id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 20304 Crash on Mac waking from sleep shiv.sahteli@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-26.4.1-arm64-arm-64bit ChimeraX Version: 1.10 (2025-06-26 08:57:52 UTC) Description Last time you used ChimeraX it crashed. This is a known crash that we are unable to fix. Here is information that may help you avoid this crash. The Qt window toolkit crashed due to a display configuration change, typically when waking from sleep or when an external display is disconnected or connected. This has only been seen on Mac computers. We hope a newer version of Qt will fix it. We update ChimeraX daily builds whenever a new Qt is released. You can check here https://www.cgl.ucsf.edu/chimerax/docs/troubleshoot.html#macdisplay to see if it has been fixed in a newer ChimeraX. 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SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 128K 1 \nActivity Tracing 256K 1 \nAttributeGraph Data 1024K 1 \nCG image 384K 11 \nColorSync 80K 5 \nCoreAnimation 3504K 209 \nCoreGraphics 48K 3 \nCoreUI image data 4864K 36 \nFoundation 32K 2 \nKernel Alloc Once 32K 1 \nMALLOC 1.4G 294 \nMALLOC guard page 4032K 4 \nMach message 64K 3 \nMemory Tag 22 64.0M 1 \nOpenGL GLSL 384K 4 \nSTACK GUARD 640K 40 \nStack 216.3M 41 \nStack Guard 56.0M 1 \nVM_ALLOCATE 331.4M 331 \nVM_ALLOCATE (reserved) 160.0M 1 reserved VM address space (unallocated)\n__AUTH 6138K 646 \n__AUTH_CONST 91.3M 1043 \n__CTF 824 1 \n__DATA 46.9M 1169 \n__DATA_CONST 45.4M 1214 \n__DATA_DIRTY 8459K 897 \n__FONT_DATA 2352 1 \n__GLSLBUILTINS 5176K 1 \n__LINKEDIT 608.5M 168 \n__OBJC_RO 79.1M 1 \n__OBJC_RW 2597K 1 \n__TEXT 1.5G 1236 \n__TPRO_CONST 128K 2 \ndyld private memory 2000K 18 \nmapped file 337.1M 72 \npage table in kernel 2003K 1 \nshared memory 3200K 27 \n=========== ======= ======= \nTOTAL 4.9G 7488 \nTOTAL, minus reserved VM space 4.8G 7488 \n"", ""legacyInfo"" : { ""threadTriggered"" : { ""name"" : ""CrBrowserMain"", ""queue"" : ""com.apple.main-thread"" } }, ""logWritingSignature"" : ""db27276803bc62b651ca5a6327cef8e2930c9261"", ""bug_type"" : ""309"", ""roots_installed"" : 0, ""trmStatus"" : 1, ""trialInfo"" : { ""rollouts"" : [ { ""rolloutId"" : ""648cada15dbc71671bb3aa1b"", ""factorPackIds"" : [ ""65a81173096f6a1f1ba46525"" ], ""deploymentId"" : 240000116 }, { ""rolloutId"" : ""67648e5334a82511f4acf879"", ""factorPackIds"" : [ ], ""deploymentId"" : 240000008 } ], ""experiments"" : [ ] } } ===== Log before crash start ===== UCSF ChimeraX version: 1.10 (2025-06-26) © 2016-2025 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /Users/sahtelis/Desktop/connexin- > str_analysis/Cx45_apo_str/cx45_hc/J315_cx45_hc_without_detergent_volume_map_xflip.mrc Opened J315_cx45_hc_without_detergent_volume_map_xflip.mrc as #1, grid size 384,384,384, pixel 0.828, shown at level 0.00407, step 2, values float32 > surface dust #1 size 8.28 > volume #1 step 1 > volume #1 level 0.02373 > volume #1 level 0.05125 > open /Users/sahtelis/Desktop/connexin- > str_analysis/Cx45_apo_str/cx45_hc/cryosparc_P2_J315_004_volume_map_xflip.mrc Opened cryosparc_P2_J315_004_volume_map_xflip.mrc as #2, grid size 384,384,384, pixel 0.828, shown at level 0.0149, step 2, values float32 > open /Users/sahtelis/Desktop/connexin- > str_analysis/Cx45_apo_str/cx45_hc/cryosparc_P2_J315_004_volume_map_sharp.mrc Opened cryosparc_P2_J315_004_volume_map_sharp.mrc