id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 14606 Qt fatal error: Failed to initialize graphics backend for OpenGL ea2941@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-13.0.1-arm64-arm-64bit ChimeraX Version: 1.8.dev202402080317 (2024-02-08 03:17:03 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. Qt fatal error: Failed to initialize graphics backend for OpenGL. Fatal Python error: Aborted Current thread 0x00000001e420e500 (most recent call first): File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 864 in rapid_access_shown File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 199 in build File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 722 in init File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1069 in File """", line 88 in _run_code File """", line 198 in _run_module_as_main Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtWebChannel, PyQt6.QtNetwork, PyQt6.QtWebEngineCore, PyQt6.QtPrintSupport, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, chimerax.surface._surface, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.pdb_lib._load_libs, chimerax.core._mac_util (total: 45) 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""base"" : 6584516608, ""size"" : 3403612160, ""uuid"" : ""2d053604-1cb6-3821-a8df-360eb2eb519b"" }, ""vmSummary"" : ""ReadOnly portion of Libraries: Total=1.5G resident=0K(0%) swapped_out_or_unallocated=1.5G(100%)\nWritable regions: Total=1.8G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=1.8G(100%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nActivity Tracing 256K 1 \nColorSync 544K 24 \nCoreGraphics 16K 1 \nFoundation 16K 1 \nKernel Alloc Once 32K 1 \nMALLOC 298.8M 59 \nMALLOC guard page 192K 10 \nMALLOC_MEDIUM (reserved) 720.0M 6 reserved VM address space (unallocated)\nMALLOC_NANO (reserved) 384.0M 1 reserved VM address space (unallocated)\nMach message 32K 2 \nSTACK GUARD 528K 33 \nStack 145.3M 34 \nStack Guard 56.0M 1 \nVM_ALLOCATE 154.2M 67 \nVM_ALLOCATE (reserved) 160.0M 3 reserved VM address space (unallocated)\n__AUTH 1815K 342 \n__AUTH_CONST 24.3M 565 \n__CTF 756 1 \n__DATA 20.5M 693 \n__DATA_CONST 36.5M 702 \n__DATA_DIRTY 1973K 224 \n__FONT_DATA 2352 1 \n__GLSLBUILTINS 5174K 1 \n__LINKEDIT 789.9M 137 \n__OBJC_CONST 4560K 307 \n__OBJC_RO 65.1M 1 \n__OBJC_RW 1981K 1 \n__TEXT 796.2M 724 \ndyld private memory 448K 3 \nmapped file 205.5M 35 \nshared memory 880K 16 \n=========== ======= ======= \nTOTAL 3.8G 3997 \nTOTAL, minus reserved VM space 2.5G 3997 \n"", ""legacyInfo"" : { ""threadTriggered"" : { ""name"" : ""CrBrowserMain"", ""queue"" : ""com.apple.main-thread"" } }, ""trialInfo"" : { ""rollouts"" : [ { ""rolloutId"" : ""60356660bbe37970735c5624"", ""factorPackIds"" : { }, ""deploymentId"" : 240000027 }, { ""rolloutId"" : ""62b4513af75dc926494899c6"", ""factorPackIds"" : { ""COREOS_ICD"" : ""62fbe3cfa9a700130f60b3ea"" }, ""deploymentId"" : 240000019 } ], ""experiments"" : [ ] } } Log: UCSF ChimeraX version: 1.8.dev202402080317 (2024-02-08) © 2016-2024 Regents of the University of California. All rights reserved. > open ""/Users/emmanuelafriyie/Documents/Cryo-EM/Cryo-EM Maps/WW4-HECT_nb > complexes/WW4-HECT_nb.C11 Complex/3.1A Map/Color maps/Recoloring of > domains/Selected color_further coloring of NLobe and CLobe/Map for > paper/orange_corniflowerblue_Forestgreen_salmon_2.cxs"" Opened cryosparc_P36_J2540_006_volume_map_sharp.mrc as #2, grid size 256,256,256, pixel 1.03, shown at level 0.087, step 1, values float32 Opened cryosparc_P36_J2540_006_volume_map_sharp.mrc as #4, grid size 256,256,256, pixel 1.03, shown at level 0.0961, step 1, values float32 Log from Sat Feb 3 20:20:01 2024UCSF ChimeraX version: 1.7rc202312120032 (2023-12-12) © 2016-2023 Regents of the University of California. All rights reserved. > open ""/Users/emmanuelafriyie/Documents/Cryo-EM/Cryo-EM Maps/WW4-HECT_nb > complexes/WW4-HECT_nb.C11 Complex/3.1A Map/Color maps/Recoloring of > domains/Selected color_further coloring of NLobe and > CLobe/orange_corniflowerblue_Forestgreen_salmon.cxs"" Opened cryosparc_P36_J2540_006_volume_map_sharp.mrc as #2, grid size 256,256,256, pixel 1.03, shown at level 0.087, step 1, values float32 Opened cryosparc_P36_J2540_006_volume_map_sharp.mrc as #4, grid size 256,256,256, pixel 1.03, shown at level 0.0961, step 1, values float32 Log from Sat Feb 3 20:12:39 2024UCSF ChimeraX version: 1.7rc202312120032 (2023-12-12) © 2016-2023 Regents of the University of California. All rights reserved. > open ""/Users/emmanuelafriyie/Documents/Cryo-EM/Cryo-EM Maps/WW4-HECT_nb > complexes/WW4-HECT_nb.C11 Complex/3.1A Map/Color maps/Recoloring of > domains/orange_corniflower_medium