id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 17718 Crash on Mac waking from sleep chimerax-bug-report@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-14.6.1-arm64-arm-64bit ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC) Description Last time you used ChimeraX it crashed. This is a known crash that we are unable to fix. Here is information that may help you avoid this crash. The Qt window toolkit crashed due to a display configuration change, typically when waking from sleep or when an external display is disconnected or connected. This has only been seen on Mac computers. We hope a newer version of Qt will fix it. We update ChimeraX daily builds whenever a new Qt is released. You can check here https://www.cgl.ucsf.edu/chimerax/docs/troubleshoot.html#macdisplay to see if it has been fixed in a newer ChimeraX. 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""SIRI_UNDERSTANDING_ATTENTION_ASSETS"" : ""65a8118e05d9422724106749"", ""SIRI_UNDERSTANDING_ASR_ASSISTANT"" : ""65a8115446dfa0720068876d"", ""SIRI_UNDERSTANDING_NL"" : ""65a811c046dfa0720068876e"", ""SIRI_EXPERIENCE_CAM"" : ""65a81173096f6a1f1ba46525"", ""SIRI_UNDERSTANDING_MORPHUN"" : ""65a811a96c2f903aa921c246"" }, ""deploymentId"" : 240000116 }, { ""rolloutId"" : ""642da32dea3b2418c750f848"", ""factorPackIds"" : { }, ""deploymentId"" : 240000004 } ], ""experiments"" : [ { ""treatmentId"" : ""28060e10-d4e5-4163-aa2b-d8bd088d5cbf"", ""experimentId"" : ""6685b283afc7c17197d69eec"", ""deploymentId"" : 400000012 } ] } } ===== Log before crash start ===== Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > windowsize 720 720 > size stickRadius 0.2 Changed 0 bond radii > open ""/Users/dellasyau/Dropbox > (HMS)/Syau_IWS1/Extended_Data_Figures/Interactions_Extended/emd_10480.map"" > name 6TEDmap Opened 6TEDmap as #1, grid size 360,360,360, pixel 1.05, shown at level 0.0148, step 2, values float32 > surface dust #1 size 10.5 > volume #1 step 1 > volume #1 level 0.016 > open 6TED 6ted title: Structure of complete, activated transcription complex Pol II-DSIF-PAF-SPT6 uncovers allosteric elongation activation by RTF1 [more info...] Chain information for 6ted #2 --- Chain | Description | UniProt A | DNA-directed RNA polymerase subunit | A0A480RVL6_PIG 1-1984 B | DNA-directed RNA polymerase subunit beta | I3LGP4_PIG -76-1174 C | RNA polymerase II subunit C | I3LCH3_PIG 1-275 D | RNA polymerase II subunit D | A0A287ADR4_PIG 1-142 E | RNA polymerase II subunit E | I3LSI7_PIG 1-210 F | RNA polymerase II subunit F | F1SKN8_PIG 1-127 G | RNA polymerase II subunit G | I3LJZ9_PIG 1-172 H | DNA-directed RNA polymerases I, II, and III subunit RPABC3 | I3LCB2_PIG 1-150 I | DNA-directed RNA polymerase II subunit RPB9 | RPB9_PIG 1-125 J | Uncharacterized protein | A0A287B432_PIG 1-67 K | Uncharacterized protein | F1RKE4_PIG 1-117 L | Uncharacterized protein | I3LN51_PIG 1-58 M | Transcription elongation factor SPT6 | SPT6H_HUMAN 1-1726 N | DNA (37-MER) | P | RNA (5'-R(P*UP*AP*AP*CP*CP*GP*GP*AP*GP*AP*GP*GP*GP*AP*AP*CP*CP*CP*AP*CP*U)-3') | Q | RNA polymerase-associated protein CTR9 homolog | CTR9_HUMAN 1-1173 R | RNA polymerase-associated protein RTF1 homolog | RTF1_HUMAN 1-710 T | Template DNA | U | RNA polymerase-associated protein LEO1 | LEO1_HUMAN 1-673 V | RNA polymerase II-associated factor 1 homolog | PAF1_HUMAN 1-531 W | WD repeat-containing protein 61 | WDR61_HUMAN 1-305 X | Parafibromin | CDC73_HUMAN 1-531 Y | Transcription elongation factor SPT4 | SPT4H_HUMAN 1-117 Z | Transcription elongation factor SPT5 | SPT5H_HUMAN 1-1087 Non-standard residues in 6ted #2 --- MG — magnesium ion ZN — zinc ion > runscript ""/Users/dellasyau/Dropbox (HMS)/Syau_IWS1/Scripts/style_sheet.cxc"" > cartoon style nucleic xsection oval width 2.5 thickness 2.5 > cartoon style protein modeHelix default arrows false xsection oval width 3 > thickness 1.2 > nucleotides fill > style stick Changed 57142 atom styles > graphics silhouettes width 3 > lighting depthCue false > lighting soft > lighting multiShadow 