id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 16528 Crash on Mac waking from sleep chimerax-bug-report@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-15.1.1-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. 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""45f4e2a5-551b-4bc2-a2dc-19c244dda8f8"", ""experimentId"" : ""6643969b3099cf28e049862f"", ""deploymentId"" : 400000007 } ] } } ===== Log before crash start ===== UCSF ChimeraX version: 1.8 (2024-06-10) © 2016-2024 Regents of the University of California. All rights reserved. > open /Users/ConstantinePetridis/Desktop/AcMNPV_Caps.cxs Opened emdb35243_ODV as #1, grid size 600,600,600, pixel 1.35, shown at level 0.284, step 1, values float32 Opened emdb43590_BV as #2, grid size 700,700,700, pixel 1.41, shown at level 0.159, step 1, values float32 Opened J1663_FE as #4, grid size 360,360,360, pixel 2.37, shown at level 0.0733, step 1, values float32 Opened J1671_PE z flip as #5, grid size 360,360,360, pixel 2.37, shown at level 0.0913, step 1, values float32 Opened J1748_FE as #3, grid size 588,588,588, pixel 1.34, shown at level 0.0321, step 1, values float32 Log from Tue Dec 24 17:47:32 2024UCSF ChimeraX version: 1.8 (2024-06-10) © 2016-2024 Regents of the University of California. All rights reserved. > open /Users/ConstantinePetridis/Desktop/AcMNPV_Caps.cxs Opened emdb35243_ODV as #1, grid size 600,600,600, pixel 1.35, shown at level 0.284, step 1, values float32 Opened emdb43590_BV as #2, grid size 700,700,700, pixel 1.41, shown at level 0.0696, step 1, values float32 Opened J1663_FE as #4, grid size 360,360,360, pixel 2.37, shown at level 0.0908, step 1, values float32 Opened J1671_PE z flip as #5, grid size 360,360,360, pixel 2.37, shown at level 0.0913, step 1, values float32 Log from Tue Dec 24 14:48:02 2024UCSF ChimeraX version: 1.8 (2024-06-10) © 2016-2024 Regents of the University of California. All rights reserved. > open /Users/ConstantinePetridis/Desktop/AcMNPV_Caps.cxs Opened emdb35243_ODV as #1, grid size 600,600,600, pixel 1.35, shown at level 0.229, step 1, values float32 Opened emdb43590_BV as #2, grid size 700,700,700, pixel 1.41, shown at level 0.167, step 1, values float32 Opened J1663_FE as #4, grid size 360,360,360, pixel 2.37, shown at level 0.254, step 1, values float32 Opened J1671_PE z flip as #5, grid size 360,360,360, pixel 2.37, shown at level 0.109, step 1, values float32 Log from Tue Dec 24 14:33:25 2024 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/ConstantinePetridis/Downloads/cryosparc_P32_J53_002_volume_map.mrc Opened cryosparc_P32_J53_002_volume_map.mrc as #1, grid size 720,720,720, pixel 1.06, shown at step 1, values float32 > volume #1 region 0,0,0,719,719,719 step 4 [Repeated 1 time(s)] > volume #1 step 1 > volume #1 change image level -0.02425,0 level 0.1837,0.8 level 0.3523,1 > volume #1 level 0.151 Drag select of 1 cryosparc_P32_J53_002_volume_map.mrc > select clear > open > /Users/ConstantinePetridis/Downloads/cryosparc_P23_J1668_003_volume_map.mrc Opened cryosparc_P23_J1668_003_volume_map.mrc as #2, grid size 360,360,360, pixel 2.37, shown at level 0.334, step 2, values float32 > hide #!1 models > volume #2 step 1 > volume #2 level 0.2509 > ui mousemode right clip > ui mousemode right translate > volume #2 level 0.2417 > volume #2 level 0.2094 > volume #2 level 0.2532 > open emdb:43590\ Fetching url ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-43590\/map/emd_43590\\.map.gz failed: > open emdb:43590 Summary of feedback from opening 43590 fetched from emdb --- notes | Fetching compressed map 43590 from ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-43590/map/emd_43590.map.gz Fetching map header 43590 from ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-43590/header/emd-43590.xml Opened emdb 43590 as #3, grid size 700,700,700, pixel 1.41, shown at step 1, values float32 > volume #3 region 0,0,0,699,699,699 step 4 [Repeated 1 time(s)] > volume #3 step 1 > volume #3 change image level -0.05584,0 level 0.4551,0.8 level 0.773,1 > hide #!3 models > show #!3 models > hide #!2 models > ui mousemode right clip > ui mousemode right translate > open emdb:43591 Summary of feedback from opening 43591 fetched from emdb --- notes | Fetching compressed map 43591 from ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-43591/map/emd_43591.map.gz Fetching map header 43591 from ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-43591/header/emd-43591.xml Opened emdb 43591 as #4, grid size 384,384,384, pixel 1.41, shown at level 0.225, step 2, values float32 > close #4 > close #1 The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > open emdb:35243 Opened emdb 35243 as #1, grid size 600,600,600, pixel 1.35, shown at level 0.35, step 4, values float32 > close #2 > rename #1 emdb35243_ODV > rename #3 emdb43590 id #2 > rename #2 emdb43590_BV > open > /Users/ConstantinePetridis/Downloads/cryosparc_P23_J1671_004_volume_map.mrc Opened