purple.cxs"" Opened cryosparc_P36_J2540_006_volume_map_sharp.mrc as #2, grid size 256,256,256, pixel 1.03, shown at level 0.087, step 1, values float32 Opened cryosparc_P36_J2540_006_volume_map_sharp.mrc as #4, grid size 256,256,256, pixel 1.03, shown at level 0.0961, step 1, values float32 Log from Tue Jan 30 09:08:53 2024UCSF ChimeraX version: 1.7rc202312120032 (2023-12-12) © 2016-2023 Regents of the University of California. All rights reserved. > open ""/Users/emmanuelafriyie/Documents/Cryo-EM/Cryo-EM Maps/WW4-HECT_nb > complexes/WW4-HECT_nb.C11 Complex/3.1A Map/Color maps/Recoloring of > domains/lightseagreen_corniflower_medium purple.cxs"" Opened cryosparc_P36_J2540_006_volume_map_sharp.mrc as #2, grid size 256,256,256, pixel 1.03, shown at level 0.087, step 1, values float32 Opened cryosparc_P36_J2540_006_volume_map_sharp.mrc as #4, grid size 256,256,256, pixel 1.03, shown at level 0.0961, step 1, values float32 Log from Tue Jan 30 08:55:37 2024UCSF ChimeraX version: 1.7rc202312120032 (2023-12-12) © 2016-2023 Regents of the University of California. All rights reserved. > open ""/Users/emmanuelafriyie/Documents/Cryo-EM/Cryo-EM Maps/WW4-HECT_nb > complexes/WW4-HECT_nb.C11 Complex/3.1A Map/Color maps/Recoloring of > domains/lightseagreen_peru_seagreen.cxs"" Opened cryosparc_P36_J2540_006_volume_map_sharp.mrc as #2, grid size 256,256,256, pixel 1.03, shown at level 0.087, step 1, values float32 Opened cryosparc_P36_J2540_006_volume_map_sharp.mrc as #4, grid size 256,256,256, pixel 1.03, shown at level 0.0961, step 1, values float32 Log from Mon Jan 29 22:44:44 2024UCSF ChimeraX version: 1.7rc202312120032 (2023-12-12) © 2016-2023 Regents of the University of California. All rights reserved. > open ""/Users/emmanuelafriyie/Documents/Cryo-EM/Cryo-EM Maps/WW4-HECT_nb > complexes/WW4-HECT_nb.C11 Complex/3.1A Map/Color maps/Recoloring of > domains/nb.C11_3.1_publication.cxs"" Opened cryosparc_P36_J2540_006_volume_map_sharp.mrc as #2, grid size 256,256,256, pixel 1.03, shown at level 0.087, step 1, values float32 Opened cryosparc_P36_J2540_006_volume_map_sharp.mrc as #4, grid size 256,256,256, pixel 1.03, shown at level 0.0961, step 1, values float32 Log from Mon Jan 29 22:27:59 2024UCSF ChimeraX version: 1.7rc202312120032 (2023-12-12) © 2016-2023 Regents of the University of California. All rights reserved. > open ""/Users/emmanuelafriyie/Documents/Cryo-EM/Cryo-EM Maps/WW4-HECT_nb > complexes/WW4-HECT_nb.C11 Complex/3.1A Map/Color maps/Cyan_colored.cxs"" Opened cryosparc_P36_J2540_006_volume_map_sharp.mrc as #2, grid size 256,256,256, pixel 1.03, shown at level 0.087, step 1, values float32 Opened cryosparc_P36_J2540_006_volume_map_sharp.mrc as #4, grid size 256,256,256, pixel 1.03, shown at level 0.0961, step 1, values float32 Log from Mon Jan 15 14:08:09 2024UCSF ChimeraX version: 1.7rc202312120032 (2023-12-12) © 2016-2023 Regents of the University of California. All rights reserved. > open ""/Users/emmanuelafriyie/Documents/Cryo-EM/Cryo-EM Maps/WW4-HECT_nb > complexes/WW4-HECT_nb.C11 Complex/3.1A Map/Color maps/3.1A map_colored > domains_soft_surface_updated_WW4_1.cxs"" Opened cryosparc_P36_J2540_006_volume_map_sharp.mrc as #2, grid size 256,256,256, pixel 1.03, shown at level 0.087, step 1, values float32 Opened cryosparc_P36_J2540_006_volume_map_sharp.mrc as #4, grid size 256,256,256, pixel 1.03, shown at level 0.0961, step 1, values float32 Log from Sat Jan 13 20:04:54 2024 > alias hid hide $1 models > alias sho show $1 models > camera ortho UCSF ChimeraX version: 1.7rc202312120032 (2023-12-12) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open ""/Users/emmanuelafriyie/Documents/Cryo-EM/Cryo-EM Maps/WW4-HECT_nb > complexes/WW4-HECT_nb.C11 Complex/3.1A Map/combine_C11_3.1A-coot-0_INC4.pdb"" Chain information for combine_C11_3.1A-coot-0_INC4.pdb #1 --- Chain | Description A | No description available B | No description available > open ""/Users/emmanuelafriyie/Documents/Cryo-EM/Cryo-EM Maps/WW4-HECT_nb > complexes/WW4-HECT_nb.C11 Complex/3.1A > Map/cryosparc_P36_J2540_006_volume_map_sharp.mrc"" Opened cryosparc_P36_J2540_006_volume_map_sharp.mrc as #2, grid size 256,256,256, pixel 1.03, shown at level 0.0253, step 1, values float32 > volume #2 level 0.1345 > ui tool show ""Hide Dust"" > surface dust #2 size 6.16 > show surfaces [Repeated 1 time(s)] > hide surfaces > open ""/Users/emmanuelafriyie/Documents/Cryo-EM/Cryo-EM Maps/WW4-HECT_nb > complexes/WW4-HECT_nb.C11 Complex/3.1A > Map/combine_C11_3.1A-coot-0_adjusted.pdb"" Chain information for combine_C11_3.1A-coot-0_adjusted.pdb #3 --- Chain | Description A | No description available B | No description available > ui