id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 14534 Crash in garbage collection mvshehat@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-10.15.7-x86_64-i386-64bit ChimeraX Version: 1.7.1 (2024-01-23 01:58:08 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. Fatal Python error: Segmentation fault Thread 0x000070000dd51000 (most recent call first): File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 324 in wait File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 622 in wait File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1392 in run File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x00007000218b1000 (most recent call first): File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 324 in wait File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 622 in wait File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1392 in run File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000070001f8a8000 (most recent call first): File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 579 in _handle_results File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000070001e8a5000 (most recent call first): File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 531 in _handle_tasks File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000070001d8a2000 (most recent call first): File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/selectors.py"", line 415 in select File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/connection.py"", line 930 in wait File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 502 in _wait_for_updates File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 522 in _handle_workers File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000070001c89f000 (most recent call first): File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000070001b89c000 (most recent call first): File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000070001a899000 (most recent call first): File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x0000700019896000 (most recent call first): File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x0000700018893000 (most recent call first): File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x0000700017890000 (most recent call first): File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000070001688d000 (most recent call first): File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000070001588a000 (most recent call first): File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Current thread 0x000000010ff1cdc0 (most recent call first): Garbage-collecting File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molarray.py"", line 97 in _atoms_pair File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molc.py"", line 209 in get_prop File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/structure.py"", line 2222 in _bond_intercept File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/structure.py"", line 1188 in first_intercept File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/structure.py"", line 736 in _position_intercepts File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/structure.py"", line 703 in first_intercept File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/drawing.py"", line 1086 in first_intercept_children File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/drawing.py"", line 1069 in first_intercept File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/models.py"", line 143 in first_intercept File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/view.py"", line 863 in picked_object_on_segment File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/view.py"", line 831 in picked_object File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/mouse_modes/std_modes.py"", line 803 in pause File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/mouse_modes/mousemodes.py"", line 641 in _mouse_pause File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/mouse_modes/mousemodes.py"", line 504 in mouse_pause_tracking File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/updateloop.py"", line 151 in _redraw_timer_callback File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 275 in event_loop File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 918 in init File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1069 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.QtWebChannel, PyQt6.QtNetwork, PyQt6.QtWebEngineCore, PyQt6.QtPrintSupport, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.surface._surface, chimerax.pdb_lib._load_libs, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, PIL._imagingmath, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, numpy.linalg.lapack_lite (total: 61) Process: ChimeraX [9780] Path: /Applications/ChimeraX-1.7.1.app/Contents/MacOS/ChimeraX Identifier: ChimeraX Version: 1.7.1 (1.7.1.0) Code Type: X86-64 (Native) Parent Process: ??? [1] Responsible: ChimeraX [9780] User ID: 501 Date/Time: 2024-02-03 17:27:25.752 -0800 OS Version: Mac OS X 10.15.7 (19H2) Report Version: 12 Bridge OS Version: 6.6 (19P6064) Anonymous UUID: F61A1488-55A7-1405-FC7D-17856118640C Sleep/Wake UUID: B11B95C9-C93C-4812-80A6-78A87067D8BD Time Awake Since Boot: 56000 seconds Time Since Wake: 870 seconds System Integrity Protection: enabled Crashed Thread: 0 CrBrowserMain Dispatch queue: com.apple.main-thread Exception Type: EXC_BAD_ACCESS (SIGSEGV) Exception Codes: KERN_INVALID_ADDRESS at 0x00000000000000a9 Exception Note: EXC_CORPSE_NOTIFY VM Regions Near 0xa9: --> __TEXT 000000010b093000-000000010b097000 [ 16K] r-x/r-x SM=COW /Applications/ChimeraX-1.7.1.app/Contents/MacOS/ChimeraX Thread 0 Crashed:: CrBrowserMain Dispatch queue: com.apple.main-thread 0 libsystem_kernel.dylib 0x00007fff6be8533a __pthread_kill + 10 1 libsystem_pthread.dylib 0x00007fff6bf41e60 pthread_kill + 430 2 libsystem_c.dylib 0x00007fff6bd9c93e raise + 26 3 org.python.python 0x000000010b3205d4 faulthandler_fatal_error + 388 4 libsystem_platform.dylib 0x00007fff6bf365fd _sigtramp + 29 5 ??? 