as #3, grid size 384,384,384, pixel 0.828, shown at level 0.0189, step 2, values float32 > surface dust #1 size 8.28 > surface dust #2 size 8.28 > surface dust #3 size 8.28 > volume #3 step 1 > volume #2 step 1 > volume #3 level 0.1324 > volume #3 level 0.05 > volume #3 level 0.08084 > volume #2 level 0.04674 > volume #2 level 0.05 > volume #3 level 0.05 > volume #2 level 0.03937 > volume #2 level 0.03381 > volume #2 level 0.035 > volume #1 level 0.03304 > volume #1 level 0.035 > volume #1 color #929292 > set bgColor white > lighting soft > lighting shadows true intensity 0.5 > lighting full > lighting shadows false > lighting soft > graphics silhouettes true > volume #1 level 0.03702 > volume #1 level 0.04 > volume #1 level 0.038 > volume #1 level 0.05 > volume #1 level 0.04 > volume #1 level 0.037 > volume #1 level 0.03346 > volume #1 level 0.0456 > volume #1 level 0.04 > graphics silhouettes false > graphics silhouettes true > volume #1 level 0.03241 > volume #1 level 0.035 > volume #3 level 0.08925 > volume #3 level 0.06962 > volume #3 level 0.04299 > volume #3 level 0.0472 > volume #1 level 0.03298 > volume #1 level 0.03702 > volume #1 level 0.035 > volume #1 level 0.038 > close #3 > close #2 > open /Users/sahtelis/Desktop/connexin- > str_analysis/Cx45_apo_str/cx45_hc/cx45_hc_volume_difference_lipids.mrc Opened cx45_hc_volume_difference_lipids.mrc as #2, grid size 384,384,384, pixel 0.828, shown at level 0.00317, step 2, values float32 > surface dust #1 size 8.28 > surface dust #2 size 8.28 > volume #2 color #0096ff > volume #2 level 0.03168 > volume #2 level 0.02113 > volume #2 step 1 > volume #2 level 0.03 > volume #2 level 0.02 > volume #2 level 0.025 > volume #2 level 0.027 > volume #2 level 0.026 > volume #2 level 0.025 > volume #2 level 0.0265 > volume #2 level 0.026 > volume #2 level 0.025 > volume #2 level 0.027 > volume #2 level 0.026 > volume #2 level 0.0265 > volume #2 level 0.025 > surface dust #2 size 10 > surface dust #2 size 9 > surface dust #1 size 9 > volume #1 level 0.02817 > volume #1 level 0.03554 > open /Users/sahtelis/Desktop/connexin- > str_analysis/Cx45_apo_str/cx45_hc/cryosparc_P2_J315_004_volume_map_sharp.mrc Opened cryosparc_P2_J315_004_volume_map_sharp.mrc as #3, grid size 384,384,384, pixel 0.828, shown at level 0.0189, step 2, values float32 > surface dust #1 size 8.28 > surface dust #3 size 8.28 > volume #3 step 1 > volume #3 level 0.1198 > volume #3 level 0.1086 > volume #3 level 0.06937 > volume flip #3 axis x Opened cryosparc_P2_J315_004_volume_map_sharp.mrc x flip as #4, grid size 384,384,384, pixel 0.828, shown at step 1, values float32 > close #3 > surface dust #1 size 8.28 > surface dust #2 size 8.28 > surface dust #4 size 8.28 > volume #4 level 0.1072 > volume #4 level 0.07778 > volume #4 level 0.05115 > volume #4 level 0.05 > volume #4 level 0.051 > volume #4 level 0.05 > volume #4 level 0.051 > volume #4 level 0.0482 > volume #4 level 0.051 > volume #2 level -0.07055 > volume #2 level 0.025 > volume #2 level 0.02 > volume #1 level 0.03048 > volume #2 level 0.025 > volume #2 level 0.023 > volume #2 level 0.022 > volume #2 level 0.021 > volume #2 level 0.02 > volume #2 level 0.021 > volume #2 level 0.02 > volume #1 level 0.035 > volume #2 level 0.025 > volume #2 level 0.022 > volume #2 level 0.023 > open /Users/sahtelis/Desktop/connexin- > str_analysis/Cx45_apo_str/cx45_hc/cx45hc_RealSpaceRefine_40/cx45_hc_real_space_refined_040-coot_7.pdb