tool show ""Model Panel"" > hide #!1 models > volume #2 level 0.08698 > volume #2 level 0.07509 > ui tool show ""Hide Dust"" > surface dust #2 size 1.03 [Repeated 1 time(s)] > ui tool show ""Hide Dust"" > surface dust #2 size 1.03 [Repeated 1 time(s)] > volume #2 level 0.08698 > ui tool show ""Hide Dust"" > surface dust #2 size 1.03 > surface dust #2 size 1.13 > surface dust #2 size 1.03 > surface dust #2 size 6.73 [Repeated 1 time(s)] > open ""/Users/emmanuelafriyie/Documents/Cryo-EM/Cryo-EM Maps/WW4-HECT_nb > complexes/WW4-HECT_nb.C11 Complex/3.1A > Map/cryosparc_P36_J2540_006_volume_map_sharp.mrc"" Opened cryosparc_P36_J2540_006_volume_map_sharp.mrc as #4, grid size 256,256,256, pixel 1.03, shown at level 0.0253, step 1, values float32 > volume #4 level 0.08167 > hide #!3 models > hide #!2 models > show #!3 models > show #!1 models > ui tool show ""Hide Dust"" > surface dust #4 size 6.16 Color zone shortcut requires 1 displayed atomic model and 1 map, got 2 atomic models, 1 maps. [Repeated 1 time(s)] > hide #!3 models > hide #!1 models > show #!1 models > show #!3 models > hide #!1 models > hide #!3 models > show #!1 models > hide #!4 models > show #!1 surfaces > transparency #1 70 > select #1/A 950 atoms, 972 bonds, 122 residues, 1 model selected > color (#!1 & sel) red > undo > show #!4 models > hide #!1 models > select add #1 4433 atoms, 4552 bonds, 539 residues, 2 models selected > select subtract #1 2 models selected > select #3/A 950 atoms, 972 bonds, 122 residues, 1 model selected > select add #3 4433 atoms, 4552 bonds, 539 residues, 1 model selected > select subtract #3 Nothing selected > select #3/B 3483 atoms, 3580 bonds, 417 residues, 1 model selected > ui tool show ""Color Zone"" > show #!3 models > select add #3 4433 atoms, 4552 bonds, 539 residues, 1 model selected > select subtract #3 Nothing selected > color zone #4 near #3 distance 6.16 > hide #!3 models > hide #!4 models > show #!4 models > select #4 2 models selected > select #4 2 models selected > select #4 2 models selected > select #4 2 models selected > select #4 2 models selected > select #4 2 models selected > select #4 2 models selected > select #4 2 models selected > select subtract #4 Nothing selected > select #4 2 models selected > select subtract #4 Nothing selected > show #!3 models > select #4 2 models selected > select #4 2 models selected No atoms selected for color zoning > hide #!3 models > select clear > hide #!4 models > show #!3 models > select #3/A 950 atoms, 972 bonds, 122 residues, 1 model selected > color sel orange red > select clear > select #3:514-542 253 atoms, 261 bonds, 29 residues, 1 model selected > color sel lime > select #3:468-504 313 atoms, 324 bonds, 37 residues, 1 model selected > color sel lime > select #3/A 950 atoms, 972 bonds, 122 residues, 1 model selected > select clear > select #3:543-end 2917 atoms, 2994 bonds, 351 residues, 1 model selected > color sel cyan > color sel magenta > select clear > show #!4 models > color zone #4 near #3 distance 6.16 > hide #!3 models > show #!3 models > hide #!4 models > show #!4 models > hide #!4 models > show #!4 models > save ""/Users/emmanuelafriyie/Documents/Cryo-EM/Cryo-EM Maps/WW4-HECT_nb > complexes/WW4-HECT_nb.C11 Complex/3.1A Map/New Folder/3.1A map.cxs"" [Errno 20] Not a directory: '/Users/emmanuelafriyie/Documents/Cryo-EM/Cryo-EM Maps/WW4-HECT_nb complexes/WW4-HECT_nb.C11 Complex/3.1A Map/New Folder' > save ""/Users/emmanuelafriyie/Documents/Cryo-EM/Cryo-EM Maps/WW4-HECT_nb > complexes/WW4-HECT_nb.C11 Complex/3.1A Map/Color maps/3.1A map_colored > domains.cxs"" > hide #!4 models > show #!4 models > lighting soft > volume #4 level 0.09607 > save ""/Users/emmanuelafriyie/Documents/Cryo-EM/Cryo-EM Maps/WW4-HECT_nb > complexes/WW4-HECT_nb.C11 Complex/3.1A Map/Color maps/3.1A map_colored > domains_soft_surface.cxs"" > undo > show #!4 models > lighting simple > lighting soft > hide #!4 models > select #3:514-533 181 atoms, 187 bonds, 20 residues, 1 model selected > color sel lime > select #3:534-end 2989 atoms, 3068 bonds, 360 residues, 1 model selected > color sel magenta > select add #3 4433 atoms, 4552 bonds, 539 residues, 1 model selected > select subtract #3 Nothing selected > show #!4 models > color zone #4 near #3 distance 6.16 > save ""/Users/emmanuelafriyie/Documents/Cryo-EM/Cryo-EM Maps/WW4-HECT_nb > complexes/WW4-HECT_nb.C11 Complex/3.1A Map/Color maps/3.1A map_colored > domains_soft_surface_updated_WW4.cxs"" > lighting soft [Repeated 1 time(s)] > preset ""overall look"" ""publication 1 (silhouettes)"" Using preset: Overall Look / Publication 1 (Silhouettes) > set bgColor #ffffff00 Preset expands to these ChimeraX