provider(session, name) File ""/private/var/folders/qn/1085xfxs3g15rmlh3q7t_w8w0000gn/T/AppTranslocation/176412EF-9F6E-400C-B8EB-4832EC1F9ACD/d/ChimeraX-1.6-rc2023.04.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/shortcuts/shortcuts.py"", line 1335, in run_provider keyboard_shortcuts(session).try_shortcut(name) File ""/private/var/folders/qn/1085xfxs3g15rmlh3q7t_w8w0000gn/T/AppTranslocation/176412EF-9F6E-400C-B8EB-4832EC1F9ACD/d/ChimeraX-1.6-rc2023.04.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/shortcuts/shortcuts.py"", line 390, in try_shortcut self.run_shortcut(keys) File ""/private/var/folders/qn/1085xfxs3g15rmlh3q7t_w8w0000gn/T/AppTranslocation/176412EF-9F6E-400C-B8EB-4832EC1F9ACD/d/ChimeraX-1.6-rc2023.04.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/shortcuts/shortcuts.py"", line 408, in run_shortcut sc.run(self.session, status = self._enabled) File ""/private/var/folders/qn/1085xfxs3g15rmlh3q7t_w8w0000gn/T/AppTranslocation/176412EF-9F6E-400C-B8EB-4832EC1F9ACD/d/ChimeraX-1.6-rc2023.04.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/shortcuts/shortcuts.py"", line 327, in run f(s) File ""/private/var/folders/qn/1085xfxs3g15rmlh3q7t_w8w0000gn/T/AppTranslocation/176412EF-9F6E-400C-B8EB-4832EC1F9ACD/d/ChimeraX-1.6-rc2023.04.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/shortcuts/shortcuts.py"", line 61, in func_plus_tip func(cmd + "" %s"")(session) File ""/private/var/folders/qn/1085xfxs3g15rmlh3q7t_w8w0000gn/T/AppTranslocation/176412EF-9F6E-400C-B8EB-4832EC1F9ACD/d/ChimeraX-1.6-rc2023.04.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/shortcuts/shortcuts.py"", line 570, in run_expanded_command run(session, cmd) File ""/private/var/folders/qn/1085xfxs3g15rmlh3q7t_w8w0000gn/T/AppTranslocation/176412EF-9F6E-400C-B8EB-4832EC1F9ACD/d/ChimeraX-1.6-rc2023.04.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/shortcuts/shortcuts.py"", line 513, in run run_command(session, command, **kw) File ""/private/var/folders/qn/1085xfxs3g15rmlh3q7t_w8w0000gn/T/AppTranslocation/176412EF-9F6E-400C-B8EB-4832EC1F9ACD/d/ChimeraX-1.6-rc2023.04.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/commands/run.py"", line 38, in run results = command.run(text, log=log, return_json=return_json) File ""/private/var/folders/qn/1085xfxs3g15rmlh3q7t_w8w0000gn/T/AppTranslocation/176412EF-9F6E-400C-B8EB-4832EC1F9ACD/d/ChimeraX-1.6-rc2023.04.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/commands/cli.py"", line 2897, in run result = ci.function(session, **kw_args) File ""/private/var/folders/qn/1085xfxs3g15rmlh3q7t_w8w0000gn/T/AppTranslocation/176412EF-9F6E-400C-B8EB-4832EC1F9ACD/d/ChimeraX-1.6-rc2023.04.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/coulombic/cmd.py"", line 88, in cmd_coulombic assign_charges(session, needs_assignment, his_scheme, charge_method, File ""/private/var/folders/qn/1085xfxs3g15rmlh3q7t_w8w0000gn/T/AppTranslocation/176412EF-9F6E-400C-B8EB-4832EC1F9ACD/d/ChimeraX-1.6-rc2023.04.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/coulombic/coulombic.py"", line 84, in assign_charges cmd_addh(session, addh_structures, hbond=hbond) File ""/private/var/folders/qn/1085xfxs3g15rmlh3q7t_w8w0000gn/T/AppTranslocation/176412EF-9F6E-400C-B8EB-4832EC1F9ACD/d/ChimeraX-1.6-rc2023.04.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/addh/cmd.py"", line 66, in cmd_addh add_h_func(session, structures, template=template, in_isolation=in_isolation, **prot_schemes) File ""/private/var/folders/qn/1085xfxs3g15rmlh3q7t_w8w0000gn/T/AppTranslocation/176412EF-9F6E-400C-B8EB-4832EC1F9ACD/d/ChimeraX-1.6-rc2023.04.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/addh/cmd.py"", line 173, in hbond_add_hydrogens add_hydrogens(session, atoms, type_info_for_atom, naming_schemas, hydrogen_totals, File ""/private/var/folders/qn/1085xfxs3g15rmlh3q7t_w8w0000gn/T/AppTranslocation/176412EF-9F6E-400C-B8EB-4832EC1F9ACD/d/ChimeraX-1.6-rc2023.04.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/addh/hbond.py"", line 248, in add_hydrogens hbonds = find_hbonds(session, s_list, dist_slop=rec_dist_slop, angle_slop=rec_angle_slop) File ""/private/var/folders/qn/1085xfxs3g15rmlh3q7t_w8w0000gn/T/AppTranslocation/176412EF-9F6E-400C-B8EB-4832EC1F9ACD/d/ChimeraX-1.6-rc2023.04.