Chain information for cx45_hc_real_space_refined_040-coot_7.pdb #3 --- Chain | Description A B C D E F | No description available > hide atoms > show cartoons > transparency #1,3 50 > close #4 > close #2 > volume #1 level 0.03 > show atoms > style stick Changed 17130 atom styles > volume #1 level 0.0359 > volume #1 level 0.035 > volume #1 level 0.02615 > ui tool show ""Side View"" > view > volume #1 level 0.02075 > volume #1 level 0.02419 > volume #1 level 0.024 > ui mousemode right ""tape measure"" > marker segment #2 position 159.1,151.8,145.8 toPosition 157.3,165.9,145.9 > color yellow radius 0.1 label 14.17 labelHeight 1.417 labelColor yellow > open /Users/sahtelis/Desktop/connexin- > str_analysis/Cx45_apo_str/cx45_gjc/RealSpaceRefine_72/D_1292153917_model- > annotate_P1.pdb D_1292153917_model-annotate_P1.pdb title: Cryo-em structure of human connexin 45 gap junction channel [more info...] Chain information for D_1292153917_model-annotate_P1.pdb #4 --- Chain | Description | UniProt A B C D E F G H I J K L | gap junction γ-1 protein,green fluorescent protein | CXG1_HUMAN 1-396, GFP_AEQVI 406-642 Non-standard residues in D_1292153917_model-annotate_P1.pdb #4 --- CLR — cholesterol > hide #!4 models > show #!4 models > matchmaker #4 to #3 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker cx45_hc_real_space_refined_040-coot_7.pdb, chain A (#3) with D_1292153917_model-annotate_P1.pdb, chain A (#4), sequence alignment score = 911 RMSD between 163 pruned atom pairs is 0.708 angstroms; (across all 194 pairs: 1.749) > style stick Changed 36440 atom styles > show cartoons > hide cartoons > marker segment #2 position 156,154.5,146 toPosition 159.4,162,146.1 color > yellow radius 0.1 label 8.174 labelHeight 0.8174 labelColor yellow > hide #!3 models > hide #!4 models > hide #!2 models > hide #!1 models > open > /Users/sahtelis/Downloads/32221101/Cx45_gjc_E41A_cryosparc_P3_J790_013_volume_map_without_micelle_xflip.mrc > /Users/sahtelis/Downloads/32221101/Cx45_gjc_apo_P2_J432_without_detergent_volume_map_xflip.mrc > /Users/sahtelis/Downloads/32221101/Cx45_gjc_ca_cryosparc_P3_J400_003_volume_map_xflip.mrc > /Users/sahtelis/Downloads/32221101/Cx45_E41A_real_space_refined_037.pdb > /Users/sahtelis/Downloads/32221101/cx45_gjc_apo_real_space_refined_072.pdb > /Users/sahtelis/Downloads/32221101/Cx45_gjc_Ca_real_space_refined_087.pdb Opened Cx45_gjc_E41A_cryosparc_P3_J790_013_volume_map_without_micelle_xflip.mrc as #5, grid size 512,512,512, pixel 0.7, shown at level 0.00637, step 2, values float32 Opened Cx45_gjc_apo_P2_J432_without_detergent_volume_map_xflip.mrc as #6, grid size 512,512,512, pixel 0.828, shown at level 0.0129, step 2, values float32 Opened Cx45_gjc_ca_cryosparc_P3_J400_003_volume_map_xflip.mrc as #7, grid size 512,512,512, pixel 0.7, shown at level 0.0275, step 2, values float32 Chain information for Cx45_E41A_real_space_refined_037.pdb #8 --- Chain | Description A B C D E F G H I J K L | No description available Chain information for cx45_gjc_apo_real_space_refined_072.pdb #9 --- Chain | Description A B C D E F G H I J K L | No description available Chain information for Cx45_gjc_Ca_real_space_refined_087.pdb #10 --- Chain | Description A B C D E F G H I J K L | No description available > surface dust #5 size 7 > surface dust #6 size 8.28 > surface dust #7 size 7 > hide #!5 models > hide #!6 models > hide #!7 