commands: set bg white graphics silhouettes t lighting depthCue f > select add #4 2 models selected > select subtract #4 Nothing selected > undo [Repeated 3 time(s)] > hide #!4 models > show #!4 models > hide #!2 models > hide #!4 models > show #!4 models > color zone #4 near #3 distance 6.16 > combine #3 > rename #5 Coot_combine_C11_3.1A_adjusted > rename #5 Coot_combine_C11_3.1A_adjusted.pdb > hide #!3 models > hide #!4 models > save ""/Users/emmanuelafriyie/Documents/Cryo-EM/Cryo-EM Maps/WW4-HECT_nb > complexes/WW4-HECT_nb.C11 Complex/3.1A Map/Color maps/3.1A map_colored > domains_soft_surface_updated_WW4_1.cxs"" ——— End of log from Sat Jan 13 20:04:54 2024 ——— opened ChimeraX session > ui tool show ""Model Panel"" > show #!4 models > hide #!5 models > show #!5 models > hide #!4 models > select :514-42 Nothing selected > select :514-442 Nothing selected > select :514-542 759 atoms, 783 bonds, 87 residues, 3 models selected > select :468-504 939 atoms, 972 bonds, 111 residues, 3 models selected > select :468-504, 514-522 1161 atoms, 1203 bonds, 138 residues, 3 models selected > select :468-504, 514-519 1068 atoms, 1107 bonds, 129 residues, 3 models selected > select :468-504, 514-522 1161 atoms, 1203 bonds, 138 residues, 3 models selected > select :521-end 9348 atoms, 9597 bonds, 1119 residues, 3 models selected > color (#!5 & sel) magenta > select :468-504, 514-523 1188 atoms, 1230 bonds, 141 residues, 3 models selected > color (#!5 & sel) lime [Repeated 1 time(s)] > combine #5 > rename #6 ""Cyan_ Coot_combine_C11_3.1A_adjusted.pdb"" > select #6/A 950 atoms, 972 bonds, 122 residues, 1 model selected > color sel cyan > color sel light sea green > undo > select clear > show #!4 models > hide #!4 models > ui tool show ""Color Zone"" > show #!2 models > hide #!2 models > show #!2 models > color zone #2 near #6 distance 6.16 > hide #!5 models > hide #!6 models > show #!1 models > hide #!1 models > show #!6 models > hide #!2 models > select :468-504, 514-526 1704 atoms, 1764 bonds, 200 residues, 4 models selected > select :468-504, 514-525 1656 atoms, 1712 bonds, 196 residues, 4 models selected > select :468-504, 514-526 1704 atoms, 1764 bonds, 200 residues, 4 models selected > color (#!6 & sel) lime > color zone #2 near #6 distance 6.16 > show #!2 models > select add #6 5711 atoms, 5875 bonds, 689 residues, 5 models selected > hide #!6 models > select subtract #6 1278 atoms, 1323 bonds, 150 residues, 4 models selected > hide #!2 models > show #!6 models > show #!1 models > hide #!1 models > show #!2 models > color zone #2 near #6 distance 5.9 > color zone #2 near #6 distance 4.07 > color zone #2 near #6 distance 3.99 > color zone #2 near #6 distance 6.15 > hide #!6 models > color zone #2 near #6 distance 6.25 > color zone #2 near #6 distance 6.35 > color zone #2 near #6 distance 6.45 > color zone #2 near #6 distance 6.55 > color zone #2 near #6 distance 6.65 > color zone #2 near #6 distance 6.75 > color zone #2 near #6 distance 6.85 > color zone #2 near #6 distance 6.95 > color zone #2 near #6 distance 7.05 > color zone #2 near #6 distance 7.15 > color zone #2 near #6 distance 7.25 > color zone #2 near #6 distance 7.35 > color zone #2 near #6 distance 7.45 > color zone #2 near #6 distance 7.55 > color zone #2 near #6 distance 7.65 > color zone #2 near #6 distance 7.75 > color zone #2 near #6 distance 7.85 > color zone #2 near #6 distance 7.95 > color zone #2 near #6 distance 8.05 > color zone #2 near #6 distance 8 > color zone #2 near #6 distance 6 > color zone #2 near #6 distance 61 > color zone #2 near #6 distance 61.5 > color zone #2 near #6 distance 61 > color zone #2 near #6 distance 6 > color zone #2 near #6 distance 6.1 > color zone #2 near #6 distance 6.15 [Repeated 1 time(s)] > save ""/Users/emmanuelafriyie/Documents/Cryo-EM/Cryo-EM Maps/WW4-HECT_nb > complexes/WW4-HECT_nb.C11 Complex/3.1A Map/Color maps/Cyan_colored.cxs"" ——— End of log from Mon Jan 15 14:08:09 2024 ——— opened ChimeraX session > ui tool show ""Model Panel"" > select add #5 5285 atoms, 5434 bonds, 639 residues, 3 models selected > select add #3 9292 atoms, 9545 bonds, 1128 residues, 3 models selected > show #!4 models > hide #!2 models > show #!2 models > hide #!4 models > select subtract #5 4859 atoms, 4993 bonds, 589 residues, 2 models selected > select subtract #3 426 atoms, 441 bonds, 50 residues, 1 model selected > show #!6 models > show #!5 models > hide #!5 models > hide #!2 models > select :468-504, 514-526 1704 atoms, 1764 bonds, 200 residues, 4 models selected > select add #3 5711 atoms, 5875 bonds, 689 residues, 5 models selected > select add #5 9718 atoms, 9986 bonds, 1178 residues, 5 models