000000000000000000 0 + 0 6 org.python.python 0x000000010b1cf8f4 tupletraverse + 52 7 org.python.python 0x000000010b31c888 gc_collect_main + 2568 8 org.python.python 0x000000010b31e102 _PyObject_GC_Link + 306 9 org.python.python 0x000000010b1e2bfd _PyType_AllocNoTrack + 125 10 org.python.python 0x000000010b1d627e PyType_GenericAlloc + 14 11 org.python.python 0x000000010b1e3264 object_new + 100 12 org.python.python 0x000000010b1d2b15 type_call + 69 13 org.python.python 0x000000010b14e3b1 _PyObject_MakeTpCall + 129 14 org.python.python 0x000000010b27c3e7 _PyEval_EvalFrameDefault + 60455 15 org.python.python 0x000000010b2824d0 _PyEval_Vector + 128 16 org.python.python 0x000000010b15eeb1 property_descr_get + 129 17 org.python.python 0x000000010b1b9f44 _PyObject_GenericGetAttrWithDict + 420 18 org.python.python 0x000000010b275222 _PyEval_EvalFrameDefault + 31330 19 org.python.python 0x000000010b2824d0 _PyEval_Vector + 128 20 org.python.python 0x000000010b152816 method_vectorcall + 454 21 QtCore.abi3.so 0x000000011a5a5f98 PyQtSlot::call(_object*, _object*) const + 40 22 QtCore.abi3.so 0x000000011a5a5e9a PyQtSlot::invoke(void**, _object*, void*, bool) const + 362 23 QtCore.abi3.so 0x000000011a5a6de5 PyQtSlotProxy::unislot(void**) + 85 24 QtCore.abi3.so 0x000000011a5a6d5a PyQtSlotProxy::qt_metacall(QMetaObject::Call, int, void**) + 58 25 QtCore 0x000000011a8bcd67 0x11a7ff000 + 777575 26 QtCore 0x000000011a8d1b57 QTimer::timerEvent(QTimerEvent*) + 199 27 QtCore.abi3.so 0x000000011a496b69 sipQTimer::timerEvent(QTimerEvent*) + 121 28 QtCore 0x000000011a8b54cd QObject::event(QEvent*) + 109 29 QtCore.abi3.so 0x000000011a4969ea sipQTimer::event(QEvent*) + 186 30 QtWidgets 0x000000011cf9ba87 QApplicationPrivate::notify_helper(QObject*, QEvent*) + 247 31 QtWidgets 0x000000011cf9ca43 QApplication::notify(QObject*, QEvent*) + 499 32 QtWidgets.abi3.so 0x000000011cab81e6 sipQApplication::notify(QObject*, QEvent*) + 230 33 QtCore 0x000000011a86cc3a QCoreApplication::notifyInternal2(QObject*, QEvent*) + 170 34 QtCore 0x000000011a9f6521 QTimerInfoList::activateTimers() + 961 35 libqcocoa.dylib 0x0000000129eb34a5 0x129e9b000 + 99493 36 com.apple.CoreFoundation 0x00007fff31ccfd52 __CFRUNLOOP_IS_CALLING_OUT_TO_A_SOURCE0_PERFORM_FUNCTION__ + 17 37 com.apple.CoreFoundation 0x00007fff31ccfcf1 __CFRunLoopDoSource0 + 103 38 com.apple.CoreFoundation 0x00007fff31ccfb0b __CFRunLoopDoSources0 + 209 39 com.apple.CoreFoundation 0x00007fff31cce83a __CFRunLoopRun + 927 40 com.apple.CoreFoundation 0x00007fff31ccde3e CFRunLoopRunSpecific + 462 41 com.apple.HIToolbox 0x00007fff308faabd RunCurrentEventLoopInMode + 292 42 com.apple.HIToolbox 0x00007fff308fa7d5 ReceiveNextEventCommon + 584 43 com.apple.HIToolbox 0x00007fff308fa579 _BlockUntilNextEventMatchingListInModeWithFilter + 64 44 com.apple.AppKit 0x00007fff2ef40039 _DPSNextEvent + 883 45 com.apple.AppKit 0x00007fff2ef3e880 -[NSApplication(NSEvent) _nextEventMatchingEventMask:untilDate:inMode:dequeue:] + 1352 46 com.apple.AppKit 0x00007fff2ef3058e -[NSApplication run] + 658 47 libqcocoa.dylib 0x0000000129eb40ac 0x129e9b000 + 102572 48 QtCore 0x000000011a876326 QEventLoop::exec(QFlags) + 486 49 QtCore 0x000000011a86d235 QCoreApplication::exec() + 133 50 QtWidgets.abi3.so 0x000000011cba4d9a meth_QApplication_exec(_object*, _object*) + 90 51 org.python.python 0x000000010b1b37ea cfunction_call + 90 52 org.python.python 0x000000010b14e3b1 _PyObject_MakeTpCall + 129 53 org.python.python 0x000000010b27c3e7 _PyEval_EvalFrameDefault + 60455 54 org.python.python 0x000000010b26c47a PyEval_EvalCode + 282 55 org.python.python 0x000000010b266ce3 builtin_exec + 483 56 org.python.python 0x000000010b1b4144 cfunction_vectorcall_FASTCALL_KEYWORDS + 68 57 org.python.python 0x000000010b27c2ef _PyEval_EvalFrameDefault + 60207 58 org.python.python 0x000000010b2824d0 _PyEval_Vector + 128 59 org.python.python 0x000000010b3196fd pymain_run_module + 253 60 org.python.python 0x000000010b3191c1 Py_RunMain + 2225 61 org.python.python 0x000000010b31a17b pymain_main + 43 62 org.python.python 0x000000010b31a14a Py_Main + 42 63 edu.ucsf.cgl.ChimeraX 0x000000010b096d9a main + 122 64 libdyld.dylib 0x00007fff6bd3dcc9 start + 1 Thread 1:: ThreadPoolServiceThread 0 libsystem_kernel.dylib 0x00007fff6be87b96 kevent64 + 10 1 QtWebEngineCore 0x0000000122397a2a 0x11e437000 + 66456106 2 QtWebEngineCore 0x0000000122397927 0x11e437000 + 66455847 3 QtWebEngineCore 0x0000000122314a5c 0x11e437000 + 65919580 4 QtWebEngineCore 0x00000001222cc998 0x11e437000 + 65624472 5 QtWebEngineCore 0x0000000122336eb8 0x11e437000 + 66059960 6 QtWebEngineCore 0x000000012231e2ad 0x11e437000 + 65958573 7 QtWebEngineCore 0x000000012233704a 0x11e437000 + 66060362 8 QtWebEngineCore 0x000000012235e908 0x11e437000 + 66222344 9 libsystem_pthread.dylib 0x00007fff6bf42109 _pthread_start + 148 10 libsystem_pthread.dylib 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60 2 QtWebEngineCore 0x0000000122365e26 0x11e437000 + 66252326 3 QtWebEngineCore 0x0000000122365bef 0x11e437000 + 66251759 4 QtWebEngineCore 0x000000012229b1c9 0x11e437000 + 65421769 5 QtWebEngineCore 0x0000000122314a5c 0x11e437000 + 65919580 6 QtWebEngineCore 0x00000001222cc998 0x11e437000 + 65624472 7 QtWebEngineCore 0x0000000122336eb8 0x11e437000 + 66059960 8 QtWebEngineCore 0x000000012233704a 0x11e437000 + 66060362 9 QtWebEngineCore 0x000000012235e908 0x11e437000 + 66222344 10 libsystem_pthread.dylib 0x00007fff6bf42109 _pthread_start + 148 11 libsystem_pthread.dylib 0x00007fff6bf3db8b thread_start + 15 Thread 26:: ThreadPoolSingleThreadSharedBackgroundBlocking1 0 libsystem_kernel.dylib 0x00007fff6be7edfa mach_msg_trap + 10 1 libsystem_kernel.dylib 0x00007fff6be7f170 mach_msg + 60 2 QtWebEngineCore 0x0000000122365e26 0x11e437000 + 66252326 3 QtWebEngineCore 0x000000012232a7bf 0x11e437000 + 66009023 4 QtWebEngineCore 0x000000012232af9a 0x11e437000 + 66011034 5 QtWebEngineCore 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1 libsystem_kernel.dylib 0x00007fff6be7f170 mach_msg + 60 2 QtWebEngineCore 0x0000000122365e26 0x11e437000 + 66252326 3 QtWebEngineCore 0x000000012232a7bf 0x11e437000 + 66009023 4 QtWebEngineCore 0x000000012232af9a 0x11e437000 + 66011034 5 QtWebEngineCore 0x000000012232ae6d 0x11e437000 + 66010733 6 QtWebEngineCore 0x000000012235e908 0x11e437000 + 66222344 7 libsystem_pthread.dylib 0x00007fff6bf42109 _pthread_start + 148 8 libsystem_pthread.dylib 0x00007fff6bf3db8b thread_start + 15 Thread 37: 0 libsystem_kernel.dylib 0x00007fff6be81882 __psynch_cvwait + 10 1 libsystem_pthread.dylib 0x00007fff6bf42425 _pthread_cond_wait + 698 2 org.python.python 0x000000010b306214 PyThread_acquire_lock_timed + 340 3 org.python.python 0x000000010b389d9e acquire_timed + 318 4 org.python.python 0x000000010b389fdc lock_PyThread_acquire_lock + 44 5 org.python.python 0x000000010b15fb07 method_vectorcall_VARARGS_KEYWORDS + 167 6 org.python.python 0x000000010b27c2ef _PyEval_EvalFrameDefault + 60207 7 org.python.python 0x000000010b2824d0 _PyEval_Vector + 128 8 org.python.python 0x000000010b152816 method_vectorcall + 454 9 org.python.python 0x000000010b38ab26 thread_run + 230 10 org.python.python 0x000000010b305ea4 pythread_wrapper + 36 11 libsystem_pthread.dylib 0x00007fff6bf42109 _pthread_start + 148 12 libsystem_pthread.dylib 0x00007fff6bf3db8b thread_start + 15 Thread 38: 0 libsystem_kernel.dylib 0x00007fff6be81882 __psynch_cvwait + 10 1 libsystem_pthread.dylib 0x00007fff6bf42425 _pthread_cond_wait + 698 2 org.python.python 0x000000010b306214 PyThread_acquire_lock_timed + 340 3 org.python.python 0x000000010b389d9e acquire_timed + 318 4 org.python.python 0x000000010b389fdc lock_PyThread_acquire_lock + 44 5 org.python.python 0x000000010b15fb07 method_vectorcall_VARARGS_KEYWORDS + 167 6 org.python.python 0x000000010b27c2ef _PyEval_EvalFrameDefault + 60207 7 