id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 16554 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. Fatal Python error: Segmentation fault Thread 0x0000000313c4b000 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 579 in _handle_results File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x0000000312c3f000 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 531 in _handle_tasks File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x0000000311c33000 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/selectors.py"", line 415 in select File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/connection.py"", line 930 in wait File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 502 in _wait_for_updates File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 522 in _handle_workers File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x0000000310c27000 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000030fc1b000 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000030ec0f000 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000030dc03000 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000030cbf7000 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000030bbeb000 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000030abdf000 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x0000000309bd3000 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Current thread 0x00000001fac23840 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 315 in event_loop File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1003 in init File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1166 in File """", line 88 in _run_code File """", line 198 in _run_module_as_main Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, 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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 0.37, step 1, values float32 Opened emdb43590_BV as #2, grid size 700,700,700, pixel 1.41, shown at level 0.292, step 1, values float32 Opened J1663_FE as #3, grid size 360,360,360, pixel 2.37, shown at level 0.211, step 1, values float32 Opened J1671_PE z flip as #4, grid size 360,360,360, pixel 2.37, shown at level 0.268, step 1, values float32 Opened J1770_FE as #5, grid size 360,360,360, pixel 2.19, shown at level 0.18, step 1, values float32 Opened cryosparc_P23_J1772_map_locres.mrc as #6, grid size 360,360,360, pixel 2.19, shown at level 7.51, step 2, values float32 Log from Fri Jan 3 17:12:52 2025UCSF 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 0.32, step 1, values float32 Opened emdb43590_BV as #2, grid size 700,700,700, pixel 1.41, shown at level 0.203, step 1, values float32 Opened J1663_FE as #3, grid size 360,360,360, pixel 2.37, shown at level 0.255, step 1, values float32 Opened J1671_PE z flip as #4, grid size 360,360,360, pixel 2.37, shown at level 0.0763, step 1, values float32 Opened J1770_FE as #5, grid size 360,360,360, pixel 2.19, shown at level 0.214, step 1, values float32 Log from Tue Dec 24 23:20:40 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 0.159, 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 [deleted to fit within ticket limits] > show #!10 models > hide #!10 models > combine #7, 10 Remapping chain ID 'A' in 8vwi #10 to 'U' Remapping chain ID 'B' in 8vwi #10 to 'l' Remapping chain ID 'C' in 8vwi #10 to 'm' Remapping chain ID 'D' in 8vwi #10 to 'n' Remapping chain ID 'E' in 8vwi #10 to 'o' Remapping chain ID 'F' in 8vwi #10 to 'p' Remapping chain ID 'G' in 8vwi #10 to 'q' Remapping chain ID 'H' in 8vwi #10 to 'r' Remapping chain ID 'I' in 8vwi #10 to 's' Remapping chain ID 'J' in 8vwi #10 to 't' Remapping chain ID 'K' in 8vwi #10 to 'u' Remapping chain ID 'L' in 8vwi #10 to 'v' Remapping chain ID 'M' in 8vwi #10 to 'w' Remapping chain ID 'N' in 8vwi #10 to 'x' Remapping chain ID 'O' in 8vwi #10 to 'y' Remapping chain ID 'P' in 8vwi #10 to 'z' Remapping chain ID 'Q' in 8vwi #10 to '1' Remapping chain ID 'R' in 8vwi #10 to '2' Remapping chain ID 'S' in 8vwi #10 to '3' Remapping chain ID 'T' in 8vwi #10 to '4' Remapping chain ID 'V' in 8vwi #10 to '5' Remapping chain ID 'W' in 8vwi #10 to '6' Remapping chain ID 'X' in 8vwi #10 to '7' Remapping chain ID 'Y' in 8vwi #10 to '8' Remapping chain ID 'Z' in 8vwi #10 to '9' Remapping chain ID 'a' in 8vwi #10 to '0' Remapping chain ID 'b' in 8vwi #10 to 'AA' Remapping chain ID 'c' in 8vwi #10 to 'AB' Remapping chain ID 'd' in 8vwi #10 to 'AC' Remapping chain ID 'e' in 8vwi #10 to 'AD' Remapping chain ID 'f' in 8vwi #10 to 'AE' Remapping chain ID 'g' in 8vwi #10 to 'AF' Remapping chain ID 'h' in 8vwi #10 to 'AG' Remapping chain ID 'i' in 8vwi #10 to 'AH' Remapping chain ID 'j' in 8vwi #10 to 'AI' Remapping chain ID 'k' in 8vwi #10 to 'AJ' > hide #!5 models > show #!5 models > close #10 > close #7 > show #8 models > hide #8 models > show #9 models > hide #9 models > select #13/G-I, b-d 20965 atoms, 21180 bonds, 2 pseudobonds, 1254 residues, 2 models selected > hide #!5 models > select #13/G-I, b-d,AC,AB,AA,q-s 41930 atoms, 42360 bonds, 4 pseudobonds, 2508 residues, 2 models selected > select ~sel & ##selected 270602 atoms, 273510 bonds, 150 pseudobonds, 16720 residues, 3 models selected > hide sel cartoons > show #!5 models > select #13/AC,AB,AA 10484 atoms, 10591 bonds, 1 pseudobond, 626 residues, 2 models selected > hide sel cartoons > select #13/AC,AB,AA 10484 atoms, 10591 bonds, 1 pseudobond, 626 residues, 2 models selected > show sel cartoons > select clear > select add #12 2274 atoms, 2302 bonds, 280 residues, 1 model selected > select subtract #12 Nothing selected > select add #13 312532 atoms, 315870 bonds, 154 pseudobonds, 19228 residues, 3 models selected > combine #13 > view matrix models > #13,-0.25724,0.96635,0.00083887,112.5,-0.96625,-0.25722,0.013732,829.67,0.013486,0.0027218,0.99991,265.44 > ui mousemode right ""rotate selected models"" > view matrix models > #13,-0.99471,0.094085,-0.041161,555.63,-0.094742,-0.9954,0.014319,663.49,-0.039624,0.018143,0.99905,281.54 > ui mousemode right ""translate selected models"" > view matrix models > #13,-0.99471,0.094085,-0.041161,619.03,-0.094742,-0.9954,0.014319,767.81,-0.039624,0.018143,0.99905,278.18 > ui mousemode right ""rotate selected models"" > view matrix models > #13,-0.95912,-0.27844,-0.05063,681.43,0.27754,-0.96041,0.024282,626.03,-0.055387,0.0092378,0.99842,285.69 > ui mousemode right ""translate selected models"" > view matrix models > #13,-0.95912,-0.27844,-0.05063,726.22,0.27754,-0.96041,0.024282,628.41,-0.055387,0.0092378,0.99842,286.46 > select subtract #13 Nothing selected > select add #13 312532 atoms, 315870 bonds, 154 pseudobonds, 19228 residues, 3 models selected > fitmap #13 inMap #5 Fit molecule combination (#13) to map J1770_FE (#5) using 312532 atoms average map value = 0.195, steps = 152 shifted from previous position = 14.1 rotated from previous position = 12.3 degrees atoms outside contour = 138721, contour level = 0.18 Position of combination (#13) relative to J1770_FE (#5) coordinates: Matrix rotation and translation -0.83439576 -0.55101692 0.01280887 638.37895402 -0.55100048 0.83448936 0.00509722 343.47486693 -0.01349752 -0.00280460 -0.99990497 663.95917314 Axis -0.28767844 0.95772687 0.00059846 Axis point 373.15541658 0.00000000 329.43330618 Rotation angle (degrees) 179.21308847 Shift along axis 145.70459849 > select clear > combine #13 #7 Remapping chain ID '0' in copy of combination #7 to 'AK' Remapping chain ID '1' in copy of combination #7 to 'AL' Remapping chain ID '2' in copy of combination #7 to 'AM' Remapping chain ID '3' in copy of combination #7 to 'AN' Remapping chain ID '4' in copy of combination #7 to 'AO' Remapping chain ID '5' in copy of combination #7 to 'AP' Remapping chain ID '6' in copy of combination #7 to 'AQ' Remapping chain ID '7' in copy of combination #7 to 'AR' Remapping chain ID '8' in copy of combination #7 to 'AS' Remapping chain ID '9' in copy of combination #7 to 'AT' Remapping chain ID 'A' in copy of combination #7 to 'AU' Remapping chain ID 'AA' in copy of combination #7 to 'AV' Remapping chain ID 'AB' in copy of combination #7 to 'AW' Remapping chain ID 'AC' in copy of combination #7 to 'AX' Remapping chain ID 'AD' in copy of combination #7 to 'AY' Remapping chain ID 'AE' in copy of combination #7 to 'AZ' Remapping chain ID 'AF' in copy of combination #7 to 'Aa' Remapping chain ID 'AG' in copy of combination #7 to 'Ab' Remapping chain ID 'AH' in copy of combination #7 to 'Ac' Remapping chain ID 'AI' in copy of combination #7 to 'Ad' Remapping chain ID 'AJ' in copy of combination #7 to 'Ae' Remapping chain ID 'B' in copy of combination #7 to 'Af' Remapping chain ID 'C' in copy of combination #7 to 'Ag' Remapping chain ID 'D' in copy of combination #7 to 'Ah' Remapping chain ID 'E' in copy of combination #7 to 'Ai' Remapping chain ID 'F' in copy of combination #7 to 'Aj' Remapping chain ID 'G' in copy of combination #7 to 'Ak' Remapping chain ID 'H' in copy of combination #7 to 'Al' Remapping chain ID 'I' in copy of combination #7 to 'Am' Remapping chain ID 'J' in copy of combination #7 to 'An' Remapping chain ID 'K' in copy of combination #7 to 'Ao' Remapping chain ID 'L' in copy of combination #7 to 'Ap' Remapping chain ID 'M' in copy of combination #7 to 'Aq' Remapping chain ID 'N' in copy of combination #7 to 'Ar' Remapping chain ID 'O' in copy of combination #7 to 'As' Remapping chain ID 'P' in copy of combination #7 to 'At' Remapping chain ID 'Q' in copy of combination #7 to 'Au' Remapping chain ID 'R' in copy of combination #7 to 'Av' Remapping chain ID 'S' in copy of combination #7 to 'Aw' Remapping chain ID 'T' in copy of combination #7 to 'Ax' Remapping chain ID 'U' in copy of combination #7 to 'Ay' Remapping chain ID 'V' in copy of combination #7 to 'Az' Remapping chain ID 'W' in copy of combination #7 to 'A1' Remapping chain ID 'X' in copy of combination #7 to 'A2' Remapping chain ID 'Y' in copy of combination #7 to 'A3' Remapping chain ID 'Z' in copy of combination #7 to 'A4' Remapping chain ID 'a' in copy of combination #7 to 'A5' Remapping chain ID 'b' in copy of combination #7 to 'A6' Remapping chain ID 'c' in copy of combination #7 to 'A7' Remapping chain ID 'd' in copy of combination #7 to 'A8' Remapping chain ID 'e' in copy of combination #7 to 'A9' Remapping chain ID 'f' in copy of combination #7 to 'A0' Remapping chain ID 'g' in copy of combination #7 to 'BA' Remapping chain ID 'h' in copy of combination #7 to 'BB' Remapping chain ID 'i' in copy of combination #7 to 'BC' Remapping chain ID 'j' in copy of combination #7 to 'BD' Remapping chain ID 'k' in copy of combination #7 to 'BE' Remapping chain ID 'l' in copy of combination #7 to 'BF' Remapping chain ID 'm' in copy of combination #7 to 'BG' Remapping chain ID 'n' in copy of combination #7 to 'BH' Remapping chain ID 'o' in copy of combination #7 to 'BI' Remapping chain ID 'p' in copy of combination #7 to 'BJ' Remapping chain ID 'q' in copy of combination #7 to 'BK' Remapping chain ID 'r' in copy of combination #7 to 'BL' Remapping chain ID 's' in copy of combination #7 to 'BM' Remapping chain ID 't' in copy of combination #7 to 'BN' Remapping chain ID 'u' in copy of combination #7 to 'BO' Remapping chain ID 'v' in copy of combination #7 to 'BP' Remapping chain ID 'w' in copy of combination #7 to 'BQ' Remapping chain ID 'x' in copy of combination #7 to 'BR' Remapping chain ID 'y' in copy of combination #7 to 'BS' Remapping chain ID 'z' in copy of combination #7 to 'BT' > hide #12 models > hide #!7 models > show #12 models > hide #12 models > hide #!10 models > show #!10 models > hide #!13 models > show #!13 models > show #!7 models > hide #!10 models > hide #!13 models > show #!13 models > hide #!5 models > show #!10 models > hide #!7 models > hide #!13 models > close #13 > close #7 > show #!5 models > show #11 models > hide #11 models > show #12 models > rainbow #12#!10 > color #12#!10 bychain > rainbow #12#!10 > save /Users/ConstantinePetridis/Desktop/AcMNPV_Caps.cxs includeMaps true > color #5 #a3a7ff74 models > color #5 #a3a7ff73 models > hide #12 models > show #12 models > hide #!10 models > show #!10 models > combine #10 > hide #!10 models > hide #!7 models > show #!7 models > show #12#!7 cartoons > color #7 #dbd3beff > color #7 #d2d2d3ff > color #7 #8c8dfcff > color #7 #8b8efcff > color #7 #8b8efceb > color #7 #8b8efcee > color #7 #8b8efcff > color #7 #b4b4fcff > hide #!7 models > show #!2 models > color #2 #d2d2d300 models > color #2 #d2d2d3ff models [Repeated 1 time(s)] > hide #!2 models > show #!10 models > hide #!10 models > show #!7 models > ui mousemode right select > ui mousemode right rotate > hide #12 models > show #12 models > show #!10 models > hide #!10 models > hide #!5 models > hide #12/A:1-40 cartoons > hide #12/B:40-200 cartoons > ui mousemode right select > select #7/AM:189 10 atoms, 9 bonds, 1 residue, 1 model selected > select up 253 atoms, 252 bonds, 16 residues, 1 model selected > select up 3607 atoms, 3640 bonds, 220 residues, 1 model selected > select up 625064 atoms, 631740 bonds, 38456 residues, 1 model selected > select down 3607 atoms, 3640 bonds, 220 residues, 1 model selected > hide sel cartoons > select #7/Av:123 10 atoms, 9 bonds, 1 residue, 1 model selected > select up 259 atoms, 260 bonds, 14 residues, 1 model selected > select up 3607 atoms, 3640 bonds, 220 residues, 1 model selected > hide sel cartoons > select #7/Au:55 17 atoms, 16 bonds, 1 residue, 1 model selected > select up 251 atoms, 252 bonds, 14 residues, 1 model selected > select up 1807 atoms, 1823 bonds, 112 residues, 1 model selected > hide sel cartoons > select #7/Ax:246 19 atoms, 18 bonds, 1 residue, 1 model selected > select up 256 atoms, 255 bonds, 15 residues, 1 model selected > select up 3658 atoms, 3692 bonds, 222 residues, 1 model selected > hide sel cartoons > select #7/Aw:137 12 atoms, 11 bonds, 1 residue, 1 model selected > select up 189 atoms, 189 bonds, 11 residues, 1 model selected > select up 2383 atoms, 2401 bonds, 148 residues, 1 model selected > hide sel cartoons > select #7/BP:298 10 atoms, 9 bonds, 1 residue, 1 model selected > select #7/Aw:228 14 atoms, 13 bonds, 1 residue, 1 model selected > select up 647 atoms, 656 bonds, 39 residues, 1 model selected > select up 1236 atoms, 1251 bonds, 75 residues, 1 model selected > hide sel cartoons > select #7/Au:205 15 atoms, 14 bonds, 1 residue, 1 model selected > select up 479 atoms, 486 bonds, 28 residues, 1 model selected > select up 1203 atoms, 1217 bonds, 73 residues, 1 model selected > select up 1279 atoms, 1293 bonds, 78 residues, 1 model selected > select up 3010 atoms, 3040 bonds, 185 residues, 1 model selected > select down 1279 atoms, 1293 bonds, 78 residues, 1 model selected > select down 1203 atoms, 1217 bonds, 73 residues, 1 model selected > select down 479 atoms, 486 bonds, 28 residues, 1 model selected > select up 1203 