models > show #!7 models > hide #!7 models > hide #!8 models > hide #!9 models > show #!9 models > hide #!10 models > show #!6 models > hide #!9 atoms > volume #6 step 1 > volume #6 level 0.1031 > volume #6 level 0.07377 > show #!7 models > toolshed show > ui tool show ""Show Volume Menu"" > ui tool show ""Volume Viewer"" > ui tool show ""Fit in Map"" > fitmap #6 inMap #7 Fit map Cx45_gjc_apo_P2_J432_without_detergent_volume_map_xflip.mrc in map Cx45_gjc_ca_cryosparc_P3_J400_003_volume_map_xflip.mrc using 223204 points correlation = 0.615, correlation about mean = 0.09893, overlap = 880.1 steps = 352, shift = 41.3, angle = 10.3 degrees Position of Cx45_gjc_apo_P2_J432_without_detergent_volume_map_xflip.mrc (#6) relative to Cx45_gjc_ca_cryosparc_P3_J400_003_volume_map_xflip.mrc (#7) coordinates: Matrix rotation and translation 0.98744533 0.12624983 0.09493529 -71.63874452 -0.13384650 0.98789465 0.07841726 -13.65411773 -0.08388590 -0.09013951 0.99239006 25.02880160 Axis -0.47105967 0.49974525 -0.72688202 Axis point -181.35019959 516.83087494 -0.00000000 Rotation angle (degrees) 10.30641308 Shift along axis 8.72955711 > hide #!7 models > show #!7 models > select add #6 2 models selected > ui mousemode right translate > ui mousemode right rotate > ui mousemode right ""translate selected models"" > view matrix models > #6,0.98745,0.12625,0.094935,-81.686,-0.13385,0.98789,0.078417,-19.126,-0.083886,-0.09014,0.99239,7.9045 > fitmap #6 inMap #7 Fit map Cx45_gjc_apo_P2_J432_without_detergent_volume_map_xflip.mrc in map Cx45_gjc_ca_cryosparc_P3_J400_003_volume_map_xflip.mrc using 223204 points correlation = 0.8263, correlation about mean = 0.3681, overlap = 1771 steps = 128, shift = 5.37, angle = 10.3 degrees Position of Cx45_gjc_apo_P2_J432_without_detergent_volume_map_xflip.mrc (#6) relative to Cx45_gjc_ca_cryosparc_P3_J400_003_volume_map_xflip.mrc (#7) coordinates: Matrix rotation and translation 1.00000000 0.00000340 -0.00006790 -32.62713856 -0.00000340 1.00000000 -0.00004979 -32.74504508 0.00006790 0.00004979 1.00000000 -32.79081531 Axis 0.59082253 -0.80579370 -0.04031453 Axis point 477873.57198542 0.00000000 -553869.20845557 Rotation angle (degrees) 0.00482822 Shift along axis 8.43084881 > volume #7 level 0.04839 > surface dust #6 size 8.28 > volume #7 step 1 > volume #7 level 0.05398 > surface dust #6 size 8.28 > select subtract #6 Nothing selected > volume #7 level 0.06171 > hide #!6 models > volume #7 level 0.06038 > volume #7 level 0.05532 > hide #!7 models > show #!5 models > volume #5 step 1 > volume #5 level 0.0211 > volume #5 level 0.03729 > volume #5 level 0.04601 > volume #5 level 0.03895 > hide #!9 models > show #!6 models > hide #!5 models > show #!7 models > hide #!6 models > volume #7 level 0.06038 > close #5-10 > show #!4 models > view #4 clip false > show #!3 models > hide #!4 models > show #!4 models > hide #!4 models > show #!1 models > ui tool show ""Volume Viewer"" > view #3 clip false > volume #1 level 0.024 > volume #1 level 0.021 > volume #1 level 0.025 > volume #1 level 0.02 > hide #!1 models > select add #3 17130 atoms, 17436 bonds, 6 pseudobonds, 1176 residues, 2 models selected > show sel surfaces > select subtract #3 6 models selected > select ::name=""CLR"" 672 atoms, 744 bonds, 24 residues, 1 model selected > select add #4 19308 atoms, 19860 bonds, 12 pseudobonds, 2424 residues, 2 models selected > select ::name=""Y01"" 504 