org.python.python 0x000000010b2824d0 _PyEval_Vector + 128 8 org.python.python 0x000000010b152816 method_vectorcall + 454 9 org.python.python 0x000000010b38ab26 thread_run + 230 10 org.python.python 0x000000010b305ea4 pythread_wrapper + 36 11 libsystem_pthread.dylib 0x00007fff6bf42109 _pthread_start + 148 12 libsystem_pthread.dylib 0x00007fff6bf3db8b thread_start + 15 Thread 39: 0 libsystem_pthread.dylib 0x00007fff6bf3db68 start_wqthread + 0 Thread 40: 0 libsystem_pthread.dylib 0x00007fff6bf3db68 start_wqthread + 0 Thread 0 crashed with X86 Thread State (64-bit): rax: 0x0000000000000000 rbx: 0x000000010ff1cdc0 rcx: 0x00007fd17c6dd9e8 rdx: 0x0000000000000000 rdi: 0x0000000000000307 rsi: 0x000000000000000b rbp: 0x00007fd17c6dda10 rsp: 0x00007fd17c6dd9e8 r8: 0x0000000000000002 r9: 0xcccccccccccccccd r10: 0x000000010ff1cdc0 r11: 0x0000000000000246 r12: 0x0000000000000307 r13: 0x000000013f3f2e01 r14: 0x000000000000000b r15: 0x0000000000000016 rip: 0x00007fff6be8533a rfl: 0x0000000000000246 cr2: 0x000000010b48c720 Logical CPU: 0 Error Code: 0x02000148 Trap Number: 133 Binary Images: 0x10b093000 - 0x10b096ff7 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/usr/lib/system/libsystem_sandbox.dylib 0x7fff6bf4c000 - 0x7fff6bf4efff libsystem_secinit.dylib (62.100.2) /usr/lib/system/libsystem_secinit.dylib 0x7fff6bf4f000 - 0x7fff6bf56ffb libsystem_symptoms.dylib (1238.120.1) /usr/lib/system/libsystem_symptoms.dylib 0x7fff6bf57000 - 0x7fff6bf6dff2 libsystem_trace.dylib (1147.120) /usr/lib/system/libsystem_trace.dylib 0x7fff6bf6f000 - 0x7fff6bf74ff7 libunwind.dylib (35.4) /usr/lib/system/libunwind.dylib 0x7fff6bf75000 - 0x7fff6bfaaffe libxpc.dylib (1738.140.1) /usr/lib/system/libxpc.dylib External Modification Summary: Calls made by other processes targeting this process: task_for_pid: 42 thread_create: 0 thread_set_state: 0 Calls made by this process: task_for_pid: 0 thread_create: 0 thread_set_state: 0 Calls made by all processes on this machine: task_for_pid: 41108 thread_create: 0 thread_set_state: 0 VM Region Summary: ReadOnly portion of Libraries: Total=1.0G resident=0K(0%) swapped_out_or_unallocated=1.0G(100%) Writable regions: Total=2.0G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=2.0G(100%) VIRTUAL REGION REGION TYPE SIZE COUNT (non-coalesced) =========== ======= ======= Accelerate framework 640K 5 Activity Tracing 256K 1 CG backing stores 1204K 3 CG image 548K 35 CoreAnimation 5048K 63 CoreGraphics 8K 1 CoreImage 40K 6 CoreUI image data 3616K 31 Foundation 20K 2 Image IO 28K 3 Kernel Alloc Once 1432K 4 MALLOC 1.0G 1315 MALLOC guard page 32K 7 MALLOC_LARGE (reserved) 384K 1 reserved VM address space (unallocated) MALLOC_NANO (reserved) 384.0M 1 reserved VM address space (unallocated) Mach message 24K 4 OpenGL GLSL 384K 4 STACK GUARD 160K 40 Stack 364.8M 41 Stack Guard 56.0M 1 VM_ALLOCATE 248.6M 269 __DATA 66.1M 616 __DATA_CONST 76K 6 __FONT_DATA 4K 1 __GLSLBUILTINS 5176K 1 __LINKEDIT 421.4M 278 __OBJC_RO 32.3M 1 __OBJC_RW 1908K 2 __TEXT 643.3M 590 __UNICODE 564K 1 mapped file 427.7M 73 shared memory 2876K 31 =========== ======= ======= TOTAL 3.6G 3437 TOTAL, minus reserved VM space 3.2G 3437 ===== 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: 1.7.1 (2024-01-23) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open ""/Users/melissashehata/Downloads/Hb_wt (1).pdb"" Hb_wt (1).pdb title: The crystal structure of human deoxyhaemoglobin At 1.74 angstroms resolution [more info...] Chain information for Hb_wt (1).pdb #1 --- Chain | Description | UniProt A C | hemoglobin (deoxy) (α chain) | HBA_HUMAN 1-141 B D | hemoglobin (deoxy) (β chain) | HBB_HUMAN 1-146 Non-standard residues in Hb_wt (1).pdb #1 --- HEM — protoporphyrin IX containing Fe (HEME) PO4 — phosphate ion > open ""/Users/melissashehata/Downloads/Hb_wt (1).pdb"" Hb_wt (1).pdb title: The crystal structure of human deoxyhaemoglobin At 1.74 angstroms resolution [more info...] Chain information for Hb_wt (1).pdb #2 --- Chain | Description | UniProt A C | hemoglobin (deoxy) (α chain) | HBA_HUMAN 1-141 B D | hemoglobin (deoxy) (β chain) | HBB_HUMAN 1-146 Non-standard residues in Hb_wt (1).pdb #2 --- HEM — protoporphyrin IX containing Fe (HEME) PO4 — phosphate ion > open ""/Users/melissashehata/Downloads/Hb_wt (1).pdb"" Hb_wt (1).pdb title: The crystal structure of human deoxyhaemoglobin At 1.74 angstroms resolution [more info...] Chain information for Hb_wt (1).pdb #3 --- Chain | Description | UniProt A C | hemoglobin (deoxy) (α chain) | HBA_HUMAN 1-141 B D | hemoglobin (deoxy) (β chain) | HBB_HUMAN 1-146 Non-standard residues in Hb_wt (1).pdb #3 --- HEM — protoporphyrin IX containing Fe (HEME) PO4 — phosphate ion > open /Users/melissashehata/Downloads/Hb_wt.pdb Hb_wt.pdb title: The crystal structure of human deoxyhaemoglobin At 1.74 angstroms resolution [more info...] Chain information for Hb_wt.pdb #4 --- Chain | Description | UniProt A C | hemoglobin (deoxy) (α chain) | HBA_HUMAN 1-141 B D | hemoglobin (deoxy) (β chain) | HBB_HUMAN 1-146 Non-standard residues in Hb_wt.pdb #4 --- HEM — protoporphyrin IX containing Fe (HEME) PO4 — phosphate ion > open /Users/melissashehata/Downloads/Hb_wt.pdb Hb_wt.pdb title: The crystal structure of human deoxyhaemoglobin At 1.74 angstroms resolution [more info...] Chain information for Hb_wt.pdb #5 --- Chain | Description | UniProt A C | hemoglobin (deoxy) (α chain) | HBA_HUMAN 1-141 B D | hemoglobin (deoxy) (β chain) | HBB_HUMAN 1-146 Non-standard residues in Hb_wt.pdb #5 --- HEM — protoporphyrin IX containing Fe (HEME) PO4 — phosphate ion > open ""/Users/melissashehata/Downloads/Hb_wt (1).pdb"" Hb_wt (1).pdb title: The crystal structure of human deoxyhaemoglobin At 1.74 angstroms resolution [more info...] Chain information for Hb_wt (1).pdb #6 --- Chain | Description | UniProt A C | hemoglobin (deoxy) (α chain) | HBA_HUMAN 1-141 B D | hemoglobin (deoxy) (β chain) | HBB_HUMAN 1-146 Non-standard residues in Hb_wt (1).pdb #6 --- HEM — protoporphyrin IX containing Fe (HEME) PO4 — phosphate ion > open ""/Users/melissashehata/Downloads/Hb_wt (1).pdb"" Hb_wt (1).pdb title: The crystal structure of human deoxyhaemoglobin At 1.74 angstroms resolution [more info...] Chain information for Hb_wt (1).pdb #7 --- Chain | Description | UniProt A C | hemoglobin (deoxy) (α chain) | HBA_HUMAN 1-141 B D | hemoglobin (deoxy) (β chain) | HBB_HUMAN 1-146 Non-standard residues in Hb_wt (1).pdb #7 --- HEM — protoporphyrin IX containing Fe (HEME) PO4 — phosphate ion > open /Users/melissashehata/Downloads/Hb_SC.pdb Hb_SC.pdb title: Crystal structure of deoxy-human hemoglobin Β6 glu->TRP [more info...] Chain information for Hb_SC.pdb #8 --- Chain | Description | UniProt A C | hemoglobin A | HBA_HUMAN 1-141 B D | hemoglobin B | HBB_HUMAN 1-146 Non-standard residues in Hb_SC.pdb #8 --- HEM — protoporphyrin IX containing Fe (HEME) > log metadata #1 Metadata for Hb_wt (1).pdb #1 --- Title | The crystal structure of human deoxyhaemoglobin At 1.74 angstroms