cryosparc_P23_J1671_004_volume_map.mrc as #3, grid size 360,360,360, pixel 2.37, shown at level 0.355, step 2, values float32 > open > /Users/ConstantinePetridis/Downloads/cryosparc_P23_J1663_003_volume_map.mrc Opened cryosparc_P23_J1663_003_volume_map.mrc as #4, grid size 360,360,360, pixel 2.37, shown at level 0.302, step 2, values float32 > hide #!4 models > hide #!3 models > rename #3 J1671_PE > rename #4 J1663_FE > ui tool show ""Fit in Map"" The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > fitmap #1 inMap #2 Fit map emdb35243_ODV in map emdb43590_BV using 42321 points correlation = 0.6504, correlation about mean = 0.07068, overlap = 3677 steps = 840, shift = 215, angle = 14.7 degrees Position of emdb35243_ODV (#1) relative to emdb43590_BV (#2) coordinates: Matrix rotation and translation 0.97285467 0.11356563 -0.20163492 106.14728499 -0.13398831 0.98682657 -0.09066670 173.53911084 0.18868208 0.11522224 0.97525530 66.06041994 Axis 0.40690739 -0.77140072 -0.48925178 Axis point 69.18299426 0.00000000 765.33059572 Rotation angle (degrees) 14.65465662 Shift along axis -122.99625756 > fitmap #1 inMap #2 Fit map emdb35243_ODV in map emdb43590_BV using 42321 points correlation = 0.6504, correlation about mean = 0.07071, overlap = 3677 steps = 104, shift = 0.0146, angle = 0.00468 degrees Position of emdb35243_ODV (#1) relative to emdb43590_BV (#2) coordinates: Matrix rotation and translation 0.97283638 0.11360386 -0.20170163 106.14959138 -0.13402943 0.98682367 -0.09063750 173.53917511 0.18874717 0.11520941 0.97524422 66.03781833 Axis 0.40672513 -0.77147305 -0.48928928 Axis point 69.36205442 0.00000000 764.99261400 Rotation angle (degrees) 14.65831075 Shift along axis -123.01868679 > fitmap #1 inMap #2 Fit map emdb35243_ODV in map emdb43590_BV using 42321 points correlation = 0.6504, correlation about mean = 0.07066, overlap = 3677 steps = 60, shift = 0.0202, angle = 0.00485 degrees Position of emdb35243_ODV (#1) relative to emdb43590_BV (#2) coordinates: Matrix rotation and translation 0.97285464 0.11356683 -0.20163440 106.14869030 -0.13397976 0.98683234 -0.09061650 173.52336845 0.18868832 0.11517161 0.97526008 66.07751356 Axis 0.40674044 -0.77147333 -0.48927612 Axis point 69.15375523 0.00000000 765.29725022 Rotation angle (degrees) 14.65346616 Shift along axis -123.02383462 > select add #2 4 models selected > select add #1 6 models selected > select subtract #2 2 models selected > ui mousemode right ""rotate selected models"" > view matrix models > #1,0.17627,0.98434,-0.00073339,8.4342,-0.98191,0.17589,0.070127,791.23,0.069158,-0.011641,0.99754,158.34 > fitmap #1 inMap #2 Fit map emdb35243_ODV in map emdb43590_BV using 42321 points correlation = 0.8508, correlation about mean = 0.2973, overlap = 5847 steps = 124, shift = 16.6, angle = 5.06 degrees Position of emdb35243_ODV (#1) relative to emdb43590_BV (#2) coordinates: Matrix rotation and translation 0.22884137 0.97346373 0.00000023 6.56644567 -0.97346373 0.22884137 0.00000059 795.07225194 0.00000052 -0.00000036 1.00000000 179.58410153 Axis -0.00000048 -0.00000015 -1.00000000 Axis point 505.10857801 393.39162659 0.00000000 Rotation angle (degrees) 76.77113185 Shift along axis -179.58422442 The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > volume #1 step 1 > ui mousemode right rotate > ui mousemode right translate > select subtract #1 Nothing selected > volume #3 level 0.2279 > select add #3 2 models selected > ui mousemode right ""rotate selected models"" > view matrix models > #3,-0.62102,0.77799,-0.095165,399.88,0.76736,0.62824,0.12834,-223.39,0.15964,0.0066773,-0.98715,777.94 > ui mousemode right ""translate selected models"" Drag select of 1 emdb35243_ODV , 2 emdb43590_BV , 3 J1671_PE > select clear > select subtract #3 Nothing selected > select add #3 2 models selected > view matrix models > #3,-0.62102,0.77799,-0.095165,386.59,0.76736,0.62824,0.12834,-139.06,0.15964,0.0066773,-0.98715,840.43 > ui mousemode right ""rotate selected models"" > view matrix models > #3,-0.59828,0.78575,0.15701,265.87,0.79956,0.59829,0.052522,-107.63,-0.05267,0.15696,-0.9862,866.45 > ui mousemode right ""translate selected models"" > view matrix models > #3,-0.59828,0.78575,0.15701,346.36,0.79956,0.59829,0.052522,-134.36,-0.05267,0.15696,-0.9862,880.56 > view matrix models > #3,-0.59828,0.78575,0.15701,-3.4192,0.79956,0.59829,0.052522,-21.834,-0.05267,0.15696,-0.9862,804.23 > vflip #3 Unknown command: vflip #3 > volume flip #3 Opened J1671_PE z flip as #5, grid size 360,360,360, pixel 2.37, shown at step 1, values float32 > close #3 > ui mousemode right ""rotate selected models"" > select add #5 2 models selected > view matrix models > #5,-0.98925,0.0012409,-0.14622,625.6,0.060453,-0.90704,-0.41668,1132.8,-0.13315,-0.42104,0.89722,289.05 > ui mousemode right ""translate selected models"" > view matrix models > #5,-0.98925,0.0012409,-0.14622,983.74,0.060453,-0.90704,-0.41668,1047,-0.13315,-0.42104,0.89722,347.49 > ui mousemode right ""rotate selected models"" > view matrix models > #5,-0.9746,0.21646,-0.05741,848.26,-0.17632,-0.89974,-0.39923,1137.4,-0.13807,-0.37897,0.91505,324.12 > view matrix models > #5,0.015509,0.99968,0.019979,59.911,-0.99511,0.013483,0.097818,887.14,0.097517,-0.021399,0.995,37.586 The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > fitmap #5 inMap #1 Fit map J1671_PE z flip in map emdb35243_ODV using 1058456 points correlation = 0.7675, correlation about mean = 0.06833, overlap = 1.003e+05 steps = 264, shift = 16.4, angle = 7.76 degrees Position of J1671_PE z flip (#5) relative to emdb35243_ODV (#1) coordinates: Matrix rotation and translation 0.95303348 0.30286496 0.00002327 -130.17331272 -0.30286496 0.95303348 0.00003703 127.93398000 -0.00001097 -0.00004234 1.00000000 -121.40095851 Axis -0.00013103 0.00005653 -0.99999999 Axis point 347.39215679 483.62545297 0.00000000 Rotation angle (degrees) 17.62976098 Shift along axis 121.42524514 > view matrix models > #5,0.30902,0.29306,0.90478,-145.34,-0.83128,-0.37894,0.40666,837.38,0.46203,-0.87779,0.12651,604.39 > undo > select add #5 3 models selected > select subtract #5 Nothing selected > ui mousemode right rotate > ui mousemode right translate > show #!4 models > select add #4 2 models selected > ui mousemode right ""translate selected models"" > view matrix models #4,1,0,0,344.93,0,1,0,0.63352,0,0,1,128.18 > volume #4 level 0.2379 > view matrix models #4,1,0,0,81.692,0,1,0,-19.877,0,0,1,125.49 > view matrix models #4,1,0,0,83.558,0,1,0,70.413,0,0,1,133.11 > view matrix models #4,1,0,0,70.873,0,1,0,70.205,0,0,1,133.5 > fitmap #4 inMap #1 Fit map J1663_FE in map emdb35243_ODV using 99734 points correlation = 0.83, correlation about mean = 0.228, overlap = 9730 steps = 88, shift = 14.2, angle = 0.0496 degrees Position of J1663_FE (#4) relative to emdb35243_ODV (#1) coordinates: Matrix rotation and translation 0.22800509 -0.97365994 -0.00000874 722.74511445 0.97365994 0.22800508 0.00010883 -107.11178091 -0.00010397 -0.00003333 0.99999999 -59.46670416 Axis -0.00007300 0.00004890 1.00000000 Axis point 428.91462448 402.21523340 0.00000000 Rotation angle (degrees) 76.82034903 Shift along axis -59.52470265 > ui mousemode right zoom > ui mousemode right rotate > select subtract #4 Nothing selected > ui mousemode right translate > volume #2 level 0.2977 > volume #1 level 0.3465 > volume #4 level 0.2335 The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > volume #4 step 1 > fitmap #4 inMap #1 Fit map J1663_FE in map emdb35243_ODV using 827535 points correlation = 0.8296, correlation about mean = 0.234, overlap = 7.948e+04 steps = 44, shift = 0.055, angle = 0.0137 degrees Position of J1663_FE (#4) relative to emdb35243_ODV (#1) coordinates: Matrix rotation and translation 0.22793154 -0.97367716 0.00001878 722.76413763 0.97367715 0.22793154 -0.00011550 -106.96571476 0.00010818 0.00004462 0.99999999 -59.55985998 Axis 0.00008222 -0.00004590 1.00000000 Axis point 428.83496900 402.26790985 0.00000000 Rotation angle (degrees) 76.82467682 Shift along axis -59.49552349 > fitmap #2 inMap #1 Fit map emdb43590_BV in map emdb35243_ODV using 3024743 points correlation = 0.7983, correlation about mean = 0.1452, overlap = 3.651e+05 steps = 44, shift = 0.128, angle = 0.0297 degrees Position of emdb43590_BV (#2) relative to emdb35243_ODV (#1) coordinates: Matrix rotation and translation 0.22934616 -0.97334492 0.00000038 772.16317142 0.97334492 0.22934616 -0.00000003 -188.52800554 -0.00000006 0.00000038 1.00000000 -179.71258188 Axis 0.00000021 0.00000022 1.00000000 Axis point 505.13813030 393.36165391 0.00000000 Rotation angle (degrees) 76.74141952 Shift along axis -179.71246293 > fitmap #4 inMap #1 Fit map J1663_FE in map emdb35243_ODV using 827535 points correlation = 0.8296, correlation about mean = 0.234, overlap = 7.948e+04 steps = 36, shift = 0.0126, angle = 0.00531 degrees Position of J1663_FE (#4) relative to emdb35243_ODV (#1) coordinates: Matrix rotation and translation 0.22793225 -0.97367699 -0.00000066 722.77597776 0.97367699 0.22793225 -0.00002493 -107.00856619 0.00002443 0.00000504 1.00000000 -59.50745513 Axis 0.00001539 -0.00001288 1.00000000 Axis point 428.86473096 402.25276864 0.00000000 Rotation angle (degrees) 76.82463471 Shift along axis -59.49495194 > fitmap #5 inMap #1 Fit map J1671_PE z flip in map emdb35243_ODV using 1058456 points correlation = 0.7675, correlation about mean = 0.06833, overlap = 1.003e+05 steps = 96, shift = 0.0142, angle = 0.00165 degrees Position of J1671_PE z flip (#5) relative to emdb35243_ODV (#1) coordinates: Matrix rotation and translation 0.95302877 0.30287977 0.00000058 -130.16785956 -0.30287977 0.95302877 0.00002874 127.93693847 0.00000815 -0.00002757 1.00000000 -121.42680505 Axis -0.00009296 -0.00001250 -1.00000000 Axis point 347.40797876 483.60691161 0.00000000 Rotation angle (degrees) 17.63065109 Shift along axis 121.43730542 > hide #!4 models > show #!4 models > hide #!5 models > show #!5 models > hide #!5 models > show #!5 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > ui mousemode right clip > volume #2 color white > volume #2 color #ff9300 > volume #2 color #942192 > volume #1 color #ff40ff > volume #1 color white > volume #2 color white > ui mousemode right translate > volume #2 level 0.1926 > volume #1 level 0.2772 > volume #2 level 0.2234 > volume #2 level 0.29 > volume #1 level 0.3743 > volume #2 level 0.3284 > volume #5 color #ff2600 > volume #5 color #00fdff > volume #5 color #7a81ff > hide #!1 models > hide #!5 models > show #!5 models > hide #!5 models > show #!5 models > volume #5 level 0.2478 > volume #1 level 0.3951 > volume #4 level 0.2535 > hide #!2 models > show #!2 models > hide #!5 models > show #!5 models > hide #!5 models > show #!5 models > show #!1 models > hide #!2 models > set bgColor white > graphics silhouettes true > lighting depthCue false > lighting soft > graphics bgColor white > graphics silhouettes width 2.3 > volume #1 level 0.2287 > show #!2 models > hide #!1 models > volume #2 level 0.1747 > volume #2 level 0.2541 > hide #!5 models > show #!5 models > hide #!5 models > show #!5 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > volume #5 level 0.1086 > volume #2 level 0.167 > save /Users/ConstantinePetridis/Desktop/AcMNPV_Caps.cxs includeMaps true ——— End of log from Tue Dec 24 14:33:25 2024 ——— opened ChimeraX session > hide #!5 models > color #2 #fffb00ff models > hide #!1 models > show #!4 models > volume #4 level 0.1109 > volume #2 level 0.2362 > show #!5 models > hide #!5 models > show #!5 models > hide #!5 models > show #!5 models > hide #!5 models > show #!5 models > hide #!5 models > show #!1 models > hide #!1 models > show #!1 models > show #!5 models > hide #!2 models > show #!2 models > hide #!2 models > hide #!4 models > show #!4 models > hide #!5 models > show #!2 models > hide #!1 models > show #!1 models > hide #!4 models > volume #1 level 0.2842 > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > volume #2 level 0.2669 > show #!4 models > volume #4 level 0.1666 > hide #!2 models > show #!2 models > hide #!1 models > show #!1 models > hide #!2 models > hide #!1 models > show #!1 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 #!2 models > hide #!1 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 #!5 models > hide #!4 models > show #!4 models > hide #!4 models > show #!4 models > hide #!5 models > show #!1 models > hide #!2 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > volume #4 level 0.09079 > hide #!4 models > show #!5 models > volume #2 level 0.1363 > volume #5 level 0.09125 > hide #!2 models > show #!2 models > show #!4 models > hide #!5 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!4 models > volume #2 level 0.003029 > volume #2 level 0.06965 > save /Users/ConstantinePetridis/Desktop/AcMNPV_Caps.cxs includeMaps true ——— End of log from Tue Dec 24 14:48:02 2024 ——— opened ChimeraX session > ui tool show ""Fit in Map"" The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. [Repeated 1 time(s)] > show #!5 models > show #!4 models > show #!1 models > fitmap #2 inMap #1 Fit map emdb43590_BV in map emdb35243_ODV using 14658219 points correlation = 0.7541, correlation about mean = 0.4206, overlap = 6.34e+05 steps = 44, shift = 0.0918, angle = 0.00815 degrees Position of emdb43590_BV (#2) relative to emdb35243_ODV (#1) coordinates: Matrix rotation and translation 0.22948454 -0.97331231 -0.00000019 772.07912980 0.97331231 0.22948454 0.00000002 -188.58027009 0.00000003 -0.00000019 1.00000000 -179.80414440 Axis -0.00000011 -0.00000011 1.00000000 Axis point 505.14652168 393.35360876 0.00000000 Rotation angle (degrees) 76.73327344 Shift along axis -179.80420481 > volume #2 level 0.1593 > fitmap #2 inMap #1 Fit map emdb43590_BV in map emdb35243_ODV using 6420765 points correlation = 0.788, correlation about mean = 0.2153, overlap = 5.315e+05 steps = 40, shift = 0.0561, angle = 0.0102 degrees Position of emdb43590_BV (#2) relative to emdb35243_ODV (#1) coordinates: Matrix rotation and translation 0.22965823 -0.97327134 0.00000041 771.97288598 0.97327134 0.22965823 0.00000005 -188.64582157 -0.00000014 0.00000039 1.00000000 -179.74825591 Axis 0.00000018 0.00000028 1.00000000 Axis point 505.15663052 393.34320391 0.00000000 Rotation angle (degrees) 76.72304870 Shift along axis -179.74817265 > fitmap #4 inMap #1 Fit map J1663_FE in map emdb35243_ODV using 3515214 points correlation = 0.7547, correlation about mean = 0.4947, overlap = 1.23e+05 steps = 44, shift = 1.44, angle = 0.00292 degrees Position of J1663_FE (#4) relative to emdb35243_ODV (#1) coordinates: Matrix rotation and translation 0.22797990 -0.97366584 0.00000032 722.75242081 0.97366584 0.22797990 -0.00001052 -107.05172737 0.00001017 0.00000271 1.00000000 -58.05938758 Axis 0.00000679 -0.00000506 1.00000000 Axis point 428.88300196 402.23914637 0.00000000 Rotation angle (degrees) 