id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 16940 Crash in event loop chimerax-bug-report@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-12.5-arm64-arm-64bit ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. Fatal Python error: Segmentation fault Thread 0x000000028c3f7000 (most recent call first): File ""/private/var/folders/8x/22q5t3l50wx6gzz5s_6bnmk00000gn/T/AppTranslocation/C13A0BEE-A79C-416B-A0CA-911A9B3949A6/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 324 in wait File ""/private/var/folders/8x/22q5t3l50wx6gzz5s_6bnmk00000gn/T/AppTranslocation/C13A0BEE-A79C-416B-A0CA-911A9B3949A6/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 622 in wait File ""/private/var/folders/8x/22q5t3l50wx6gzz5s_6bnmk00000gn/T/AppTranslocation/C13A0BEE-A79C-416B-A0CA-911A9B3949A6/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1392 in run File ""/private/var/folders/8x/22q5t3l50wx6gzz5s_6bnmk00000gn/T/AppTranslocation/C13A0BEE-A79C-416B-A0CA-911A9B3949A6/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/private/var/folders/8x/22q5t3l50wx6gzz5s_6bnmk00000gn/T/AppTranslocation/C13A0BEE-A79C-416B-A0CA-911A9B3949A6/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000028805b000 (most recent call first): File ""/private/var/folders/8x/22q5t3l50wx6gzz5s_6bnmk00000gn/T/AppTranslocation/C13A0BEE-A79C-416B-A0CA-911A9B3949A6/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 579 in _handle_results File ""/private/var/folders/8x/22q5t3l50wx6gzz5s_6bnmk00000gn/T/AppTranslocation/C13A0BEE-A79C-416B-A0CA-911A9B3949A6/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/private/var/folders/8x/22q5t3l50wx6gzz5s_6bnmk00000gn/T/AppTranslocation/C13A0BEE-A79C-416B-A0CA-911A9B3949A6/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/private/var/folders/8x/22q5t3l50wx6gzz5s_6bnmk00000gn/T/AppTranslocation/C13A0BEE-A79C-416B-A0CA-911A9B3949A6/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000028704f000 (most recent call first): File ""/private/var/folders/8x/22q5t3l50wx6gzz5s_6bnmk00000gn/T/AppTranslocation/C13A0BEE-A79C-416B-A0CA-911A9B3949A6/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 531 in _handle_tasks File ""/private/var/folders/8x/22q5t3l50wx6gzz5s_6bnmk00000gn/T/AppTranslocation/C13A0BEE-A79C-416B-A0CA-911A9B3949A6/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/private/var/folders/8x/22q5t3l50wx6gzz5s_6bnmk00000gn/T/AppTranslocation/C13A0BEE-A79C-416B-A0CA-911A9B3949A6/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/private/var/folders/8x/22q5t3l50wx6gzz5s_6bnmk00000gn/T/AppTranslocation/C13A0BEE-A79C-416B-A0CA-911A9B3949A6/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x0000000286043000 (most recent call first): File ""/private/var/folders/8x/22q5t3l50wx6gzz5s_6bnmk00000gn/T/AppTranslocation/C13A0BEE-A79C-416B-A0CA-911A9B3949A6/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/selectors.py"", line 415 in select File ""/private/var/folders/8x/22q5t3l50wx6gzz5s_6bnmk00000gn/T/AppTranslocation/C13A0BEE-A79C-416B-A0CA-911A9B3949A6/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/connection.py"", line 930 in wait File ""/private/var/folders/8x/22q5t3l50wx6gzz5s_6bnmk00000gn/T/AppTranslocation/C13A0BEE-A79C-416B-A0CA-911A9B3949A6/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 502 in _wait_for_updates File ""/private/var/folders/8x/22q5t3l50wx6gzz5s_6bnmk00000gn/T/AppTranslocation/C13A0BEE-A79C-416B-A0CA-911A9B3949A6/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 522 in _handle_workers File ""/private/var/folders/8x/22q5t3l50wx6gzz5s_6bnmk00000gn/T/AppTranslocation/C13A0BEE-A79C-416B-A0CA-911A9B3949A6/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/private/var/folders/8x/22q5t3l50wx6gzz5s_6bnmk00000gn/T/AppTranslocation/C13A0BEE-A79C-416B-A0CA-911A9B3949A6/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/private/var/folders/8x/22q5t3l50wx6gzz5s_6bnmk00000gn/T/AppTranslocation/C13A0BEE-A79C-416B-A0CA-911A9B3949A6/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x0000000285037000 (most recent call first): File ""/private/var/folders/8x/22q5t3l50wx6gzz5s_6bnmk00000gn/T/AppTranslocation/C13A0BEE-A79C-416B-A0CA-911A9B3949A6/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/private/var/folders/8x/22q5t3l50wx6gzz5s_6bnmk00000gn/T/AppTranslocation/C13A0BEE-A79C-416B-A0CA-911A9B3949A6/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/private/var/folders/8x/22q5t3l50wx6gzz5s_6bnmk00000gn/T/AppTranslocation/C13A0BEE-A79C-416B-A0CA-911A9B3949A6/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/private/var/folders/8x/22q5t3l50wx6gzz5s_6bnmk00000gn/T/AppTranslocation/C13A0BEE-A79C-416B-A0CA-911A9B3949A6/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000028402b000 (most recent call first): File ""/private/var/folders/8x/22q5t3l50wx6gzz5s_6bnmk00000gn/T/AppTranslocation/C13A0BEE-A79C-416B-A0CA-911A9B3949A6/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/private/var/folders/8x/22q5t3l50wx6gzz5s_6bnmk00000gn/T/AppTranslocation/C13A0BEE-A79C-416B-A0CA-911A9B3949A6/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/private/var/folders/8x/22q5t3l50wx6gzz5s_6bnmk00000gn/T/AppTranslocation/C13A0BEE-A79C-416B-A0CA-911A9B3949A6/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/private/var/folders/8x/22q5t3l50wx6gzz5s_6bnmk00000gn/T/AppTranslocation/C13A0BEE-A79C-416B-A0CA-911A9B3949A6/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000028301f000 (most recent call first): File ""/private/var/folders/8x/22q5t3l50wx6gzz5s_6bnmk00000gn/T/AppTranslocation/C13A0BEE-A79C-416B-A0CA-911A9B3949A6/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/private/var/folders/8x/22q5t3l50wx6gzz5s_6bnmk00000gn/T/AppTranslocation/C13A0BEE-A79C-416B-A0CA-911A9B3949A6/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/private/var/folders/8x/22q5t3l50wx6gzz5s_6bnmk00000gn/T/AppTranslocation/C13A0BEE-A79C-416B-A0CA-911A9B3949A6/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/private/var/folders/8x/22q5t3l50wx6gzz5s_6bnmk00000gn/T/AppTranslocation/C13A0BEE-A79C-416B-A0CA-911A9B3949A6/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x0000000282013000 (most recent call first): File ""/private/var/folders/8x/22q5t3l50wx6gzz5s_6bnmk00000gn/T/AppTranslocation/C13A0BEE-A79C-416B-A0CA-911A9B3949A6/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/private/var/folders/8x/22q5t3l50wx6gzz5s_6bnmk00000gn/T/AppTranslocation/C13A0BEE-A79C-416B-A0CA-911A9B3949A6/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/private/var/folders/8x/22q5t3l50wx6gzz5s_6bnmk00000gn/T/AppTranslocation/C13A0BEE-A79C-416B-A0CA-911A9B3949A6/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/private/var/folders/8x/22q5t3l50wx6gzz5s_6bnmk00000gn/T/AppTranslocation/C13A0BEE-A79C-416B-A0CA-911A9B3949A6/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x0000000281007000 (most recent call first): File ""/private/var/folders/8x/22q5t3l50wx6gzz5s_6bnmk00000gn/T/AppTranslocation/C13A0BEE-A79C-416B-A0CA-911A9B3949A6/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/private/var/folders/8x/22q5t3l50wx6gzz5s_6bnmk00000gn/T/AppTranslocation/C13A0BEE-A79C-416B-A0CA-911A9B3949A6/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/private/var/folders/8x/22q5t3l50wx6gzz5s_6bnmk00000gn/T/AppTranslocation/C13A0BEE-A79C-416B-A0CA-911A9B3949A6/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/private/var/folders/8x/22q5t3l50wx6gzz5s_6bnmk00000gn/T/AppTranslocation/C13A0BEE-A79C-416B-A0CA-911A9B3949A6/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000017f427000 (most recent call first): File ""/private/var/folders/8x/22q5t3l50wx6gzz5s_6bnmk00000gn/T/AppTranslocation/C13A0BEE-A79C-416B-A0CA-911A9B3949A6/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/private/var/folders/8x/22q5t3l50wx6gzz5s_6bnmk00000gn/T/AppTranslocation/C13A0BEE-A79C-416B-A0CA-911A9B3949A6/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/private/var/folders/8x/22q5t3l50wx6gzz5s_6bnmk00000gn/T/AppTranslocation/C13A0BEE-A79C-416B-A0CA-911A9B3949A6/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/private/var/folders/8x/22q5t3l50wx6gzz5s_6bnmk00000gn/T/AppTranslocation/C13A0BEE-A79C-416B-A0CA-911A9B3949A6/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000017e41b000 (most recent call first): File ""/private/var/folders/8x/22q5t3l50wx6gzz5s_6bnmk00000gn/T/AppTranslocation/C13A0BEE-A79C-416B-A0CA-911A9B3949A6/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/private/var/folders/8x/22q5t3l50wx6gzz5s_6bnmk00000gn/T/AppTranslocation/C13A0BEE-A79C-416B-A0CA-911A9B3949A6/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/private/var/folders/8x/22q5t3l50wx6gzz5s_6bnmk00000gn/T/AppTranslocation/C13A0BEE-A79C-416B-A0CA-911A9B3949A6/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/private/var/folders/8x/22q5t3l50wx6gzz5s_6bnmk00000gn/T/AppTranslocation/C13A0BEE-A79C-416B-A0CA-911A9B3949A6/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000017d40f000 (most recent call first): File 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_bootstrap Current thread 0x0000000100268580 (most recent call first): File ""/private/var/folders/8x/22q5t3l50wx6gzz5s_6bnmk00000gn/T/AppTranslocation/C13A0BEE-A79C-416B-A0CA-911A9B3949A6/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 330 in event_loop File ""/private/var/folders/8x/22q5t3l50wx6gzz5s_6bnmk00000gn/T/AppTranslocation/C13A0BEE-A79C-416B-A0CA-911A9B3949A6/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1054 in init File ""/private/var/folders/8x/22q5t3l50wx6gzz5s_6bnmk00000gn/T/AppTranslocation/C13A0BEE-A79C-416B-A0CA-911A9B3949A6/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1217 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, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.surface._surface, chimerax.pdb_lib._load_libs, chimerax.map._map, charset_normalizer.md, requests.packages.charset_normalizer.md, requests.packages.chardet.md, PIL._imaging, kiwisolver._cext, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.pdb._pdbio, PIL._imagingmath, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.atom_search.ast, chimerax.chem_group._chem_group, chimerax.mlp._mlp, chimerax.coulombic._esp (total: 56) {""app_name"":""ChimeraX"",""timestamp"":""2025-02-22 19:09:36.00 -0800"",""app_version"":""1.9.0"",""slice_uuid"":""17982d98-65bc-3327-8526-577ec996453c"",""build_version"":""1.9.0.0"",""platform"":1,""bundleID"":""edu.ucsf.cgl.ChimeraX"",""share_with_app_devs"":1,""is_first_party"":0,""bug_type"":""309"",""os_version"":""macOS 12.5 (21G72)"",""incident_id"":""952BB2E4-8144-4156-8982-CF22BEBCF3A7"",""name"":""ChimeraX""} { ""uptime"" : 310000, ""procLaunch"" : ""2025-02-22 14:53:18.4401 -0800"", ""procRole"" : ""Foreground"", ""version"" : 2, ""userID"" : 501, ""deployVersion"" : 210, 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swapped_out=0K(0%) unallocated=5.1G(100%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 640K 5 \nActivity Tracing 256K 1 \nCG backing stores 3328K 4 \nCG image 7888K 88 \nCG raster data 288K 6 \nColorSync 640K 28 \nCoreAnimation 17.6M 114 \nCoreGraphics 32K 2 \nCoreUI image data 5408K 37 \nFoundation 16K 1 \nKernel Alloc Once 1424K 4 \nMALLOC 3.3G 169 \nMALLOC guard page 192K 11 \nMALLOC_MEDIUM (reserved) 928.0M 9 reserved VM address space (unallocated)\nMALLOC_NANO (reserved) 128.0M 1 reserved VM address space (unallocated)\nMach message 64K 2 \nOpenGL GLSL 384K 4 \nSTACK GUARD 56.8M 52 \nStack 393.2M 52 \nVM_ALLOCATE 234.9M 219 \nVM_ALLOCATE (reserved) 128.0M 1 reserved VM address space (unallocated)\n__AUTH 3382K 406 \n__AUTH_CONST 24.0M 623 \n__CTF 756 1 \n__DATA 26.9M 774 \n__DATA_CONST 33.1M 780 \n__DATA_DIRTY 2187K 267 \n__FONT_DATA 4K 1 \n__GLSLBUILTINS 5176K 1 \n__LINKEDIT 607.3M 161 \n__OBJC_CONST 5144K 371 \n__OBJC_RO 83.0M 1 \n__OBJC_RW 3168K 1 \n__TEXT 847.5M 798 \n__UNICODE 592K 1 \ndyld private memory 1072K 3 \nmapped file 204.6M 57 \nshared memory 3344K 29 \n=========== ======= ======= \nTOTAL 7.0G 5085 \nTOTAL, minus reserved VM space 5.8G 5085 \n"", ""legacyInfo"" : { ""threadTriggered"" : { ""name"" : ""CrBrowserMain"", ""queue"" : ""com.apple.main-thread"" } }, ""trialInfo"" : { ""rollouts"" : [ { ""rolloutId"" : ""6112e14f37f5d11121dcd519"", ""factorPackIds"" : { ""SIRI_TEXT_TO_SPEECH"" : ""634710168e8be655c1316aaa"" }, ""deploymentId"" : 240000229 }, { ""rolloutId"" : ""6297d96be2c9387df974efa4"", ""factorPackIds"" : { }, ""deploymentId"" : 240000032 } ], ""experiments"" : [ ] } } ===== Log before crash start ===== Startup Messages --- warning | QCoreApplication::postEvent: Unexpected null receiver 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: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > help help:quickstart Cell requested for row 0 is out of bounds for table with 0 rows! Resizing table model. > open /Users/nurnisajanybek/Desktop/2hyy.cif Summary of feedback from opening /Users/nurnisajanybek/Desktop/2hyy.cif --- note | Fetching CCD STI from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/I/STI/STI.cif 2hyy.cif title: Human Abl kinase domain in complex with imatinib (STI571, Glivec) [more info...] Chain information for 2hyy.cif #1 --- Chain | Description | UniProt A B C D | Proto-oncogene tyrosine-protein kinase ABL1 | ABL1_HUMAN 228-500 Non-standard residues in 2hyy.cif #1 --- STI — 4-(4-methyl-piperazin-1-ylmethyl)-N-[4-methyl-3-(4-pyridin-3-yl- pyrimidin-2-ylamino)-phenyl]-benzamide (sti-571; imatinib) 2hyy.cif mmCIF Assemblies --- 1| author_defined_assembly 2| author_defined_assembly 3| author_defined_assembly 4| author_defined_assembly > select ::name=""HOH"" 200 atoms, 200 residues, 1 model selected > hide sel atoms > select clear > open /Users/nurnisajanybek/Desktop/1lpa.pdb 1lpa.pdb title: Interfacial activation of the lipase-procolipase complex by mixed micelles revealed by X-ray crystallography [more info...] Chain information for 1lpa.pdb #2 --- Chain | Description | UniProt A | colipase | COL_PIG 1-95 B | lipase | LIPP_HUMAN 1-449 Non-standard residues in 1lpa.pdb #2 --- BNG — nonyl β-D-glucopyranoside (β-nonylglucoside; nonyl β-D-glucoside; nonyl D-glucoside; nonyl glucoside) CA — calcium ion PLC — diundecyl phosphatidyl choline > select add #1 8702 atoms, 8736 bonds, 5 pseudobonds, 1258 residues, 3 models selected > close > open /Users/nurnisajanybek/Desktop/1lpa.pdb format pdb 1lpa.pdb title: Interfacial activation of the lipase-procolipase complex by mixed micelles revealed by X-ray crystallography [more info...] Chain information for 1lpa.pdb #1 --- Chain | Description | UniProt A | colipase | COL_PIG 1-95 B | lipase | LIPP_HUMAN 1-449 Non-standard residues in 1lpa.pdb #1 --- BNG — nonyl β-D-glucopyranoside (β-nonylglucoside; nonyl β-D-glucoside; nonyl D-glucoside; nonyl glucoside) CA — calcium ion PLC — diundecyl phosphatidyl choline > select nucleic-acid Nothing selected > show atoms > hide atoms > select nucleic-acid Nothing selected > set bgColor white > lighting simple > lighting soft > lighting simple > lighting full > set bgColor black > select /B 3554 atoms, 3648 bonds, 5 pseudobonds, 452 residues, 2 models selected > color (#!1 & sel) purple > color (#!1 & sel) hot pink > ui tool show H-Bonds > hbonds sel color #2ca3fa twoColors true reveal true 434 hydrogen bonds found 222 strict hydrogen bonds found > save /Users/nurnisajanybek/Desktop/image1.png supersample 3 > select clear > save /Users/nurnisajanybek/Desktop/image2.png supersample 3 > mlp Map values for surface ""1lpa.pdb_A SES surface"": minimum -24.79, mean -3.881, maximum 21.98 Map values for surface ""1lpa.pdb_B SES surface"": minimum -30.59, mean -5.371, maximum 23.16 To also show corresponding color key, enter the above mlp command and add key true > save /Users/nurnisajanybek/Desktop/image3.png supersample 3 > hbonds reveal true 498 hydrogen bonds found > mlp Map values for surface ""1lpa.pdb_A SES surface"": minimum -24.79, mean -3.881, maximum 21.98 Map values for surface ""1lpa.pdb_B SES surface"": minimum -30.59, mean -5.371, maximum 23.16 To also show corresponding color key, enter the above mlp command and add key true > coulombic Using Amber 20 recommended default charges and atom types for standard residues Coulombic values for 1lpa.pdb_A SES surface #1.3: minimum, -14.79, mean -1.46, maximum 9.59 Coulombic values for 1lpa.pdb_B SES surface #1.4: minimum, -18.17, mean -1.81, maximum 15.04 To also show corresponding color key, enter the above coulombic command and add key true > save /Users/nurnisajanybek/Desktop/image4.png supersample 3 > preset cartoons/nucleotides ribbons/slabs Using preset: Cartoons/Nucleotides / Ribbons/Slabs Changed 0 atom styles Preset expands to these ChimeraX commands: show nucleic hide protein|solvent|H surf hide style (protein|nucleic|solvent) & @@draw_mode=0 stick ~worm cartoon cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20 cartoon style ~(nucleic|strand) x round cartoon style (nucleic|strand) x rect nucleotides tube/slab shape box > ui tool show ""Show Sequence Viewer"" > sequence chain /B Alignment identifier is 1/B ===== Log before crash end ===== Log: Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 Metal - 76.3 OpenGL renderer: Apple M2 OpenGL vendor: Apple Python: 3.11.4 Locale: UTF-8 Qt version: PyQt6 6.7.1, Qt 6.7.1 Qt runtime version: 6.7.3 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Air Model Identifier: Mac14,2 Chip: Apple M2 Total Number of Cores: 8 (4 performance and 4 efficiency) Memory: 8 GB System Firmware Version: 7459.141.1 OS Loader Version: 7459.141.1 Software: System Software Overview: System Version: macOS 12.5 (21G72) Kernel Version: Darwin 21.6.0 Time since boot: 27 days 5:11 Graphics/Displays: Apple M2: Chipset Model: Apple M2 Type: GPU Bus: Built-In Total Number of Cores: 8 Vendor: Apple (0x106b) Metal Family: Supported, Metal GPUFamily Apple 7 Displays: Color LCD: Display Type: Built-in Liquid Retina Display Resolution: 2560 x 1664 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: No Connection Type: Internal Installed Packages: alabaster: 1.0.0 anyio: 4.7.0 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 3.0.0 auditwheel: 6.1.0 babel: 2.16.0 beautifulsoup4: 4.12.3 blockdiag: 3.0.0 blosc2: 3.0.0 build: 1.2.1 certifi: 2023.11.17 cftime: 1.6.4.post1 charset-normalizer: 3.4.0 ChimeraX-AddCharge: 1.5.18 ChimeraX-AddH: 2.2.6 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.5 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.16.1 ChimeraX-AlphaFold: 1.0.1 ChimeraX-AltlocExplorer: 1.1.2 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.58.8 ChimeraX-AtomicLibrary: 14.1.11 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 3.0.0 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.13.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.4.0 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.4 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.4 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.3 ChimeraX-ColorActions: 1.0.5 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.6 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.9 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.4 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2.6 ChimeraX-DistMonitor: 1.4.2 ChimeraX-DockPrep: 1.1.3 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 ChimeraX-Help: 1.3 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.3 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-KVFinder: 1.2.1 ChimeraX-Label: 1.1.14 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.2 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 ChimeraX-Map: 1.3 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0.1 ChimeraX-MapFilter: 2.0.1 