512 > graphics silhouettes true > graphics bgColor white > color /Y pale green > color /Z forest green > hide atoms > show /Z:163-268 /Y cartoons > color zone #1 near /Z:163-268 /Y distance 2.5 > view matrix camera > 0.01311,-0.39465,0.91874,375.79,0.77299,-0.57883,-0.25967,96.813,0.63428,0.71358,0.29747,280.11 > show /Z:163-268 /Y surfaces > hide /Y,Z cartoons > transparency /Y,Z 80 > transparency /Y,Z 90 > view matrix camera > 0.01311,-0.39465,0.91874,375.79,0.77299,-0.57883,-0.25967,96.813,0.63428,0.71358,0.29747,280.11 > volume #1 level 0.02275 > view matrix camera > 0.01311,-0.39465,0.91874,375.79,0.77299,-0.57883,-0.25967,96.813,0.63428,0.71358,0.29747,280.11 > volume #1 level 0.025 > volume #1 level 0.026 > save ""/Users/dellasyau/Dropbox > (HMS)/Syau_IWS1/Extended_Data_Figures/Interactions_Extended/6TEDNGN.png"" > format png width 1440 height 1440 supersample 4 transparentBackground true > volume #1 level 0.02 > save ""/Users/dellasyau/Dropbox > (HMS)/Syau_IWS1/Extended_Data_Figures/Interactions_Extended/6TEDNGN.png"" > format png width 1440 height 1440 supersample 4 transparentBackground true > show /Y,Z cartoons > open ""/Users/dellasyau/Dropbox (HMS)/Syau_IWS1/Figures/IWS1 > interactions/cryosparc_P146_J525_007_volume_map.mrc"" name J525 Opened J525 as #3, grid size 460,460,460, pixel 1.19, shown at level 0.014, step 2, values float32 > surface dust #3 size 11.9 > volume #3 step 1 > volume #3 level 0.05 > hide #!1 models > hide #!2 models > open ""/Users/dellasyau/Dropbox (HMS)/Syau_IWS1/Structures/Revision 1 > modeling intermediates/250509_model_it062.pdb"" name EC Chain information for EC #4 --- 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 H | No description available I | No description available J | No description available K | No description available L | No description available M | No description available N | No description available O | No description available P | No description available Q | No description available R | No description available S | No description available T | No description available U | No description available V | No description available W | No description available X | No description available Y | No description available Z | No description available a | No description available b | No description available c g | No description available d h | No description available e | No description available f | No description available i | No description available l | No description available > runscript ""/Users/dellasyau/Dropbox (HMS)/Syau_IWS1/Scripts/style_sheet.cxc"" > cartoon style nucleic xsection oval width 2.5 thickness 2.5 > cartoon style protein modeHelix default arrows false xsection oval width 3 > thickness 1.2 > nucleotides fill > style stick Changed 201822 atom styles > graphics silhouettes width 3 > lighting depthCue false > lighting soft > lighting multiShadow 512 > graphics silhouettes true > graphics bgColor white > runscript ""/Users/dellasyau/Dropbox (HMS)/Syau_IWS1/Scripts/naming.cxc"" > name PolII ##name=""EC""/A-L > name SPT6 ##name=""EC""/M > name ELOF1 ##name=""EC""/O > name CTR9 ##name=""EC""/Q > name RTF1 ##name=""EC""/R > name TFIIS ##name=""EC""/S > name LEO1 ##name=""EC""/U > name PAF1 ##name=""EC""/V > name WDR61 ##name=""EC""/W > name CDC73 ##name=""EC""/X > name SPT4 ##name=""EC""/Y > name SPT5 ##name=""EC""/Z > name IWS1 ##name=""EC""/i > name H2A ##name=""EC""/c,g > name H2B ##name=""EC""/d,h > name H3 ##name=""EC""/a,e > name H4 ##name=""EC""/b,f > name LEDGF ##name=""EC""/l > name Nucleic-acids ##name=""EC""/T,N,P > name template ##name=""EC""/T > name nontemplate ##name=""EC""/N > name RNA ##name=""EC""/P > runscript ""/Users/dellasyau/Dropbox (HMS)/Syau_IWS1/Scripts/coloring.cxc"" > color PolII silver > color ELOF1 cyan > color SPT4 pale green > color SPT5 forest green > color SPT6 dark blue > color RTF1 hot pink > color CDC73 brown > color PAF1 green yellow > color LEO1 purple > color CTR9 orange > color WDR61 teal > color TFIIS #ffc300 > color IWS1 pink > color