selected > select subtract #3 5285 atoms, 5434 bonds, 639 residues, 4 models selected > select subtract #5 852 atoms, 882 bonds, 100 residues, 3 models selected > ui tool show ""Color Actions"" > color sel hot pink > undo > color sel steel blue [Repeated 1 time(s)] > ui tool show ""Color Actions"" [Repeated 2 time(s)] > color sel green > color sel lime green > select clear > select #6/a:1-end 950 atoms, 972 bonds, 122 residues, 1 model selected > select #6/a 950 atoms, 972 bonds, 122 residues, 1 model selected > color sel deep sky blue > select clear > lighting simple > select #6/b 3483 atoms, 3580 bonds, 417 residues, 1 model selected > select #6/b: 527-end 3057 atoms, 3138 bonds, 367 residues, 1 model selected > ui tool show ""Color Actions"" > color sel rosy brown > select clear > select #6/b: 527-end 3057 atoms, 3138 bonds, 367 residues, 1 model selected > ui tool show ""Color Actions"" > color sel burly wood > select clear > ui tool show ""Color Actions"" > color tan > undo > select #6/b: 527-end 3057 atoms, 3138 bonds, 367 residues, 1 model selected > ui tool show ""Color Actions"" > color sel tan > color sel burly wood > color sel wheat > undo > select clear > ui tool show ""Color Actions"" > select #6/b: 527-end 3057 atoms, 3138 bonds, 367 residues, 1 model selected > ui tool show ""Color Actions"" > color sel peru > select clear > dssp #6 > lighting soft > lighting simple > select #6/a 950 atoms, 972 bonds, 122 residues, 1 model selected > ui tool show ""Color Actions"" > color sel turquoise > select clear > undo > select clear > ui tool show ""Color Zone"" > color zone #2 near #6 distance 1.03 [Repeated 1 time(s)] > show #!2 models > hide #!6 models > hide #!2 models > show #!2 models > show #!1 models > hide #!2 models > show #!2 models > hide #!2 models > hide #!1 models > show #!2 models > hide #!2 models > show #!6 models > color single #2 > show #!2 models > color zone #2 near #6 distance 1.03 > combine #2 No structures specified > hide #!6 models > hide #!2 models > show #!2 models > show #!1 models > hide #!1 models > hide #!2 models > show #!2 models > show #!5 models > hide #!2 models > hide #!5 models > show #!6 models > combine #6 > hide #!6 models > ui tool show ""Color Actions"" > select #7/a 950 atoms, 972 bonds, 122 residues, 1 model selected > color sel turquoise [Repeated 1 time(s)] > undo > select clear > color zone #2 near #7 distance 1.03 > show #!2 models > hide #!7 models > color zone #2 near #7 distance 3.11 > color zone #2 near #7 distance 7.19 > color zone #2 near #7 distance 6.85 > color zone #2 near #7 distance 10.37 > color zone #2 near #7 distance 12.76 > show #!6 models > hide #!2 models > hide #!6 models > show #!7 models > show #!2 models > color zone #2 near #7 distance 12.51 > color zone #2 near #7 distance 5.79 > color zone #2 near #7 distance 5.51 > color zone #2 near #7 distance 7.71 > color zone #2 near #7 distance 7.41 > color zone #2 near #7 distance 10.69 > save ""/Users/emmanuelafriyie/Documents/Cryo-EM/Cryo-EM Maps/WW4-HECT_nb > complexes/WW4-HECT_nb.C11 Complex/3.1A Map/Color maps/Recoloring of > domains/nb.C11_3.1_publication.cxs"" ——— End of log from Mon Jan 29 22:27:59 2024 ——— opened ChimeraX session > select #2 2 models selected > select #2 2 models selected > select #2 2 models selected > ui tool show ""Color Zone"" > color zone #2 near #7 distance 1.03 No atoms selected for color zoning > undo > color single #2 > undo > select clear > ui tool show ""Model Panel"" > hide #!7 models > ui tool show ""Color Actions"" > select #7/a 950 atoms, 972 bonds, 122 residues, 1 model selected > select #7/a 950 atoms, 972 bonds, 122 residues, 1 model selected > show #!7 models > select add #7 4433 atoms, 4552 bonds, 539 residues, 1 model selected > select subtract #7 Nothing selected > hide #!2 models > select #7/a 950 atoms, 972 bonds, 122 residues, 1 model selected > ui tool show ""Color Actions"" > color sel light sea green > select clear > ui tool show ""Color Zone"" No atoms selected for color zoning > color zone #2 near #7 distance 1.04 > show #!2 models > color zone #2 near #7 distance 1.03 > color zone #2 near #7 distance 4.61 > color zone #2 near #7 distance 4.57 > color zone #2 near #7 distance 11.45 > save ""/Users/emmanuelafriyie/Documents/Cryo-EM/Cryo-EM Maps/WW4-HECT_nb > complexes/WW4-HECT_nb.C11 Complex/3.1A Map/Color maps/Recoloring of > domains/lightseagreen_peru_forestgreen.cxs"" > hide #!7 models > select :468-504, 514-526: Expected an objects specifier or a keyword > select #7:468-504, 514-526 426 atoms, 441 bonds, 50 residues, 1 model selected > show #!7 models > show #!3 models > hide #!2 models > hide #!3 models > ui