76.82183100 Shift along axis -58.05393872 > fitmap #5 inMap #1 Fit map J1671_PE z flip in map emdb35243_ODV using 2887742 points correlation = 0.7439, correlation about mean = 0.3608, overlap = 1.359e+05 steps = 84, shift = 0.0126, angle = 0.0165 degrees Position of J1671_PE z flip (#5) relative to emdb35243_ODV (#1) coordinates: Matrix rotation and translation 0.95294192 0.30315291 -0.00002329 -130.23084526 -0.30315291 0.95294192 0.00003337 128.08923520 0.00003231 -0.00002474 1.00000000 -121.44780533 Axis -0.00009584 -0.00009171 -0.99999999 Axis point 347.50822763 483.49288311 0.00000000 Rotation angle (degrees) 17.64707305 Shift along axis 121.44853799 > save /Users/ConstantinePetridis/Desktop/AcMNPV_Caps.cxs includeMaps true > open > /Users/ConstantinePetridis/Downloads/cryosparc_P23_J1748_004_volume_map.mrc Opened cryosparc_P23_J1748_004_volume_map.mrc as #3, grid size 588,588,588, pixel 1.34, shown at level 0.129, step 4, values float32 > hide #!4 models > hide #!5 models > hide #!3 models > hide #!2 models > show #!3 models The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > volume #3 step 1 > ui mousemode right clip > ui mousemode right translate > select add #3 3 models selected > ui mousemode right ""rotate selected models"" > view matrix models > #3,0.40948,-0.77865,-0.47542,760.83,-0.71746,-0.59673,0.35938,744.31,-0.56353,0.19394,-0.80301,985.38 > view matrix models > #3,0.32041,-0.69825,0.64014,244.66,-0.90173,-0.43184,-0.019699,928.51,0.2902,-0.57093,-0.768,934.07 > view matrix models > #3,0.39371,-0.91284,-0.10826,648.9,-0.91524,-0.37831,-0.1386,968.12,0.085564,0.15365,-0.98441,830.02 > ui mousemode right ""translate selected models"" > view matrix models > #3,0.39371,-0.91284,-0.10826,762.28,-0.91524,-0.37831,-0.1386,1064.7,0.085564,0.15365,-0.98441,801.88 > ui mousemode right ""rotate selected models"" > view matrix models > #3,0.37861,-0.92556,-0.0013901,723.46,-0.91898,-0.37574,-0.11957,1056.3,0.11015,0.046549,-0.99282,838.31 > ui mousemode right ""translate selected models"" > view matrix models > #3,0.37861,-0.92556,-0.0013901,717.57,-0.91898,-0.37574,-0.11957,1053,0.11015,0.046549,-0.99282,889.03 > view matrix models > #3,0.37861,-0.92556,-0.0013901,714.64,-0.91898,-0.37574,-0.11957,1041.5,0.11015,0.046549,-0.99282,889.68 > fitmap #3 inMap #1 Fit map cryosparc_P23_J1748_004_volume_map.mrc in map emdb35243_ODV using 2033906 points correlation = 0.8586, correlation about mean = 0.213, overlap = 1.155e+05 steps = 176, shift = 23, angle = 7.82 degrees Position of cryosparc_P23_J1748_004_volume_map.mrc (#3) relative to emdb35243_ODV (#1) coordinates: Matrix rotation and translation 0.99578155 0.09175521 0.00000256 -23.45858541 0.09175519 -0.99578156 -0.00000778 761.14443305 0.00000183 0.00000798 -0.99999997 760.15790824 Axis 0.99892332 0.04637151 -0.00137005 Axis point 0.00000000 381.11520699 380.06436878 Rotation angle (degrees) 179.99954802 Shift along axis 10.82063276 > fitmap #3 inMap #1 Fit map cryosparc_P23_J1748_004_volume_map.mrc in map emdb35243_ODV using 2033906 points correlation = 0.8586, correlation about mean = 0.2131, overlap = 1.155e+05 steps = 36, shift = 0.0092, angle = 0.00079 degrees Position of cryosparc_P23_J1748_004_volume_map.mrc (#3) relative to emdb35243_ODV (#1) coordinates: Matrix rotation and translation 0.99578150 0.09175583 0.00001530 -23.45998132 0.09175581 -0.99578151 -0.00000256 761.14824253 0.00001500 0.00000396 -0.99999997 760.15889297 Axis 0.99888925 0.04700335 -0.00330788 Axis point 0.00000000 381.12546248 380.04122309 Rotation angle (degrees) 179.99981308 Shift along axis 9.82808080 > select subtract #3 Nothing selected > volume #3 level 0.03398 > volume #3 level 0.04519 > volume #3 color #3b8fff > ui mousemode right clip > ui mousemode right translate > hide #!1 models > volume #3 level 0.05546 > volume #4 level 0.1149 > volume #4 level 0.1236 > show #!4 models > hide #!3 models > show #!3 models > hide #!4 models > show #!4 models > hide #!3 models > show #!3 models > hide #!4 models > show #!4 models > hide #!4 models > show #!4 models > hide #!4 models > show #!4 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!4 models > show #!4 models > hide #!4 models > show #!4 models > hide #!4 models > show #!4 models > hide #!4 models > volume #3 level 0.05173 > volume #3 level 0.03211 > volume #4 level 0.07328 > hide #!4 models > show #!4 models > hide #!4 models > rename #3 J1748_FE > show #!5 models > hide #!5 models > save /Users/ConstantinePetridis/Desktop/AcMNPV_Caps.cxs includeMaps true ——— End of log from Tue Dec 24 17:47:32 2024 ——— opened ChimeraX session > show #!2 models > show #!1 models > hide #!2 models > hide #!1 models > volume #3 level 0.04733 > volume #3 level 0.06065 > ui mousemode right clip > show #!1 models > show #!2 models > show #!5 models > volume #5 level 0.1186 > volume #5 level 0.1111 > volume #2 level 0.1926 > show #!4 models > volume #4 level 0.1535 > hide #!5 models > close #4 > volume #2 level 0.2003 > volume #1 level 0.2218 > hide #!2 models > hide #!3 models > show #!2 models > hide #!2 models > show #!3 models > volume #1 level 0.1698 > hide #!3 models > volume #1 level 0.2252 > volume #1 level 0.2703 > hide #!5 models > show #!3 models > volume #3 level 0.06804 > volume #3 level 0.07359 > volume #3 level 0.05788 > ui tool show ""Hide Dust"" > surface dust #3 size 8.04 > surface dust #3 size 8.8 > surface dust #3 size 18.45 > surface dust #3 size 18.75 > surface dust #3 size 37.37 > volume #1 level 0.2495 > volume #1 level 0.246 > surface dust #3 size 37.37 The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > surface dust #1 size 8.1 > surface dust #1 size 8.02 > surface dust #1 size 20.2 > surface dust #1 size 18.89 > surface dust #1 size 23.12 > volume #2 level 0.2054 > volume #2 color #dfd9fc > volume #2 color #c2cafd > volume #2 color #f34d8f > volume #2 color #3b8fff > volume #2 color #7a81ff > volume #2 color #d2d2d3 > volume #2 color #dfd9fc > volume #2 color #c2cafd > volume #2 color #f34d8f > volume #2 color #235091 > volume #2 color #d2d2d3 > volume #2 color #d9776e > volume #5 level 0.1409 > ui mousemode right rotate > ui mousemode right translate > surface dust #2 size 8.46 > surface dust #2 size 8.3 > transparency #3 50 > transparency #3 40 > volume #2 level 0.2403 > volume #3 level 0.06527 > volume #1 level 0.2595 > volume #1 color #c2cafd > ui tool show ""Hide Dust"" > surface dust #1 size 1.35 The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > surface dust #5 size 14.2 > surface dust #5 size 15.03 > surface dust #5 size 37.91 > surface dust #1 size 12.83 > surface dust #1 size 13.96 > surface dust #1 size 33.45 > surface dust #1 size 14.19 > surface dust #1 size 27.82 > surface dust #1 size 33.45 > surface dust #1 size 58.26 > ui mousemode right clip > volume #5 level 0.02913 > volume #5 level 0.1086 > volume #5 level 0.07634 > transparency #3 0 > volume #3 level 0.0158 > volume #3 level 0.03958 > open > /Users/ConstantinePetridis/Downloads/cryosparc_P23_J1663_003_volume_map.mrc Opened cryosparc_P23_J1663_003_volume_map.mrc as #4, grid size 360,360,360, pixel 2.37, shown at level 0.302, step 2, values float32 The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > volume #4 step 1 > volume #4 level 0.09233 > volume #4 level 0.1146 > ui mousemode right translate > volume #4 level 0.0901 > ui mousemode right clip > select add #4 3 models selected > ui mousemode right ""translate selected models"" > view matrix models #4,1,0,0,65.037,0,1,0,-9.76,0,0,1,122.44 > ui tool show ""Fit in Map"" > surface dust #1 size 58.3 > surface dust #1 size 58.42 > surface dust #1 size 58.58 The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > fitmap #4 inMap #3 Fit map cryosparc_P23_J1663_003_volume_map.mrc in map J1748_FE using 3557522 points correlation = 0.4347, correlation about mean = -0.02198, overlap = 1.693e+04 steps = 188, shift = 24, angle = 3.93 degrees Position of cryosparc_P23_J1663_003_volume_map.mrc (#4) relative to J1748_FE (#3) coordinates: Matrix rotation and translation 0.33050798 -0.94178203 0.06173458 681.45164000 -0.94275723 -0.33251334 -0.02537203 979.22027943 0.04442248 -0.04981506 -0.99777009 818.62961298 Axis -0.81561934 0.57767311 -0.03254049 Axis point 0.00000000 734.69129100 391.17873063 Rotation angle (degrees) 179.14142847 Shift along axis -16.77451928 > view matrix models > #4,0.99891,0.016612,0.043643,30.823,-0.014401,0.99862,-0.050483,34.399,-0.044421,0.049799,0.99777,106.43 > ui mousemode right ""rotate selected models"" > view matrix models > #4,0.99791,-0.016664,-0.062458,89.788,0.016304,0.99985,-0.0062726,2.309,0.062553,0.0052411,0.99803,79.721 > fitmap #4 inMap #3 Fit map cryosparc_P23_J1663_003_volume_map.mrc in map J1748_FE using 3557522 points correlation = 0.4361, correlation about mean = -0.01796, overlap = 1.701e+04 steps = 152, shift = 17, angle = 1.78 degrees Position of cryosparc_P23_J1663_003_volume_map.mrc (#4) relative to J1748_FE (#3) coordinates: Matrix rotation and translation 0.31830062 -0.94776499 -0.02064779 722.74851077 -0.94395812 -0.31887832 0.08520406 917.64991711 -0.08733756 -0.00762985 -0.99614958 857.77294072 Axis -0.81170878 0.58311312 0.03328592 Axis point 0.00000000 733.56123549 427.29369258 Rotation angle (degrees) 176.72179560 Shift along axis -23.01584556 > volume #4 level 0.1302 > ui mousemode right clip > ui mousemode right ""translate selected models"" > view matrix models > #4,0.99618,0.0017832,-0.087354,122.51,-0.0024414,0.99997,-0.0074289,67.89,0.087338,0.0076138,0.99615,82.111 > view matrix models > #4,0.99618,0.0017832,-0.087354,111.55,-0.0024414,0.99997,-0.0074289,66.848,0.087338,0.0076138,0.99615,83.851 > ui mousemode right ""rotate selected models"" > view matrix models > #4,0.99989,-0.012706,0.0079521,78.608,0.012717,0.99992,-0.0013316,58.009,-0.0079345,0.0014326,0.99997,125.58 > ui mousemode right ""translate selected models"" > view