id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 19822 Crash in swap_buffers when status line exposed in macOS 26.2 chimerax-bug-report@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-26.2-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 Thread 0x0000000309067000 (most recent call first): File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 579 in _handle_results File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 982 in run File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1045 in _bootstrap_inner File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1002 in _bootstrap Thread 0x000000030805b000 (most recent call first): File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 531 in _handle_tasks File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 982 in run File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1045 in _bootstrap_inner File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1002 in _bootstrap Thread 0x000000030704f000 (most recent call first): File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/selectors.py"", line 415 in select File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/connection.py"", line 948 in wait File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 502 in _wait_for_updates File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 522 in _handle_workers File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 982 in run File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1045 in _bootstrap_inner File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1002 in _bootstrap Thread 0x0000000306043000 (most recent call first): File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 982 in run File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1045 in _bootstrap_inner File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1002 in _bootstrap Thread 0x0000000305037000 (most recent call first): File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 982 in run File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1045 in _bootstrap_inner File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1002 in _bootstrap Thread 0x000000030402b000 (most recent call first): File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 982 in run File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1045 in _bootstrap_inner File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1002 in _bootstrap Thread 0x000000030301f000 (most recent call first): File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 982 in run File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1045 in _bootstrap_inner File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1002 in _bootstrap Thread 0x0000000302013000 (most recent call first): File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 982 in run File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1045 in _bootstrap_inner File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1002 in _bootstrap Thread 0x0000000301007000 (most recent call first): File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 982 in run File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1045 in _bootstrap_inner File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1002 in _bootstrap Thread 0x000000017f18f000 (most recent call first): File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 982 in run File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1045 in _bootstrap_inner File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1002 in _bootstrap Thread 0x000000017e183000 (most recent call first): File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 982 in run File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1045 in _bootstrap_inner File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1002 in _bootstrap Thread 0x000000017d177000 (most recent call first): File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 982 in run File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1045 in _bootstrap_inner File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1002 in _bootstrap Thread 0x000000017c16b000 (most recent call first): File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 982 in run File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1045 in _bootstrap_inner File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1002 in _bootstrap Current thread 0x000000020c55ec40 (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, psutil._psutil_osx, psutil._psutil_posix, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, chimerax.surface._surface, 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resident=0K(0%) swapped_out_or_unallocated=2.1G(100%) Writable regions: Total=1.3G written=22.2M(2%) resident=1410K(0%) swapped_out=20.8M(2%) unallocated=1.3G(98%) VIRTUAL REGION REGION TYPE SIZE COUNT (non-coalesced) =========== ======= ======= Accelerate framework 128K 1 Activity Tracing 256K 1 AttributeGraph Data 1024K 1 CG image 2464K 68 ColorSync 336K 20 CoreAnimation 4960K 150 CoreGraphics 32K 2 CoreImage 96K 3 CoreUI image data 5344K 38 Foundation 32K 2 Kernel Alloc Once 96K 2 MALLOC 515.1M 135 MALLOC guard page 3744K 4 Mach message 64K 3 OpenGL GLSL 256K 3 PROTECTED_MEMORY 16K 1 STACK GUARD 56.8M 52 Stack 408.7M 52 VM_ALLOCATE 236.8M 161 VM_ALLOCATE (reserved) 192.0M 1 reserved VM address space (unallocated) __AUTH 5939K 654 __AUTH_CONST 90.0M 1044 __CTF 824 1 __DATA 43.5M 1138 __DATA_CONST 59.5M 1185 __DATA_DIRTY 8790K 903 __FONT_DATA 2352 1 __GLSLBUILTINS 5176K 1 __INFO_FILTER 8 1 __LINKEDIT 621.0M 137 __OBJC_RO 78.4M 1 __OBJC_RW 2570K 1 __TEXT 1.5G 1202 __TEXT (graphics) 5408K 6 __TPRO_CONST 128K 2 dyld private memory 1200K 12 mapped file 356.6M 91 page table in kernel 1410K 1 shared memory 4976K 37 =========== ======= ======= TOTAL 4.1G 7118 TOTAL, minus reserved VM space 3.9G 7118 "", ""legacyInfo"" : { ""threadTriggered"" : { ""name"" : ""CrBrowserMain"", ""queue"" : ""com.apple.main-thread"" } }, ""logWritingSignature"" : ""2ea17296aaca76f5a2777138864eb25a8e48dc39"", ""bug_type"" : ""309"", ""roots_installed"" : 0, ""trmStatus"" : 1, ""trialInfo"" : { ""rollouts"" : [ { ""rolloutId"" : ""5fb4245a1bbfe8005e33a1e1"", ""factorPackIds"" : [ ], ""deploymentId"" : 240000021 }, { ""rolloutId"" : ""6410af69ed1e1e7ab93ed169"", ""factorPackIds"" : [ ], ""deploymentId"" : 240000011 } ], ""experiments"" : [ ] } } ===== Log before crash start ===== Startup Messages --- note | available bundle cache has not been initialized yet You can double click a model's Name or ID in the model panel to edit those fields 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 > open ""/Users/paulminges/Library/CloudStorage/OneDrive- > Personal/Documents/ResearchStuff/AG-Eder/2. Research/5. Endometriosis/1. > Target Development/Structure_Analysis/MMP-10.pdb"" MMP-10.pdb title: Alphafold monomer V2.0 prediction for stromelysin-2 (P09238) [more info...] Chain information for MMP-10.pdb #1 --- Chain | Description | UniProt A | stromelysin-2 | MMP10_HUMAN 1-476 Computing secondary structure > set bgColor white > set bgColor black > lighting simple > lighting soft > lighting simple > lighting soft > lighting full > lighting soft > rainbow > sequence chain #1/A Alignment identifier is 1/A > select > /A:21-41,55-69,80-87,126-143,211-222,245-247,252-262,328-330,346-348,375-378,425-427,470-474 837 atoms, 837 bonds, 106 residues, 1 model selected > select /A:1-2 16 atoms, 15 bonds, 2 residues, 1 model selected > select /A:1-12 95 atoms, 96 bonds, 12 residues, 1 model selected > select /A:1-2 16 atoms, 15 bonds, 2 residues, 1 model selected > select /A:1-95 758 atoms, 769 bonds, 95 residues, 1 model selected > select /A:1 8 atoms, 7 bonds, 1 residue, 1 model selected > select /A:1-98 779 atoms, 791 bonds, 98 residues, 1 model selected > color sel bychain > color sel bypolymer > color sel bychain > color sel bypolymer > rainbow sel > color sel bypolymer > color sel bynucleotide > interfaces select & ~solvent Missing or invalid ""atoms"" argument: invalid atoms specifier > color #1 #7ad600ff > color #1 #2fd605ff > select /A:1-2 16 atoms, 15 bonds, 2 residues, 1 model selected > select /A:1-99 790 atoms, 803 bonds, 99 residues, 1 model selected > color #1 #942192ff > select /A:1-99 790 atoms, 803 bonds, 99 residues, 1 model selected > color #1 #ff9300ff > select > /A:21-41,55-69,80-87,126-143,211-222,245-247,252-262,328-330,346-348,375-378,425-427,470-474 837 atoms, 837 bonds, 106 residues, 1 model selected > select /A:1 8 atoms, 7 bonds, 1 residue, 1 model selected > select /A:1-99 790 atoms, 803 bonds, 99 residues, 1 model selected > nucleotides sel atoms > style nucleic & sel stick Changed 0 atom styles > select /A:1 8 atoms, 7 bonds, 1 residue, 1 model selected > select /A:1-99 790 atoms, 803 bonds, 99 residues, 1 model selected > color sel gray > select /A:2 8 atoms, 7 bonds, 1 residue, 1 model selected > select /A:2-50 391 atoms, 398 bonds, 49 residues, 1 model selected > select /A:1 8 atoms, 7 bonds, 1 residue, 1 model selected > select /A:1-99 790 atoms, 803 bonds, 99 residues, 1 model selected > label sel attribute label_specifier > undo > select /A:1 8 atoms, 7 bonds, 1 residue, 1 model selected > select /A:1-99 790 atoms, 803 bonds, 99 residues, 1 model selected > ~label sel residues > ui windowfill toggle > volume style surface No volumes specified > select /A:1-2 16 atoms, 15 bonds, 2 residues, 1 model selected > select /A 3833 atoms, 3955 bonds, 476 residues, 1 model selected > volume style surface No volumes specified > coulombic sel Using Amber 20 recommended default charges and atom types for standard residues Coulombic values for MMP-10.pdb_A SES surface #1.1: minimum, -19.89, mean -3.03, maximum 9.23 To also show corresponding color key, enter the above coulombic command and add key true > coulombic sel Coulombic values for MMP-10.pdb_A SES surface #1.1: minimum, -19.89, mean -3.03, maximum 9.23 To also show corresponding color key, enter the above coulombic command and add key true > mlp sel Map values for surface ""MMP-10.pdb_A SES surface"": minimum -31.22, mean -4.877, maximum 23.98 To also show corresponding color key, enter the above mlp command and add key true > style sel stick Changed 3833 atom styles > style sel stick Changed 3833 atom styles > style sel stick Changed 3833 atom styles > style sel stick Changed 3833 atom styles > color sel byhetero > color sel bynucleotide > color sel bychain > nucleotides sel atoms > style nucleic & sel stick Changed 0 atom styles > style sel stick Changed 3833 atom styles > style sel sphere Changed 3833 atom styles > style sel ball Changed 3833 atom styles > select /A:1 8 atoms, 7 bonds, 1 residue, 1 model selected > select /A 3833 atoms, 3955 bonds, 476 residues, 1 model selected > style sel stick Changed 3833 atom styles > style sel ball Changed 3833 atom styles > style sel stick Changed 3833 atom styles > cartoon (#!1 & sel) > select /A:1 8 atoms, 7 bonds, 1 residue, 1 model selected > select /A 3833 atoms, 3955 bonds, 476 residues, 1 model selected > cartoon style (#!1 & sel) xsection oval modeHelix default > color all grey > hide surfaces > show cartoons > hide all > name ""Signal Peptide"" :1-17 Not registering illegal selector name ""Signal Peptide"" > name ""Signal Peptide"" :1-17 Not registering illegal selector name ""Signal Peptide"" > name ""Signal Peptide"" :1-17 Not registering illegal selector name ""Signal Peptide"" > name list There are no user-defined specifier names. > name list There are no user-defined specifier names. > list models Unknown command: list models > list models Unknown command: list models > select /A:1-2 16 atoms, 15 bonds, 2 residues, 1 model selected > select /A 3833 atoms, 3955 bonds, 476 residues, 1 model selected > select /A:1 8 atoms, 7 bonds, 1 residue, 1 model selected > select /A:1-20 153 atoms, 157 bonds, 20 residues, 1 model selected > select clear > select /A:140 14 atoms, 15 bonds, 1 residue, 1 model selected > select /A:140-222 654 atoms, 678 bonds, 83 residues, 1 model selected > ui hideFloating toggle > select clear > name""Signal Peptide"":1-17 incomplete quoted text > name ""Signal Peptide"" :1-17 Not registering illegal selector name ""Signal Peptide"" > color ""Signal Peptide"" orange Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', 'fromcartoons', 'fromribbons', or 'random' or a keyword > color ""Signal Peptide"" red Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', 'fromcartoons', 'fromribbons', or 'random' or a keyword > name list There are no user-defined specifier names. > ui windowfill toggle > name SignalPeptide : 1-17 > name list SignalPeptide : 1-17 > name ProPeptide : 18-98 > color ""SignalPeptide"" lightgrey > color ""ProPeptide"" lightgrey > transparency ""ProPeptide"" 50 > transparency ""ProPeptide"" 5 > transparency ""ProPeptide"" 50 target c > transparency ""SignalPeptide"" 50 target c > name Main 99-476 ""99-476"": invalid atom specifier > name""Main"": 99-476 incomplete quoted text > name Main : 99-476 > color ""Main"" green > select /A:100 6 atoms, 5 bonds, 1 residue, 1 model selected > select /A:100-476 3043 atoms, 3151 bonds, 377 residues, 1 model selected > close session > open ""/Users/paulminges/Library/CloudStorage/OneDrive- > Personal/Documents/ResearchStuff/AG-Eder/2. Research/5. Endometriosis/1. > Target > Development/Structure_Analysis/MMP-10_99-476/fold_2026_02_06_14_30_job_request.json"" Failed opening file /Users/paulminges/Library/CloudStorage/OneDrive- Personal/Documents/ResearchStuff/AG-Eder/2. Research/5. Endometriosis/1. Target Development/Structure_Analysis/MMP-10_99-476/fold_2026_02_06_14_30_job_request.json: Opening an AlphaFold PAE file requires first opening the predicted atomic model. Did not find an open atomic model from the same directory. If the atomic model is already open choose it using menu Tools / Structure Prediction / AlphaFold Error Plot or use the open command structure option, for example open /Users/paulminges/Library/CloudStorage/OneDrive- Personal/Documents/ResearchStuff/AG-Eder/2. Research/5. Endometriosis/1. Target Development/Structure_Analysis/MMP-10_99-476/fold_2026_02_06_14_30_job_request.json structure #1 If you are trying to open a JSON file that is not AlphaFold PAE data then you need to specify the specific JSON format such as open mole_channels.json format mole > open ""/Users/paulminges/Library/CloudStorage/OneDrive- > Personal/Documents/ResearchStuff/AG-Eder/2. Research/5. Endometriosis/1. > Target > Development/Structure_Analysis/MMP-10_01-476/AF-P09238-F1-model_v6.cif"" Chain information for AF-P09238-F1-model_v6.cif #1 --- Chain | Description | UniProt A | Stromelysin-2 | MMP10_HUMAN 1-476 Color AF-P09238-F1-model_v6.cif by residue attribute pLDDT_score > color bfactor palette alphafold 3833 atoms, 476 residues, atom bfactor range 31 to 98.6 > ui windowfill toggle > open ""/Users/paulminges/Library/CloudStorage/OneDrive- > Personal/Documents/ResearchStuff/AG-Eder/2. Research/5. Endometriosis/1. > Target > Development/Structure_Analysis/MMP-10_99-476/fold_2026_02_06_14_30_full_data_0.json"" Opening an AlphaFold PAE file requires first opening the predicted atomic model. Did not find an open atomic model from the same directory. If the atomic model is already open choose it using menu Tools / Structure Prediction / AlphaFold Error Plot or use the open command structure option, for example open /Users/paulminges/Library/CloudStorage/OneDrive- Personal/Documents/ResearchStuff/AG-Eder/2. Research/5. Endometriosis/1. Target Development/Structure_Analysis/MMP-10_99-476/fold_2026_02_06_14_30_full_data_0.json structure #1 If you are trying to open a JSON file that is not AlphaFold PAE data then you need to specify the specific JSON format such as open mole_channels.json format mole > open ""/Users/paulminges/Library/CloudStorage/OneDrive- > Personal/Documents/ResearchStuff/AG-Eder/2. Research/5. Endometriosis/1. > Target > Development/Structure_Analysis/MMP-10_99-476/fold_2026_02_06_14_30_model_0.cif"" Chain information for fold_2026_02_06_14_30_model_0.cif #2 --- Chain | Description A | . Computing secondary structure > open ""/Users/paulminges/Library/CloudStorage/OneDrive- > Personal/Documents/ResearchStuff/AG-Eder/2. Research/5. Endometriosis/1. > Target > Development/Structure_Analysis/MMP-10_99-476/fold_2026_02_06_14_30_model_0.cif"" > format mmcif Chain information for fold_2026_02_06_14_30_model_0.cif #3 --- Chain | Description A | . Computing secondary structure > list models Unknown command: list models > hide #1 > ui tool show ""Model Panel"" > ui tool show ""Selection Inspector"" ===== 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 M4 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 Air Model Identifier: Mac16,13 Model Number: MC6L4D/A Chip: Apple M4 Total Number of Cores: 10 (4 performance and 6 efficiency) Memory: 24 GB System Firmware Version: 13822.61.10 OS Loader Version: 13822.61.10 Software: System Software Overview: System Version: macOS 26.2 (25C56) Kernel Version: Darwin 25.2.0 Time since boot: 6 days, 21 hours, 46 minutes Graphics/Displays: Apple M4: Chipset Model: Apple M4 Type: GPU Bus: Built-In Total Number of Cores: 10 Vendor: Apple (0x106b) Metal Support: Metal 4 Displays: N27p: Resolution: 5120 x 2880 (5K/UHD+ - Ultra High Definition Plus) UI Looks like: 2560 x 1440 @ 60.00Hz Main Display: Yes Mirror: Off Online: Yes Rotation: Supported Automatically Adjust Brightness: No Color LCD: Display Type: Built-in Liquid Retina Display Resolution: 2880 x 1864 Retina Mirror: Off Online: Yes Automatically Adjust Brightness: Yes 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 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