template navy > color nontemplate light steel blue > color RNA red > color H2A yellow > color H2B red > color H3 dodger blue > color H4 chartreuse > color LEDGF orchid > color Mg deeppink > style Mg sphere Changed 2 atom styles > show Mg atoms > size Mg atomRadius 1.5 Changed 2 atom radii > hide atoms > show ##name=EC/Z:163-268 ##name=EC/Y cartoons > color zone #3 near #4/A,B,O,i,M #4/Z:163-268 #4/Y distance 2.5 > view matrix camera > -0.87789,0.47882,0.0061785,314.26,-0.45091,-0.83094,0.32591,322.65,0.16118,0.28333,0.94538,506.43 > volume #3 level 0.0695 > volume #3 level 0.07 > view matrix camera > -0.87789,0.47882,0.0061785,314.26,-0.45091,-0.83094,0.32591,322.65,0.16118,0.28333,0.94538,506.43 > hide cartoons > color zone #3 near #4/A,B,O,i,M #4/Z:163-268 #4/Y distance 2.75 > color zone #3 near #4/A,B,O,i,M #4/Z:163-268 #4/Y distance 3 > color #3 silver > color zone #3 near #4/A,B,O,i,M #4/Z:163-268 #4/Y distance 3 > save ""/Users/dellasyau/Dropbox > (HMS)/Syau_IWS1/Extended_Data_Figures/Interactions_Extended/NGNdensity.png"" > format png width 1440 height 1440 supersample 4 transparentBackground true > show #!1 models > show #!2 models > hide #!3 models > hide #!4 models > view matrix camera > 0.01311,-0.39465,0.91874,375.79,0.77299,-0.57883,-0.25967,96.813,0.63428,0.71358,0.29747,280.11 > show #2/B cartoons > hide #2/B cartoons > volume #1 level 0.02811 > close #3 > open ""/Users/dellasyau/Dropbox > (HMS)/Syau_IWS1/Extended_Data_Figures/IWS1_classification_tree/cryosparc_P146_J154_007_volume_map.mrc"" Opened cryosparc_P146_J154_007_volume_map.mrc as #3, grid size 460,460,460, pixel 1.19, shown at level 0.0136, step 2, values float32 > surface dust #3 size 11.9 > volume #3 step 1 > volume #3 level 0.07 > color #3 silver > color zone #3 near #4/A,B,O,i,M #4/Z:163-268 #4/Y distance 3 > view matrix camera > -0.87789,0.47882,0.0061785,314.26,-0.45091,-0.83094,0.32591,322.65,0.16118,0.28333,0.94538,506.43 > hide #!1 models > hide #!2 models > volume #3 level 0.06044 > volume #3 level 0.05 > save ""/Users/dellasyau/Dropbox > (HMS)/Syau_IWS1/Extended_Data_Figures/Interactions_Extended/NGNdensity.png"" > format png width 1440 height 1440 supersample 4 transparentBackground true > mmaker #4/A to #2/A Computing secondary structure Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 6ted, chain A (#2) with EC, chain A (#4), sequence alignment score = 6599.3 RMSD between 1363 pruned atom pairs is 0.496 angstroms; (across all 1393 pairs: 0.713) > hide #!3 models > show #!2 models > show #!1 models > show #4 cartoons > view matrix camera > 0.01311,-0.39465,0.91874,375.79,0.77299,-0.57883,-0.25967,96.813,0.63428,0.71358,0.29747,280.11 > show #!4 models > hide #!4 models > show #!4 models > hide #!4 models > close #1-4 > open /Users/dellasyau/Downloads/cryosparc_P146_J685_007_volume_map.mrc Opened cryosparc_P146_J685_007_volume_map.mrc as #1, grid size 360,360,360, pixel 1.72, shown at level 0.102, step 2, values float32 > open /Users/dellasyau/Downloads/cryosparc_P146_J686_005_volume_map.mrc Opened cryosparc_P146_J686_005_volume_map.mrc as #2, grid size 360,360,360, pixel 1.72, shown at level 0.109, step 2, values float32 > open /Users/dellasyau/Downloads/cryosparc_P146_J687_006_volume_map.mrc Opened cryosparc_P146_J687_006_volume_map.mrc as #3, grid size 360,360,360, pixel 1.72, shown at level 0.142, step 2, values float32 > volume #1 step 1 > volume #2 step 1 > volume #3 step 1 > hide #!2 models > hide #!3 models > volume #1 level 0.1771 > volume #1 level 0.2087 > volume #2 level 0.2054 > show #!3 models > hide #!2 models > volume #3 level 0.2778 > volume #3 level 0.2559 > volume #3 level 0.2075 > volume #2 level 0.228 > volume #1 level 0.1857 > close #1-3 > open /Users/dellasyau/Downloads/cryosparc_P146_J688_003_volume_map.mrc Opened cryosparc_P146_J688_003_volume_map.mrc as #1, grid size 360,360,360, pixel 1.72, shown at level 0.0948, step 2, values float32 > open /Users/dellasyau/Downloads/cryosparc_P146_J689_002_volume_map.mrc Opened