id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 20320 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 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 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 0x000000030704f000 (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 0x0000000306043000 (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 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 0x000000017f2b3000 (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 0x000000017e2a7000 (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 0x000000017d29b000 (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 0x000000017c28f000 (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 0x000000017b283000 (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 0x00000001fb28b100 (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, PIL._imaging, chimerax.map._map, chimerax.surface._surface, 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swapped_out_or_unallocated=2.1G(100%) Writable regions: Total=1.2G written=65.6M(5%) resident=1301K(0%) swapped_out=64.3M(5%) unallocated=1.1G(95%) VIRTUAL REGION REGION TYPE SIZE COUNT (non-coalesced) =========== ======= ======= .note.gnu.proper 320 1 Accelerate framework 256K 2 Activity Tracing 256K 1 AttributeGraph Data 1024K 1 CG image 48K 3 ColorSync 240K 15 CoreAnimation 1440K 79 CoreGraphics 48K 3 CoreUI image data 5488K 50 Foundation 32K 2 Kernel Alloc Once 112K 3 MALLOC 370.8M 93 MALLOC guard page 3568K 4 Mach message 64K 2 OpenGL GLSL 256K 3 PROTECTED_MEMORY 16K 1 STACK GUARD 56.8M 52 Stack 401.2M 52 VM_ALLOCATE 264.4M 278 VM_ALLOCATE (reserved) 192.0M 1 reserved VM address space (unallocated) __AUTH 5964K 654 __AUTH_CONST 90.5M 1040 __CTF 824 1 __DATA 42.6M 1126 __DATA_CONST 59.4M 1174 __DATA_DIRTY 8497K 897 __FONT_DATA 2352 1 __GLSLBUILTINS 5176K 1 __INFO_FILTER 8 1 __LINKEDIT 617.8M 130 __OBJC_RO 78.4M 1 __OBJC_RW 2571K 1 __TEXT 1.5G 1172 __TEXT (graphics) 21.6M 24 __TPRO_CONST 128K 2 dyld private memory 432K 4 mapped file 315.9M 64 page table in kernel 1301K 1 shared memory 3712K 26 =========== ======= ======= TOTAL 4.0G 6966 TOTAL, minus reserved VM space 3.8G 6966 "", ""legacyInfo"" : { ""threadTriggered"" : { ""name"" : ""CrBrowserMain"", ""queue"" : ""com.apple.main-thread"" } }, ""logWritingSignature"" : ""fba21231002d31b7c937df348626334c597af8f4"", ""roots_installed"" : 0, ""bug_type"" : ""309"", ""trmStatus"" : 1, ""trialInfo"" : { ""rollouts"" : [ { ""rolloutId"" : ""661464ecda55e5192b100804"", ""factorPackIds"" : [ ], ""deploymentId"" : 240000005 }, { ""rolloutId"" : ""644114de41e7236e6177f9bd"", ""factorPackIds"" : [ ], ""deploymentId"" : 240000013 } ], ""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/nitrogenousbase/Desktop/cgas- > patches/32x32x32/roi1_patch_32x32x32.mrc Opened roi1_patch_32x32x32.mrc as #1, grid size 32,32,32, pixel 8, shown at level 4.48, step 1, values float32 > volume #1 level 3.608 > volume #1 level 1.426 > volume #1 step 2 > volume #1 step 1 > volume #1 level 1.956 > volume #1 level 2.425 > open /Users/nitrogenousbase/Desktop/cgas- > patches/48x48x48/roi1_patch_48x48x48.mrc Opened roi1_patch_48x48x48.mrc as #2, grid size 48,48,48, pixel 8, shown at level 4.56, step 1, values float32 > open /Users/nitrogenousbase/Desktop/cgas- > patches/64x64x64/roi1_patch_64x64x64.mrc Opened roi1_patch_64x64x64.mrc as #3, grid size 64,64,64, pixel 8, shown at level 4.48, step 1, values float32 > hide #!1 models > hide #!2 models > show #!2 models > volume #2 level 2.848 > volume #3 level 3.292 > volume #3 level 3 > volume #1 level 3.139 > volume #2 level -3.876 > volume #3 level 3.225 > volume #2 level 2.826 > hide #!3 models > hide #!2 models > volume #1 level 3.118 > show #!2 models > hide #!2 models > show #!2 models > volume #1 level 2.467 > open /Users/nitrogenousbase/Desktop/cgas- > patches/48x48x48/roi2_patch_48x48x48.mrc Opened roi2_patch_48x48x48.mrc as #4, grid size 48,48,48, pixel 8, shown at level 4.34, step 1, values float32 > hide #!1 models > hide #!2 models > volume #4 level 3.982 > volume #4 level 3.139 > volume #4 level 2.078 > volume #4 level 2.681 > volume #4 level 2.271 > volume #4 level 2.391 > open /Users/nitrogenousbase/Downloads/6LRJ.cif Summary of feedback from opening /Users/nitrogenousbase/Downloads/6LRJ.cif --- notes | Fetching CCD EQX from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/X/EQX/EQX.cif Fetching CCD ZN from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/N/ZN/ZN.cif 6LRJ.cif title: Human cGAS catalytic domain bound with compound 23 [more info...] Chain information for 6LRJ.cif #5 --- Chain | Description | UniProt A B | Cyclic GMP-AMP synthase | CGAS_HUMAN 157-522 Non-standard residues in 6LRJ.cif #5 --- EQX — 4-[2-(2-methyl-[1,2,4]triazolo[1,5-c]quinazolin-5-yl)hydrazinyl]-4-oxidanylidene- butanoic acid ZN — zinc ion 5260 atoms have anisotropic B-factors. Depict anisotropic information with Thermal Ellipsoids [start tool...] or the aniso command. > hide #!4 models > hide #!5 models > show #!5 models > show #!5 target m > view #5 clip false > show #!4 models > show #!4 target m > view #4 clip false > select add #5 5260 atoms, 5359 bonds, 22 pseudobonds, 666 residues, 4 models selected > hide #!4 models > show #!4 models > select subtract #5 Nothing selected > view #5 clip false > ui mousemode right ""translate selected models"" > fitmap #5 inMap #3 Fit molecule 6LRJ.cif (#5) to map roi1_patch_64x64x64.mrc (#3) using 5260 atoms average map value = 0, steps = 24 shifted from previous position = 0 rotated from previous position = 0 degrees atoms outside contour = 5260, contour level = 3.2249 Position of 6LRJ.cif (#5) relative to roi1_patch_64x64x64.mrc (#3) coordinates: Matrix rotation and translation 1.00000000 0.00000000 0.00000000 0.00000000 0.00000000 1.00000000 0.00000000 0.00000000 0.00000000 0.00000000 1.00000000 0.00000000 Axis 0.00000000 0.00000000 1.00000000 Axis point 0.00000000 0.00000000 0.00000000 Rotation angle (degrees) 0.00000000 Shift along axis 0.00000000 > hide #!4 models > show #!4 models > view #4 clip false > select add #5 5260 atoms, 5359 bonds, 22 pseudobonds, 666 residues, 4 models selected > move #5 center #4 Missing or invalid ""axis"" argument: Axis argument requires 2 atoms, got 5260 atoms > move cofr models #5 toCenter #4 Missing or invalid ""models"" argument: invalid models specifier > align #5 toAtoms #4 Unequal number of atoms to pair, 5260 and 0 > show #4 > show #5 > view all > view matrix models #5,1,0,0,1084.3,0,1,0,2037.1,0,0,1,3614.1 > view matrix models #5,1,0,0,3711.8,0,1,0,6100.3,0,0,1,1225 > view matrix models #5,1,0,0,5634.4,0,1,0,5024.7,0,0,1,1204.3 > view matrix models #5,1,0,0,5619.4,0,1,0,5034.4,0,0,1,1196.1 > ui mousemode right zoom > ui mousemode right rotate > ui mousemode right translate > ui mousemode right ""rotate selected models"" > view matrix models > #5,0.80382,0.58124,-0.12663,5632.8,-0.56285,0.81202,0.15438,5040.7,0.19256,-0.052823,0.97986,1191.9 > select add #4 5260 atoms, 5359 bonds, 22 pseudobonds, 666 residues, 6 models selected > ui mousemode right rotate > select subtract #4 5260 atoms, 5359 bonds, 22 pseudobonds, 666 residues, 4 models selected > select subtract #5 Nothing selected > ui mousemode right ""rotate selected models"" > view #4 clip false > select add #5 5260 atoms, 5359 bonds, 22 pseudobonds, 666 residues, 4 models selected > view matrix models > #5,0.85602,-0.10972,-0.50517,5634.2,0.44019,0.66709,0.60102,5006.2,0.27105,-0.73686,0.61934,1192.4 > ui mousemode right ""translate selected models"" > view matrix models > #5,0.85602,-0.10972,-0.50517,5907,0.44019,0.66709,0.60102,5001.8,0.27105,-0.73686,0.61934,1323.7 > view matrix models > #5,0.85602,-0.10972,-0.50517,6145.1,0.44019,0.66709,0.60102,5267.6,0.27105,-0.73686,0.61934,1361.8 > view matrix models > #5,0.85602,-0.10972,-0.50517,5896,0.44019,0.66709,0.60102,5554.9,0.27105,-0.73686,0.61934,1343 > view matrix models > #5,0.85602,-0.10972,-0.50517,5824.7,0.44019,0.66709,0.60102,5542.5,0.27105,-0.73686,0.61934,1413.3 > show #!1 models > hide #!4 models > show #!4 target m > view matrix models > #5,0.85602,-0.10972,-0.50517,5691.5,0.44019,0.66709,0.60102,5482.6,0.27105,-0.73686,0.61934,1260.6 > hide #!4 models > select add #1 5260 atoms, 5359 bonds, 22 pseudobonds, 666 residues, 6 models selected > hide #!1 models > show #!1 models > show #!1 target m > view #1 clip false > show #!4 models > undo > show #!4 models > hide #!4 models > show #!4 models > hide #!4 models > show #!1 target m > view #1 clip false > view matrix models > #1,1,0,0,2.2626,0,1,0,-9.4427,0,0,1,4.3031,#5,0.85602,-0.10972,-0.50517,5693.8,0.44019,0.66709,0.60102,5473.1,0.27105,-0.73686,0.61934,1264.9 > select subtract #1 5260 atoms, 5359 bonds, 22 pseudobonds, 666 residues, 4 models selected > view matrix models > #5,0.85602,-0.10972,-0.50517,5693.8,0.44019,0.66709,0.60102,5473,0.27105,-0.73686,0.61934,1265 > view matrix models > #5,0.85602,-0.10972,-0.50517,5760.8,0.44019,0.66709,0.60102,5135,0.27105,-0.73686,0.61934,1516.3 > view matrix models > #5,0.85602,-0.10972,-0.50517,5701.6,0.44019,0.66709,0.60102,4835.4,0.27105,-0.73686,0.61934,1551.9 > view matrix models > #5,0.85602,-0.10972,-0.50517,5526,0.44019,0.66709,0.60102,4557.3,0.27105,-0.73686,0.61934,1541.9 > view matrix models > #5,0.85602,-0.10972,-0.50517,5235.9,0.44019,0.66709,0.60102,4389.2,0.27105,-0.73686,0.61934,1468.5 > view matrix models > #5,0.85602,-0.10972,-0.50517,5034.4,0.44019,0.66709,0.60102,4376.8,0.27105,-0.73686,0.61934,1431.8 > view matrix models > #5,0.85602,-0.10972,-0.50517,4852,0.44019,0.66709,0.60102,4435,0.27105,-0.73686,0.61934,1458.8 > view matrix models > #5,0.85602,-0.10972,-0.50517,4740.3,0.44019,0.66709,0.60102,4630.6,0.27105,-0.73686,0.61934,1473.6 > view matrix models > #5,0.85602,-0.10972,-0.50517,4741.3,0.44019,0.66709,0.60102,4630.4,0.27105,-0.73686,0.61934,1475.6 > view matrix models > #5,0.85602,-0.10972,-0.50517,4717.2,0.44019,0.66709,0.60102,4641.5,0.27105,-0.73686,0.61934,1442 > view matrix models > #5,0.85602,-0.10972,-0.50517,4697.1,0.44019,0.66709,0.60102,4664.7,0.27105,-0.73686,0.61934,1382.5 > view matrix models > #5,0.85602,-0.10972,-0.50517,4979.7,0.44019,0.66709,0.60102,4760.1,0.27105,-0.73686,0.61934,1379.7 > view matrix models > #5,0.85602,-0.10972,-0.50517,4970.5,0.44019,0.66709,0.60102,4766,0.27105,-0.73686,0.61934,1372.4 > ui