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/hbonds/hbond.py"", line 574, in find_hbonds donor_hyds = hyd_positions(donor_atom) File ""/private/var/folders/qn/1085xfxs3g15rmlh3q7t_w8w0000gn/T/AppTranslocation/176412EF-9F6E-400C-B8EB-4832EC1F9ACD/d/ChimeraX-1.6-rc2023.04.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/hbonds/hydpos.py"", line 77, in hyd_positions bond_positions(heavy_loc, geom, bond_len, bonded_locs, coplanar=coplanar)) File ""/private/var/folders/qn/1085xfxs3g15rmlh3q7t_w8w0000gn/T/AppTranslocation/176412EF-9F6E-400C-B8EB-4832EC1F9ACD/d/ChimeraX-1.6-rc2023.04.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/atomic/bond_geom.py"", line 73, in bond_positions return planar_pos(bondee, bonded, bond_len, coplanar, toward, away, toward2, away2) File ""/private/var/folders/qn/1085xfxs3g15rmlh3q7t_w8w0000gn/T/AppTranslocation/176412EF-9F6E-400C-B8EB-4832EC1F9ACD/d/ChimeraX-1.6-rc2023.04.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/atomic/bond_geom.py"", line 129, in planar_pos pos = angle_pos(bondee, cur_bonded[0], bond_len, 120.0, coplanar) File ""/private/var/folders/qn/1085xfxs3g15rmlh3q7t_w8w0000gn/T/AppTranslocation/176412EF-9F6E-400C-B8EB-4832EC1F9ACD/d/ChimeraX-1.6-rc2023.04.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/atomic/bond_geom.py"", line 231, in angle_pos raise ValueError(""More than 2 coplanar positions specified!"") ValueError: More than 2 coplanar positions specified! ValueError: More than 2 coplanar positions specified! File ""/private/var/folders/qn/1085xfxs3g15rmlh3q7t_w8w0000gn/T/AppTranslocation/176412EF-9F6E-400C-B8EB-4832EC1F9ACD/d/ChimeraX-1.6-rc2023.04.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/atomic/bond_geom.py"", line 231, in angle_pos raise ValueError(""More than 2 coplanar positions specified!"") See log for complete Python traceback. Unsupported scale factor (0.000000) detected on Display0 QPainter::begin: Paint device returned engine == 0, type: 3 ===== Log before crash end ===== Log: UCSF ChimeraX version: 1.6rc202304072249 (2023-04-07) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open > /Users/karlaivettedelaobecerra/Documents/For_Mac/C5PAPER/C5B3G8_FINAL/C5-UC5Nb1-UC5Nb2.pdb Chain information for C5-UC5Nb1-UC5Nb2.pdb #1 --- Chain | Description A | No description available B | No description available C | No description available > open > /Users/karlaivettedelaobecerra/Downloads/C5-UC5Nb1-UC5Nb2-Final1-coot-0.pdb Chain information for C5-UC5Nb1-UC5Nb2-Final1-coot-0.pdb #2 --- Chain | Description A | No description available B | No description available C | No description available D | No description available > open > /Users/karlaivettedelaobecerra/Documents/For_Mac/C5PAPER/C5B3G8_FINAL/C5-UC5Nb1-UC5Nb2-Final1-coot-0.pdb Chain information for C5-UC5Nb1-UC5Nb2-Final1-coot-0.pdb #3 --- Chain | Description A | No description available B | No description available C | No description available D | No description available OpenGL version: 4.1 Metal - 76.3 OpenGL renderer: Apple M1 Pro OpenGL vendor: Apple Python: 3.9.11 Locale: UTF-8 Qt version: PyQt6 6.4.2, Qt 6.4.2 Qt runtime version: 6.4.3 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro18,3 Chip: Apple M1 Pro Total Number of Cores: 8 (6 performance and 2 efficiency) Memory: 16 GB System Firmware Version: 7459.141.1 OS Loader Version: 7459.141.1 Software: System Software Overview: System Version: macOS 12.5 (21G72) Kernel Version: Darwin 21.6.0 Time since boot: 147 days 4:58 Graphics/Displays: Apple M1 Pro: Chipset Model: Apple M1 Pro Type: GPU Bus: Built-In Total Number of Cores: 14 Vendor: Apple (0x106b) Metal Family: Supported, Metal GPUFamily Apple 7 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: Yes Connection Type: Internal HP E272q: Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition) UI Looks like: 2560 x 1440 @ 60.00Hz Mirror: Off Online: Yes Rotation: Supported Installed Packages: alabaster: 0.7.13 appdirs: 1.4.4 appnope: 0.1.3 asttokens: 2.2.1 Babel: 2.12.1 backcall: 0.2.0 beautifulsoup4: 4.11.2 blockdiag: 3.0.0 build: 0.10.0 certifi: 2021.10.8 cftime: 1.6.2 charset-normalizer: 3.1.0 ChimeraX-AddCharge: 1.5.9 ChimeraX-AddH: 2.2.4 ChimeraX-AlignmentAlgorithms: 2.0.1 ChimeraX-AlignmentHdrs: 3.3.1 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.9.3 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.0.3 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.43.10 ChimeraX-AtomicLibrary: 10.0.6 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.3.2 