cryosparc_P146_J689_002_volume_map.mrc as #2, grid size 360,360,360, pixel 1.72, shown at level 0.079, step 2, values float32 > open /Users/dellasyau/Downloads/cryosparc_P146_J690_004_volume_map.mrc Opened cryosparc_P146_J690_004_volume_map.mrc as #3, grid size 360,360,360, pixel 1.72, shown at level 0.102, step 2, values float32 > open /Users/dellasyau/Downloads/cryosparc_P146_J691_002_volume_map.mrc Opened cryosparc_P146_J691_002_volume_map.mrc as #4, grid size 360,360,360, pixel 1.72, shown at level 0.078, step 2, values float32 > volume step 1 > volume level 0.2 > volume #2 level 0.1121 > volume #3 level 0.182 > volume #3 level 0.2067 > volume #4 level 0.1365 > show #!2 models > open ""/Users/dellasyau/HMS Dropbox/Della Syau/Syau_IWS1/Structures/Revision > 1 modeling intermediates/250509_model_it062.pdb"" Chain information for 250509_model_it062.pdb #5 --- 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 H | No description available I | No description available J | No description available K | No description available L | No description available M | No description available N | No description available O | No description available P | No description available Q | No description available R | No description available S | No description available T | No description available U | No description available V | No description available W | No description available X | No description available Y | No description available Z | No description available a | No description available b | No description available c g | No description available d h | No description available e | No description available f | No description available i | No description available l | No description available > hide atoms > show cartoons > show #!1 models > hide #!2 models > vop flip #2 Opened cryosparc_P146_J689_002_volume_map.mrc z flip as #6, grid size 360,360,360, pixel 1.72, shown at step 1, values float32 > vop flip #1 Opened cryosparc_P146_J688_003_volume_map.mrc z flip as #7, grid size 360,360,360, pixel 1.72, shown at step 1, values float32 > hide #!6 models > ui mousemode right ""rotate selected models"" > select add #5 144680 atoms, 146848 bonds, 67 pseudobonds, 9652 residues, 3 models selected > view matrix models > #5,0.94375,-0.33067,0.0014512,104.46,0.29593,0.84263,-0.44988,97.324,0.14754,0.425,0.89309,-123.16 > view matrix models > #5,0.41477,-0.87257,0.25805,313.92,0.90802,0.41525,-0.055389,-56.191,-0.058825,0.25729,0.96454,-45.125 > view matrix models > #5,-0.73785,-0.60384,-0.3016,696.79,0.66378,-0.73016,-0.16204,350.53,-0.12237,-0.31976,0.93956,136.26 > view matrix models > #5,-0.79426,-0.53592,-0.28625,688.19,0.59084,-0.79111,-0.15829,384.78,-0.14163,-0.29485,0.94499,132.8 > view matrix models > #5,-0.84,-0.4017,-0.36474,685.83,0.51314,-0.80659,-0.29343,447.92,-0.17632,-0.43364,0.88367,197.36 > ui mousemode right ""translate selected models"" > view matrix models > #5,-0.84,-0.4017,-0.36474,738.06,0.51314,-0.80659,-0.29343,424.09,-0.17632,-0.43364,0.88367,244.98 > view matrix models > #5,-0.84,-0.4017,-0.36474,770.67,0.51314,-0.80659,-0.29343,466.28,-0.17632,-0.43364,0.88367,244.11 > view matrix models > #5,-0.84,-0.4017,-0.36474,758.23,0.51314,-0.80659,-0.29343,470.63,-0.17632,-0.43364,0.88367,222.8 > fitmap #5 inMap #7 Fit molecule 250509_model_it062.pdb (#5) to map cryosparc_P146_J688_003_volume_map.mrc z flip (#7) using 144680 atoms average map value = 0.2114, steps = 196 shifted from previous position = 11.9 rotated from previous position = 21.7 degrees atoms outside contour = 75738, contour level = 0.2 Position of 250509_model_it062.pdb (#5) relative to cryosparc_P146_J688_003_volume_map.mrc z flip (#7) coordinates: Matrix rotation and translation -0.96811951 -0.18441872 -0.16951205 671.63770620 0.24826891 -0.79634080 -0.55154681 614.09702817 -0.03327381 -0.57604780 0.81673850 251.83379040 Axis -0.05393246 -0.29989243 0.95244728 Axis point 305.49792027 387.33310436 0.00000000 Rotation angle (degrees) 166.87094482 Shift along axis 19.47228748 > select subtract #5 Nothing selected > ui mousemode right translate > volume #6 color #ffffb2b0 > vop flip #4 Opened cryosparc_P146_J691_002_volume_map.mrc z flip as #8, grid size 360,360,360, pixel 1.72, shown at step 1, values float32 > volume #6 color #ffffb2 > volume #6 level 0.1346 > volume #8 level 0.1141 > volume #8 level 0.1533 > open 6s01 6s01 title: Structure of LEDGF PWWP domain bound H3K36 methylated nucleosome [more info...] Chain information for 6s01 #9 --- Chain | Description | UniProt A E | Histone H3 | A0A310TTQ1_XENLA 1-135 B F | Histone H4 | H4_XENLA 1-102 C G | Histone H2A | Q6AZJ8_XENLA 1-129 D H | Histone H2B 1.1 | H2B11_XENLA 1-122 I | Wisdom 601 DNA (165-MER) | J | Wisdom 601 DNA (165-MER) | K | PC4 and SFRS1-interacting protein | PSIP1_HUMAN 1-530 > mmaker #9/A to #5/a Computing secondary structure Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 250509_model_it062.pdb, chain a (#5) with 6s01, chain A (#9), sequence alignment score = 486.4 RMSD between 97 pruned atom pairs is 0.111 angstroms; (across all 97 pairs: 0.111) > hide atoms > show cartoons > select add #9 12959 atoms, 13814 bonds, 351 pseudobonds, 1153 residues, 3 models selected > ui mousemode right ""rotate selected models"" > view matrix models > #9,0.31482,0.76562,0.56099,136.88,-0.39512,0.64311,-0.65596,322.33,-0.863,-0.015154,0.50498,462.16 > view matrix models > #9,-0.053111,0.85546,0.51514,180.06,-0.52896,0.41345,-0.74113,382.23,-0.84699,-0.31185,0.43054,509.6 > view matrix models > #9,-0.28695,0.89323,0.34613,227.84,-0.7913,-0.017375,-0.61118,459.41,-0.53991,-0.44927,0.7118,451.24 > view matrix models > #9,-0.34821,0.8712,0.34606,239.07,-0.71158,-0.0053326,-0.70258,458.62,-0.61025,-0.49089,0.62179,477.74 > ui mousemode right ""translate selected models"" > view matrix models > #9,-0.34821,0.8712,0.34606,240.7,-0.71158,-0.0053326,-0.70258,432.09,-0.61025,-0.49089,0.62179,455.62 > view matrix models > #9,-0.34821,0.8712,0.34606,241.63,-0.71158,-0.0053326,-0.70258,427.75,-0.61025,-0.49089,0.62179,453.6 > volume #8 level 0.1664 > open /Users/dellasyau/Downloads/cryosparc_P146_J589_006_volume_map.mrc Opened cryosparc_P146_J589_006_volume_map.mrc as #10, grid size 460,460,460, pixel 1.19, shown at level 0.0198, step 2, values float32 > close #9 > close #7-8,10 > close #4-6 > close #1-3 > open ""/Users/dellasyau/Dropbox (HMS)/Syau_IWS1/Structures/Revision 1 > modeling intermediates/250509_model_it062.pdb"" format pdb Chain information for 250509_model_it062.pdb #1 --- 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 H | No description available I | No description available J | No description available K | No description available L | No description available M | No description available N | No description available O | No description available P | No description available Q | No description available R | No description available S | No description available T | No description available U | No description available V | No description available W | No description available X | No description available Y | No description available Z | No description available a | No description available b | No description available c g | No description available d h | No description available e | No description available f | No description available i | No description available l | No description available > open /Users/dellasyau/Downloads/cryosparc_P146_J589_006_volume_map_sharp.mrc Opened cryosparc_P146_J589_006_volume_map_sharp.mrc as #2, grid size 460,460,460, pixel 1.19, shown at level 0.0674, step 2, values float32 > open /Users/dellasyau/Downloads/cryosparc_P146_J589_006_volume_map.mrc Opened cryosparc_P146_J589_006_volume_map.mrc as #3, grid size 460,460,460, pixel 1.19, shown at level 0.0198, step 2, values float32 > hide atoms > show cartoons > volume step 1 Color zone shortcut requires 1 displayed atomic model and 1 map, got 1 atomic models, 2 maps. > surface dust #2 size 11.9 > surface dust #3 size 11.9 > volume #3 level 0.3 > volume #3 level 0.1 > hide #!1 models > show #!1 