atoms, 1217 bonds, 73 residues, 1 model selected > hide sel cartoons > show #!5 models > select #5 2 models selected > select subtract #5 Nothing selected > hide #!5 models > select #7/2:280 24 atoms, 23 bonds, 1 residue, 1 model selected > select up 188 atoms, 189 bonds, 10 residues, 1 model selected > select up 3607 atoms, 3640 bonds, 220 residues, 1 model selected > hide sel cartoons > select #7/1:47 19 atoms, 18 bonds, 1 residue, 1 model selected > select up 251 atoms, 252 bonds, 14 residues, 1 model selected > select up 1807 atoms, 1823 bonds, 112 residues, 1 model selected > hide sel cartoons Drag select of 81 residues, 1 pseudobonds > select up 2894 atoms, 2918 bonds, 1 pseudobond, 175 residues, 2 models selected > select up 13213 atoms, 13338 bonds, 1 pseudobond, 811 residues, 2 models selected > hide sel cartoons [Repeated 1 time(s)]Drag select of 14 residues > select up 484 atoms, 484 bonds, 29 residues, 1 model selected > select up 4766 atoms, 4802 bonds, 296 residues, 1 model selected > hide sel cartoons > show #!5 models > hide #!5 models Drag select of 128 residues > select up 4549 atoms, 4574 bonds, 275 residues, 1 model selected > select up 14682 atoms, 14829 bonds, 891 residues, 1 model selected > hide sel cartoons > select #7/AE:203 19 atoms, 18 bonds, 1 residue, 1 model selected > select up 254 atoms, 255 bonds, 16 residues, 1 model selected > select up 3841 atoms, 3875 bonds, 234 residues, 1 model selected > select clear > show #!5 models > hide #!5 models > show #!5 models > save /Users/ConstantinePetridis/Desktop/AcMNPV_Caps.cxs includeMaps true > hide #12 models > show #!10 models > hide #!10 models > hide #!7 models > show #!7 models > show #!10 models > hide #!7 models > show #!7 models > color #5 #d2d2d3ff models > hide #!5 models > show #!5 models > color #5 #8c8dfcff models > color #5 #8c8dfc70 models > color #5 #8c8dfc73 models > color #7 #d2d2d3ff > fitmap #7 inMap #5 Fit molecule copy of combination (#7) to map J1770_FE (#5) using 625064 atoms average map value = 0.195, steps = 44 shifted from previous position = 0.0274 rotated from previous position = 0.00223 degrees atoms outside contour = 277443, contour level = 0.18 Position of copy of combination (#7) relative to J1770_FE (#5) coordinates: Matrix rotation and translation -0.83437907 -0.55104211 0.01281242 638.36011778 -0.55102535 0.83447279 0.00512188 343.47189580 -0.01351399 -0.00278638 -0.99990480 663.94176171 Axis -0.28769283 0.95772254 0.00060966 Axis point 373.15013012 0.00000000 329.42077578 Rotation angle (degrees) 179.21248605 Shift along axis 145.70392280 > hide #!10 models > color #5 #8c8dfc96 models > save /Users/ConstantinePetridis/Desktop/AcMNPV_Caps.cxs includeMaps true > combine #5 No structures specified > mcopy #5 Missing required ""to_atoms"" argument > colume copy #5 Unknown command: colume copy #5 > volume copy #5 Opened J1770_FE copy as #13, grid size 360,360,360, pixel 2.19, shown at step 1, values float32 > color zone #13 near #7 > hide #!13 models > show #!13 models > color zone #13 near #7 transparency 50 Expected a keyword > color zone #13 near #7 red transparency 50 Expected a keyword > color zone #13 near #7 farColor red transparency 50 Expected a keyword > color zone #13 near #7 farColor red transparency 50 | keep Expected a keyword > color zone #13 near #7 farColor red | keep Expected a keyword > color zone #13 near #7 red Expected a keyword > select zone #13 near #7 Missing or invalid ""range"" argument: Expected a number > hide #!13 models > show #!13 models > hide #!7 models > select zone #13 near #7 distance 2.5 Missing or invalid ""range"" argument: Expected a number > show #!7 models > select zone #13 near #7 distance 2.5 Missing or invalid ""range"" argument: Expected a number > color zone #13 near #7 distance 2.5 > color zone #13 near #7 distance 2.8 > hide #!7 models > color #13 #8c8dfcff models > color #13 #8c8dfcb0 models > color #13 #8c8dfcd5 models > color #13 #8c8dfc40 models > hide #!13 models > show #!5 models > show #!7 models > show #12 models > view name AC104 > show matrix Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword > view matrix view matrix camera 0.22366,0.054139,-0.97316,-514.33,-0.97457,-0.002007,-0.22409,253.96,-0.014085,0.99853,0.052313,593.01 view matrix models #1,0.22884,0.97346,2.2675e-07,6.5664,-0.97346,0.22884,5.8736e-07,795.07,5.199e-07,-3.5514e-07,1,179.58,#1.1,1,0,0,0,0,1,0,0,0,0,1,0,#2,1,0.00083921,3.6674e-07,-0.41412,-0.00083921,1,1.9537e-07,0.41458,-3.6657e-07,-1.9568e-07,1,-0.16369,#2.1,1,0,0,0,0,1,0,0,0,0,1,0,#2.2,1,0,0,0,0,1,0,0,0,0,1,0,#3,1,-0.00067234,5.3385e-06,67.653,0.00067234,1,2.164e-05,67.085,-5.353e-06,-2.1636e-05,1,119.77,#3.1,1,0,0,0,0,1,0,0,0,0,1,0,#4,-0.077036,0.99703,2.7381e-05,101.45,-0.99703,-0.077036,3.09e-05,951.16,3.2916e-05,-2.4918e-05,1,58.136,#4.1,1,0,0,0,0,1,0,0,0,0,1,0,#5,0.99509,0.098993,-3.3983e-05,62.481,0.098993,-0.99509,3.2042e-05,846.52,-3.0643e-05,-3.5249e-05,-1,939.76,#5.1,1,0,0,0,0,1,0,0,0,0,1,0,#6,0.66683,-0.74518,0.0062522,524.05,-0.74518,-0.66686,-0.0035196,1050.6,0.006792,-0.002312,-0.99997,936.44,#6.1,1,0,0,0,0,1,0,0,0,0,1,0,#8,0.4645,-0.88458,0.041929,663.55,0.73537,0.41167,0.5383,185.13,-0.49342,-0.21921,0.84171,641.73,#9,0.82925,0.50292,0.24376,304.29,-0.54973,0.65541,0.51791,428.54,0.1007,-0.56348,0.81997,561.86,#11,-0.46204,0.77531,-0.4306,308.8,0.86303,0.50486,-0.017036,453.11,0.20419,-0.37949,-0.90238,570.23,#12,0.82925,0.50292,0.24376,304.29,-0.54973,0.65541,0.51791,428.54,0.1007,-0.56348,0.81997,561.86,#10,-0.88484,-0.4657,0.013285,731.7,0.46569,-0.88494,-0.0038362,567.95,0.013543,0.0027921,0.9999,275.77,#10.1,1,0,0,0,0,1,0,0,0,0,1,0,#10.2,1,0,0,0,0,1,0,0,0,0,1,0,#7,-0.88483,-0.46573,0.01329,731.68,0.46572,-0.88492,-0.0038604,567.95,0.013559,0.0027739,0.9999,275.79,#7.1,1,0,0,0,0,1,0,0,0,0,1,0,#7.2,1,0,0,0,0,1,0,0,0,0,1,0,#13,0.99509,0.098993,-3.3983e-05,62.481,0.098993,-0.99509,3.2042e-05,846.52,-3.0643e-05,-3.5249e-05,-1,939.76,#13.1,1,0,0,0,0,1,0,0,0,0,1,0 > hide #12 models > show #12 models > color #12 #c1153cff > color #12 #7b2734ff > color #12 #ff506dff > color #12 #ee4a65ff > color #12 #ec4a64ff > color #12 #ff506dff > color #12 #e64862ff > color #12 #dda235ff > color #12 #dda174ff > color #12 #c1153cff > hide #12 models > show #!10 models > hide #!10 models > show #!10 models > hide #!7 models > hide #!10 models > show #!7 models > color #5 #8c8dfcc6 models > color #5 #8c8dfca7 models > color #5 #8c8dfcb3 models > color #5 #8c8dfca9 models > color #5 #8c8dfcb5 models > color #5 #8c8dfcb1 models > color #5 #8c8dfca8 models > color #5 #8c8dfca5 models > color #7 #bbbbbdff > color #7 #cacbcdff > color #7 #d2d2d3ff > color #7 #cfcfd2ff > color #7 #cecfd1ff > color #7 #cacaccff > color #7 #c3c4c6ff > save /Users/ConstantinePetridis/Desktop/BV_FE_AC104density.png width 3000 > height 1873 supersample 4 [Repeated 1 time(s)] > color #5 #d2d2d3ff models > color #5 #d2d2d3ac models > color #5 #d2d2d3ab models > color #5 #d2d2d3a6 models > color #7 #7a81ffff > color #5 #d2d2d356 models > color #5 #d2d2d37b models > color #5 #d2d2d37e models > color #5 #d2d2d380 models > color #7 #c1153cff > color #7 #75ff79ff > hide #!7 models > show #!10 models > color #5 #8c8dfcff models > color #5 #8c8dfc8e models > color #5 #8c8dfc4f models > color #5 #8c8dfc56 models > color #5 #8d90ff56 models > color #5 #a5aaff56 models > color #5 #a5aaff66 models > color #5 #a5aaff88 models > color #5 #a5aaff80 models > view AC104 > color #5 #d2d2d3ff models > color #5 #d2d2d35f models > color #5 #d2d2d391 models > color #5 #d2d2d3a7 models > color #5 #d2d2d398 models > color #5 #8c8dfcff models > color #5 #8c8dfc29 models > color #5 #8c8dfc24 models > color #5 #8c8dfc21 models > color #5 #8c8dfc5e models > color #5 #8c8dfc5d models > color #5 #8d90ff5d models > color #5 #bcbbff5d models > color #5 #bcbbff6f models > color #5 #bcbbff7c models > color #5 #bcbbff80 models > save /Users/ConstantinePetridis/Desktop/BV_FE_AC104density.png width 3000 > height 1873 supersample 4 > view front > color #3 #d2d2d3ff models > show #!2 models > color #5 #8c8dfcff models > color #5 #8c8dfc83 models > color #5 #8c8dfc80 models > close #13 > show #12 models > hide #12 models > color zone #2 near #10 distance 2.8 > hide #!10 models > show #!10 models > color zone #2 near #10 distance 5 > hide #!10 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!7 models > show #!7 surfaces > hide #!7 models > show #!10 models > show #!7 models > color #7 #75ff79fe > color #7 #75ff79e0 > color #7 #75ff79ff > hide #!7 models > color #5 #8c8dfc5b models > color #5 #8c8dfc66 models > show #12 models > hide #12 models > show #12 models > hide #12 models > show #12 models > hide #12 models > show #12 models > hide #12 models > show #12 models > hide #12 models > show #12 models > hide #12 models > show #12 models > hide #12 models > show #!3 models > hide #!3 models > show #!2 models > color #2 #8C8DFC surfaces > color #2 #D2D2D3 surfaces > hide #!2 models > save /Users/ConstantinePetridis/Desktop/BV_FE_AC104density.png width 3000 > height 1873 supersample 4 > view name AC104 > view camera matrix Expected an objects specifier or a view name or a keyword > view matrix view matrix camera 0.32828,0.086655,-0.9406,-314.61,-0.94454,0.021045,-0.32772,216.96,-0.0086042,0.99602,0.088758,595.15 view matrix models 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> ui tool show ""Side View"" > save /Users/ConstantinePetridis/Desktop/BV_FE_AC104density.png width 3000 > height 1873 supersample 4 > view name AC104 > view matrix view matrix camera 0.24029,0.0028905,-0.9707,-407.99,-0.97064,-0.010592,-0.2403,271.05,-0.010977,0.99994,0.00026049,546.45 view matrix models 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> save /Users/ConstantinePetridis/Desktop/AcMNPV_Caps.cxs includeMaps true > save /Users/ConstantinePetridis/Desktop/BV_FE_AC104density.png width 1984 > height 1239 supersample 3 > hide #!5 models Drag select of 703 residues, 1 pseudobonds > select ~sel & ##selected 614421 atoms, 620987 bonds, 307 pseudobonds, 37818 residues, 3 models selected > hide sel cartoons > select #10/AX:658 11 atoms, 10 bonds, 1 residue, 1 model selected > select up 395 atoms, 396 bonds, 23 residues, 1 model selected > hide sel cartoons > select clear Drag select of 4 residues > hide sel cartoons > show #!5 models > show #12 models > hide #12 models > show #12 models > hide #12 models > show #12 models > hide #12 models > show #12 models > hide #12 models > show #12 models > hide #12 models > hide #!5 models > select add #10 625064 atoms, 631740 bonds, 308 pseudobonds, 38456 residues, 3 models selected > select subtract #10 Nothing selected > show #10 cartoons > show #12 models > show #!5 models > hide #!5 models > select #10/b-d 10484 atoms, 10591 bonds, 1 pseudobond, 626 residues, 2 models selected > select ~sel & ##selected 614580 atoms, 621149 bonds, 307 pseudobonds, 37830 residues, 3 models selected > hide sel cartoons > show #!5 models > hide #!5 models > show #!5 models > select #10/A-C 370085 atoms, 374051 bonds, 176 pseudobonds, 22751 residues, 3 models selected > show sel cartoons > select add #10 625064 atoms, 631740 bonds, 308 pseudobonds, 38456 residues, 3 models selected > select subtract #10 Nothing selected > select add #10 625064 atoms, 631740 bonds, 308 pseudobonds, 38456 residues, 3 models selected > select subtract #10 Nothing selected > select add #10 625064 atoms, 631740 bonds, 308 pseudobonds, 38456 residues, 3 models selected > show sel cartoons > hide #!5 models > select #10/G-I 10481 atoms, 10589 bonds, 1 pseudobond, 628 residues, 2 models selected > select ~sel & ##selected 614583 atoms, 621151 bonds, 307 pseudobonds, 37828 residues, 3 models selected > hide sel cartoons > graphics silhouettes width 2.3 > cartoon style protein modeHelix tube radius 1.9 sides 24 > show #!5 models > graphics silhouettes width 2.3 > cartoon style protein modeHelix tube radius 2 sides 24 > view name AC104 > view matrix view matrix camera 0.25887,0.036214,-0.96523,-403.96,-0.96583,-0.0028951,-0.25914,268.43,-0.012179,0.99934,0.034228,563.34 view matrix models #1,0.22884,0.97346,2.2675e-07,6.5664,-0.97346,0.22884,5.8736e-07,795.07,5.199e-07,-3.5514e-07,1,179.58,#1.1,1,0,0,0,0,1,0,0,0,0,1,0,#2,1,0.00083921,3.6674e-07,-0.41412,-0.00083921,1,1.9537e-07,0.41458,-3.6657e-07,-1.9568e-07,1,-0.16369,#2.1,1,0,0,0,0,1,0,0,0,0,1,0,#2.2,1,0,0,0,0,1,0,0,0,0,1,0,#3,1,-0.00067234,5.3385e-06,67.653,0.00067234,1,2.164e-05,67.085,-5.353e-06,-2.1636e-05,1,119.77,#3.1,1,0,0,0,0,1,0,0,0,0,1,0,#4,-0.077036,0.99703,2.7381e-05,101.45,-0.99703,-0.077036,3.09e-05,951.16,3.2916e-05,-2.4918e-05,1,58.136,#4.1,1,0,0,0,0,1,0,0,0,0,1,0,#5,0.99509,0.098993,-3.3983e-05,62.481,0.098993,-0.99509,3.2042e-05,846.52,-3.0643e-05,-3.5249e-05,-1,939.76,#5.1,1,0,0,0,0,1,0,0,0,0,1,0,#6,0.66683,-0.74518,0.0062522,524.05,-0.74518,-0.66686,-0.0035196,1050.6,0.006792,-0.002312,-0.99997,936.44,#6.1,1,0,0,0,0,1,0,0,0,0,1,0,#8,0.4645,-0.88458,0.041929,663.55,0.73537,0.41167,0.5383,185.13,-0.49342,-0.21921,0.84171,641.73,#9,0.82925,0.50292,0.24376,304.29,-0.54973,0.65541,0.51791,428.54,0.1007,-0.56348,0.81997,561.86,#11,-0.46204,0.77531,-0.4306,308.8,0.86303,0.50486,-0.017036,453.11,0.20419,-0.37949,-0.90238,570.23,#12,0.82925,0.50292,0.24376,304.29,-0.54973,0.65541,0.51791,428.54,0.1007,-0.56348,0.81997,561.86,#10,-0.88484,-0.4657,0.013285,731.7,0.46569,-0.88494,-0.0038362,567.95,0.013543,0.0027921,0.9999,275.77,#10.1,1,0,0,0,0,1,0,0,0,0,1,0,#10.2,1,0,0,0,0,1,0,0,0,0,1,0,#7,-0.88483,-0.46573,0.01329,731.68,0.46572,-0.88492,-0.0038604,567.95,0.013559,0.0027739,0.9999,275.79,#7.1,1,0,0,0,0,1,0,0,0,0,1,0,#7.2,1,0,0,0,0,1,0,0,0,0,1,0,#7.3,1,0,0,0,0,1,0,0,0,0,1,0,#7.4,1,0,0,0,0,1,0,0,0,0,1,0,#7.5,1,0,0,0,0,1,0,0,0,0,1,0,#7.6,1,0,0,0,0,1,0,0,0,0,1,0,#7.7,1,0,0,0,0,1,0,0,0,0,1,0,#7.8,1,0,0,0,0,1,0,0,0,0,1,0,#7.9,1,0,0,0,0,1,0,0,0,0,1,0,#7.10,1,0,0,0,0,1,0,0,0,0,1,0,#7.11,1,0,0,0,0,1,0,0,0,0,1,0,#7.12,1,0,0,0,0,1,0,0,0,0,1,0,#7.13,1,0,0,0,0,1,0,0,0,0,1,0,#7.14,1,0,0,0,0,1,0,0,0,0,1,0,#7.15,1,0,0,0,0,1,0,0,0,0,1,0,#7.16,1,0,0,0,0,1,0,0,0,0,1,0,#7.17,1,0,0,0,0,1,0,0,0,0,1,0,#7.18,1,0,0,0,0,1,0,0,0,0,1,0,#7.19,1,0,0,0,0,1,0,0,0,0,1,0,#7.20,1,0,0,0,0,1,0,0,0,0,1,0,#7.21,1,0,0,0,0,1,0,0,0,0,1,0,#7.22,1,0,0,0,0,1,0,0,0,0,1,0,#7.23,1,0,0,0,0,1,0,0,0,0,1,0,#7.24,1,0,0,0,0,1,0,0,0,0,1,0,#7.25,1,0,0,0,0,1,0,0,0,0,1,0,#7.26,1,0,0,0,0,1,0,0,0,0,1,0,#7.27,1,0,0,0,0,1,0,0,0,0,1,0,#7.28,1,0,0,0,0,1,0,0,0,0,1,0,#7.29,1,0,0,0,0,1,0,0,0,0,1,0,#7.30,1,0,0,0,0,1,0,0,0,0,1,0,#7.31,1,0,0,0,0,1,0,0,0,0,1,0,#7.32,1,0,0,0,0,1,0,0,0,0,1,0,#7.33,1,0,0,0,0,1,0,0,0,0,1,0,#7.34,1,0,0,0,0,1,0,0,0,0,1,0,#7.35,1,0,0,0,0,1,0,0,0,0,1,0,#7.36,1,0,0,0,0,1,0,0,0,0,1,0,#7.37,1,0,0,0,0,1,0,0,0,0,1,0,#7.38,1,0,0,0,0,1,0,0,0,0,1,0,#7.39,1,0,0,0,0,1,0,0,0,0,1,0,#7.40,1,0,0,0,0,1,0,0,0,0,1,0,#7.41,1,0,0,0,0,1,0,0,0,0,1,0,#7.42,1,0,0,0,0,1,0,0,0,0,1,0,#7.43,1,0,0,0,0,1,0,0,0,0,1,0,#7.44,1,0,0,0,0,1,0,0,0,0,1,0,#7.45,1,0,