id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 20010 Crash in swap_buffers exposing status line during Mac wakeup, macOS 26 chimerax-bug-report@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-26.3.1-arm64-arm-64bit ChimeraX Version: 1.11.1 (2026-01-23 05:51:34 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. Fatal Python error: Bus error Current thread 0x0000000206f57100 (most recent call first): File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/opengl.py"", line 248 in swap_buffers File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/opengl.py"", line 561 in swap_buffers File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/statusbar.py"", line 166 in status File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/statusbar.py"", line 98 in _expose_event File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 414 in event_loop File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1064 in init File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1229 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.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, 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""bug_type"" : ""309"", ""roots_installed"" : 0, ""trmStatus"" : 1, ""trialInfo"" : { ""rollouts"" : [ { ""rolloutId"" : ""645eb1d0417dab722a215927"", ""factorPackIds"" : [ ], ""deploymentId"" : 240000005 }, { ""rolloutId"" : ""661464ecda55e5192b100804"", ""factorPackIds"" : [ ], ""deploymentId"" : 240000005 } ], ""experiments"" : [ ] } } ===== Log before crash start ===== UCSF ChimeraX version: 1.11.1 (2026-01-23) © 2016-2025 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > close session > open > /Users/shantigangwar/Downloads/cryosparc_P52_J396_volume_class_09_map_sharp.mrc > /Users/shantigangwar/Downloads/cryosparc_P52_J396_volume_class_08_map_sharp.mrc > /Users/shantigangwar/Downloads/cryosparc_P52_J396_volume_class_07_map_sharp.mrc > /Users/shantigangwar/Downloads/cryosparc_P52_J396_volume_class_06_map_sharp.mrc > /Users/shantigangwar/Downloads/cryosparc_P52_J396_volume_class_05_map_sharp.mrc > /Users/shantigangwar/Downloads/cryosparc_P52_J396_volume_class_04_map_sharp.mrc > /Users/shantigangwar/Downloads/cryosparc_P52_J396_volume_class_03_map_sharp.mrc > /Users/shantigangwar/Downloads/cryosparc_P52_J396_volume_class_02_map_sharp.mrc > /Users/shantigangwar/Downloads/cryosparc_P52_J396_volume_class_01_map_sharp.mrc > /Users/shantigangwar/Downloads/cryosparc_P52_J396_volume_class_00_map_sharp.mrc Opened cryosparc_P52_J396_volume_class_09_map_sharp.mrc as #1.1, grid size 416,416,416, pixel 0.86, shown at level 0.0566, step 2, values float32 Opened cryosparc_P52_J396_volume_class_08_map_sharp.mrc as #1.2, grid size 416,416,416, pixel 0.86, shown at level 0.057, step 2, values float32 Opened cryosparc_P52_J396_volume_class_07_map_sharp.mrc as #1.3, grid size 416,416,416, pixel 0.86, shown at level 0.057, step 2, values float32 Opened cryosparc_P52_J396_volume_class_06_map_sharp.mrc as #1.4, grid size 416,416,416, pixel 0.86, shown at level 0.0567, step 2, values float32 Opened cryosparc_P52_J396_volume_class_05_map_sharp.mrc as #1.5, grid size 416,416,416, pixel 0.86, shown at level 0.0573, step 2, values float32 Opened cryosparc_P52_J396_volume_class_04_map_sharp.mrc as #1.6, grid size 416,416,416, pixel 0.86, shown at level 0.0573, step 2, values float32 Opened cryosparc_P52_J396_volume_class_03_map_sharp.mrc as #1.7, grid size 416,416,416, pixel 0.86, shown at level 0.0565, step 2, values float32 Opened