id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 20359 ChimeraX bug report submission chimerax-bug-report@… "{{{ 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 0x0000000209527100 (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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All rights reserved. How to cite UCSF ChimeraX > open > /Users/guidopetrovich/Documents/DmelIR25a_IR93a-VcarIR40a/DmelIR25a_IR93a-VcarIR40a-Isolde5.pdb Chain information for DmelIR25a_IR93a-VcarIR40a-Isolde5.pdb #1 --- Chain | Description A | No description available B | No description available C | No description available D | No description available > open > /Users/guidopetrovich/Documents/DmelIR25a_IR93a-VcarIR40a/cryosparc_P54_J755_004_volume_map_sharp.mrc Opened cryosparc_P54_J755_004_volume_map_sharp.mrc as #2, grid size 360,360,360, pixel 0.987, shown at level 0.0686, step 2, values float32 > open /Users/guidopetrovich/Documents/DmelIR25a_IR93a-VcarIR40a/IR40a_LBD- > lobe2.pdb Chain information for IR40a_LBD-lobe2.pdb #3 --- Chain | Description A | No description available > isolde start > set selectionWidth 4 Done loading forcefield > isolde set simFidelityMode Medium/Medium ISOLDE: setting sim fidelity mode to Medium/Medium nonbonded_cutoff_distance = 0.900000 use_gbsa = True gbsa_cutoff = 1.100000 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 1 residues in model #1 to IUPAC-IUB standards. Chain information for DmelIR25a_IR93a-VcarIR40a-Isolde5.pdb #1.2 --- Chain | Description A | No description available B | No description available C | No description available D | No description available > clipper associate #2 toModel #1 Opened cryosparc_P54_J755_004_volume_map_sharp.mrc as #1.1.1.1, grid size 360,360,360, pixel 0.987, shown at step 1, values float32 > set bgColor white > lighting soft > graphics silhouettes true > select clear > sequence chain #1.2/A Alignment identifier is 1.2/A > select #1.2/A:23 20 atoms, 20 bonds, 1 residue, 1 model selected > select #1.2/A:23 20 atoms, 20 bonds, 1 residue, 1 model selected > isolde stepto #1.2/A:23 > transparency 50 > volume style surface > volume #1.1.1.1 level 0.1 > isolde stepto next > select #1.2/A:24-25 33 atoms, 32 bonds, 2 residues, 1 model selected > select #1.2/A:24-27 58 atoms, 57 bonds, 4 residues, 1 model selected > select #1.2/A:23 20 atoms, 20 bonds, 1 residue, 1 model selected > select #1.2/A:23-67 717 atoms, 721 bonds, 45 residues, 1 model selected > isolde sim start #1.2/A:23-67 ISOLDE: started sim > select #1.2/A:39 12 atoms, 11 bonds, 1 residue, 1 model selected > select #1.2/A:39-40 32 atoms, 32 bonds, 2 residues, 1 model selected > select #1.2/A:43 10 atoms, 9 bonds, 1 residue, 1 model selected > select #1.2/A:43-44 29 atoms, 28 bonds, 2 residues, 1 model selected > select #1.2/A:40 20 atoms, 20 bonds, 1 residue, 1 model selected > select #1.2/A:40-50 156 atoms, 157 bonds, 11 residues, 1 model selected > isolde stepto prev > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB standards. ISOLDE: stopped sim > isolde stepto next > volume #1.1.1.1 level 0.2 > isolde stepto next > isolde stepto prev > isolde sim start #1.2/A:108 ISOLDE: started sim > select #1.2/A:109 14 atoms, 13 bonds, 1 residue, 1 model selected > select #1.2/A:109-111 40 atoms, 39 bonds, 3 residues, 1 model selected > select #1.2/A:93 10 atoms, 9 bonds, 1 residue, 1 model selected > select #1.2/A:93-108 264 atoms, 266 bonds, 16 residues, 1 model selected > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde stepto next > isolde stepto prev > isolde sim start #1.2/A:120 ISOLDE: started sim > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde stepto next > isolde sim start #1.2/A:123 ISOLDE: started sim > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB standards. ISOLDE: stopped sim > isolde stepto next > isolde stepto prev > isolde sim start #1.2/A:179 ISOLDE: started sim > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde stepto next > select #1.2/A:182 14 atoms, 13 bonds, 1 residue, 1 model selected > select #1.2/A:182-183 31 atoms, 30 bonds, 2 residues, 1 model selected > isolde sim start #1.2/A:182-183 ISOLDE: started sim > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde stepto next > select #1.2/A:185 14 atoms, 13 bonds, 1 residue, 1 model selected > select #1.2/A:185-192 131 atoms, 132 bonds, 8 residues, 1 model selected > isolde sim start #1.2/A:185-192 ISOLDE: started sim > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde stepto next > isolde sim start #1.2/A:192 ISOLDE: started sim > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde stepto next > select #1.2/A:199 11 atoms, 10 bonds, 1 residue, 1 model selected > select #1.2/A:199-200 18 atoms, 17 bonds, 2 residues, 1 model selected > isolde sim start #1.2/A:199-200 ISOLDE: started sim > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde stepto next > isolde sim start #1.2/A:259 ISOLDE: started