mousemode right ""rotate selected models"" > view matrix models > #5,-0.1653,-0.92974,-0.32904,4979.5,-0.65724,0.3526,-0.66612,4818.7,0.73533,0.10615,-0.66934,1404 > ui mousemode right ""translate selected models"" > view matrix models > #5,-0.1653,-0.92974,-0.32904,4967.1,-0.65724,0.3526,-0.66612,4833,0.73533,0.10615,-0.66934,1402.6 > view matrix models > #5,-0.1653,-0.92974,-0.32904,4839.9,-0.65724,0.3526,-0.66612,4868,0.73533,0.10615,-0.66934,1449.7 > ui mousemode right ""rotate selected models"" > view matrix models > #5,0.41775,-0.76089,0.49652,4808.1,-0.6109,-0.63975,-0.4664,4851.7,0.67252,-0.10848,-0.73208,1450.4 > view matrix models > #5,0.59389,-0.42991,0.68005,4803,-0.36932,-0.89662,-0.24429,4838.2,0.71477,-0.10608,-0.69127,1448.5 > ui mousemode right ""translate selected models"" > view matrix models > #5,0.59389,-0.42991,0.68005,4790.6,-0.36932,-0.89662,-0.24429,4877.8,0.71477,-0.10608,-0.69127,1451.5 > view matrix models > #5,0.59389,-0.42991,0.68005,4802.5,-0.36932,-0.89662,-0.24429,4898.4,0.71477,-0.10608,-0.69127,1452.5 > volume #1 level 4.042 > view matrix models > #5,0.59389,-0.42991,0.68005,4882.2,-0.36932,-0.89662,-0.24429,4848.3,0.71477,-0.10608,-0.69127,1455.3 > view matrix models > #5,0.59389,-0.42991,0.68005,4850.3,-0.36932,-0.89662,-0.24429,4867.4,0.71477,-0.10608,-0.69127,1445.7 > ui mousemode right ""rotate selected models"" > view matrix models > #5,0.57221,-0.69926,0.42849,4854.4,-0.28198,-0.65838,-0.69787,4879.5,0.7701,0.27851,-0.57391,1445.5 > view matrix models > #5,0.62872,-0.090123,-0.77239,4890,0.10523,0.99399,-0.030323,4871.1,0.77048,-0.062213,0.63442,1411.1 > ui mousemode right ""translate selected models"" > view matrix models > #5,0.62872,-0.090123,-0.77239,4861.2,0.10523,0.99399,-0.030323,4896.1,0.77048,-0.062213,0.63442,1430.3 > volume #1 level 3.748 > view matrix models > #5,0.62872,-0.090123,-0.77239,5035.6,0.10523,0.99399,-0.030323,4810.9,0.77048,-0.062213,0.63442,1328.2 > view matrix models > #5,0.62872,-0.090123,-0.77239,5021.6,0.10523,0.99399,-0.030323,4800.9,0.77048,-0.062213,0.63442,1322 > view matrix models > #5,0.62872,-0.090123,-0.77239,5029.4,0.10523,0.99399,-0.030323,4806.5,0.77048,-0.062213,0.63442,1308.5 > volume #1 level 2.866 > view matrix models > #5,0.62872,-0.090123,-0.77239,5030.9,0.10523,0.99399,-0.030323,4808.1,0.77048,-0.062213,0.63442,1327.3 > view matrix models > #5,0.62872,-0.090123,-0.77239,4998.5,0.10523,0.99399,-0.030323,4791.4,0.77048,-0.062213,0.63442,1397.4 > view matrix models > #5,0.62872,-0.090123,-0.77239,4850.6,0.10523,0.99399,-0.030323,4914.6,0.77048,-0.062213,0.63442,1443.9 > ui mousemode right ""rotate selected models"" > view matrix models > #5,0.69089,-0.091611,-0.71713,4847.8,0.24182,0.96409,0.10982,4907.8,0.68131,-0.24929,0.68823,1442.5 > view matrix models > #5,0.80169,-0.10417,-0.5886,4842,0.50003,0.65641,0.56489,4887.5,0.32752,-0.74718,0.57832,1447.8 > view matrix models > #5,-0.69644,-0.29731,0.65313,4840.6,0.23512,-0.95444,-0.18376,4895.7,0.678,0.025586,0.73461,1444.2 > ui mousemode right ""translate selected models"" > view matrix models > #5,-0.69644,-0.29731,0.65313,4849.8,0.23512,-0.95444,-0.18376,4888.8,0.678,0.025586,0.73461,1440 > view matrix models > #5,-0.69644,-0.29731,0.65313,4842.5,0.23512,-0.95444,-0.18376,4876.7,0.678,0.025586,0.73461,1440.4 > view matrix models > #5,-0.69644,-0.29731,0.65313,4810.9,0.23512,-0.95444,-0.18376,4948,0.678,0.025586,0.73461,1399.4 > view matrix models > #5,-0.69644,-0.29731,0.65313,4866,0.23512,-0.95444,-0.18376,4914.6,0.678,0.025586,0.73461,1381.5 > view matrix models > #5,-0.69644,-0.29731,0.65313,4858.4,0.23512,-0.95444,-0.18376,4907.2,0.678,0.025586,0.73461,1402.1 > view matrix models > #5,-0.69644,-0.29731,0.65313,4836.5,0.23512,-0.95444,-0.18376,4889.9,0.678,0.025586,0.73461,1397.6 > view matrix models > #5,-0.69644,-0.29731,0.65313,4834,0.23512,-0.95444,-0.18376,4893.7,0.678,0.025586,0.73461,1382.2 > ui mousemode right ""rotate selected models"" > view matrix models > #5,-0.73872,-0.60587,-0.29531,4855.9,0.40145,-0.74745,0.5293,4874.1,-0.54141,0.27245,0.79539,1409.4 > view matrix models > #5,-0.76139,-0.50981,-0.40048,4860.1,0.22962,-0.78976,0.56881,4876.3,-0.60627,0.34113,0.71838,1413.4 > view matrix models > #5,-0.75861,-0.44689,-0.47413,4862.5,0.25194,-0.8723,0.41908,4878.8,-0.60087,0.19846,0.77432,1410.4 > view matrix models > #5,-0.73986,-0.5703,-0.35687,4857.9,0.35424,-0.78121,0.51402,4875.1,-0.57194,0.25389,0.78002,1410.2 > view matrix models > #5,-0.7136,-0.064842,-0.69754,4871.2,-0.13334,0.99008,0.044373,4915.7,0.68775,0.12467,-0.71517,1420 > volume #1 style mesh > view matrix models > #5,-0.684,-0.37304,-0.62689,4865.6,-0.40666,0.90843,-0.096876,4924.4,0.60562,0.18867,-0.77307,1423.9 > view matrix models > #5,-0.72931,0.03445,-0.68332,4872.2,-0.052032,0.99305,0.1056,4912.5,0.68221,0.11257,-0.72244,1420.2 > view matrix models > #5,0.19429,-0.72512,0.66064,4810.3,0.97481,0.21794,-0.047478,4886.4,-0.10955,0.65322,0.7492,1405.2 > view matrix models > #5,-0.49484,-0.14142,0.8574,4826.1,-0.055129,-0.97957,-0.19339,4899.9,0.86723,-0.14297,0.47693,1383 > view matrix models > #5,-0.47699,-0.12885,0.86941,4825.5,0.0079755,-0.98979,-0.14231,4897.2,0.87887,-0.060947,0.47315,1383.7 > view matrix models > #5,-0.47494,-0.061501,0.87787,4825.9,0.091407,-0.99561,-0.020296,4892.2,0.87526,0.070603,0.47848,1384.9 > view matrix models > #5,-0.67058,-0.38661,0.63313,4833,0.40645,-0.90544,-0.12241,4889,0.62059,0.17525,0.7643,1384.2 > view matrix models > #5,-0.6673,-0.38497,0.63758,4832.9,0.40588,-0.90574,-0.12209,4889,0.62448,0.17731,0.76065,1384.2 > ui mousemode right ""translate selected models"" > view matrix models > #5,-0.6673,-0.38497,0.63758,4840,0.40588,-0.90574,-0.12209,4884.4,0.62448,0.17731,0.76065,1383.5 > volume #1 level 4.063 > volume #1 level 3.601 > view matrix models > #5,-0.6673,-0.38497,0.63758,4835.4,0.40588,-0.90574,-0.12209,4888.2,0.62448,0.17731,0.76065,1408.4 > view matrix models > #5,-0.6673,-0.38497,0.63758,4834.3,0.40588,-0.90574,-0.12209,4884.3,0.62448,0.17731,0.76065,1408.6 > ui mousemode right ""rotate selected models"" > view matrix models > #5,-0.58509,-0.36049,0.72644,4830.5,0.39949,-0.90766,-0.12866,4884.6,0.70575,0.21493,0.67507,1409.5 ===== 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 M1 Pro 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: MacBookPro18,3 Model Number: Z15G001X8LL/A Chip: Apple M1 Pro Total Number of Cores: 10 (8 Performance and 2 Efficiency) Memory: 32 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: 16 days, 56 minutes Graphics/Displays: Apple M1 Pro: Chipset Model: Apple M1 Pro Type: GPU Bus: Built-In Total Number of Cores: 16 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: Yes Connection Type: Internal LG ULTRAWIDE: Resolution: 2560 x 1080 (UW-UXGA - Ultra Wide - Ultra Extended Graphics Array) UI Looks like: 2560 x 1080 @ 50.00Hz 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