models > open /Users/dellasyau/Downloads/cryosparc_P146_J670_004_volume_map_sharp.mrc Opened cryosparc_P146_J670_004_volume_map_sharp.mrc as #4, grid size 460,460,460, pixel 1.19, shown at level 0.0446, step 2, values float32 > open /Users/dellasyau/Downloads/cryosparc_P146_J670_004_volume_map.mrc Opened cryosparc_P146_J670_004_volume_map.mrc as #5, grid size 460,460,460, pixel 1.19, shown at level 0.0185, step 2, values float32 > volume step 1 > surface dust #3 size 11.9 > surface dust #4 size 11.9 > surface dust #5 size 11.9 > volume #5 level 0.1 > volume #3 level 0.04843 > volume #3 level 0.04029 > volume #3 level 0.04843 > hide #!1 models > ui tool show ""Side View"" > show #!1 models > volume #3 level 0.03215 > volume #3 level 0.02265 > hide #!3 models > show #!3 models > hide #!3 models > ui tool show ""Side View"" > volume #3 level 0.03215 > volume #3 level 0.03622 > volume #3 level 0.04436 > volume #3 level 0.03758 > volume #3 level 0.04708 > volume #3 level 0.09864 > volume #3 level 0.04708 > volume #3 level 0.0475 > volume #5 level 0.475 > volume #5 level 0.0475 > volume #2 level 0.07845 > volume #2 level 0.1079 > volume #2 level 0.06003 > volume #2 level 0.04528 > close #2-3 > show #!4 models > volume #4 level 0.07 > volume #5 level 0.07 > hide #!5 models > fitmap #1 inMap #4 Fit molecule 250509_model_it062.pdb (#1) to map cryosparc_P146_J670_004_volume_map_sharp.mrc (#4) using 144680 atoms average map value = 0.06737, steps = 84 shifted from previous position = 0.615 rotated from previous position = 0.61 degrees atoms outside contour = 103215, contour level = 0.07 Position of 250509_model_it062.pdb (#1) relative to cryosparc_P146_J670_004_volume_map_sharp.mrc (#4) coordinates: Matrix rotation and translation 0.99994636 0.00550710 0.00877235 -4.38159006 -0.00548537 0.99998183 -0.00249942 2.38927378 -0.00878595 0.00245117 0.99995840 2.03757886 Axis 0.23243578 0.82438184 -0.51610870 Axis point 223.65792196 0.00000000 498.18540782 Rotation angle (degrees) 0.61017583 Shift along axis -0.10037659 > isolde start > set selectionWidth 4 Done loading forcefield > isolde set simFidelityMode Medium/Medium ISOLDE: setting sim fidelity mode to Medium/Medium nonbonded_cutoff_distance = 0.900000 use_gbsa = True gbsa_cutoff = 1.100000 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... Chain information for 250509_model_it062.pdb --- Chain | Description 1.2/A | No description available 1.2/B | No description available 1.2/C | No description available 1.2/D | No description available 1.2/E | No description available 1.2/F | No description available 1.2/G | No description available 1.2/H | No description available 1.2/I | No description available 1.2/J | No description available 1.2/K | No description available 1.2/L | No description available 1.2/M | No description available 1.2/N | No description available 1.2/O | No description available 1.2/P | No description available 1.2/Q | No description available 1.2/R | No description available 1.2/S | No description available 1.2/T | No description available 1.2/U | No description available 1.2/V | No description available 1.2/W | No description available 1.2/X | No description available 1.2/Y | No description available 1.2/Z | No description available 1.2/a | No description available 1.2/b | No description available 1.2/c 1.2/g | No description available 1.2/d 1.2/h | No description available 1.2/e | No description available 1.2/f | No description available 1.2/i | No description available 1.2/l | No description available > clipper associate #4 toModel #1 Opened cryosparc_P146_J670_004_volume_map_sharp.mrc as #1.1.1.1, grid size 460,460,460, pixel 1.19, shown at step 1, values float32 > select /A:10 14 atoms, 13 bonds, 1 residue, 1 model selected > isolde stepto /A:10 > isolde stepto prev > isolde stepto next > select /A:1 Nothing selected > select /A:9 Nothing selected > volume #5 level 0.06368 > volume #1.1.1.1 level 0.06591 > select clear > select up 10 atoms, 9 bonds, 1 residue, 2 models selected > select up 158 atoms, 158 bonds, 10 residues, 2 models selected > isolde sim start /A:10-19 ISOLDE: started sim > isolde stepto /A:14 > isolde stepto next > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB standards. ISOLDE: stopped sim > isolde stepto next > isolde sim start /A:29 ISOLDE: started sim > isolde stepto next > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde stepto next > isolde sim start /A:42 ISOLDE: started sim > isolde stepto next > isolde stepto prev > isolde stepto next > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB standards. ISOLDE: stopped sim > isolde sim start /A:48 ISOLDE: started sim > select clear > isolde stepto next > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde stepto next > isolde sim start /A:57 ISOLDE: started sim > isolde stepto next > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde sim start /A:65 ISOLDE: started sim > isolde stepto next > isolde stepto /A:69 > isolde stepto next > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde sim start /A:74 ISOLDE: started sim > isolde stepto next > isolde stepto prev > isolde stepto next > isolde stepto prev > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB standards. ISOLDE: stopped sim > isolde sim start /A:80 ISOLDE: started sim > isolde stepto next > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB standards. ISOLDE: stopped sim > isolde stepto next > isolde sim start /A:90 ISOLDE: started sim > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde stepto next > isolde sim start /A:97 ISOLDE: started sim > isolde stepto next > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde stepto next > isolde sim start /A:113 ISOLDE: started sim > select clear > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB standards. ISOLDE: stopped sim > save ""/Users/dellasyau/HMS Dropbox/Della Syau/Syau_IWS1/Structures/Revision > 1 modeling intermediates/250517_model_it063.pdb"" ===== Log before crash end ===== Log: Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 1.9 (2024-12-11) © 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 M1 Pro OpenGL vendor: Apple Python: 3.11.4 Locale: UTF-8 Qt version: PyQt6 6.7.1, Qt 6.7.1 Qt runtime version: 6.7.3 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro18,3 Model Number: Z15H00105LL/A Chip: Apple M1 Pro Total Number of Cores: 10 (8 performance and 2 efficiency) Memory: 32 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: 12 days, 57 minutes Graphics/Displays: Apple M1 Pro: Chipset Model: Apple M1 Pro Type: GPU Bus: Built-In Total Number of Cores: 16 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-in Liquid Retina XDR Display Resolution: 3024 x 1964 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal DELL U2723QE: Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition) UI Looks like: 1920 x 1080 @ 60.00Hz Mirror: Off Online: Yes Rotation: Supported Installed Packages: alabaster: 1.0.0 anyio: 4.7.0 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 3.0.0 auditwheel: 6.1.0 autocommand: 2.2.2 babel: 2.16.0 backports.tarfile: 1.2.0 beautifulsoup4: 4.12.3 blockdiag: 3.0.0 blosc2: 3.0.0 build: 1.2.1 certifi: 2023.11.17 cftime: 1.6.4.post1 charset-normalizer: 3.4.0 ChimeraX-AddCharge: 1.5.18 ChimeraX-AddH: 2.2.6 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.5 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.16.1 ChimeraX-AlphaFold: 1.0.1 ChimeraX-AltlocExplorer: 1.1.2 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.58.8 ChimeraX-AtomicLibrary: 14.1.11 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 3.0.0 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.13.