sim > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde stepto next > isolde sim start #1.2/A:267 ISOLDE: started sim > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde stepto next > isolde stepto prev > isolde stepto next > isolde stepto prev > isolde stepto next > isolde sim start #1.2/A:293 ISOLDE: started sim > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > save > /Users/guidopetrovich/Documents/DmelIR25a_IR93a-VcarIR40a/DmelIR25a_IR93a-VcarIR40a-Isolde6.pdb > models #1 > isolde stepto next > isolde sim start #1.2/A:299 ISOLDE: started sim > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde stepto next > isolde stepto prev > isolde sim start #1.2/A:319 ISOLDE: started sim > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde stepto next > isolde sim start #1.2/A:320 ISOLDE: started sim > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde stepto next > isolde stepto prev > isolde sim start #1.2/A:330 ISOLDE: started sim > select #1.2/A:329 19 atoms, 18 bonds, 1 residue, 1 model selected > select #1.2/A:329-331 50 atoms, 50 bonds, 3 residues, 1 model selected > select #1.2/A:320 19 atoms, 18 bonds, 1 residue, 1 model selected > select #1.2/A:320-331 172 atoms, 173 bonds, 12 residues, 1 model selected > isolde stepto prev > isolde stepto next > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB standards. ISOLDE: stopped sim > isolde stepto next > select #1.2/A:263 14 atoms, 13 bonds, 1 residue, 1 model selected > select #1.2/A:263-346 1341 atoms, 1360 bonds, 84 residues, 1 model selected > select #1.2/A:263-264 34 atoms, 34 bonds, 2 residues, 1 model selected > select #1.2/A:263-347 1365 atoms, 1384 bonds, 85 residues, 1 model selected > isolde sim start #1.2/A:263-347 ISOLDE: started sim > select #1.2/A:260 22 atoms, 21 bonds, 1 residue, 1 model selected > select #1.2/A:260 22 atoms, 21 bonds, 1 residue, 1 model selected > isolde stepto #1.2/A:260 > isolde stepto next > select #1.2/A:319-320 39 atoms, 39 bonds, 2 residues, 1 model selected > select #1.2/A:319-320 39 atoms, 39 bonds, 2 residues, 1 model selected > select #1.2/A:321 14 atoms, 13 bonds, 1 residue, 1 model selected > select #1.2/A:319-321 53 atoms, 53 bonds, 3 residues, 1 model selected > select #1.2/A:331 17 atoms, 17 bonds, 1 residue, 1 model selected > select #1.2/A:319-331 192 atoms, 194 bonds, 13 residues, 1 model selected > select #1.2/A:319 20 atoms, 20 bonds, 1 residue, 1 model selected > select #1.2/A:319 20 atoms, 20 bonds, 1 residue, 1 model selected > select #1.2/A:320-321 33 atoms, 32 bonds, 2 residues, 1 model selected > select #1.2/A:320-321 33 atoms, 32 bonds, 2 residues, 1 model selected > select #1.2/A:320 19 atoms, 18 bonds, 1 residue, 1 model selected > select #1.2/A:320 19 atoms, 18 bonds, 1 residue, 1 model selected > isolde stepto next > select #1.2/A:322 19 atoms, 18 bonds, 1 residue, 1 model selected > select #1.2/A:322-331 139 atoms, 140 bonds, 10 residues, 1 model selected > select #1.2/A:321 14 atoms, 13 bonds, 1 residue, 1 model selected > select #1.2/A:321-328 103 atoms, 103 bonds, 8 residues, 1 model selected > select #1.2/A:320 19 atoms, 18 bonds, 1 residue, 1 model selected > select #1.2/A:320-331 172 atoms, 173 bonds, 12 residues, 1 model selected > select #1.2/A:320 19 atoms, 18 bonds, 1 residue, 1 model selected > select #1.2/A:320 19 atoms, 18 bonds, 1 residue, 1 model selected > select #1.2/A:321 14 atoms, 13 bonds, 1 residue, 1 model selected > select #1.2/A:321 14 atoms, 13 bonds, 1 residue, 1 model selected > isolde stepto next > isolde stepto prev > isolde stepto next > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB standards. ISOLDE: stopped sim > select #1.2/A:342 19 atoms, 18 bonds, 1 residue, 1 model selected > select #1.2/A:342-343 38 atoms, 37 bonds, 2 residues, 1 model selected > select #1.2/A:347 24 atoms, 23 bonds, 1 residue, 1 model selected > select #1.2/A:341-347 130 atoms, 131 bonds, 7 residues, 1 model selected > isolde sim start #1.2/A:341-347 ISOLDE: started sim > isolde stepto next > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > save > /Users/guidopetrovich/Documents/DmelIR25a_IR93a-VcarIR40a/DmelIR25a_IR93a-VcarIR40a-Isolde7.pdb > models #1 ===== 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 M5 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: Mac17,2 Model Number: MDE34LL/A Chip: Apple M5 Total Number of Cores: 10 (4 Super and 6 Efficiency) Memory: 24 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, 5 hours, 51 minutes Graphics/Displays: Apple M5: Chipset Model: Apple M5 Type: GPU Bus: Built-In Total Number of Cores: 10 Vendor: Apple (0x106b) Metal Support: Metal 4 Displays: Color LCD: Display Type: Built-in Liquid Retina XDR Display Resolution: 3024 x 1964 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: No Connection Type: Internal 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 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