matrix models > #4,0.99989,-0.012706,0.0079521,73.359,0.012717,0.99992,-0.0013316,57.418,-0.0079345,0.0014326,0.99997,127 > fitmap #4 inMap #3 Fit map cryosparc_P23_J1663_003_volume_map.mrc in map J1748_FE using 1934742 points correlation = 0.9722, correlation about mean = 0.8889, overlap = 4.877e+04 steps = 72, shift = 7.35, angle = 0.83 degrees Position of cryosparc_P23_J1663_003_volume_map.mrc (#4) relative to J1748_FE (#3) coordinates: Matrix rotation and translation 0.31655931 -0.94857276 -0.00000334 663.27925709 -0.94857276 -0.31655929 -0.00000757 933.06974962 0.00000612 0.00000557 -1.00000003 819.98524864 Axis 0.81162632 -0.58417690 0.00025913 Axis point 0.00000000 705.23406850 409.88905627 Rotation angle (degrees) 179.99953615 Shift along axis -6.53039807 > select subtract #4 Nothing selected > ui mousemode right translate > volume #3 level 0.05385 > transparency #3 50 > transparency #3 0 > volume #3 level 0.051 > ui mousemode right clip > volume #3 level 0.03007 > volume #3 level 0.04434 > volume #3 level 0.03958 > volume #3 level 0.04 > volume #3 level 0.042 > show #!2 models > show #!1 models > hide #!3 models > hide #!2 models > show #!2 models > hide #!2 models > volume #1 level 0.2422 > volume #1 level 0.25 > volume #2 level 0.248 > ui mousemode right translate > volume #2 level 0.275 > volume #1 level 0.24 > volume #2 level 0.28 > ui mousemode right clip > ui mousemode right ""clip rotate"" > ui mousemode right clip > ui mousemode right ""clip rotate"" > ui mousemode right clip > ui tool show ""Side View"" > ui mousemode right translate > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!5 models > hide #!5 models > show #!3 models > show #!4 models > hide #!3 models > show #!3 models > hide #!4 models > show #!4 models > hide #!2 models > hide #!1 models > volume #4 level 0.1035 > hide #!3 models > show #!3 models > hide #!4 models > show #!4 models > hide #!3 models > volume #4 level 0.1146 > show #!3 models > hide #!4 models > show #!4 models > hide #!3 models > hide #!4 models > show #!3 models > show #!2 models > show #!1 models > hide #!3 models > transparency #2 50 > transparency #2 40 > volume #1 level 0.2712 > show #!5 models > hide #!5 models > color #2 #d2d2d3ff models > color #2 #c2cafdff models > color #1 #f34d8fff models > color #1 #c1153cff models > color #1 #f34d8fff models > color #1 white models > color #1 #5f90e2ff models > color #1 #74fad9ff models > color #1 white models > color #1 #71ed4eff models > color #1 white models > color #1 #6057e0ff models > transparency #2 40 > transparency #2 0 > transparency #1 40 > transparency #2 40 > transparency #1 0 > color #1 #7f51e0ff models > color #1 #5573e1ff models > color #1 #4e5ce0ff models > color #2 #c3b2e9ff models > color #2 #c9b8eaff models > color #2 #7a81ffff models > color #2 #fefefeff models > color #2 white models > transparency #2 0 > color #2 #f6f0e1ff models > color #2 #d2d2d3ff models > color #2 #d2d2d366 models > transparency #2 0 > transparency #1 40 > transparency #2 40 > transparency #1 40 > transparency #1 0 > lighting gentle > lighting soft > lighting gentle > lighting flat > lighting gentle > lighting soft > lighting gentle > lighting soft > color #1 #d2d2d3ff models > color #2 #3b8fffff models > color #2 #c2cafdff models > color #2 #7a81ffff models > transparency #1 40 > transparency #1 0 > transparency #2 40 > color #1 #fafcfbff models > color #1 #f7eef5ff models > color #1 #f1dcedff models > color #1 #f9f3f0ff models > color #1 #f8f7ebff models > color #1 #edf8caff models > color #1 #f0f8cbff models > color #1 #f8f1d9ff models > color #1 #f8efd7ff models > color #1 #e1d8c3ff models > color #1 #f2e9d2ff models > color #1 #dfd7c2ff models > color #1 #dbd3beff models > color #1 #7a81ffff models > color #2 #dbd3beff models > transparency #2 40 > transparency #2 0 > transparency #1 40 > color #2 #d2e2d7ff models > color #2 #c9e2c2ff models > color #2 #dcd9e2ff models > color #2 #f8f4ffff models > color #2 #e4e0eaff models > transparency #1 50 > transparency #1 35 > name view front ""front"": invalid atom specifier > view name front > save /Users/ConstantinePetridis/Desktop/BV_ODV.png width 3000 height 1962 > supersample 4 > color #2 #8d8b91ff models > color #2 #a3a1a8ff models > transparency #1 35 > transparency #2 0 > color #2 #f7f5ffff models > color #2 #cbc9d1ff models > color #2 #cbc9d2ff models > lighting soft > lighting gentle > lighting soft > ui mousemode right rotate > ui mousemode right zoom > ui mousemode right rotate > ui mousemode right translate > ui mousemode right ""clip rotate"" > ui mousemode right clip > ui mousemode right translate > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > volume #1 level 0.3024 > color #1 #7a81ffff models > color #1 #7a81ff00 models > color #1 #7a81ff34 models > color #1 #7a81ffff models > ui mousemode right clip > ui mousemode right ""clip rotate"" > ui mousemode right clip > ui mousemode right translate > show #!2 