cryosparc_P52_J396_volume_class_02_map_sharp.mrc as #1.8, grid size 416,416,416, pixel 0.86, shown at level 0.0569, step 2, values float32 Opened cryosparc_P52_J396_volume_class_01_map_sharp.mrc as #1.9, grid size 416,416,416, pixel 0.86, shown at level 0.0574, step 2, values float32 Opened cryosparc_P52_J396_volume_class_00_map_sharp.mrc as #1.10, grid size 416,416,416, pixel 0.86, shown at level 0.0579, step 2, values float32 > surface dust #1.1 size 8.6 > surface dust #1.2 size 8.6 > surface dust #1.3 size 8.6 > surface dust #1.4 size 8.6 > surface dust #1.5 size 8.6 > surface dust #1.6 size 8.6 > surface dust #1.7 size 8.6 > surface dust #1.8 size 8.6 > surface dust #1.9 size 8.6 > surface dust #1.10 size 8.6 > lighting soft > set bgColor white > volume step 1 level 0.1 > volume step 1 level 0.09 > hide #!1.1 models > hide #!1.2 models > hide #!1.3 models > hide #!1.4 models > hide #!1.5 models > hide #!1.6 models > hide #!1.7 models > hide #!1.8 models > hide #!1.9 models > hide #!1.10 models > show #!1.1 models > volume step 1 level 0.08 > hide #!1.1 models > show #!1.2 models > show #!1.1 models > hide #!1.1 models > show #!1.1 models > hide #!1.2 models > open 8FWS Summary of feedback from opening 8FWS fetched from pdb --- warnings | Cannot find consistent set of bond orders for ring system containing atom CAG in residue 2J9 /A:1009 Cannot find consistent set of bond orders for ring system containing atom CAG in residue 2J9 /C:1001 Cannot find consistent set of bond orders for ring system containing atom CAG in residue 2J9 /A:1001 Cannot find consistent set of bond orders for ring system containing atom CAG in residue 2J9 /C:1002 8fws title: Structure of the ligand-binding and transmembrane domains of kainate receptor GluK2 in complex with the positive allosteric modulator BPAM344 [more info...] Chain information for 8fws #2 --- Chain | Description | UniProt A B C D | Glutamate receptor ionotropic, kainate 2 | GRIK2_RAT 1-908 Non-standard residues in 8fws #2 --- 2J9 — 4-cyclopropyl-7-fluoro-3,4-dihydro-2H-1,2,4-benzothiadiazine 1,1-dioxide BMA — beta-D-mannopyranose (beta-D-mannose; D-mannose; mannose) CL — chloride ion NA — sodium ion NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine; 2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose; 2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE) POV — (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate (POPC) > hide atoms > ui mousemode right ""move picked models"" > view matrix models #2,1,0,0,-0.56799,0,1,0,0.26858,0,0,1,12.097 > ui mousemode right ""rotate selected models"" > ui mousemode right ""move picked models"" > ui mousemode right ""rotate selected models"" > ui mousemode right ""move picked models"" > view matrix models #2,1,0,0,-89.763,0,1,0,12.863,0,0,1,51.288 > ui mousemode right ""rotate selected models"" > select add #2 14416 atoms, 14732 bonds, 8 pseudobonds, 1726 residues, 2 models selected > view matrix models > #2,0.42726,-0.90385,0.022325,168.83,-0.89957,-0.42746,-0.089758,439.93,0.090671,0.018267,-0.99571,344.09 > ui mousemode right ""move picked models"" > view matrix models > #2,0.42726,-0.90385,0.022325,259.33,-0.89957,-0.42746,-0.089758,419.64,0.090671,0.018267,-0.99571,344.99 > ui tool show ""Fit in Map"" > fitmap #2 inMap #1.1 Fit molecule 8fws (#2) to map cryosparc_P52_J396_volume_class_09_map_sharp.mrc (#1.1) using 14416 atoms average map value = 0.08332, steps = 120 shifted from previous position = 9.52 rotated from previous position = 5.77 degrees atoms outside