resolution Citation | The crystal structure of human deoxyhaemoglobin At 1.74 aresolution PMID: 6726807 Non-standard residues | HEM — protoporphyrin IX containing Fe (HEME) PO4 — phosphate ion Source (natural) | Homo sapiens (human) Experimental method | X-ray diffraction Resolution | 1.74Å > log chains #1 Chain information for Hb_wt (1).pdb #1 --- Chain | Description | UniProt A C | hemoglobin (deoxy) (α chain) | HBA_HUMAN 1-141 B D | hemoglobin (deoxy) (β chain) | HBB_HUMAN 1-146 > log metadata #2 Metadata for Hb_wt (1).pdb #2 --- Title | The crystal structure of human deoxyhaemoglobin At 1.74 angstroms resolution Citation | The crystal structure of human deoxyhaemoglobin At 1.74 aresolution PMID: 6726807 Non-standard residues | HEM — protoporphyrin IX containing Fe (HEME) PO4 — phosphate ion Source (natural) | Homo sapiens (human) Experimental method | X-ray diffraction Resolution | 1.74Å > log chains #2 Chain information for Hb_wt (1).pdb #2 --- Chain | Description | UniProt A C | hemoglobin (deoxy) (α chain) | HBA_HUMAN 1-141 B D | hemoglobin (deoxy) (β chain) | HBB_HUMAN 1-146 > log metadata #3 Metadata for Hb_wt (1).pdb #3 --- Title | The crystal structure of human deoxyhaemoglobin At 1.74 angstroms resolution Citation | The crystal structure of human deoxyhaemoglobin At 1.74 aresolution PMID: 6726807 Non-standard residues | HEM — protoporphyrin IX containing Fe (HEME) PO4 — phosphate ion Source (natural) | Homo sapiens (human) Experimental method | X-ray diffraction Resolution | 1.74Å > log chains #3 Chain information for Hb_wt (1).pdb #3 --- Chain | Description | UniProt A C | hemoglobin (deoxy) (α chain) | HBA_HUMAN 1-141 B D | hemoglobin (deoxy) (β chain) | HBB_HUMAN 1-146 > log metadata #4 Metadata for Hb_wt.pdb #4 --- Title | The crystal structure of human deoxyhaemoglobin At 1.74 angstroms resolution Citation | The crystal structure of human deoxyhaemoglobin At 1.74 aresolution PMID: 6726807 Non-standard residues | HEM — protoporphyrin IX containing Fe (HEME) PO4 — phosphate ion Source (natural) | Homo sapiens (human) Experimental method | X-ray diffraction Resolution | 1.74Å > log chains #4 Chain information for Hb_wt.pdb #4 --- Chain | Description | UniProt A C | hemoglobin (deoxy) (α chain) | HBA_HUMAN 1-141 B D | hemoglobin (deoxy) (β chain) | HBB_HUMAN 1-146 > log metadata #5 Metadata for Hb_wt.pdb #5 --- Title | The crystal structure of human deoxyhaemoglobin At 1.74 angstroms resolution Citation | The crystal structure of human deoxyhaemoglobin At 1.74 aresolution PMID: 6726807 Non-standard residues | HEM — protoporphyrin IX containing Fe (HEME) PO4 — phosphate ion Source (natural) | Homo sapiens (human) Experimental method | X-ray diffraction Resolution | 1.74Å > log chains #5 Chain information for Hb_wt.pdb #5 --- Chain | Description | UniProt A C | hemoglobin (deoxy) (α chain) | HBA_HUMAN 1-141 B D | hemoglobin (deoxy) (β chain) | HBB_HUMAN 1-146 > log metadata #6 Metadata for Hb_wt (1).pdb #6 --- Title | The crystal structure of human deoxyhaemoglobin At 1.74 angstroms resolution Citation | The crystal structure of human deoxyhaemoglobin At 1.74 aresolution PMID: 6726807 Non-standard residues | HEM — protoporphyrin IX containing Fe (HEME) PO4 — phosphate ion Source (natural) | Homo sapiens (human) Experimental method | X-ray diffraction Resolution | 1.74Å > log chains #6 Chain information for Hb_wt (1).pdb #6 --- Chain | Description | UniProt A C | hemoglobin (deoxy) (α chain) | HBA_HUMAN 1-141 B D | hemoglobin (deoxy) (β chain) | HBB_HUMAN 1-146 > log metadata #7 Metadata for Hb_wt (1).pdb #7 --- Title | The crystal structure of human deoxyhaemoglobin At 1.74 angstroms resolution Citation | The crystal structure of human deoxyhaemoglobin At 1.74 aresolution PMID: 6726807 Non-standard residues | HEM — protoporphyrin IX containing Fe (HEME) PO4 — phosphate ion Source (natural) | Homo sapiens (human) Experimental method | X-ray diffraction Resolution | 1.74Å > log chains #7 Chain information for Hb_wt (1).pdb #7 --- Chain | Description | UniProt A C | hemoglobin (deoxy) (α chain) | HBA_HUMAN 1-141 B D | hemoglobin (deoxy) (β chain) | HBB_HUMAN 1-146 > log metadata #8 Metadata for Hb_SC.pdb #8 --- Title | Crystal structure of deoxy-human hemoglobin Β6 glu->TRP Citation | Crystal structure of deoxy-human hemoglobin Β6 glu -->TRP. Implications for the structure and formation of thesickle cell fiber. PMID: 9830011 Non-standard residue | HEM — protoporphyrin IX containing Fe (HEME) Gene source | Homo sapiens (human) Experimental method | X-ray diffraction Resolution | 2.00Å > log chains #8 Chain information for Hb_SC.pdb #8 --- Chain | Description | UniProt A C | hemoglobin A | HBA_HUMAN 1-141 B D | hemoglobin B | HBB_HUMAN 1-146 > view clip false > show target m > hide target m > show target m > ui tool show ""Selection Inspector"" > ui tool show Matchmaker > matchmaker #!2 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker Hb_wt (1).pdb, chain B (#1) with Hb_wt (1).pdb, chain B (#2), sequence alignment score = 789.7 RMSD between 146 pruned atom pairs is 0.000 angstroms; (across all 146 pairs: 0.000) > matchmaker #!8 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker Hb_wt (1).pdb, chain B (#1) with Hb_SC.pdb, chain B (#8), sequence alignment score = 771.5 RMSD between 146 pruned atom pairs is 0.316 angstroms; (across all 146 pairs: 0.316) > matchmaker #!8 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker Hb_wt (1).pdb, chain B (#1) with Hb_SC.pdb, chain B (#8), sequence alignment score = 771.5 RMSD between 146 pruned atom pairs is 0.316 angstroms; (across all 146 pairs: 0.316) > ui tool show ""Show Sequence Viewer"" > sequence chain #1/A #1/C #2/A #2/C #3/A #3/C #4/A #4/C #5/A #5/C #6/A #6/C > #7/A #7/C #8/A #8/C Alignment identifier is 1 > ui tool show ""Show Sequence Viewer"" > sequence chain #8/B #8/D Alignment identifier is 2 > ui tool show ""Show Sequence Viewer"" > sequence chain #1/B #1/D #2/B #2/D #3/B #3/D #4/B #4/D #5/B #5/D #6/B #6/D > #7/B #7/D Alignment identifier is 1 > sequence chain #8/B #8/D Alignment identifier is 3 > ui tool show ""Show Sequence Viewer"" > sequence chain #1/B #1/D #2/B #2/D #3/B #3/D #4/B #4/D #5/B #5/D #6/B #6/D > #7/B #7/D Alignment identifier is 1 > sequence chain #8/B #8/D Alignment identifier is 3 > hide #!6 models > hide #!5 models > hide #!4 models > hide #!3 models > hide #!2 models > hide #!1 models > view clip false > help help:user/tools/sequenceviewer.html > ui tool show ""Show Sequence Viewer"" > sequence chain #8/B #8/D Alignment identifier is 3 > ui tool show Matchmaker > matchmaker #!8 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker Hb_wt (1).pdb, chain B (#1) with Hb_SC.pdb, chain B (#8), sequence alignment score = 771.5 RMSD between 146 pruned atom pairs is 0.316 angstroms; (across all 146 pairs: 0.316) > matchmaker #!8 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker Hb_wt (1).pdb, chain B (#1) with Hb_SC.pdb, chain