atoms, 522 bonds, 6 residues, 1 model selected > select add #3 17130 atoms, 17436 bonds, 6 pseudobonds, 1176 residues, 2 models selected > select subtract #3 6 models selected > select add #3 17130 atoms, 17436 bonds, 6 pseudobonds, 1176 residues, 2 models selected > select subtract #3 6 models selected > hide #!3 models > show #!1 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > select add #3 17130 atoms, 17436 bonds, 6 pseudobonds, 1176 residues, 2 models selected > hide sel surfaces > select subtract #3 6 models selected > volume #1 level 0.0245 > volume #1 level 0.024 > hide #!3 models > show #!3 models > hide #!1 models > show #!1 models > hide #!1 models > show #!4 models > hide #!4 models > show #!4 models > color #4 #ffd479ff > color #3 #ff7e79ff > color #3 #d4fb79ff > color #3 #73fa79ff > color #3 #7a81ffff > show #!1 models > hide #!1 models > show #!1 models > volume #1 level 0.025 > hide #!1 models > select #3/A 2855 atoms, 2906 bonds, 1 pseudobond, 196 residues, 2 models selected > combine sel > hide #!3 models > select add #3 17130 atoms, 17436 bonds, 6 pseudobonds, 1176 residues, 3 models selected > hide #!5 models > hide #!4 models > show #!5 models > close #5 > select #3/A 2855 atoms, 2906 bonds, 1 pseudobond, 196 residues, 2 models selected > show #!3 models > combine sel > select add #3 17130 atoms, 17436 bonds, 6 pseudobonds, 1176 residues, 3 models selected > hide #!3 models > select subtract #3 6 models selected > hide #!5 models > show #!5 models > select #3/B-F 14275 atoms, 14530 bonds, 5 pseudobonds, 980 residues, 2 models selected > select add #3 17130 atoms, 17436 bonds, 6 pseudobonds, 1176 residues, 7 models selected > select subtract #3 6 models selected > select #5/B-F 14275 atoms, 14530 bonds, 5 pseudobonds, 980 residues, 2 models selected > delete sel > hide #!5 models > combine #4 > select #6/B-F 8044 atoms, 8275 bonds, 5 pseudobonds, 1009 residues, 2 models selected > delete sel > hide #!6 models > show #!5 models > show #!6 models > select #6/B-L 9654 atoms, 9930 bonds, 6 pseudobonds, 1212 residues, 2 models selected > delete sel > view #6 clip false > show #!1 models > volume #1 level 0.03699 > ui tool show ""Side View"" > view > volume #1 level 0.03184 > hide #!1 models > hide #!6 models > show #!6 models > hide #!6 models > show #!6 models > hide #!6 models > show #!6 models > hide #!6 models > show #!6 models > hide #!6 models > show #!6 models ===== Log before crash end ===== Log: UCSF ChimeraX version: 1.10 (2025-06-26) © 2016-2025 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 Metal - 90.5 OpenGL renderer: Apple M3 OpenGL vendor: Apple Python: 3.11.4 Locale: en_US.UTF-8 Qt version: PyQt6 6.8.1, Qt 6.8.2 Qt runtime version: 6.8.2 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Air Model Identifier: Mac15,12 Model Number: MC8G4KS/A Chip: Apple M3 Total Number of Cores: 8 (4 Performance and 4 Efficiency) Memory: 16 GB System Firmware Version: 18000.101.7 OS Loader Version: 18000.101.7 Software: System Software Overview: System Version: macOS 26.4.1 (25E253) Kernel Version: Darwin 25.4.0 Time since boot: 6 days, 12 hours, 40 minutes Graphics/Displays: Apple M3: Chipset Model: Apple M3 Type: GPU Bus: Built-In Total Number of Cores: 8 Vendor: Apple (0x106b) Metal Support: Metal 4 Displays: Color LCD: Display Type: Built-in Liquid Retina Display Resolution: 2560 x 1664 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal Installed Packages: alabaster: 1.0.0 annotated-types: 0.7.0 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 3.0.0 auditwheel: 6.4.0 babel: 2.17.0 beautifulsoup4: 4.13.3 blockdiag: 3.0.0 blosc2: 3.5.0 build: 1.2.2.post1 certifi: 2023.11.17 cftime: 1.6.4.post1 charset-normalizer: 3.4.2 ChimeraX-AddCharge: 1.5.19 ChimeraX-AddH: 2.2.7 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.6.1 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.20.2 ChimeraX-AlphaFold: 1.0.1 ChimeraX-AltlocExplorer: 1.1.2 ChimeraX-AmberInfo: 1.0 ChimeraX-Aniso: 1.1.4 ChimeraX-Arrays: 1.1 ChimeraX-ArtiaX: 0.6.0 ChimeraX-Atomic: 1.60.7 ChimeraX-AtomicLibrary: 14.1.18 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.3 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 3.0.0 ChimeraX-Boltz: 1.0 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.2 ChimeraX-BuildStructure: 2.13.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.5.1 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.4 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.5 ChimeraX-ChemGroup: 2.0.2 ChimeraX-Clashes: 2.3 ChimeraX-Clipper: 0.25.2 ChimeraX-ColorActions: 1.0.5 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.8 ChimeraX-CommandLine: 1.3 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.10 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.5 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DAQplugin: 0.13.60 ChimeraX-DataFormats: 1.2.4 ChimeraX-Dicom: 1.2.7 ChimeraX-DistMonitor: 1.4.2 ChimeraX-DockPrep: 1.1.4 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ESMFold: 1.0 ChimeraX-FileHistory: 1.0.1 ChimeraX-FunctionKey: 1.0.1 ChimeraX-Geometry: 1.3 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.4.1 ChimeraX-Hbonds: 2.5.1 ChimeraX-Help: 1.3 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.3 ChimeraX-ISOLDE: 1.10.1 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-KVFinder: 1.6.2 ChimeraX-Label: 1.1.14 ChimeraX-ListInfo: 1.2.2 ChimeraX-locscalesurfer: 0.1.3 ChimeraX-Log: 1.2 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 ChimeraX-Map: 1.3 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0.1 ChimeraX-MapFilter: 2.0.1 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1.1 ChimeraX-Markers: 1.0.1 ChimeraX-Mask: 1.0.2 ChimeraX-MatchMaker: 2.2.2 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.10.1 ChimeraX-MedicalToolbar: 1.1 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.16 ChimeraX-MMTF: 2.2 ChimeraX-ModelArchive: 1.0 ChimeraX-Modeller: 1.5.19 ChimeraX-ModelPanel: 1.5.1 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0.3 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.2 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0 ChimeraX-MutationScores: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.2 ChimeraX-NMRSTAR: 1.0.2 ChimeraX-NRRD: 1.2 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.14.1 ChimeraX-OrthoPick: 1.0.1 ChimeraX-PDB: 2.7.10 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: 1.1.3 ChimeraX-ProfileGrids: 1.1.2 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.6.3 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.3.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 4.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.3 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-Segmentations: 3.5.7 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.17.1 ChimeraX-Shape: 1.