contour = 7407, contour level = 0.08 Position of 8fws (#2) relative to cryosparc_P52_J396_volume_class_09_map_sharp.mrc (#1.1) coordinates: Matrix rotation and translation 0.39346993 -0.91933693 -0.00101108 272.39053553 -0.91933722 -0.39347042 0.00033005 411.85590925 -0.00070125 0.00079966 -0.99999943 365.20158362 Axis 0.83470644 -0.55069491 -0.00051220 Axis point 0.00000000 295.75157917 182.71908258 Rotation angle (degrees) 179.98388250 Shift along axis 0.37212339 > select subtract #2 Nothing selected > volume #1.1 level 0.1569 > volume #1.1 level 0.09521 > fitmap #2 inMap #1.1 Fit molecule 8fws (#2) to map cryosparc_P52_J396_volume_class_09_map_sharp.mrc (#1.1) using 14416 atoms average map value = 0.08332, steps = 44 shifted from previous position = 0.016 rotated from previous position = 0.0116 degrees atoms outside contour = 8711, contour level = 0.095211 Position of 8fws (#2) relative to cryosparc_P52_J396_volume_class_09_map_sharp.mrc (#1.1) coordinates: Matrix rotation and translation 0.39349738 -0.91932520 -0.00099026 272.38503835 -0.91932560 -0.39349769 0.00013085 411.87604997 -0.00050996 0.00085889 -0.99999950 365.15779760 Axis 0.83471468 -0.55068248 -0.00044890 Axis point 0.00000000 295.73999552 182.70596590 Rotation angle (degrees) 179.97501349 Shift along axis 0.38694562 > fitmap #2 inMap #1.1 Fit molecule 8fws (#2) to map cryosparc_P52_J396_volume_class_09_map_sharp.mrc (#1.1) using 14416 atoms average map value = 0.08332, steps = 44 shifted from previous position = 0.0168 rotated from previous position = 0.00302 degrees atoms outside contour = 8714, contour level = 0.095211 Position of 8fws (#2) relative to cryosparc_P52_J396_volume_class_09_map_sharp.mrc (#1.1) coordinates: Matrix rotation and translation 0.39347821 -0.91933345 -0.00094609 272.38098844 -0.91933380 -0.39347852 0.00015072 411.88751387 -0.00051083 0.00081047 -0.99999954 365.16631783 Axis 0.83470894 -0.55069120 -0.00043589 Axis point 0.00000000 295.75090335 182.70305577 Rotation angle (degrees) 179.97735682 Shift along axis 0.37684553 > hide #!1.1 models > show #!1.1 models > fitmap #2 inMap #1.1 Fit molecule 8fws (#2) to map cryosparc_P52_J396_volume_class_09_map_sharp.mrc (#1.1) using 14416 atoms average map value = 0.08332, steps = 40 shifted from previous position = 0.0201 rotated from previous position = 0.00629 degrees atoms outside contour = 8703, contour level = 0.095211 Position of 8fws (#2) relative to cryosparc_P52_J396_volume_class_09_map_sharp.mrc (#1.1) coordinates: Matrix rotation and translation 0.39347233 -0.91933587 -0.00104067 272.39713852 -0.91933633 -0.39347263 0.00009551 411.87584129 -0.00049728 0.00091915 -0.99999945 365.14522875 Axis 0.83470718 -0.55069384 -0.00046025 Axis point 0.00000000 295.74028095 182.70860686 Rotation angle (degrees) 179.97173192 Shift along axis 0.38630002 > hide #!1.1 models > show #!1.1 models > hide #!1.1 models > show #!1.1 models > hide #!1.1 models > show #!1.2 models > fitmap #2 inMap #1.2 Fit molecule 8fws (#2) to map cryosparc_P52_J396_volume_class_08_map_sharp.mrc (#1.2) using 14416 atoms average map value = 0.08909, steps = 48 shifted from previous position = 0.358 rotated from previous position = 0.0473 degrees atoms outside contour = 6653, contour level = 0.08 Position of 8fws (#2) relative to cryosparc_P52_J396_volume_class_08_map_sharp.mrc (#1.2) coordinates: Matrix rotation and translation 0.39276532 -0.91963800 -0.00115909 272.57734310 -0.91963839 -0.39276595 0.00037360 411.81326000 -0.00079883 0.00091920 -0.99999926 364.84562255 