B (#8), sequence alignment score = 771.5 RMSD between 146 pruned atom pairs is 0.316 angstroms; (across all 146 pairs: 0.316) > ui tool show ""Side View"" > ui tool show ""File History"" > ui tool show ""Command Line Interface"" > ui tool show ""Model Panel"" > ui autostart false ""Model Panel"" > ui dockable false ""Model Panel"" > ui tool show ""Model Panel"" > close #1-6 > select #8/B,D:9-10 22 atoms, 20 bonds, 4 residues, 1 model selected > select #8/B,D:9-17 130 atoms, 132 bonds, 18 residues, 1 model selected > select #8/B,D:4-41,50-76,85-93,99-117,123-143 1720 atoms, 1758 bonds, 228 residues, 1 model selected > select #8/B,D:100 14 atoms, 14 bonds, 2 residues, 1 model selected > select #8/B,D:100-117 284 atoms, 290 bonds, 36 residues, 1 model selected > select #8/B,D:99-100 30 atoms, 30 bonds, 4 residues, 1 model selected > select #8/B,D:99-117 300 atoms, 306 bonds, 38 residues, 1 model selected > color sel blue > ui windowfill toggle > hide sel cartoons > hide sel atoms > hide sel cartoons > hide sel atoms > hide sel cartoons > hide sel surfaces > hide sel atoms > close session > open /Users/melissashehata/Downloads/Hb_SC.pdb format pdb Hb_SC.pdb title: Crystal structure of deoxy-human hemoglobin Β6 glu->TRP [more info...] Chain information for Hb_SC.pdb #1 --- Chain | Description | UniProt A C | hemoglobin A | HBA_HUMAN 1-141 B D | hemoglobin B | HBB_HUMAN 1-146 Non-standard residues in Hb_SC.pdb #1 --- HEM — protoporphyrin IX containing Fe (HEME) > open /Users/melissashehata/Downloads/Hb_wt.pdb Hb_wt.pdb title: The crystal structure of human deoxyhaemoglobin At 1.74 angstroms resolution [more info...] Chain information for Hb_wt.pdb #2 --- Chain | Description | UniProt A C | hemoglobin (deoxy) (α chain) | HBA_HUMAN 1-141 B D | hemoglobin (deoxy) (β chain) | HBB_HUMAN 1-146 Non-standard residues in Hb_wt.pdb #2 --- HEM — protoporphyrin IX containing Fe (HEME) PO4 — phosphate ion > open /Users/melissashehata/Downloads/Hb_SC.pdb Hb_SC.pdb title: Crystal structure of deoxy-human hemoglobin Β6 glu->TRP [more info...] Chain information for Hb_SC.pdb #3 --- Chain | Description | UniProt A C | hemoglobin A | HBA_HUMAN 1-141 B D | hemoglobin B | HBB_HUMAN 1-146 Non-standard residues in Hb_SC.pdb #3 --- HEM — protoporphyrin IX containing Fe (HEME) > open /Users/melissashehata/Downloads/Hb_SC.pdb Hb_SC.pdb title: Crystal structure of deoxy-human hemoglobin Β6 glu->TRP [more info...] Chain information for Hb_SC.pdb #4 --- Chain | Description | UniProt A C | hemoglobin A | HBA_HUMAN 1-141 B D | hemoglobin B | HBB_HUMAN 1-146 Non-standard residues in Hb_SC.pdb #4 --- HEM — protoporphyrin IX containing Fe (HEME) > open ""/Users/melissashehata/Library/Mobile > Documents/com~apple~CloudDocs/Downloads/Hb_wt.pdb"" Hb_wt.pdb title: The crystal structure of human deoxyhaemoglobin At 1.74 angstroms resolution [more info...] Chain information for Hb_wt.pdb #5 --- Chain | Description | UniProt A C | hemoglobin (deoxy) (α chain) | HBA_HUMAN 1-141 B D | hemoglobin (deoxy) (β chain) | HBB_HUMAN 1-146 Non-standard residues in Hb_wt.pdb #5 --- HEM — protoporphyrin IX containing Fe (HEME) PO4 — phosphate ion > ui tool show Matchmaker > matchmaker #!5 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker Hb_SC.pdb, chain B (#1) with Hb_wt.pdb, chain B (#5), sequence alignment score = 771.5 RMSD between 146 pruned atom pairs is 0.316 angstroms; (across all 146 pairs: 0.316) > ui tool show Matchmaker > matchmaker #!2 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker Hb_SC.pdb, chain B (#1) with Hb_wt.pdb, chain B (#2), sequence alignment score = 771.5 RMSD between 146 pruned atom pairs is 0.316 angstroms; (across all 146 pairs: 0.316) > matchmaker #!2 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker Hb_SC.pdb, chain B (#1) with Hb_wt.pdb, chain B (#2), sequence alignment score = 771.5 RMSD between 146 pruned atom pairs is 0.316 angstroms; (across all 146 pairs: 0.316) > ui tool show ""Show Sequence Viewer"" > sequence chain #1/B #1/D #3/B #3/D #4/B #4/D Alignment identifier is 1 > sequence chain #2/B #2/D #5/B #5/D Alignment identifier is 2 > select #1/B,D:4-41,50-76,85-93,99-117,123-143 > #3/B,D:4-41,50-76,85-93,99-117,123-143 > #4/B,D:4-41,50-76,85-93,99-117,123-143 5160 atoms, 5274 bonds, 684 residues, 3 models selected > hide sel atoms > show sel atoms > hide sel atoms > hide sel cartoons > ui tool show ""Show Sequence Viewer"" > sequence chain #1/B #1/D #3/B #3/D #4/B #4/D Alignment identifier is 1 > sequence chain #2/B #2/D #5/B #5/D Alignment identifier is 2 > select #2/B,D:1-2 #5/B,D:1-2 68 atoms, 68 bonds, 8 residues, 2 models selected > select #2/B,D:1 #5/B,D:1 28 atoms, 24 bonds, 4 residues, 2 models selected > select #2/B,D:1-2 #5/B,D:1-2 68 atoms, 68 bonds, 8 residues, 2 models selected > select #2/B,D:1 #5/B,D:1 28 atoms, 24 bonds, 4 residues, 2 models selected Hemoglobin (Deoxy) (Β Chain) [ID: 2] region 4 chains [1] RMSD: 0.000 > select #2/B,D:4 #5/B,D:4 28 atoms, 24 bonds, 4 residues, 2 models selected > select #2/B,D:4-41 #5/B,D:4-41 1192 atoms, 1220 bonds, 152 residues, 2 models selected Hemoglobin (Deoxy) (Β Chain) [ID: 2] region 4 chains [4-41] RMSD: 0.000 > color sel red > select #1/B,D:4 #3/B,D:4 #4/B,D:4 42 atoms, 36 bonds, 6 residues, 3 models selected > select #1/B,D:4-41 #3/B,D:4-41 #4/B,D:4-41 1818 atoms, 1872 bonds, 228 residues, 3 models selected Hemoglobin B [ID: 1] region 6 chains [4-41] RMSD: 0.000 > select #1/B,D:58 #3/B,D:58 #4/B,D:58 42 atoms, 42 bonds, 6 residues, 3 models selected > select #1/B,D:58-61 #3/B,D:58-61 #4/B,D:58-61 192 atoms, 192 bonds, 24 residues, 3 models selected Hemoglobin B [ID: 1] region 6 chains [58-61] RMSD: 0.000 > select #1/B,D:4 #3/B,D:4 #4/B,D:4 42 atoms, 36 bonds, 6 residues, 3 models selected > select #1/B,D:4-41 #3/B,D:4-41 #4/B,D:4-41 1818 atoms, 1872 bonds, 228 residues, 3 models selected Hemoglobin B [ID: 1] region 6 chains [4-41] RMSD: 0.000 > color sel blue > color sel medium blue > color sel orange > color sel blue > color sel yellow > select #1/B,D:4-41,50-76,85-93,99-117,123-143 > #3/B,D:4-41,50-76,85-93,99-117,123-143 > #4/B,D:4-41,50-76,85-93,99-117,123-143 5160 atoms, 5274 bonds, 684 residues, 3 models selected > select #1/B,D:6 #3/B,D:6 #4/B,D:6 84 atoms, 90 bonds, 6 residues, 3 models selected > select #1/B,D:6-9 #3/B,D:6-9 #4/B,D:6-9 228 atoms, 234 bonds, 24 residues, 3 models selected Hemoglobin B [ID: 1] region 6 chains [6-9] RMSD: 0.000 > select #1/B,D:50 #3/B,D:50 #4/B,D:50 42 atoms, 36 bonds, 6 residues, 3 models selected > select #1/B,D:50-60 #3/B,D:50-60 #4/B,D:50-60 462 atoms, 468 bonds, 66 residues, 3 models selected Hemoglobin B [ID: 1] region 6 chains [50-60] RMSD: 0.000 > color sel blue > select #1/B,D:4-41,50-76,85-93,99-117,123-143 > #3/B,D:4-41,50-76,85-93,99-117,123-143 > #4/B,D:4-41,50-76,85-93,99-117,123-143 5160 atoms, 5274 bonds, 684 residues, 3 models selected > select #1/B,D:2-3 #3/B,D:2-3 #4/B,D:2-3 108 atoms, 108 bonds, 