tool show ""Color Actions"" > color sel chartreuse > color sel sea green > select clear > show #!2 models > color zone #2 near #7 distance 11.45 > save ""/Users/emmanuelafriyie/Documents/Cryo-EM/Cryo-EM Maps/WW4-HECT_nb > complexes/WW4-HECT_nb.C11 Complex/3.1A Map/Color maps/Recoloring of > domains/lightseagreen_peru_seagreen.cxs"" ——— End of log from Mon Jan 29 22:44:44 2024 ——— opened ChimeraX session > ui tool show ""Model Panel"" > hide #!7 models > hide #!2 models > show #!2 models > show #!7 models > select #7:468-504, 514-526 426 atoms, 441 bonds, 50 residues, 1 model selected > ui tool show ""Color Actions"" > color sel sea green [Repeated 3 time(s)] > hide #!7 models > select add #7 4433 atoms, 4552 bonds, 539 residues, 1 model selected > hide #!2 models > select subtract #7 Nothing selected > show #!7 models > select add #7 4433 atoms, 4552 bonds, 539 residues, 1 model selected > select subtract #7 Nothing selected > ui tool show ""Color Zone"" > color zone #2 near #7 distance 1.03 > show #!2 models > color zone #2 near #7 distance 4.22 > color zone #2 near #7 distance 4.1 > color zone #2 near #7 distance 8.77 [Repeated 1 time(s)] > save ""/Users/emmanuelafriyie/Documents/Cryo-EM/Cryo-EM Maps/WW4-HECT_nb > complexes/WW4-HECT_nb.C11 Complex/3.1A Map/Color maps/Recoloring of > domains/lightseagreen_peru_seagreen_1.cxs"" > ui tool show ""Color Actions"" > select #7/b 3483 atoms, 3580 bonds, 417 residues, 1 model selected > select #7/b:1-527 434 atoms, 449 bonds, 51 residues, 1 model selected > select #7/b:1-527 434 atoms, 449 bonds, 51 residues, 1 model selected > hide #!2 models > select clear > select #7/b:1-527 434 atoms, 449 bonds, 51 residues, 1 model selected > select #7/b:527-end 3057 atoms, 3138 bonds, 367 residues, 1 model selected > color sel thistle > show #!2 models > ui tool show ""Color Zone"" > color zone #2 near #7 distance 1.03 [Repeated 1 time(s)] > color zone #2 near #7 distance 10.17 > color zone #2 near #7 distance 10.37 > color zone #2 near #7 distance 19.33 > ui tool show ""Color Actions"" [Repeated 1 time(s)] > save ""/Users/emmanuelafriyie/Documents/Cryo-EM/Cryo-EM Maps/WW4-HECT_nb > complexes/WW4-HECT_nb.C11 Complex/3.1A Map/Color maps/Recoloring of > domains/lightseagreen_Thistle_seagreen.cxs"" > select add #7 4433 atoms, 4552 bonds, 539 residues, 1 model selected > hide #!7 models > select subtract #7 Nothing selected > hide #!2 models > show #!7 models > preset ""overall look"" ""publication 1 (silhouettes)"" Using preset: Overall Look / Publication 1 (Silhouettes) Preset expands to these ChimeraX commands: set bg white graphics silhouettes t lighting depthCue f > select #7/b:527-end 3057 atoms, 3138 bonds, 367 residues, 1 model selected > color sel rosy brown > select clear > ui tool show ""Color Zone"" > color zone #2 near #7 distance 1.03 [Repeated 1 time(s)] > show #!2 models > color zone #2 near #7 distance 4.57 > color zone #2 near #7 distance 4.43 > color zone #2 near #7 distance 5.4 > save ""/Users/emmanuelafriyie/Documents/Cryo-EM/Cryo-EM Maps/WW4-HECT_nb > complexes/WW4-HECT_nb.C11 Complex/3.1A Map/Color maps/Recoloring of > domains/lightseagreen_Rosybrown_seagreen.cxs"" > hide #!2 models > select #7/b:527-end 3057 atoms, 3138 bonds, 367 residues, 1 model selected > color sel peru > undo > color sel lightblue peru Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > color sel peru > select clear > color medium purple > undo [Repeated 1 time(s)] > select clear > select #7/b:527-end 3057 atoms, 3138 bonds, 367 residues, 1 model selected > color sel medium purple > color sel cornflower blue > select clear > ui tool show ""Color Zone"" > color zone #2 near #7 distance 1.03 [Repeated 1 time(s)] > show #!2 models > color zone #2 near #7 distance 6.33 > save ""/Users/emmanuelafriyie/Documents/Cryo-EM/Cryo-EM Maps/WW4-HECT_nb > complexes/WW4-HECT_nb.C11 Complex/3.1A Map/Color maps/Recoloring of > domains/lightseagreen_cauliflower_seagreen.cxs"" > hide #!7 models > show #!7 models > hide #!2 models > show #!2 models > select #7/b:1-526 426 atoms, 441 bonds, 50 residues, 1 model selected > ui tool show ""Color Actions"" [Repeated 1 time(s)] > color sel medium purple > hide #!2 models > show #!2 models > ui tool show ""Color Zone"" > color zone #2 near #7 distance 1.03 [Repeated 1 time(s)] > color zone #2 near #7 distance 5.04 > color zone #2 near #7 distance 4.89 > color zone #2 near #7 distance 6.39 > color zone #2 near #7 distance 6.33 > color zone #2 near #7 distance 7.86 > color zone #2 near #7 distance 8.02 > color zone #2 near #7 distance 9.3 > ui tool show ""Color Actions"" > save ""/Users/emmanuelafriyie/Documents/Cryo-EM/Cryo-EM