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.4.0 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: 2.3 ChimeraX-Clipper: 0.24.0 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: 1.9 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.4 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2.6 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: 1.4.1 ChimeraX-Hbonds: 2.5 ChimeraX-Help: 1.3 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.3 ChimeraX-ISOLDE: 1.9 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-KVFinder: 1.2.1 ChimeraX-Label: 1.1.14 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.2 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 ChimeraX-Map: 1.3 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: 2.1.6 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.7.2 ChimeraX-MedicalToolbar: 1.1 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.14.2 ChimeraX-MMTF: 2.2 ChimeraX-ModelArchive: 1.0 ChimeraX-Modeller: 1.5.18 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-MutationScores: 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: 1.14 ChimeraX-OrthoPick: 1.0.1 ChimeraX-PDB: 2.7.6 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: 1.1.2 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.6.2 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.3.1 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: 3.5.6 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.14 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.2.0 ChimeraX-ShowSequences: 1.0.3 ChimeraX-SideView: 1.0.1 ChimeraX-SimilarStructures: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.18.1 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: 1.2.3 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.41 ChimeraX-Umap: 1.0 ChimeraX-uniprot: 2.3.1 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.4.4 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: 1.3.1 cxservices: 1.2.3 cycler: 0.12.1 Cython: 3.0.10 debugpy: 1.8.9 decorator: 5.1.1 docutils: 0.21.2 executing: 2.1.0 filelock: 3.15.4 fonttools: 4.55.3 funcparserlib: 2.0.0a0 glfw: 2.8.0 grako: 3.16.5 h11: 0.14.0 h5py: 3.12.1 html2text: 2024.2.26 httpcore: 1.0.7 httpx: 0.28.1 idna: 3.10 ihm: 1.3 imagecodecs: 2024.6.1 imagesize: 1.4.1 importlib_metadata: 8.0.0 importlib_resources: 6.4.0 inflect: 7.3.1 ipykernel: 6.29.5 ipython: 8.26.0 ipywidgets: 8.1.5 jaraco.context: 5.3.0 jaraco.functools: 4.0.1 jaraco.text: 3.12.1 jedi: 0.19.1 Jinja2: 3.1.4 jupyter_client: 8.6.2 jupyter_core: 5.7.2 jupyterlab_widgets: 3.0.13 kiwisolver: 1.4.7 line_profiler: 4.1.3 lxml: 5.2.2 lz4: 4.3.3 MarkupSafe: 3.0.2 matplotlib: 3.9.2 matplotlib-inline: 0.1.7 more-itertools: 10.3.0 msgpack: 1.0.8 ndindex: 1.9.2 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.10.2 numpy: 1.26.4 openvr: 1.26.701 ordered-set: 4.1.0 packaging: 23.2 packaging: 24.1 ParmEd: 4.2.2 parso: 0.8.4 pep517: 0.13.1 pexpect: 4.9.0 pillow: 10.4.0 pip: 24.2 pkginfo: 1.11.1 platformdirs: 4.3.6 platformdirs: 4.2.2 prompt_toolkit: 3.0.48 psutil: 6.0.0 ptyprocess: 0.7.0 pure_eval: 0.2.3 py-cpuinfo: 9.0.0 pycollada: 0.8 pydicom: 2.4.4 pyelftools: 0.31 Pygments: 2.18.0 pynmrstar: 3.3.4 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.3401 pyparsing: 3.2.0 pyproject_hooks: 1.2.0 PyQt6-commercial: 6.7.1 PyQt6-Qt6: 6.7.3 PyQt6-WebEngine-commercial: 6.7.0 PyQt6-WebEngine-Qt6: 6.7.3 PyQt6-WebEngineSubwheel-Qt6: 6.7.3 PyQt6_sip: 13.8.0 python-dateutil: 2.9.0.post0 pytz: 2024.2 pyzmq: 26.2.0 qtconsole: 5.5.2 QtPy: 2.4.2 qtshim: 1.0 RandomWords: 0.4.0 requests: 2.32.3 scipy: 1.14.0 setuptools: 72.1.0 sfftk-rw: 0.8.1 six: 1.16.0 sniffio: 1.3.1 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.6 Sphinx: 8.0.2 sphinx-autodoc-typehints: 2.2.3 sphinxcontrib-applehelp: 2.0.0 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 2.0.0 sphinxcontrib-htmlhelp: 2.1.0 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 2.0.0 sphinxcontrib-serializinghtml: 2.0.0 stack-data: 0.6.3 superqt: 0.6.3 tables: 3.10.1 tcia_utils: 1.5.1 tifffile: 2024.7.24 tinyarray: 1.2.4 tomli: 2.0.1 tornado: 6.4.2 traitlets: 5.14.3 typeguard: 4.3.0 typing_extensions: 4.12.2 typing_extensions: 4.12.2 tzdata: 2024.2 urllib3: 2.2.3 wcwidth: 0.2.13 webcolors: 24.6.0 wheel: 0.43.0 wheel: 0.43.0 wheel-filename: 1.4.1 widgetsnbextension: 4.0.13 zipp: 3.19.2 }}} " defect closed normal Window Toolkit duplicate all ChimeraX