12 residues, 3 models selected > select #1/B,D:2-7 #3/B,D:2-7 #4/B,D:2-7 330 atoms, 348 bonds, 36 residues, 3 models selected Hemoglobin B [ID: 1] region 6 chains [2-7] RMSD: 0.000 > select #1/B,D:4 #3/B,D:4 #4/B,D:4 42 atoms, 36 bonds, 6 residues, 3 models selected > select #1/B,D:4-41 #3/B,D:4-41 #4/B,D:4-41 1818 atoms, 1872 bonds, 228 residues, 3 models selected Hemoglobin B [ID: 1] region 6 chains [4-41] RMSD: 0.000 > color sel yellow > select #2/B,D:61 #5/B,D:61 36 atoms, 32 bonds, 4 residues, 2 models selected > select #2/B,D:61-76 #5/B,D:61-76 448 atoms, 452 bonds, 64 residues, 2 models selected Hemoglobin (Deoxy) (Β Chain) [ID: 2] region 4 chains [61-76] RMSD: 0.000 > color sel blue > color sel yellow > hide sel atoms > show sel atoms > hide sel cartoons > show sel cartoons > color sel bynucleotide > ui mousemode right ""delete markers"" > select #2/B,D:64 #5/B,D:64 16 atoms, 12 bonds, 4 residues, 2 models selected > select #2/B,D:64-71 #5/B,D:64-71 228 atoms, 228 bonds, 32 residues, 2 models selected Hemoglobin (Deoxy) (Β Chain) [ID: 2] region 4 chains [64-71] RMSD: 0.000 > select #2/B,D:61 #5/B,D:61 36 atoms, 32 bonds, 4 residues, 2 models selected > select #2/B,D:61-76 #5/B,D:61-76 448 atoms, 452 bonds, 64 residues, 2 models selected Hemoglobin (Deoxy) (Β Chain) [ID: 2] region 4 chains [61-76] RMSD: 0.000 > ui mousemode right ""delete markers"" > undo > select #2/B,D:61 #5/B,D:61 36 atoms, 32 bonds, 4 residues, 2 models selected > select #2/B,D:61-62 #5/B,D:61-62 56 atoms, 52 bonds, 8 residues, 2 models selected Hemoglobin (Deoxy) (Β Chain) [ID: 2] region 4 chains [61-62] RMSD: 0.000 > select #2/B,D:78 #5/B,D:78 32 atoms, 28 bonds, 4 residues, 2 models selected > select #2/B,D:78-83 #5/B,D:78-83 180 atoms, 176 bonds, 24 residues, 2 models selected Hemoglobin (Deoxy) (Β Chain) [ID: 2] region 4 chains [78-83] RMSD: 0.000 > select #2/B,D:136 #5/B,D:136 16 atoms, 12 bonds, 4 residues, 2 models selected > select #2/B,D:136-141 #5/B,D:136-141 148 atoms, 144 bonds, 24 residues, 2 models selected Hemoglobin (Deoxy) (Β Chain) [ID: 2] region 4 chains [136-141] RMSD: 0.000 > select #2/B,D:78 #5/B,D:78 32 atoms, 28 bonds, 4 residues, 2 models selected > select #2/B,D:78-82 #5/B,D:78-82 164 atoms, 160 bonds, 20 residues, 2 models selected Hemoglobin (Deoxy) (Β Chain) [ID: 2] region 4 chains [78-82] RMSD: 0.000 > select #1/B,D:79 #3/B,D:79 #4/B,D:79 48 atoms, 42 bonds, 6 residues, 3 models selected > select #1/B,D:79-85 #3/B,D:79-85 #4/B,D:79-85 330 atoms, 330 bonds, 42 residues, 3 models selected Hemoglobin B [ID: 1] region 6 chains [79-85] RMSD: 0.000 > hide sel atoms > hide sel cartoons > hide sel atoms > close session > open /Users/melissashehata/Downloads/Hb_SC.pdb format pdb Hb_SC.pdb title: Crystal structure of deoxy-human hemoglobin Β6 glu->TRP [more info...] Chain information for Hb_SC.pdb #1 --- Chain | Description | UniProt A C | hemoglobin A | HBA_HUMAN 1-141 B D | hemoglobin B | HBB_HUMAN 1-146 Non-standard residues in Hb_SC.pdb #1 --- HEM — protoporphyrin IX containing Fe (HEME) > open ""/Users/melissashehata/Library/Mobile > Documents/com~apple~CloudDocs/Downloads/Hb_wt.pdb"" Hb_wt.pdb title: The crystal structure of human deoxyhaemoglobin At 1.74 angstroms resolution [more info...] Chain information for Hb_wt.pdb #2 --- Chain | Description | UniProt A C | hemoglobin (deoxy) (α chain) | HBA_HUMAN 1-141 B D | hemoglobin (deoxy) (β chain) | HBB_HUMAN 1-146 Non-standard residues in Hb_wt.pdb #2 --- HEM — protoporphyrin IX containing Fe (HEME) PO4 — phosphate ion > open /Users/melissashehata/Downloads/Hb_SC.pdb Hb_SC.pdb title: Crystal structure of deoxy-human hemoglobin Β6 glu->TRP [more info...] Chain information for Hb_SC.pdb #3 --- Chain | Description | UniProt A C | hemoglobin A | HBA_HUMAN 1-141 B D | hemoglobin B | HBB_HUMAN 1-146 Non-standard residues in Hb_SC.pdb #3 --- HEM — protoporphyrin IX containing Fe (HEME) > ui tool show Matchmaker > matchmaker #!2 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker Hb_SC.pdb, chain B (#1) with Hb_wt.pdb, chain B (#2), sequence alignment score = 771.5 RMSD between 146 pruned atom pairs is 0.316 angstroms; (across all 146 pairs: 0.316) > matchmaker #!2 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker Hb_SC.pdb, chain B (#1) with Hb_wt.pdb, chain B (#2), sequence alignment score = 771.5 RMSD between 146 pruned atom pairs is 0.316 angstroms; (across all 146 pairs: 0.316) > ui tool show ""Show Sequence Viewer"" > sequence chain #1/B #1/D #3/B #3/D Alignment identifier is 1 > sequence chain #2/B #2/D Alignment identifier is 2 > select #1/B,D:4-41,50-76,85-93,99-117,123-143 > #3/B,D:4-41,50-76,85-93,99-117,123-143 3440 atoms, 3516 bonds, 456 residues, 2 models selected > select #2/B,D:4 14 atoms, 12 bonds, 2 residues, 1 model selected > select #2/B,D:4-41 596 atoms, 610 bonds, 76 residues, 1 model selected > color sel red > select #1/B,D:4 #3/B,D:4 28 atoms, 24 bonds, 4 residues, 2 models selected > select #1/B,D:4-41 #3/B,D:4-41 1212 atoms, 1248 bonds, 152 residues, 2 models selected Hemoglobin B [ID: 1] region 4 chains [4-41] RMSD: 0.000 > color sel blue > save /Users/melissashehata/Desktop/image1.png supersample 3 > save /Users/melissashehata/Desktop/image2.png supersample 3 > ui mousemode right ""clip rotate"" > select #2/B,D:4-41 596 atoms, 610 bonds, 76 residues, 1 model selected > undo > select #2/B,D:50 14 atoms, 12 bonds, 2 residues, 1 model selected > select #2/B,D:50-60 154 atoms, 156 bonds, 22 residues, 1 model selected > select #2/B,D:50 14 atoms, 12 bonds, 2 residues, 1 model selected > select #2/B,D:50-76 378 atoms, 384 bonds, 54 residues, 1 model selected > color sel blue > close session > open /Users/melissashehata/Downloads/Hb_SC.pdb format pdb Hb_SC.pdb title: Crystal structure of deoxy-human hemoglobin Β6 glu->TRP [more info...] Chain information for Hb_SC.pdb #1 --- Chain | Description | UniProt A C | hemoglobin A | HBA_HUMAN 1-141 B D | hemoglobin B | HBB_HUMAN 1-146 Non-standard residues in Hb_SC.pdb #1 --- HEM — protoporphyrin IX containing Fe (HEME) > open > /Users/melissashehata/Downloads/ProteinStructure2_6202f/ProteinStructure2_6202f_scores_rank_001_alphafold2_ptm_model_1_seed_000.json Failed opening file /Users/melissashehata/Downloads/ProteinStructure2_6202f/ProteinStructure2_6202f_scores_rank_001_alphafold2_ptm_model_1_seed_000.json: ProteinStructure2_6202f_scores_rank_001_alphafold2_ptm_model_1_seed_000.json does not look like Mole Online json file, does not contain Channels. > open > /Users/melissashehata/Downloads/ProteinStructure2_6202f/ProteinStructure2_6202f_scores_rank_001_alphafold2_ptm_model_1_seed_000.json Failed opening file /Users/melissashehata/Downloads/ProteinStructure2_6202f/ProteinStructure2_6202f_scores_rank_001_alphafold2_ptm_model_1_seed_000.json: ProteinStructure2_6202f_scores_rank_001_alphafold2_ptm_model_1_seed_000.json does not look like Mole Online json file, does not contain Channels. > open > /Users/melissashehata/Downloads/ProteinStructure2_6202f/ProteinStructure2_6202f_scores_rank_001_alphafold2_ptm_model_1_seed_000.json Failed opening file /Users/melissashehata/Downloads/ProteinStructure2_6202f/ProteinStructure2_6202f_scores_rank_001_alphafold2_ptm_model_1_seed_000.json: ProteinStructure2_6202f_scores_rank_001_alphafold2_ptm_model_1_seed_000.json does not look like Mole Online json file, does not contain Channels. > close session > open /Users/melissashehata/Downloads/Hb_SC.pdb format pdb Hb_SC.pdb title: Crystal structure of deoxy-human hemoglobin Β6 glu->TRP [more info...] Chain information for Hb_SC.pdb #1 --- Chain | Description | UniProt A C | hemoglobin A | HBA_HUMAN 1-141 B D | hemoglobin B | HBB_HUMAN 1-146 Non-standard residues in Hb_SC.pdb #1 --- HEM — protoporphyrin IX containing Fe (HEME) > open > /Users/melissashehata/Downloads/ProteinStructure2_6202f/ProteinStructure2_6202f_scores_rank_001_alphafold2_ptm_model_1_seed_000.json ProteinStructure2_6202f_scores_rank_001_alphafold2_ptm_model_1_seed_000.json does not look like Mole Online json file, does not contain Channels. > open > /Users/melissashehata/Downloads/ProteinStructure2_6202f/ProteinStructure2_6202f_scores_rank_001_alphafold2_ptm_model_1_seed_000.json Failed opening file /Users/melissashehata/Downloads/ProteinStructure2_6202f/ProteinStructure2_6202f_scores_rank_001_alphafold2_ptm_model_1_seed_000.json: ProteinStructure2_6202f_scores_rank_001_alphafold2_ptm_model_1_seed_000.json does not look like Mole Online json file, does not contain Channels. > open > /Users/melissashehata/Downloads/ProteinStructure2_6202f/ProteinStructure2_6202f_unrelaxed_rank_001_alphafold2_ptm_model_1_seed_000.pdb Chain information for ProteinStructure2_6202f_unrelaxed_rank_001_alphafold2_ptm_model_1_seed_000.pdb #2 --- Chain | Description A | No description available > open ""/Users/melissashehata/Downloads/1scj - Pro-Subtilisin E7.pdb"" 1scj - Pro-Subtilisin E7.pdb title: Crystal structure of subtilisin-propeptide complex [more info...] Chain information for 1scj - Pro-Subtilisin E7.pdb #3 --- Chain | Description | UniProt A | serine protease | SUBT_BACSU 1-275 B | serine protease | SUBT_BACSU 307-377 Non-standard residues in 1scj - Pro-Subtilisin E7.pdb #3 --- CA — calcium ion > open ""/Users/melissashehata/Downloads/1scj - Pro-Subtilisin E7.pdb"" 1scj - Pro-Subtilisin E7.pdb title: Crystal structure of subtilisin-propeptide complex [more info...] Chain information for 1scj - Pro-Subtilisin E7.pdb #4 --- Chain | Description | UniProt A | serine protease | SUBT_BACSU 1-275 B | serine protease | SUBT_BACSU 307-377 Non-standard residues in 1scj - Pro-Subtilisin E7.pdb #4 --- CA — calcium ion > select 12795 atoms, 12316 bonds, 46 pseudobonds, 2362 residues, 7 models selected > hide (#2#!1,3-4 & sel) target a > hide sel atoms > close session > open ""/Users/melissashehata/Downloads/1scj - Pro-Subtilisin E7.pdb"" format > pdb 1scj - Pro-Subtilisin E7.pdb title: Crystal structure of subtilisin-propeptide complex [more info...] Chain information for 1scj - Pro-Subtilisin E7.pdb #1 --- Chain | Description | UniProt A | serine protease | SUBT_BACSU 1-275 B | serine protease | SUBT_BACSU 307-377 Non-standard residues in 1scj - Pro-Subtilisin E7.pdb #1 --- CA — calcium ion > close session > open ""/Users/melissashehata/Downloads/1scj - Pro-Subtilisin E7.pdb"" format > pdb 1scj - Pro-Subtilisin E7.pdb title: Crystal structure of subtilisin-propeptide complex [more info...] Chain information for 1scj - Pro-Subtilisin E7.pdb #1 --- Chain | Description | UniProt A | serine protease | SUBT_BACSU 1-275 B | serine protease | SUBT_BACSU 307-377 Non-standard residues in 1scj - Pro-Subtilisin E7.pdb #1 --- CA — calcium ion > select 2703 atoms, 2559 bonds, 13 pseudobonds, 537 residues, 2 models selected > hide (#!1 & sel) target a > select clear > ui tool show ""Show Sequence Viewer"" > sequence chain /A Alignment identifier is 1/A > select /A:27-32,44-49,89-94,121-124,148-152,175-180,198-201,205-209,213-217 329 atoms, 324 bonds, 47 residues, 1 model selected > select /A:272 5 atoms, 4 bonds, 1 residue, 1 model selected > select /A:272-273 10 atoms, 9 bonds, 2 residues, 1 model selected > select /A:31-32 16 atoms, 15 bonds, 2 residues, 1 model selected > select /A:31-32 16 atoms, 15 bonds, 2 residues, 1 model selected > select /A:33-34 10 atoms, 9 bonds, 2 residues, 1 model selected > select /A:32-34 18 atoms, 17 bonds, 3 residues, 1 model selected > select /A:32 8 atoms, 7 bonds, 1 residue, 1 model selected > select /A:32 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > hide sel atoms > show sel atoms > show sel cartoons > hide sel cartoons > show sel cartoons > hide sel cartoons > show sel cartoons > hide sel cartoons > show sel cartoons > style sel stick Changed 8 atom styles > style sel sphere Changed 8 atom styles > style sel ball Changed 8 atom styles > style sel sphere Changed 8 atom styles > style sel stick Changed 8 atom styles > hide sel atoms > select /A:64 10 atoms, 10 bonds, 1 residue, 1 model selected > show sel atoms > style sel ball Changed 10 atom styles > select /A:125 6 atoms, 5 bonds, 1 residue, 1 model selected > select /A:125 6 atoms, 5 bonds, 1 residue, 1 model selected > show sel atoms > style sel ball Changed 6 atom styles > select /A:32 8 atoms, 7 bonds, 1 residue, 1 model selected > select /A:32 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > style sel ball Changed 8 atom styles > close session > open ""/Users/melissashehata/Downloads/Protease sequence – Active.txt"" Unrecognized file suffix '.txt' > open ""/Users/melissashehata/Downloads/1scj - Pro-Subtilisin E7.pdb"" format > pdb 1scj - Pro-Subtilisin E7.pdb title: Crystal structure of subtilisin-propeptide complex [more info...] Chain information for 1scj - Pro-Subtilisin E7.pdb #1 --- Chain | Description | UniProt A | serine protease | SUBT_BACSU 1-275 B | serine protease | SUBT_BACSU 307-377 Non-standard residues in 1scj - Pro-Subtilisin E7.pdb #1 --- CA — calcium ion > open > /Users/melissashehata/Downloads/ProteaseSequence_0b095/ProteaseSequence_0b095_unrelaxed_rank_001_alphafold2_ptm_model_5_seed_000.pdb Chain information for ProteaseSequence_0b095_unrelaxed_rank_001_alphafold2_ptm_model_5_seed_000.pdb #2 --- Chain | Description A | No description available > ui tool show Matchmaker > matchmaker #2 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 1scj - Pro-Subtilisin E7.pdb, chain A (#1) with ProteaseSequence_0b095_unrelaxed_rank_001_alphafold2_ptm_model_5_seed_000.pdb, chain A (#2), sequence alignment score = 1287.8 RMSD between 264 pruned atom pairs is 0.330 angstroms; (across all 264 pairs: 0.330) > matchmaker #2 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 1scj - Pro-Subtilisin E7.pdb, chain A (#1) with ProteaseSequence_0b095_unrelaxed_rank_001_alphafold2_ptm_model_5_seed_000.pdb, chain A (#2), sequence alignment score = 1287.8 RMSD between 264 pruned atom pairs is 0.330 