Maps/WW4-HECT_nb > complexes/WW4-HECT_nb.C11 Complex/3.1A Map/Color maps/Recoloring of > domains/lightseagreen_corniflower_seagreen.cxs"" > save ""/Users/emmanuelafriyie/Documents/Cryo-EM/Cryo-EM Maps/WW4-HECT_nb > complexes/WW4-HECT_nb.C11 Complex/3.1A Map/Color maps/Recoloring of > domains/lightseagreen_corniflower_medium purple.cxs"" ——— End of log from Tue Jan 30 08:55:37 2024 ——— opened ChimeraX session > ui tool show ""Color Actions"" > ui tool show ""Model Panel"" > select #7/a 950 atoms, 972 bonds, 122 residues, 1 model selected > hide #!2 models > color sel orange > select clear > ui tool show ""Color Zone"" > color zone #2 near #7 distance 1.03 > show #!2 models > color zone #2 near #7 distance 1.03 > color zone #2 near #7 distance 11.33 > color zone #2 near #7 distance 11.45 > color zone #2 near #7 distance 28.42 > save ""/Users/emmanuelafriyie/Documents/Cryo-EM/Cryo-EM Maps/WW4-HECT_nb > complexes/WW4-HECT_nb.C11 Complex/3.1A Map/Color maps/Recoloring of > domains/orange_corniflower_medium purple.cxs"" ——— End of log from Tue Jan 30 09:08:53 2024 ——— opened ChimeraX session > ui tool show ""Model Panel"" > hide #!2 models > show #!2 models > hide #!2 models > 468-504, 514-520 Unknown command: 468-504, 514-520 > select #7:468-504, 514-520 367 atoms, 380 bonds, 44 residues, 1 model selected > ui tool show ""Color Actions"" > color sel salmon > select clear > select #7:521-end 3116 atoms, 3199 bonds, 373 residues, 1 model selected > color sel cornflower blue > select clear > select #7 468-504 Expected a keyword > select #7: 468-504 313 atoms, 324 bonds, 37 residues, 1 model selected > ui tool show ""Show Sequence Viewer"" > sequence chain #1/B #3/B #5/B #6/B #7/B Alignment identifier is 1 > select #7: 468-504 313 atoms, 324 bonds, 37 residues, 1 model selected > select clear > select #7: 468-504 313 atoms, 324 bonds, 37 residues, 1 model selected > select #7:514-521 63 atoms, 65 bonds, 8 residues, 1 model selected > select #7:514-520 54 atoms, 56 bonds, 7 residues, 1 model selected > show sel atoms > hide sel atoms > select #7:785-end 902 atoms, 930 bonds, 109 residues, 1 model selected > ui tool show ""Color Actions"" > color sel salmon > select clear > select #7:785-end 902 atoms, 930 bonds, 109 residues, 1 model selected > color sel forest green > select clear > select #7:468-504 313 atoms, 324 bonds, 37 residues, 1 model selected > ui tool show ""Color Actions"" > color sel salmon > select clear > select #7:514-520 54 atoms, 56 bonds, 7 residues, 1 model selected > ui tool show ""Color Actions"" > color sel cornflower blue > select clear > ui tool show ""Model Panel"" > show #!6 models > hide #!6 models > show #!2 models > ui tool show ""Model Panel"" > ui tool show ""Color Zone"" > color zone #2 near #7 distance 1.03 > ui tool show ""Model Panel"" > hide #!2 models > save ""/Users/emmanuelafriyie/Documents/Cryo-EM/Cryo-EM Maps/WW4-HECT_nb > complexes/WW4-HECT_nb.C11 Complex/3.1A Map/Color maps/Recoloring of > domains/Selected color_further coloring of NLobe and > CLobe/orange_corniflowerblue_Forestgreen_salmon.cxs"" ——— End of log from Sat Feb 3 20:12:39 2024 ——— opened ChimeraX session > ui tool show ""Color Zone"" > color zone #2 near #7 distance 1.03 [Repeated 1 time(s)] > ui tool show ""Model Panel"" > show #!2 models > color zone #2 near #7 distance 1.03 > color zone #2 near #7 distance 8.43 > save ""/Users/emmanuelafriyie/Documents/Cryo-EM/Cryo-EM Maps/WW4-HECT_nb > complexes/WW4-HECT_nb.C11 Complex/3.1A Map/Color maps/Recoloring of > domains/Selected color_further coloring of NLobe and > CLobe/orange_corniflowerblue_Forestgreen_salmon_1.cxs"" > color zone #2 near #7 distance 8.43 > ui tool show ""Model Panel"" > hide #!2 models > show #!2 models > hide #!7 models > save ""/Users/emmanuelafriyie/Documents/Cryo-EM/Cryo-EM Maps/WW4-HECT_nb > complexes/WW4-HECT_nb.C11 Complex/3.1A Map/Color maps/Recoloring of > domains/Selected color_further coloring of NLobe and > CLobe/orange_corniflowerblue_Forestgreen_salmon_2.cxs"" ——— End of log from Sat Feb 3 20:20:01 2024 ——— opened ChimeraX session OpenGL version: 4.1 Metal - 83 OpenGL renderer: Apple M1 OpenGL vendor: Apple Python: 3.11.4 Locale: UTF-8 Qt version: PyQt6 6.3.1, Qt 6.3.1 Qt runtime version: 6.3.2 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Air Model Identifier: MacBookAir10,1 Model Number: Z125000HMLL/A Chip: Apple M1 Total Number of Cores: 8 (4 performance and 4 efficiency) Memory: 16 GB System Firmware Version: 8419.41.10 OS Loader Version: 8419.41.10 Software: System Software Overview: System Version: macOS 13.0.1 (22A400) Kernel Version: Darwin 22.1.0 Time since boot: 3 minutes, 13 seconds