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!1 models > show #!1 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!1 models > hide #!2 models > show #!1 models > show #!4 models > hide #!4 models > show #!3 models > hide #!3 models > show #!2 models > hide #!2 models > volume #1 level 0.2885 > volume #1 level 0.2469 > show #!2 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > volume #2 level 0.2031 > hide #!1 models > show #!1 models > hide #!2 models > show #!2 models > hide #!1 models > show #!1 models > hide #!1 models > show #!3 models > hide #!3 models > show #!4 models > hide #!4 models > show #!5 models > hide #!5 models > show #!5 models > hide #!5 models > show #!3 models > show #!1 models > hide #!1 models > show #!1 models > hide #!3 models > hide #!2 models > show #!3 models > volume #1 level 0.3197 > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > volume #3 level 0.05913 > volume #3 level 0.05722 > hide #!1 models > show #!1 models > hide #!3 models > show #!3 models > hide #!1 models > volume #3 level 0.07815 > volume #3 level 0.08481 > volume #3 level 0.08 > hide #!1 models > volume #3 level 0.1009 > show #!4 models > volume #4 level 0.2261 > volume #4 level 0.235 > volume #3 level 0.09998 > volume #3 level 0.08856 > volume #4 level 0.2551 > volume #3 level 0.1019 > show #!4 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!4 models > show #!4 models > hide #!4 models > show #!4 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!4 models > show #!4 models > hide #!4 models > show #!4 models > hide #!4 models > show #!4 models > close #3 > rename #4 J1663_FE > rename #4 J1663_FE id #3 > rename #5 id #4 > save /Users/ConstantinePetridis/Desktop/AcMNPV_Caps.cxs includeMaps true > open > /Users/ConstantinePetridis/Downloads/cryosparc_P23_J1770_003_volume_map.mrc Opened cryosparc_P23_J1770_003_volume_map.mrc as #5, grid size 360,360,360, pixel 2.19, shown at level 0.277, step 2, values float32 > hide #!3 models The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > volume #5 step 1 > volume #5 level 0.1721 > show #!3 models > hide #!4 models > volume #5 level 0.2115 > volume #5 level 0.2174 > ui mousemode right ""rotate selected models"" > select add #5 3 models selected > view matrix models > #5,0.95745,0.28858,0.0043312,-98.953,0.28414,-0.93989,-0.18942,741.06,-0.050591,0.18259,-0.98189,876.7 > ui mousemode right ""translate selected models"" > view matrix models > #5,0.95745,0.28858,0.0043312,-4.1809,0.28414,-0.93989,-0.18942,804.6,-0.050591,0.18259,-0.98189,869.49 > ui mousemode right ""rotate selected models"" > view matrix models > #5,0.9971,0.066566,0.037008,52.351,0.073264,-0.97107,-0.22728,917.7,0.020808,0.22933,-0.97313,818.85 > view matrix models > #5,0.99854,-0.036256,0.040116,90.834,-0.024169,-0.96292,-0.26869,972.29,0.048371,0.26733,-0.96239,787.99 > view matrix models > #5,0.99559,-0.055166,-0.07586,153.79,-0.070768,-0.97259,-0.22149,972.33,-0.061562,0.22588,-0.97221,852.22 > ui mousemode right ""translate selected models"" > view matrix models > #5,0.99559,-0.055166,-0.07586,138.73,-0.070768,-0.97259,-0.22149,972.47,-0.061562,0.22588,-0.97221,837.2 > fitmap #5 inMap #3 Fit map cryosparc_P23_J1770_003_volume_map.mrc in map J1663_FE using 822201 points correlation = 0.9965, correlation about mean = 0.9334, overlap = 9.029e+04 steps = 208, shift = 47.2, angle = 16.4 degrees Position of cryosparc_P23_J1770_003_volume_map.mrc (#5) relative to J1663_FE (#3) coordinates: Matrix rotation and translation 0.99517678 0.09809776 0.00003947 -4.57853809 0.09809776 -0.99517678 -0.00003620 779.53497612 0.00003573 0.00003990 -1.00000000 819.70376405 Axis 0.99879463 0.04908453 0.00003744 Axis point 0.00000000 389.87217475 409.85938563 Rotation angle (degrees) 179.99781716 Shift along axis 33.72077697 > select subtract #5 Nothing selected > ui mousemode right translate > volume #5 level 0.2155 > volume #5 level 0.2135 > ui mousemode right clip > ui mousemode right translate > rename #5 J1770_FE > save /Users/ConstantinePetridis/Desktop/AcMNPV_Caps.cxs includeMaps true ===== 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 - 89.3 OpenGL renderer: Apple M1 Pro 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: MacBookPro18,3 Model Number: MKGP3LL/A Chip: Apple M1 Pro Total Number of Cores: 8 (6 performance and 2 efficiency) Memory: 16 GB System Firmware Version: 11881.41.5 OS Loader Version: 11881.41.5 Software: System Software Overview: System Version: macOS 15.1.1 (24B91) Kernel Version: Darwin 24.1.0 Time since boot: 20 days, 11 hours, 53 minutes Graphics/Displays: Apple M1 Pro: Chipset Model: Apple M1 Pro Type: GPU Bus: Built-In Total Number of Cores: 14 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 LG ULTRAGEAR: Resolution: 1920 x 1080 (1080p FHD - Full High Definition) UI Looks like: 1920 x 1080 @ 120.00Hz Mirror: Off Online: Yes Rotation: Supported 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