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1.1 ChimeraX-Markers: 1.0.1 ChimeraX-Mask: 1.0.2 ChimeraX-MatchMaker: 2.1.6 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.7.2 ChimeraX-MedicalToolbar: 1.1 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.14.2 ChimeraX-MMTF: 2.2 ChimeraX-ModelArchive: 1.0 ChimeraX-Modeller: 1.5.18 ChimeraX-ModelPanel: 1.5 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0.3 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.2 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0 ChimeraX-MutationScores: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.2 ChimeraX-NMRSTAR: 1.0.2 ChimeraX-NRRD: 1.2 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.14 ChimeraX-OrthoPick: 1.0.1 ChimeraX-PDB: 2.7.6 ChimeraX-PDBBio: 1.0.1 ChimeraX-PDBLibrary: 1.0.4 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1.2 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.6.2 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.3.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 4.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.2 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-Segmentations: 3.5.6 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.14 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.2.0 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: 1.18.1 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 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: 1.41 ChimeraX-Umap: 1.0 ChimeraX-uniprot: 2.3.1 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.4.4 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-vrml: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.4 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.2.2 contourpy: 1.3.1 cxservices: 1.2.3 cycler: 0.12.1 Cython: 3.0.10 debugpy: 1.8.9 decorator: 5.1.1 docutils: 0.21.2 executing: 2.1.0 filelock: 3.15.4 fonttools: 4.55.3 funcparserlib: 2.0.0a0 glfw: 2.8.0 grako: 3.16.5 h11: 0.14.0 h5py: 3.12.1 html2text: 2024.2.26 httpcore: 1.0.7 httpx: 0.28.1 idna: 3.10 ihm: 1.3 imagecodecs: 2024.6.1 imagesize: 1.4.1 ipykernel: 6.29.5 ipython: 8.26.0 ipywidgets: 8.1.5 jedi: 0.19.1 Jinja2: 3.1.4 jupyter_client: 8.6.2 jupyter_core: 5.7.2 jupyterlab_widgets: 3.0.13 kiwisolver: 1.4.7 line_profiler: 4.1.3 lxml: 5.2.2 lz4: 4.3.3 MarkupSafe: 3.0.2 matplotlib: 3.9.2 matplotlib-inline: 0.1.7 msgpack: 1.0.8 ndindex: 1.9.2 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.10.2 numpy: 1.26.4 openvr: 1.26.701 packaging: 23.2 ParmEd: 4.2.2 parso: 0.8.4 pep517: 0.13.1 pexpect: 4.9.0 pillow: 10.4.0 pip: 24.2 pkginfo: 1.11.1 platformdirs: 4.3.6 prompt_toolkit: 3.0.48 psutil: 6.0.0 ptyprocess: 0.7.0 pure_eval: 0.2.3 py-cpuinfo: 9.0.0 pycollada: 0.8 pydicom: 2.4.4 pyelftools: 0.31 Pygments: 2.18.0 pynmrstar: 3.3.4 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.3401 pyparsing: 3.2.0 pyproject_hooks: 1.2.0 PyQt6-commercial: 6.7.1 PyQt6-Qt6: 6.7.3 PyQt6-WebEngine-commercial: 6.7.0 PyQt6-WebEngine-Qt6: 6.7.3 PyQt6-WebEngineSubwheel-Qt6: 6.7.3 PyQt6_sip: 13.8.0 python-dateutil: 2.9.0.post0 pytz: 2024.2 pyzmq: 26.2.0 qtconsole: 5.5.2 QtPy: 2.4.2 qtshim: 1.0 RandomWords: 0.4.0 requests: 2.32.3 scipy: 1.14.0 setuptools: 72.1.0 sfftk-rw: 0.8.1 six: 1.16.0 sniffio: 1.3.1 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.6 Sphinx: 8.0.2 sphinx-autodoc-typehints: 2.2.3 sphinxcontrib-applehelp: 2.0.0 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 2.0.0 sphinxcontrib-htmlhelp: 2.1.0 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 2.0.0 sphinxcontrib-serializinghtml: 2.0.0 stack-data: 0.6.3 superqt: 0.6.3 tables: 3.10.1 tcia_utils: 1.5.1 tifffile: 2024.7.24 tinyarray: 1.2.4 tornado: 6.4.2 traitlets: 5.14.3 typing_extensions: 4.12.2 tzdata: 2024.2 urllib3: 2.2.3 wcwidth: 0.2.13 webcolors: 24.6.0 wheel: 0.43.0 wheel-filename: 1.4.1 widgetsnbextension: 4.0.13 }}} " defect closed normal Window Toolkit can't reproduce Tom Goddard all ChimeraX