Axis 0.83449539 -0.55101461 -0.00058599 Axis point 0.00000000 295.86186877 182.55886379 Rotation angle (degrees) 179.98126986 Shift along axis 0.33561558 > fitmap #2 inMap #1.2 Fit molecule 8fws (#2) to map cryosparc_P52_J396_volume_class_08_map_sharp.mrc (#1.2) using 14416 atoms average map value = 0.08909, steps = 44 shifted from previous position = 0.0169 rotated from previous position = 0.0131 degrees atoms outside contour = 6660, contour level = 0.08 Position of 8fws (#2) relative to cryosparc_P52_J396_volume_class_08_map_sharp.mrc (#1.2) coordinates: Matrix rotation and translation 0.39275880 -0.91964057 -0.00132159 272.60626895 -0.91964096 -0.39275974 0.00053534 411.76926131 -0.00101139 0.00100513 -0.99999898 364.86825721 Axis 0.83449343 -0.55101745 -0.00069827 Axis point 0.00000000 295.85505734 182.58292065 Rotation angle (degrees) 179.98387230 Shift along axis 0.34131457 > volume #1.2 level 0.09456 > show atoms > transparency #1.2.1 50 > transparency #1.2.1 0 > hide atoms > hide #!1.2 models > show #!1.3 models > fitmap #2 inMap #1.3 Fit molecule 8fws (#2) to map cryosparc_P52_J396_volume_class_07_map_sharp.mrc (#1.3) using 14416 atoms average map value = 0.08362, steps = 60 shifted from previous position = 0.208 rotated from previous position = 0.131 degrees atoms outside contour = 7308, contour level = 0.08 Position of 8fws (#2) relative to cryosparc_P52_J396_volume_class_07_map_sharp.mrc (#1.3) coordinates: Matrix rotation and translation 0.39481382 -0.91876073 -0.00087644 272.10397125 -0.91876079 -0.39481433 0.00050375 411.99898666 -0.00080885 0.00060635 -0.99999949 365.08953904 Axis 0.83510861 -0.55008486 -0.00050152 Axis point 0.00000000 295.61002865 182.63405603 Rotation angle (degrees) 179.99648023 Shift along axis 0.41886677 > color #2 #ea4125ff > show #!1.2 models > hide #!1.2 models > show #!1.2 models > hide #!1.2 models > show #!1.2 models > hide #!1.3 models > show #!1.3 models > hide #!1.2 models > hide #!1.3 models > show #!1.3 models > show #!1.2 models > hide #!1.3 models > volume step 1 level 0.08 > show #!1.3 models > hide #!1.2 models > show #!1.2 models > hide #!1.2 models > show #!1.2 models > volume #1.3 level 0.08636 > show #!1.1 models > hide #!1.2 models > hide #!1.3 models > show #!1.3 models > hide #!1.3 models > show #!1.3 models > hide #!1.3 models > show #!1.3 models > hide #!1.3 models > show #!1.3 models > hide #!1.3 models > show #!1.3 models > show #!1.2 models > hide #!1.1 models > hide #!1.2 models > show #!1.2 models > hide #!1.3 models > hide #!1.2 models > show #!1.3 models > show #!1.4 models > hide #!1.3 models > show #!1.5 models > hide #!1.4 models > hide #!1.5 models > show #!1.6 models > hide #!1.6 models > show #!1.7 models > hide #!1.7 models > show #!1.8 models > hide #!1.8 models > show #!1.9 models > hide #!1.9 models > hide #!2 models > show #!1.10 models > show #!1.9 models > show #!1.8 models > show #!1.7 models > show #!1.6 models > show #!1.5 models > show #!1.4 models > show #!1.3 models > show #!1.2 models > show #!1.1 models > ui tool show ""Side View"" > hide #!1.1 models > hide #!1.2 models > hide #!1.3 models > hide #!1.4 models > hide #!1.5 models > hide #!1.6 models > hide #!1.7 models > hide #!1.8 models > hide #!1.9 models > hide #!1.10 models > show #!1.1 models > hide #!1.1 models > show #!1.2 models > hide #!1.2 models > show #!1.3 models > hide #!1.3 models > show #!1.4 models > hide #!1.4 models > show #!1.5 models > hide #!1.5 models > show #!1.6 models > hide #!1.6 models > show #!1.7 models > hide #!1.7 models > show #!1.8 models > hide #!1.8 models > show #!1.9 models > hide #!1.9 models > show #!1.10 models > hide #!1.10 models > show #!2 models > hide #!2 models > hide #!1 models > show #!1 models > hide #!1 models Unsupported scale factor (0.000000) detected on Display1 ===== Log before crash end ===== Log: UCSF ChimeraX version: 1.11.1 (2026-01-23) © 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 Max OpenGL vendor: Apple Python: 3.11.9 Locale: en_US.UTF-8 Qt version: PyQt6 6.9.1, Qt 6.9.0 Qt runtime version: 6.9.2 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: Mac15,9 Model Number: MUW63LL/A Chip: Apple M3 Max Total Number of Cores: 16 (12 Performance and 4 Efficiency) Memory: 48 GB System Firmware Version: 13822.81.10 OS Loader Version: 13822.81.10 Software: System Software Overview: System Version: macOS 26.3.1 (a) (25D771280a) Kernel Version: Darwin 25.3.0 Time since boot: 1 day, 1 hour, 12 minutes Graphics/Displays: Apple M3 Max: Chipset Model: Apple M3 Max Type: GPU Bus: Built-In Total Number of Cores: 40 Vendor: Apple (0x106b) Metal Support: Metal 4 Displays: Color LCD: Display Type: Built-in Liquid Retina XDR Display Resolution: 3456 x 2234 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal DELL U2415: Resolution: 1920 x 1200 (WUXGA - Widescreen Ultra eXtended Graphics Array) UI Looks like: 1920 x 1200 @ 60.00Hz Mirror: Off Online: Yes Rotation: Supported Installed Packages: aiohappyeyeballs: 2.6.1 aiohttp: 3.13.1 aiosignal: 1.4.0 alabaster: 1.0.0 annotated-types: 0.7.0 anyio: 4.12.1 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 3.0.1 attrs: 25.4.0 babel: 2.17.0 beautifulsoup4: 4.13.5 blockdiag: 3.0.0 blosc2: 3.12.2 build: 1.3.0 certifi: 2025.7.14 cftime: 1.6.5 charset-normalizer: 3.4.4 ChimeraX-AddCharge: 1.5.20 ChimeraX-AddH: 2.2.8 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.6.1 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 3.1.1 ChimeraX-AlphaFold: 1.0.1 ChimeraX-AltlocExplorer: 1.2 ChimeraX-AmberInfo: 1.0 ChimeraX-Animations: 1.0 ChimeraX-Aniso: 1.3.2 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.61.4 ChimeraX-AtomicLibrary: 14.2.1 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: 1.1 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.2 ChimeraX-BuildStructure: 2.13.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.6.0 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.4 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.5 ChimeraX-ChemGroup: 2.0.2 ChimeraX-Clashes: 2.3 ChimeraX-ColorActions: 1.0.5 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.8 ChimeraX-CommandLine: 1.3.0 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.11.1 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.5 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 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: 2.5.3 ChimeraX-Help: 1.3 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.4 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-KVFinder: 1.7.3 ChimeraX-Label: 1.2 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.2.2 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.2 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-MCPServer: 0.1.0 ChimeraX-MDcrds: 2.17.2 ChimeraX-MedicalToolbar: 1.1 ChimeraX-Meeting: 1.0.1 ChimeraX-Minimize: 1.3.2 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.16 ChimeraX-MMTF: 2.2 ChimeraX-ModelArchive: 1.0 ChimeraX-Modeller: 1.5.22 ChimeraX-ModelPanel: 1.6 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: 1.0.1 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: 1.15.2 ChimeraX-OrthoPick: 1.0.1 ChimeraX-PDB: 2.7.12 ChimeraX-PDBBio: 1.0.1 ChimeraX-PDBLibrary: 1.0.5 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1.4 ChimeraX-ProfileGrids: 1.4.2 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.6.5 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.3.3 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 4.