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.2.1 ChimeraX-ShowSequences: 1.0.3 ChimeraX-SideView: 1.0.1 ChimeraX-SimilarStructures: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.19.1 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.2.1 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.5.2 ChimeraX-TapeMeasure: 1.0 ChimeraX-TaskManager: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.2.3 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.45.2 ChimeraX-Umap: 1.0 ChimeraX-uniprot: 2.3.1 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.4.4 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-vrml: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.5 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 coloredlogs: 15.0.1 comm: 0.2.2 contourpy: 1.3.2 coverage: 7.9.1 cxservices: 1.2.3 cycler: 0.12.1 Cython: 3.0.12 debugpy: 1.8.14 decorator: 5.2.1 docutils: 0.21.2 einops: 0.3.2 executing: 2.2.0 filelock: 3.18.0 flatbuffers: 25.12.19 fonttools: 4.58.4 fsspec: 2025.7.0 funcparserlib: 2.0.0a0 geomdl: 5.4.0 glfw: 2.9.0 grako: 3.16.5 h5py: 3.14.0 html2text: 2024.2.26 humanfriendly: 10.0 idna: 3.10 ihm: 2.2 imagecodecs: 2024.6.1 imagesize: 1.4.1 iniconfig: 2.1.0 ipykernel: 6.29.5 ipython: 8.26.0 ipywidgets: 8.1.7 jedi: 0.19.1 Jinja2: 3.1.6 jupyter_client: 8.6.3 jupyter_core: 5.8.1 jupyterlab_widgets: 3.0.15 kiwisolver: 1.4.8 line_profiler: 4.2.0 lxml: 5.3.1 lz4: 4.4.4 MarkupSafe: 3.0.2 matplotlib: 3.10.1 matplotlib-inline: 0.1.7 mpmath: 1.3.0 mrcfile: 1.5.4 msgpack: 1.1.0 ndindex: 1.10.0 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.11.0 numpy: 1.24.4 numpy: 1.26.4 onnxruntime: 1.23.2 OpenMM: 8.2.0 openvr: 1.26.701 packaging: 24.2 pandas: 2.3.2 ParmEd: 4.2.2 parso: 0.8.4 pep517: 0.13.1 pexpect: 4.9.0 pickleshare: 0.7.5 pillow: 10.4.0 pip: 25.0.1 pkginfo: 1.11.1 platformdirs: 4.3.8 pluggy: 1.6.0 prompt_toolkit: 3.0.51 protobuf: 6.33.4 psutil: 7.0.0 ptyprocess: 0.7.0 pure_eval: 0.2.3 py-cpuinfo: 9.0.0 pyarrow: 21.0.0 pycollada: 0.8 pydantic: 2.11.7 pydantic_core: 2.33.2 pydicom: 2.4.4 pyelftools: 0.32 Pygments: 2.18.0 pynmrstar: 3.3.5 pynrrd: 1.0.0 PyOpenGL: 3.1.9 PyOpenGL-accelerate: 3.1.9 pyopenxr: 1.1.4501 pyparsing: 3.2.3 pyproject_hooks: 1.2.0 PyQt6-commercial: 6.8.1 PyQt6-Qt6: 6.8.2 PyQt6-WebEngine-commercial: 6.8.0 PyQt6-WebEngine-Qt6: 6.8.2 PyQt6_sip: 13.10.0 pytest: 8.4.1 pytest-cov: 6.2.1 python-dateutil: 2.9.0.post0 pytz: 2025.2 pyzmq: 27.0.0 qtconsole: 5.5.2 QtPy: 2.4.3 qtshim: 1.1 RandomWords: 0.4.0 requests: 2.32.3 roman-numerals-py: 3.1.0 scipy: 1.10.1 scipy: 1.14.0 setuptools: 78.1.0 sfftk-rw: 0.8.1 six: 1.16.0 snowballstemmer: 3.0.1 sortedcontainers: 2.4.0 soupsieve: 2.7 Sphinx: 8.2.3 sphinx-autodoc-typehints: 3.1.0 sphinxcontrib-applehelp: 2.0.0 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 2.0.0 sphinxcontrib-htmlhelp: 2.1.0 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 2.0.0 sphinxcontrib-serializinghtml: 2.0.0 stack-data: 0.6.3 starfile: 0.5.13 superqt: 0.7.1 sympy: 1.14.0 tables: 3.10.2 tcia_utils: 1.5.1 tifffile: 2025.3.13 timm: 0.4.12 tinyarray: 1.2.4 torch: 2.2.2 torchvision: 0.17.2 tornado: 6.5.1 tqdm: 4.66.6 traitlets: 5.14.3 typing-inspection: 0.4.1 typing_extensions: 4.14.0 tzdata: 2025.2 urllib3: 2.5.0 wcwidth: 0.2.13 webcolors: 24.11.1 wheel: 0.45.1 wheel-filename: 1.4.2 widgetsnbextension: 4.0.14 }}} " defect closed normal Window Toolkit duplicate all ChimeraX