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.1.2 ChimeraX-BondRot: 2.0.1 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.8 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: 1.3.2 ChimeraX-ChangeChains: 1.0.2 ChimeraX-CheckWaters: 1.3.1 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.2.4 ChimeraX-ColorActions: 1.0.3 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.3 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.6rc202304072249 ChimeraX-CoreFormats: 1.1 ChimeraX-coulombic: 1.4.2 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 ChimeraX-DockPrep: 1.1.1 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: 1.2.1 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-Label: 1.1.7 ChimeraX-ListInfo: 1.1.1 ChimeraX-Log: 1.1.5 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.8.2 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: 2.0.12 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.2 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.12 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.9 ChimeraX-ModelPanel: 1.3.7 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.2 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.0 ChimeraX-NRRD: 1.0 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.10.1 ChimeraX-PDB: 2.7 ChimeraX-PDBBio: 1.0 ChimeraX-PDBLibrary: 1.0.2 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1 ChimeraX-PubChem: 2.1 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.1 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.1 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 3.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.1 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.8.3 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.1 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.10.2 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.1.2 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.2.1 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1.2 ChimeraX-ToolshedUtils: 1.2.1 ChimeraX-Topography: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.28.4 ChimeraX-uniprot: 2.2.2 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.2 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.1 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.1.3 contourpy: 1.0.7 cxservices: 1.2.2 cycler: 0.11.0 Cython: 0.29.33 debugpy: 1.6.7 decorator: 5.1.1 docutils: 0.19 executing: 1.2.0 filelock: 3.9.0 fonttools: 4.39.3 funcparserlib: 1.0.1 grako: 3.16.5 h5py: 3.8.0 html2text: 2020.1.16 idna: 3.4 ihm: 0.35 imagecodecs: 2022.2.22 imagesize: 1.4.1 importlib-metadata: 6.3.0 ipykernel: 6.21.1 ipython: 8.10.0 ipython-genutils: 0.2.0 ipywidgets: 8.0.6 jedi: 0.18.2 Jinja2: 3.1.2 jupyter-client: 8.0.2 jupyter-core: 5.3.0 jupyterlab-widgets: 3.0.7 kiwisolver: 1.4.4 line-profiler: 4.0.2 lxml: 4.9.2 lz4: 4.3.2 MarkupSafe: 2.1.2 matplotlib: 3.6.3 matplotlib-inline: 0.1.6 msgpack: 1.0.4 nest-asyncio: 1.5.6 netCDF4: 1.6.2 networkx: 2.8.8 nibabel: 5.0.1 nptyping: 2.5.0 numexpr: 2.8.4 numpy: 1.23.5 openvr: 1.23.701 packaging: 21.3 ParmEd: 3.4.3 parso: 0.8.3 pep517: 0.13.0 pexpect: 4.8.0 pickleshare: 0.7.5 Pillow: 9.3.0 pip: 23.0 pkginfo: 1.9.6 platformdirs: 3.2.0 prompt-toolkit: 3.0.38 psutil: 5.9.4 ptyprocess: 0.7.0 pure-eval: 0.2.2 pycollada: 0.7.2 pydicom: 2.3.0 Pygments: 2.14.0 pynrrd: 1.0.0 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 3.0.9 pyproject-hooks: 1.0.0 PyQt6-commercial: 6.4.2 PyQt6-Qt6: 6.4.3 PyQt6-sip: 13.4.1 PyQt6-WebEngine-commercial: 6.4.0 PyQt6-WebEngine-Qt6: 6.4.3 python-dateutil: 2.8.2 pytz: 2023.3 pyzmq: 25.0.2 qtconsole: 5.4.0 QtPy: 2.3.1 RandomWords: 0.4.0 requests: 2.28.2 scipy: 1.9.3 setuptools: 67.4.0 setuptools-scm: 7.0.5 sfftk-rw: 0.7.3 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.4 sphinx: 6.1.3 sphinx-autodoc-typehints: 1.22 sphinxcontrib-applehelp: 1.0.4 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.2 sphinxcontrib-htmlhelp: 2.0.1 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.3 sphinxcontrib-serializinghtml: 1.1.5 stack-data: 0.6.2 tables: 3.7.0 tcia-utils: 1.2.0 tifffile: 2022.10.10 tinyarray: 1.2.4 tomli: 2.0.1 tornado: 6.2 traitlets: 5.9.0 typing-extensions: 4.5.0 tzdata: 2023.3 urllib3: 1.26.15 wcwidth: 0.2.6 webcolors: 1.12 wheel: 0.38.4 wheel-filename: 1.4.1 widgetsnbextension: 4.0.7 zipp: 3.15.0 }}} " defect closed normal Window Toolkit can't reproduce Tom Goddard all ChimeraX