0,0,0,1,0,0,0,0,1,0,#7.46,1,0,0,0,0,1,0,0,0,0,1,0,#7.47,1,0,0,0,0,1,0,0,0,0,1,0,#7.48,1,0,0,0,0,1,0,0,0,0,1,0,#7.49,1,0,0,0,0,1,0,0,0,0,1,0,#7.50,1,0,0,0,0,1,0,0,0,0,1,0,#7.51,1,0,0,0,0,1,0,0,0,0,1,0,#7.52,1,0,0,0,0,1,0,0,0,0,1,0,#7.53,1,0,0,0,0,1,0,0,0,0,1,0,#7.54,1,0,0,0,0,1,0,0,0,0,1,0,#7.55,1,0,0,0,0,1,0,0,0,0,1,0,#7.56,1,0,0,0,0,1,0,0,0,0,1,0,#7.57,1,0,0,0,0,1,0,0,0,0,1,0,#7.58,1,0,0,0,0,1,0,0,0,0,1,0,#7.59,1,0,0,0,0,1,0,0,0,0,1,0,#7.60,1,0,0,0,0,1,0,0,0,0,1,0,#7.61,1,0,0,0,0,1,0,0,0,0,1,0,#7.62,1,0,0,0,0,1,0,0,0,0,1,0,#7.63,1,0,0,0,0,1,0,0,0,0,1,0,#7.64,1,0,0,0,0,1,0,0,0,0,1,0,#7.65,1,0,0,0,0,1,0,0,0,0,1,0,#7.66,1,0,0,0,0,1,0,0,0,0,1,0,#7.67,1,0,0,0,0,1,0,0,0,0,1,0,#7.68,1,0,0,0,0,1,0,0,0,0,1,0,#7.69,1,0,0,0,0,1,0,0,0,0,1,0,#7.70,1,0,0,0,0,1,0,0,0,0,1,0,#7.71,1,0,0,0,0,1,0,0,0,0,1,0,#7.72,1,0,0,0,0,1,0,0,0,0,1,0,#7.73,1,0,0,0,0,1,0,0,0,0,1,0,#7.74,1,0,0,0,0,1,0,0,0,0,1,0,#7.75,1,0,0,0,0,1,0,0,0,0,1,0,#7.76,1,0,0,0,0,1,0,0,0,0,1,0,#7.77,1,0,0,0,0,1,0,0,0,0,1,0,#7.78,1,0,0,0,0,1,0,0,0,0,1,0,#7.79,1,0,0,0,0,1,0,0,0,0,1,0,#7.80,1,0,0,0,0,1,0,0,0,0,1,0,#7.81,1,0,0,0,0,1,0,0,0,0,1,0,#7.82,1,0,0,0,0,1,0,0,0,0,1,0,#7.83,1,0,0,0,0,1,0,0,0,0,1,0,#7.84,1,0,0,0,0,1,0,0,0,0,1,0,#7.85,1,0,0,0,0,1,0,0,0,0,1,0,#7.86,1,0,0,0,0,1,0,0,0,0,1,0,#7.87,1,0,0,0,0,1,0,0,0,0,1,0,#7.88,1,0,0,0,0,1,0,0,0,0,1,0,#7.89,1,0,0,0,0,1,0,0,0,0,1,0,#7.90,1,0,0,0,0,1,0,0,0,0,1,0,#7.91,1,0,0,0,0,1,0,0,0,0,1,0,#7.92,1,0,0,0,0,1,0,0,0,0,1,0,#7.93,1,0,0,0,0,1,0,0,0,0,1,0,#7.94,1,0,0,0,0,1,0,0,0,0,1,0,#7.95,1,0,0,0,0,1,0,0,0,0,1,0,#7.96,1,0,0,0,0,1,0,0,0,0,1,0,#7.97,1,0,0,0,0,1,0,0,0,0,1,0,#7.98,1,0,0,0,0,1,0,0,0,0,1,0,#7.99,1,0,0,0,0,1,0,0,0,0,1,0,#7.100,1,0,0,0,0,1,0,0,0,0,1,0,#7.101,1,0,0,0,0,1,0,0,0,0,1,0,#7.102,1,0,0,0,0,1,0,0,0,0,1,0,#7.103,1,0,0,0,0,1,0,0,0,0,1,0,#7.104,1,0,0,0,0,1,0,0,0,0,1,0,#7.105,1,0,0,0,0,1,0,0,0,0,1,0,#7.106,1,0,0,0,0,1,0,0,0,0,1,0,#7.107,1,0,0,0,0,1,0,0,0,0,1,0,#7.108,1,0,0,0,0,1,0,0,0,0,1,0,#7.109,1,0,0,0,0,1,0,0,0,0,1,0,#7.110,1,0,0,0,0,1,0,0,0,0,1,0,#7.111,1,0,0,0,0,1,0,0,0,0,1,0,#7.112,1,0,0,0,0,1,0,0,0,0,1,0,#7.113,1,0,0,0,0,1,0,0,0,0,1,0,#7.114,1,0,0,0,0,1,0,0,0,0,1,0,#7.115,1,0,0,0,0,1,0,0,0,0,1,0,#7.116,1,0,0,0,0,1,0,0,0,0,1,0,#7.117,1,0,0,0,0,1,0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> hide #12 models > save /Users/ConstantinePetridis/Desktop/BV_FE_AC104density.png width 3000 > height 1873 supersample 4 Alignment identifier is 1 Alignment identifier is 2 Alignment identifier is 3 Alignment identifier is 4 Alignment identifier is 5 Alignment identifier is 6 Alignment identifier is 7 Populating font family aliases took 157 ms. Replace uses of missing font family ""Times"" with one that exists to avoid this cost. > hide #!5 models > show #!5 models > view name AC104 > view matrix camera > 0.25887,0.036214,-0.96523,-403.96,-0.96583,-0.0028951,-0.25914,268.43,-0.012179,0.99934,0.034228,563.34 > view name AC104 > save /Users/ConstantinePetridis/Desktop/AcMNPV_Caps.cxs includeMaps true > show #12 models > hide #!5 models > show #!5 models > color #10 #f34d8fff > select add #12 616857 atoms, 623453 bonds, 307 pseudobonds, 38108 residues, 4 models selected > rainbow sel > select clear > view name AC104 > view matrix camera > 0.25887,0.036214,-0.96523,-403.96,-0.96583,-0.0028951,-0.25914,268.43,-0.012179,0.99934,0.034228,563.34 > view name AC104 > save /Users/ConstantinePetridis/Desktop/BV_FE_AC104densitymissing.png width > 3000 height 1873 supersample 4 > show #8 models > show #8 cartoons > color #8 #c2cafdff > lighting gentle > lighting soft > open > /Users/ConstantinePetridis/Desktop/fold_2025_01_03_16_08_vp80x1/fold_2025_01_03_16_08_vp80x1_summary_confidences_0.json Failed opening file /Users/ConstantinePetridis/Desktop/fold_2025_01_03_16_08_vp80x1/fold_2025_01_03_16_08_vp80x1_summary_confidences_0.json: expected str, bytes or os.PathLike object, not NoneType > open > /Users/ConstantinePetridis/Desktop/fold_2025_01_03_16_08_vp80x1/fold_2025_01_03_16_08_vp80x1_summary_confidences_0.json Traceback (most recent call last): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/ui/graphics.py"", line 54, in event if self.handle_drag_and_drop(event): ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/ui/graphics.py"", line 124, in handle_drag_and_drop mw.dropEvent(event) File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/ui/gui.py"", line 697, in dropEvent _open_dropped_file(self.session, p) File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/ui/gui.py"", line 2075, in _open_dropped_file run(session, 'open %s' % FileNameArg.unparse(path)) File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/commands/run.py"", line 49, in run results = command.run(text, log=log, return_json=return_json) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/commands/cli.py"", line 3213, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/open_command/cmd.py"", line 131, in cmd_open models = Command(session, registry=registry).run(provider_cmd_text, log=log)[0] ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/commands/cli.py"", line 3213, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/open_command/cmd.py"", line 213, in provider_open models, status = collated_open(session, None, [data], data_format, _add_models, ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/open_command/cmd.py"", line 513, in collated_open return remember_data_format() ^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/open_command/cmd.py"", line 484, in remember_data_format models, status = func(*func_args, **func_kw) ^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/alphafold/__init__.py"", line 129, in open structs = [m for m in session.models.list(type = AtomicStructure) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/alphafold/__init__.py"", line 130, in if hasattr(m, 'filename') and dirname(m.filename) == dirname(path)] ^^^^^^^^^^^^^^^^^^^ File """", line 152, in dirname TypeError: expected str, bytes or os.PathLike object, not NoneType TypeError: expected str, bytes or os.PathLike object, not NoneType File """", line 152, in dirname See log for complete Python traceback. > ui tool show ""Render/Select by Attribute"" > open > /Users/ConstantinePetridis/Desktop/fold_2025_01_03_16_08_vp80x1/fold_2025_01_03_16_08_vp80x1_full_data_0.json Traceback (most recent call last): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/ui/graphics.py"", line 54, in event if self.handle_drag_and_drop(event): ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/ui/graphics.py"", line 124, in handle_drag_and_drop mw.dropEvent(event) File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/ui/gui.py"", line 697, in dropEvent _open_dropped_file(self.session, p) File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/ui/gui.py"", line 2075, in _open_dropped_file run(session, 'open %s' % FileNameArg.unparse(path)) File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/commands/run.py"", line 49, in run results = command.run(text, log=log, return_json=return_json) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/commands/cli.py"", line 3213, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/open_command/cmd.py"", line 131, in cmd_open models = Command(session, registry=registry).run(provider_cmd_text, log=log)[0] ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/commands/cli.py"", line 3213, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/open_command/cmd.py"", line 213, in provider_open models, status = collated_open(session, None, [data], data_format, _add_models, ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/open_command/cmd.py"", line 513, in collated_open return remember_data_format() ^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/open_command/cmd.py"", line 484, in remember_data_format models, status = func(*func_args, **func_kw) ^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/alphafold/__init__.py"", line 129, in open structs = [m for m in session.models.list(type = AtomicStructure) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/alphafold/__init__.py"", line 130, in if hasattr(m, 'filename') and dirname(m.filename) == dirname(path)] ^^^^^^^^^^^^^^^^^^^ File """", line 152, in dirname TypeError: expected str, bytes or os.PathLike object, not NoneType TypeError: expected str, bytes or os.PathLike object, not NoneType File """", line 152, in dirname See log for complete Python traceback. > colorConfidence #8 Unknown command: colorConfidence #8 > open > /Users/ConstantinePetridis/Downloads/fold_2025_01_03_18_42_vp80x1_60_200/fold_2025_01_03_18_42_vp80x1_60_200_summary_confidences_4.json Failed opening file /Users/ConstantinePetridis/Downloads/fold_2025_01_03_18_42_vp80x1_60_200/fold_2025_01_03_18_42_vp80x1_60_200_summary_confidences_4.json: expected str, bytes or os.PathLike object, not NoneType > save /Users/ConstantinePetridis/Desktop/AcMNPV_Caps.cxs includeMaps true > view name AC104 > view matrix camera > 0.25887,0.036214,-0.96523,-403.96,-0.96583,-0.0028951,-0.25914,268.43,-0.012179,0.99934,0.034228,563.34 > view name AC104 [Repeated 1 time(s)] > view matrix camera > 0.25887,0.036214,-0.96523,-403.96,-0.96583,-0.0028951,-0.25914,268.43,-0.012179,0.99934,0.034228,563.34 > view name AC104 > hide #!10 models > show #!10 models > rainbow #8,12#!10 > hide #12 models > show #12 models > hide #12 models > show #11 models > hide #11 models > show #11 models > hide #11 models > show #9 models > close #9 > close #11 > show #12 models > hide #12 models > hide #!10 models > show #!10 models > hide #8 models > show #8 models > hide #8 models > show #8 models > hide #8 models > show #8 models > hide #8 models > show #8 models > hide #8 models > show #8 models > hide #8 models > show #8 models > hide #8 models > show #!7 models > show #12 models > hide #12 models > hide #!7 models > show #8 models > hide #8 models > combine #8 > select #8/A:1-50 383 atoms, 382 bonds, 50 residues, 1 model selected > show #8 models > show #12 models > hide #12 models > select ~sel & ##selected 5226 atoms, 5316 bonds, 641 residues, 1 model selected > hide sel cartoons > hide #!10 models > show #!10 models > hide #8 models > show #8 models > select add #8 5609 atoms, 5698 bonds, 691 residues, 1 model selected > select subtract #8 Nothing selected > hide #!10 models > show #!10 models > hide #9 models > show #12 models > hide #12 models > select add #8 5609 atoms, 5698 bonds, 691 residues, 1 model selected > show #12 models > rainbow sel > select subtract #8 Nothing selected > select add #8 5609 atoms, 5698 bonds, 691 residues, 1 model selected > select #8/A:1-50 383 atoms, 382 bonds, 50 residues, 1 model selected > rainbow sel > ui mousemode right ""translate selected models"" > view matrix models > #8,0.4645,-0.88458,0.041929,597.01,0.73537,0.41167,0.5383,442.19,-0.49342,-0.21921,0.84171,528.35 > view matrix models > #8,0.4645,-0.88458,0.041929,479.42,0.73537,0.41167,0.5383,379.58,-0.49342,-0.21921,0.84171,462.17 > view matrix models > #8,0.4645,-0.88458,0.041929,330.83,0.73537,0.41167,0.5383,581.7,-0.49342,-0.21921,0.84171,553.5 > view matrix models > #8,0.4645,-0.88458,0.041929,330.7,0.73537,0.41167,0.5383,405.56,-0.49342,-0.21921,0.84171,598.46 > save /Users/ConstantinePetridis/Desktop/AcMNPV_Caps.cxs includeMaps true > view matrix models > #8,0.4645,-0.88458,0.041929,345.09,0.73537,0.41167,0.5383,441.25,-0.49342,-0.21921,0.84171,600.5 > ui mousemode right ""rotate selected models"" > view matrix models > #8,0.073912,-0.64111,-0.76389,361.14,0.94556,-0.19838,0.25798,468.77,-0.31693,-0.74137,0.59154,624.36 > view matrix models > #8,-0.76704,0.44957,0.45775,303.09,-0.41714,0.19264,-0.88819,503.94,-0.48749,-0.87222,0.039769,645.64 > show #!2 models > hide #!2 models > show #!7 models > hide sel surfaces [Repeated 1 time(s)] > select add #7 625447 atoms, 632122 bonds, 308 pseudobonds, 38506 residues, 4 models selected > hide sel surfaces > select subtract #7 383 atoms, 382 bonds, 50 residues, 145 models selected > info #7 147 models #7, copy of combination, shown 625064 atoms, 631740 bonds, 38456 residues, 144 chains (A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,V,W,X,Y,Z,a,b,c,d,e,f,g,h,i,j,k,U,l,m,n,o,p,q,r,s,t,u,v,w,x,y,z,1,2,3,4,5,6,7,8,9,0,AA,AB,AC,AD,AE,AF,AG,AH,AI,AJ,AU,Af,Ag,Ah,Ai,Aj,Ak,Al,Am,An,Ao,Ap,Aq,Ar,As,At,Au,Av,Aw,Ax,Az,A1,A2,A3,A4,A5,A6,A7,A8,A9,A0,BA,BB,BC,BD,BE,Ay,BF,BG,BH,BI,BJ,BK,BL,BM,BN,BO,BP,BQ,BR,BS,BT,AL,AM,AN,AO,AP,AQ,AR,AS,AT,AK,AV,AW,AX,AY,AZ,Aa,Ab,Ac,Ad,Ae) 180 metal coordination bonds, 128 missing structure #7.1, metal coordination bonds, shown, 180 pseudobonds #7.2, missing structure, shown, 128 pseudobonds #7.3, copy of combination_0 SES surface, shown, 441042 triangles #7.4, copy of combination_1 SES surface, shown, 301274 triangles #7.5, copy of combination_2 SES surface, shown, 383162 triangles #7.6, copy of combination_3 SES surface, shown, 378278 triangles #7.7, copy of combination_4 SES surface, shown, 380646 triangles #7.8, copy of combination_5 SES surface, shown, 394392 triangles #7.9, copy of combination_6 SES surface, shown, 402638 triangles #7.10, copy of combination_7 SES surface, shown, 428132 triangles #7.11, copy of combination_8 SES surface, shown, 432104 triangles #7.12, copy of combination_9 SES surface, shown, 421392 triangles #7.13, copy of combination_A SES surface, shown, 394406 triangles #7.14, copy of combination_A0 SES surface, shown, 414598 triangles #7.15, copy of combination_A1 SES surface, shown, 403638 triangles #7.16, copy of combination_A2 SES surface, shown, 427114 triangles #7.17, copy of combination_A3 SES surface, shown, 430666 triangles #7.18, copy of combination_A4 SES surface, shown, 421538 triangles #7.19, copy of combination_A5 SES surface, shown, 442202 triangles #7.20, copy of combination_A6 SES surface, shown, 339168 triangles #7.21, copy of combination_A7 SES surface, shown, 326894 triangles #7.22, copy of combination_A8 SES surface, shown, 339632 triangles #7.23, copy of combination_A9 SES surface, shown, 336968 triangles #7.24, copy of combination_AA SES surface, shown, 336818 triangles #7.25, copy of combination_AB SES surface, shown, 326798 triangles #7.26, copy of combination_AC SES surface, shown, 340796 triangles #7.27, copy of combination_AD SES surface, shown, 336220 triangles #7.28, copy of combination_AE SES surface, shown, 416230 triangles #7.29, copy of combination_AF SES surface, shown, 397872 triangles #7.30, copy of combination_AG SES surface, shown, 399022 triangles #7.31, copy of combination_AH SES surface, shown, 552932 triangles #7.32, copy of combination_AI SES surface, shown, 688910 triangles #7.33, copy of combination_AJ SES surface, shown, 441388 triangles #7.34, copy of combination_AK SES surface, shown, 437792 triangles #7.35, copy of combination_AL SES surface, shown, 301700 triangles #7.36, copy of combination_AM SES surface, shown, 384260 triangles #7.37, copy of combination_AN SES surface, shown, 379014 triangles #7.38, copy