Graphics/Displays: Apple M1: Chipset Model: Apple M1 Type: GPU Bus: Built-In Total Number of Cores: 8 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-In Retina LCD Resolution: 2560 x 1600 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal Installed Packages: alabaster: 0.7.16 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 2.4.1 Babel: 2.14.0 beautifulsoup4: 4.12.3 blockdiag: 3.0.0 blosc2: 2.0.0 build: 1.0.3 certifi: 2023.11.17 cftime: 1.6.3 charset-normalizer: 3.3.2 ChimeraX-AddCharge: 1.5.15 ChimeraX-AddH: 2.2.5 ChimeraX-AlignmentAlgorithms: 2.0.1 ChimeraX-AlignmentHdrs: 3.4.3 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.12.4 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.1.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.53 ChimeraX-AtomicLibrary: 12.1.11 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.1.2 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.11 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2.2 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.4 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.3.2 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.2.4 ChimeraX-ColorActions: 1.0.3 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.5 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.8.dev202402080317 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 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: 1.1.9 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.1.6 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 ChimeraX-Map: 1.1.4 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0.1 ChimeraX-MapFilter: 2.0.1 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1.1 ChimeraX-Markers: 1.0.1 ChimeraX-Mask: 1.0.2 ChimeraX-MatchMaker: 2.1.2 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.6.2 ChimeraX-MedicalToolbar: 1.0.2 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.12.2 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.15 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: 1.1 ChimeraX-NMRSTAR: 1.0.2 ChimeraX-NRRD: 1.1 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.13.2 ChimeraX-PDB: 2.7.3 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 ChimeraX-PubChem: 2.1 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.2.1 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: 1.0 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: 1.0.2 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.15 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.1.2 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.3 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: 1.33.7 ChimeraX-uniprot: 2.3 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.3.2 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: 1.1.3 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.2.1 contourpy: 1.2.0 cxservices: 1.2.2 cycler: 0.12.1 Cython: 3.0.8 debugpy: 1.8.0 decorator: 5.1.1 docutils: 0.20.1 executing: 2.0.1 filelock: 3.13.1 fonttools: 4.48.1 funcparserlib: 2.0.0a0 glfw: 2.6.5 grako: 3.16.5 h5py: 3.10.0 html2text: 2020.1.16 idna: 3.6 ihm: 0.43 imagecodecs: 2024.1.1 imagesize: 1.4.1 ipykernel: 6.29.2 ipython: 8.21.0 ipywidgets: 8.1.1 jedi: 0.19.1 Jinja2: 3.1.3 jupyter-client: 8.6.0 jupyter-core: 5.7.1 jupyterlab-widgets: 3.0.9 kiwisolver: 1.4.5 line-profiler: 4.1.2 lxml: 5.1.0 lz4: 4.3.3 MarkupSafe: 2.1.5 matplotlib: 3.8.2 matplotlib-inline: 0.1.6 msgpack: 1.0.7 ndindex: 1.7 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.2.1 nibabel: 5.0.1 nptyping: 2.5.0 numexpr: 2.9.0 numpy: 1.26.3 openvr: 1.26.701 packaging: 23.2 ParmEd: 3.4.3 parso: 0.8.3 pep517: 0.13.1 pexpect: 4.9.0 pillow: 10.2.0 pip: 23.3.2 pkginfo: 1.9.6 platformdirs: 4.2.0 prompt-toolkit: 3.0.43 psutil: 5.9.8 ptyprocess: 0.7.0 pure-eval: 0.2.2 py-cpuinfo: 9.0.0 pycollada: 0.8 pydicom: 2.3.0 pygments: 2.17.2 pynmrstar: 3.3.2 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.3301 pyparsing: 3.1.1 pyproject-hooks: 1.0.0 PyQt6-commercial: 6.3.1 PyQt6-Qt6: 6.3.2 PyQt6-sip: 13.6.0 PyQt6-WebEngine-commercial: 6.3.1 PyQt6-WebEngine-Qt6: 6.3.2 python-dateutil: 2.8.2 pytz: 2024.1 pyzmq: 25.1.2 qtconsole: 5.5.1 QtPy: 2.4.1 RandomWords: 0.4.0 requests: 2.31.0 scipy: 1.11.4 setuptools: 69.0.3 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: 1.25.3 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: 0.6.1 tables: 3.8.0 tcia-utils: 1.5.1 tifffile: 2023.12.9 tinyarray: 1.2.4 tornado: 6.4 traitlets: 5.14.1 typing-extensions: 4.9.0 tzdata: 2023.4 urllib3: 2.2.0 wcwidth: 0.2.13 webcolors: 1.13 wheel: 0.42.0 wheel-filename: 1.4.1 widgetsnbextension: 4.0.9 }}} " defect feedback normal Window Toolkit Tom Goddard all ChimeraX