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.2 ChimeraX-Scenes: 0.3.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.3 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-Segmentations: 3.5.10 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.17.3 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: 1.49.1 ChimeraX-Umap: 1.0 ChimeraX-uniprot: 2.3.2 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDock: 1.5.2 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: 1.1.5 ChimeraX-Zone: 1.0.1 click: 8.3.1 colorama: 0.4.6 comm: 0.2.3 contourpy: 1.3.3 coverage: 7.13.1 cxservices: 1.2.3 cycler: 0.12.1 Cython: 3.1.4 debugpy: 1.8.19 decorator: 5.2.1 docutils: 0.21.2 executing: 2.2.1 filelock: 3.19.1 fonttools: 4.61.1 frozenlist: 1.8.0 funcparserlib: 2.0.0a0 glfw: 2.10.0 grako: 3.16.5 h11: 0.16.0 h5py: 3.15.1 html2text: 2025.4.15 httpcore: 1.0.9 httpx: 0.28.1 httpx-sse: 0.4.3 idna: 3.11 ihm: 2.2 imagecodecs: 2024.6.1 imagesize: 1.4.1 iniconfig: 2.3.0 ipykernel: 6.30.1 ipython: 9.5.0 ipython_pygments_lexers: 1.1.1 ipywidgets: 8.1.8 jedi: 0.19.2 Jinja2: 3.1.6 jsonschema: 4.26.0 jsonschema-specifications: 2025.9.1 jupyter_client: 8.6.3 jupyter_core: 5.9.1 jupyterlab_widgets: 3.0.16 kiwisolver: 1.4.9 line_profiler: 5.0.0 lxml: 6.0.2 lz4: 4.3.2 Markdown: 3.8.2 MarkupSafe: 3.0.3 matplotlib: 3.10.7 matplotlib-inline: 0.2.1 mcp: 1.18.0 msgpack: 1.1.1 multidict: 6.7.0 ndindex: 1.10.1 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.14.1 numpy: 1.26.4 OpenMM: 8.2.0 openvr: 1.26.701 packaging: 25.0 ParmEd: 4.2.2 parso: 0.8.5 pep517: 0.13.1 pexpect: 4.9.0 pickleshare: 0.7.5 pillow: 11.3.0 pip: 25.2 pkginfo: 1.12.1.2 platformdirs: 4.5.1 pluggy: 1.6.0 prompt_toolkit: 3.0.52 propcache: 0.4.1 psutil: 7.0.0 ptyprocess: 0.7.0 pure_eval: 0.2.3 py-cpuinfo: 9.0.0 pybind11: 3.0.1 pycollada: 0.8 pydantic: 2.12.5 pydantic-settings: 2.12.0 pydantic_core: 2.41.5 pydicom: 2.4.4 Pygments: 2.18.0 pynmrstar: 3.3.6 pynrrd: 1.0.0 PyOpenGL: 3.1.10 PyOpenGL-accelerate: 3.1.10 pyopenxr: 1.1.4501 pyparsing: 3.3.2 pyproject_hooks: 1.2.0 PyQt6-commercial: 6.9.1 PyQt6-Qt6: 6.9.2 PyQt6-WebEngine-commercial: 6.9.0 PyQt6-WebEngine-Qt6: 6.9.2 PyQt6_sip: 13.10.2 pytest: 9.0.2 pytest-cov: 7.0.0 python-dateutil: 2.9.0.post0 python-dotenv: 1.2.1 python-multipart: 0.0.21 pyzmq: 27.1.0 qtconsole: 5.7.0 QtPy: 2.4.3 qtshim: 1.2 RandomWords: 0.4.0 referencing: 0.37.0 requests: 2.32.5 roman-numerals: 4.1.0 roman-numerals-py: 4.1.0 rpds-py: 0.30.0 scipy: 1.14.0 setuptools: 80.9.0 sfftk-rw: 0.8.1 six: 1.17.0 snowballstemmer: 3.0.1 sortedcontainers: 2.4.0 soupsieve: 2.8.3 Sphinx: 8.2.3 sphinx-autodoc-typehints: 3.2.0 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 sse-starlette: 3.2.0 stack-data: 0.6.3 starlette: 0.52.1 superqt: 0.7.6 tables: 3.10.2 tcia_utils: 1.5.1 tifffile: 2025.3.13 tinyarray: 1.2.5 tornado: 6.5.4 traitlets: 5.14.3 typing-inspection: 0.4.2 typing_extensions: 4.15.0 urllib3: 2.6.3 uvicorn: 0.40.0 wcwidth: 0.3.2 webcolors: 24.11.1 wheel: 0.45.1 wheel-filename: 1.4.2 widgetsnbextension: 4.0.15 yarl: 1.22.0 }}} " defect closed normal Graphics duplicate all ChimeraX