of combination_AO SES surface, shown, 381682 triangles #7.39, copy of combination_AP SES surface, shown, 394636 triangles #7.40, copy of combination_AQ SES surface, shown, 404790 triangles #7.41, copy of combination_AR SES surface, shown, 426260 triangles #7.42, copy of combination_AS SES surface, shown, 432524 triangles #7.43, copy of combination_AT SES surface, shown, 422334 triangles #7.44, copy of combination_AU SES surface, shown, 395262 triangles #7.45, copy of combination_AV SES surface, shown, 338364 triangles #7.46, copy of combination_AW SES surface, shown, 327684 triangles #7.47, copy of combination_AX SES surface, shown, 341268 triangles #7.48, copy of combination_AY SES surface, shown, 335382 triangles #7.49, copy of combination_AZ SES surface, shown, 416356 triangles #7.50, copy of combination_Aa SES surface, shown, 398232 triangles #7.51, copy of combination_Ab SES surface, shown, 398654 triangles #7.52, copy of combination_Ac SES surface, shown, 556970 triangles #7.53, copy of combination_Ad SES surface, shown, 685808 triangles #7.54, copy of combination_Ae SES surface, shown, 441266 triangles #7.55, copy of combination_Af SES surface, shown, 402464 triangles #7.56, copy of combination_Ag SES surface, shown, 423734 triangles #7.57, copy of combination_Ah SES surface, shown, 437526 triangles #7.58, copy of combination_Ai SES surface, shown, 421098 triangles #7.59, copy of combination_Aj SES surface, shown, 431524 triangles #7.60, copy of combination_Ak SES surface, shown, 336818 triangles #7.61, copy of combination_Al SES surface, shown, 334900 triangles #7.62, copy of combination_Am SES surface, shown, 338522 triangles #7.63, copy of combination_An SES surface, shown, 337260 triangles #7.64, copy of combination_Ao SES surface, shown, 408020 triangles #7.65, copy of combination_Ap SES surface, shown, 395562 triangles #7.66, copy of combination_Aq SES surface, shown, 407482 triangles #7.67, copy of combination_Ar SES surface, shown, 564248 triangles #7.68, copy of combination_As SES surface, shown, 695322 triangles #7.69, copy of combination_At SES surface, shown, 445872 triangles #7.70, copy of combination_Au SES surface, shown, 300236 triangles #7.71, copy of combination_Av SES surface, shown, 382412 triangles #7.72, copy of combination_Aw SES surface, shown, 379678 triangles #7.73, copy of combination_Ax SES surface, shown, 380742 triangles #7.74, copy of combination_Ay SES surface, shown, 394856 triangles #7.75, copy of combination_Az SES surface, shown, 393592 triangles #7.76, copy of combination_B SES surface, shown, 403756 triangles #7.77, copy of combination_BA SES surface, shown, 398538 triangles #7.78, copy of combination_BB SES surface, shown, 399466 triangles #7.79, copy of combination_BC SES surface, shown, 553302 triangles #7.80, copy of combination_BD SES surface, shown, 688636 triangles #7.81, copy of combination_BE SES surface, shown, 441754 triangles #7.82, copy of combination_BF SES surface, shown, 403834 triangles #7.83, copy of combination_BG SES surface, shown, 423790 triangles #7.84, copy of combination_BH SES surface, shown, 436268 triangles #7.85, copy of combination_BI SES surface, shown, 417754 triangles #7.86, copy of combination_BJ SES surface, shown, 432254 triangles #7.87, copy of combination_BK SES surface, shown, 337312 triangles #7.88, copy of combination_BL SES surface, shown, 334872 triangles #7.89, copy of combination_BM SES surface, shown, 338280 triangles #7.90, copy of combination_BN SES surface, shown, 335276 triangles #7.91, copy of combination_BO SES surface, shown, 405282 triangles #7.92, copy of combination_BP SES surface, shown, 395888 triangles #7.93, copy of combination_BQ SES surface, shown, 407044 triangles #7.94, copy of combination_BR SES surface, shown, 563834 triangles #7.95, copy of combination_BS SES surface, shown, 694784 triangles #7.96, copy of combination_BT SES surface, shown, 448270 triangles #7.97, copy of combination_C SES surface, shown, 422870 triangles #7.98, copy of combination_D SES surface, shown, 436998 triangles #7.99, copy of combination_E SES surface, shown, 422306 triangles #7.100, copy of combination_F SES surface, shown, 430806 triangles #7.101, copy of combination_G SES surface, shown, 335592 triangles #7.102, copy of combination_H SES surface, shown, 333562 triangles #7.103, copy of combination_I SES surface, shown, 340406 triangles #7.104, copy of combination_J SES surface, shown, 335494 triangles #7.105, copy of combination_K SES surface, shown, 406364 triangles #7.106, copy of combination_L SES surface, shown, 395280 triangles #7.107, copy of combination_M SES surface, shown, 408874 triangles #7.108, copy of combination_N SES surface, shown, 563488 triangles #7.109, copy of combination_O SES surface, shown, 695856 triangles #7.110, copy of combination_P SES surface, shown, 447202 triangles #7.111, copy of combination_Q SES surface, shown, 302488 triangles #7.112, copy of combination_R SES surface, shown, 382574 triangles #7.113, copy of combination_S SES surface, shown, 379040 triangles #7.114, copy of combination_T SES surface, shown, 381940 triangles #7.115, copy of combination_U SES surface, shown, 395870 triangles #7.116, copy of combination_V SES surface, shown, 393816 triangles #7.117, copy of combination_W SES surface, shown, 402682 triangles #7.118, copy of combination_X SES surface, shown, 428078 triangles #7.119, copy of combination_Y SES surface, shown, 432120 triangles #7.120, copy of combination_Z SES surface, shown, 422002 triangles #7.121, copy of combination_a SES surface, shown, 440468 triangles #7.122, copy of combination_b SES surface, shown, 337778 triangles #7.123, copy of combination_c SES surface, shown, 326636 triangles #7.124, copy of combination_d SES surface, shown, 340196 triangles #7.125, copy of combination_e SES surface, shown, 335754 triangles #7.126, copy of combination_f SES surface, shown, 416262 triangles #7.127, copy of combination_g SES surface, shown, 397890 triangles #7.128, copy of combination_h SES surface, shown, 400350 triangles #7.129, copy of combination_i SES surface, shown, 556078 triangles #7.130, copy of combination_j SES surface, shown, 686334 triangles #7.131, copy of combination_k SES surface, shown, 443078 triangles #7.132, copy of combination_l SES surface, shown, 402376 triangles #7.133, copy of combination_m SES surface, shown, 424388 triangles #7.134, copy of combination_n SES surface, shown, 438008 triangles #7.135, copy of combination_o SES surface, shown, 420850 triangles #7.136, copy of combination_p SES surface, shown, 429698 triangles #7.137, copy of combination_q SES surface, shown, 337644 triangles #7.138, copy of combination_r SES surface, shown, 333252 triangles #7.139, copy of combination_s SES surface, shown, 340104 triangles #7.140, copy of combination_t SES surface, shown, 335536 triangles #7.141, copy of combination_u SES surface, shown, 406656 triangles #7.142, copy of combination_v SES surface, shown, 395108 triangles #7.143, copy of combination_w SES surface, shown, 408752 triangles #7.144, copy of combination_x SES surface, shown, 563796 triangles #7.145, copy of combination_y SES surface, shown, 693396 triangles #7.146, copy of combination_z SES surface, shown, 449318 triangles > info #7/J 1 models #7, copy of combination, shown 625064 atoms, 631740 bonds, 38456 residues, 144 chains (A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,V,W,X,Y,Z,a,b,c,d,e,f,g,h,i,j,k,U,l,m,n,o,p,q,r,s,t,u,v,w,x,y,z,1,2,3,4,5,6,7,8,9,0,AA,AB,AC,AD,AE,AF,AG,AH,AI,AJ,AU,Af,Ag,Ah,Ai,Aj,Ak,Al,Am,An,Ao,Ap,Aq,Ar,As,At,Au,Av,Aw,Ax,Az,A1,A2,A3,A4,A5,A6,A7,A8,A9,A0,BA,BB,BC,BD,BE,Ay,BF,BG,BH,BI,BJ,BK,BL,BM,BN,BO,BP,BQ,BR,BS,BT,AL,AM,AN,AO,AP,AQ,AR,AS,AT,AK,AV,AW,AX,AY,AZ,Aa,Ab,Ac,Ad,Ae) 180 metal coordination bonds, 128 missing structure > open 8VWI Summary of feedback from opening 8VWI fetched from pdb --- warnings | Atom H1 is not in the residue template for MET /N:1 Atom H1 is not in the residue template for MET /i:1 8vwi title: The base complex of the AcMNPV baculovirus nucleocapsid (Class 1, localised reconstruction) [more info...] Chain information for 8vwi #11 --- Chain | Description | UniProt A B C D E F V W X Y Z a | Major capsid protein | MCP_NPVAC 1-347 G H I b c d | Capsid-associated protein VP80 | VP80_NPVAC 1-691 J M Q S e h | Occlusion-derived virus envelope protein E27 | E27_NPVAC 1-290 K L R T f g | Protein C42 | C42_NPVAC 1-361 N i | Protein AC109 | AC109_NPVAC 1-390 O j | Protein AC142 | AC142_NPVAC 1-477 P k | 38K (AC98) protein in P143-LEF5 intergenic region | 38K_NPVAC 1-320 Non-standard residues in 8vwi #11 --- ZN — zinc ion > hide #!5 models > show #!5 models > open 8VWJ Summary of feedback from opening 8VWJ fetched from pdb --- warnings | Atom H1 is not in the residue template for MET /N:1 Atom H1 is not in the residue template for MET /i:1 note | Fetching compressed mmCIF 8vwj from http://files.rcsb.org/download/8vwj.cif 8vwj title: The base complex of the AcMNPV baculovirus nucleocapsid (Class 2, localised reconstruction) [more info...] Chain information for 8vwj #13 --- Chain | Description | UniProt A B C D E F V W X Y Z a | Major capsid protein | MCP_NPVAC 1-347 G H I b c d | Capsid-associated protein VP80 | VP80_NPVAC 1-691 J M Q S e h | Occlusion-derived virus envelope protein E27 | E27_NPVAC 1-290 K L R T f g | Protein C42 | C42_NPVAC 1-361 N i | Protein AC109 | AC109_NPVAC 1-390 O j | Protein AC142 | AC142_NPVAC 1-477 P k | 38K (AC98) | 38K_NPVAC 1-320 Non-standard residues in 8vwj #13 --- ZN — zinc ion > color #11 #c1153cff > color #13 #d2d2d3ff > select add #8 5609 atoms, 5698 bonds, 691 residues, 1 model selected > select subtract #8 Nothing selected > select add #13 156295 atoms, 157964 bonds, 79 pseudobonds, 9616 residues, 3 models selected > select add #11 312561 atoms, 315899 bonds, 156 pseudobonds, 19230 residues, 6 models selected > hide sel surfaces > show sel cartoons > hide sel surfaces > select subtract #11 156295 atoms, 157964 bonds, 79 pseudobonds, 9616 residues, 3 models selected > select add #11 312561 atoms, 315899 bonds, 156 pseudobonds, 19230 residues, 6 models selected > select subtract #11 156295 atoms, 157964 bonds, 79 pseudobonds, 9616 residues, 3 models selected > hide sel surfaces > hide #11,13 surfaces > select add #11 312561 atoms, 315899 bonds, 156 pseudobonds, 19230 residues, 6 models selected > hide #!11 models > show #!11 models > hide #!13 models > show #!13 models > hide #!13 models > show #!13 models > hide sel atoms > select clear > close #11 > close #13 > hide #!7 models > select add #8 5609 atoms, 5698 bonds, 691 residues, 1 model selected > view matrix models > #8,0.083188,0.40998,0.90829,279.15,0.11175,0.90186,-0.41732,454.97,-0.99025,0.13622,0.029207,614.06 > view matrix models > #8,0.81284,-0.03746,0.58129,292.11,0.10848,0.99021,-0.087881,443.7,-0.5723,0.13449,0.80894,588.4 > ui mousemode right ""translate selected models"" > view matrix models > #8,0.81284,-0.03746,0.58129,287.17,0.10848,0.99021,-0.087881,444.62,-0.5723,0.13449,0.80894,589.41 > view matrix models > #8,0.81284,-0.03746,0.58129,290.91,0.10848,0.99021,-0.087881,447.96,-0.5723,0.13449,0.80894,591.44 > view matrix models > #8,0.81284,-0.03746,0.58129,290.58,0.10848,0.99021,-0.087881,446.43,-0.5723,0.13449,0.80894,590.62 > view matrix models > #8,0.81284,-0.03746,0.58129,288.8,0.10848,0.99021,-0.087881,445.64,-0.5723,0.13449,0.80894,592.11 > view matrix models > #8,0.81284,-0.03746,0.58129,291.27,0.10848,0.99021,-0.087881,443.3,-0.5723,0.13449,0.80894,589.38 > view matrix models > #8,0.81284,-0.03746,0.58129,293.55,0.10848,0.99021,-0.087881,444.6,-0.5723,0.13449,0.80894,588.43 > view matrix models > #8,0.81284,-0.03746,0.58129,291.25,0.10848,0.99021,-0.087881,443.24,-0.5723,0.13449,0.80894,591.17 > view matrix models > #8,0.81284,-0.03746,0.58129,291.17,0.10848,0.99021,-0.087881,444.94,-0.5723,0.13449,0.80894,595.63 > view matrix models > #8,0.81284,-0.03746,0.58129,289.09,0.10848,0.99021,-0.087881,446.3,-0.5723,0.13449,0.80894,593.55 > ui mousemode right ""rotate selected models"" > view matrix models > #8,0.6871,-0.71532,0.12731,329.33,0.71566,0.63609,-0.28847,454.66,0.12537,0.28932,0.94899,571.77 > view matrix models > #8,0.00053363,-0.96751,-0.25284,360.51,0.54193,0.21277,-0.81304,487.15,0.84042,-0.13659,0.52444,586.42 > view matrix models > #8,-0.30516,-0.91798,-0.25335,363.88,0.4295,0.10477,-0.89697,495.45,0.84995,-0.38253,0.3623,600 > view matrix models > #8,-0.24893,-0.93213,-0.26299,363.7,0.488,0.11384,-0.86539,493.31,0.8366,-0.34376,0.42654,597.15 > view matrix models > #8,-0.19214,-0.94383,-0.26883,363.31,0.54111,0.12664,-0.83136,491.06,0.81871,-0.3052,0.48638,594.5 > view matrix models > #8,-0.20671,-0.86948,-0.44863,364.81,0.58605,0.25714,-0.76839,483.53,0.78347,-0.42175,0.4564,600.52 > ui mousemode right ""translate selected models"" > view matrix models > #8,-0.20671,-0.86948,-0.44863,366.25,0.58605,0.25714,-0.76839,484.43,0.78347,-0.42175,0.4564,603.16 > ui mousemode right ""rotate selected models"" > view matrix models > #8,-0.11267,-0.88882,-0.4442,365.28,0.61651,0.28806,-0.73276,481.81,0.77925,-0.35641,0.5155,599.2 > view matrix models > #8,-0.060239,-0.89886,-0.43408,364.53,0.62854,0.30367,-0.71605,480.58,0.77544,-0.31597,0.54667,596.9 > view matrix models > #8,0.012777,-0.83467,-0.5506,363.41,0.45111,0.49624,-0.74179,476.53,0.89238,-0.23891,0.38287,595.61 > ui mousemode right ""translate selected models"" > view matrix models > #8,0.012777,-0.83467,-0.5506,361.51,0.45111,0.49624,-0.74179,474.78,0.89238,-0.23891,0.38287,594.64 > select add #12 7883 atoms, 8000 bonds, 971 residues, 2 models selected > combine #8, 12 Remapping chain ID 'A' in combination #12 to 'C' > select subtract #8 2274 atoms, 2302 bonds, 280 residues, 1 model selected > hide #8 models > select subtract #12 Nothing selected > hide #12 models > hide #11 models > show #11 models > hide #11 models > show #11 models > rainbow #11#!10 > view matrix models > #8,0.4645,-0.88458,0.041929,597.01,0.73537,0.41167,0.5383,442.19,-0.49342,-0.21921,0.84171,528.35 > ""view matrix"" Unknown command: ""view matrix"" > view matrix camera > 0.25887,0.036214,-0.96523,-403.96,-0.96583,-0.0028951,-0.25914,268.43,-0.012179,0.99934,0.034228,563.34 > view name AC104 > save /Users/ConstantinePetridis/Desktop/AcMNPV_Caps.cxs includeMaps true ——— End of log from Sat Jan 4 03:05:47 2025 ——— opened ChimeraX session > hide #11 models > show #11 models > hide #!10 models > show #!10 models > color #10 #c1153cff > save /Users/ConstantinePetridis/Desktop/BV_FE_AC104densitymissing.png width > 3000 height 1873 supersample 4 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: 31 days, 14 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: XV272U V3: Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition) UI Looks like: 2560 x 1440 @ 180.00Hz Main Display: Yes 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