angstroms; (across all 264 pairs: 0.330) > ui tool show ""Show Sequence Viewer"" > sequence chain #1/A Alignment identifier is 1/A > sequence chain #2/A Alignment identifier is 2/A > open ""/Users/melissashehata/Downloads/ProteinStructure2_6202f > 2/ProteinStructure2_6202f_scores_rank_001_alphafold2_ptm_model_1_seed_000.json"" Failed opening file /Users/melissashehata/Downloads/ProteinStructure2_6202f 2/ProteinStructure2_6202f_scores_rank_001_alphafold2_ptm_model_1_seed_000.json: ProteinStructure2_6202f_scores_rank_001_alphafold2_ptm_model_1_seed_000.json does not look like Mole Online json file, does not contain Channels. > open ""/Users/melissashehata/Downloads/ProteinStructure2_6202f > 2/ProteinStructure2_6202f_scores_rank_001_alphafold2_ptm_model_1_seed_000.json"" Failed opening file /Users/melissashehata/Downloads/ProteinStructure2_6202f 2/ProteinStructure2_6202f_scores_rank_001_alphafold2_ptm_model_1_seed_000.json: ProteinStructure2_6202f_scores_rank_001_alphafold2_ptm_model_1_seed_000.json does not look like Mole Online json file, does not contain Channels. > close session > open > /Users/melissashehata/Downloads/ProteinStructure2_6202f/ProteinStructure2_6202f_unrelaxed_rank_001_alphafold2_ptm_model_1_seed_000.pdb > format pdb Chain information for ProteinStructure2_6202f_unrelaxed_rank_001_alphafold2_ptm_model_1_seed_000.pdb #1 --- Chain | Description A | No description available > close session > open ""/Users/melissashehata/Downloads/1scj - Pro-Subtilisin E7.pdb"" format > pdb 1scj - Pro-Subtilisin E7.pdb title: Crystal structure of subtilisin-propeptide complex [more info...] Chain information for 1scj - Pro-Subtilisin E7.pdb #1 --- Chain | Description | UniProt A | serine protease | SUBT_BACSU 1-275 B | serine protease | SUBT_BACSU 307-377 Non-standard residues in 1scj - Pro-Subtilisin E7.pdb #1 --- CA — calcium ion > open > /Users/melissashehata/Downloads/ProteaseSequence_0b095/ProteaseSequence_0b095_unrelaxed_rank_001_alphafold2_ptm_model_5_seed_000.pdb Chain information for ProteaseSequence_0b095_unrelaxed_rank_001_alphafold2_ptm_model_5_seed_000.pdb #2 --- Chain | Description A | No description available > ui tool show Matchmaker > matchmaker #2 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 1scj - Pro-Subtilisin E7.pdb, chain A (#1) with ProteaseSequence_0b095_unrelaxed_rank_001_alphafold2_ptm_model_5_seed_000.pdb, chain A (#2), sequence alignment score = 1287.8 RMSD between 264 pruned atom pairs is 0.330 angstroms; (across all 264 pairs: 0.330) > matchmaker #2 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 1scj - Pro-Subtilisin E7.pdb, chain A (#1) with ProteaseSequence_0b095_unrelaxed_rank_001_alphafold2_ptm_model_5_seed_000.pdb, chain A (#2), sequence alignment score = 1287.8 RMSD between 264 pruned atom pairs is 0.330 angstroms; (across all 264 pairs: 0.330) > save /Users/melissashehata/Downloads/predicted.pro-pro.known.pro-sub.cxs > close session > open > /Users/melissashehata/Downloads/ProteaseSequence_0b095/ProteaseSequence_0b095_unrelaxed_rank_001_alphafold2_ptm_model_5_seed_000.pdb Chain information for ProteaseSequence_0b095_unrelaxed_rank_001_alphafold2_ptm_model_5_seed_000.pdb #1 --- Chain | Description A | No description available > open ""/Users/melissashehata/Downloads/ProteinStructure2_6202f > 2/ProteinStructure2_6202f_unrelaxed_rank_001_alphafold2_ptm_model_1_seed_000.pdb"" Chain information for ProteinStructure2_6202f_unrelaxed_rank_001_alphafold2_ptm_model_1_seed_000.pdb #2 --- Chain | Description A | No description available > ui tool show Matchmaker > matchmaker #2 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker ProteaseSequence_0b095_unrelaxed_rank_001_alphafold2_ptm_model_5_seed_000.pdb, chain A (#1) with ProteinStructure2_6202f_unrelaxed_rank_001_alphafold2_ptm_model_1_seed_000.pdb, chain A (#2), sequence alignment score = 1319.1 RMSD between 264 pruned atom pairs is 0.257 angstroms; (across all 264 pairs: 0.257) > matchmaker #2 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker ProteaseSequence_0b095_unrelaxed_rank_001_alphafold2_ptm_model_5_seed_000.pdb, chain A (#1) with ProteinStructure2_6202f_unrelaxed_rank_001_alphafold2_ptm_model_1_seed_000.pdb, chain A (#2), sequence alignment score = 1319.1 RMSD between 264 pruned atom pairs is 0.257 angstroms; (across all 264 pairs: 0.257) > ui tool show ""Show Sequence Viewer"" > sequence chain #1/A Alignment identifier is 1/A > sequence chain #2/A Alignment identifier is 2/A > select > #2/A:25-29,36-39,93-98,110-115,155-160,187-190,214-218,241-246,264-267,271-275,279-283 397 atoms, 390 bonds, 56 residues, 1 model selected > select #2/A:98 8 atoms, 7 bonds, 1 residue, 1 model selected > select #2/A:98 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > style sel ball Changed 8 atom styles > select #2/A:130 10 atoms, 10 bonds, 1 residue, 1 model selected > select #2/A:130 10 atoms, 10 bonds, 1 residue, 1 model selected > show sel atoms > style sel ball Changed 10 atom styles > select #2/A:191 6 atoms, 5 bonds, 1 residue, 1 model selected > select #2/A:191 6 atoms, 5 bonds, 1 residue, 1 model selected > show sel atoms > style sel ball Changed 6 atom styles > select #1/A:21 8 atoms, 7 bonds, 1 residue, 1 model selected > select #1/A:21 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > style sel ball Changed 8 atom styles > select #1/A:53 10 atoms, 10 bonds, 1 residue, 1 model selected > select #1/A:53 10 atoms, 10 bonds, 1 residue, 1 model selected > show sel atoms > style sel ball Changed 10 atom styles > select #1/A:114 6 atoms, 5 bonds, 1 residue, 1 model selected > select #1/A:114 6 atoms, 5 bonds, 1 residue, 1 model selected > show sel atoms > style sel ball Changed 6 atom styles > open ""/Users/melissashehata/Downloads/ProteaseSequence_0b095 2/config.json"" Failed opening file /Users/melissashehata/Downloads/ProteaseSequence_0b095 2/config.json: config.json does not look like Mole Online json file, does not contain Channels. > select #2/A:191 6 atoms, 5 bonds, 1 residue, 1 model selected > select #2/A:191 6 atoms, 5 bonds, 1 residue, 1 model selected ===== Log before crash end ===== Log: UCSF ChimeraX version: 1.7.1 (2024-01-23) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 INTEL-14.7.8 OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 645 OpenGL vendor: Intel Inc. Python: 3.11.2 Locale: UTF-8 Qt version: PyQt6 6.3.1, Qt 6.3.1 Qt runtime version: 6.3.2 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro15,4 Processor Name: Quad-Core Intel Core i5 Processor Speed: 1.4 GHz Number of Processors: 1 Total Number of Cores: 4 L2 Cache (per Core): 256 KB L3 Cache: 6 MB Hyper-Threading Technology: Enabled Memory: 8 GB Boot ROM Version: 1731.140.2.0.0 (iBridge: 19.16.16064.0.0,0) Software: System Software Overview: System Version: macOS 10.15.7 (19H2) Kernel Version: Darwin 19.6.0 Time since boot: 8 days 6:42 Graphics/Displays: Intel Iris Plus Graphics 645: Chipset Model: Intel Iris Plus Graphics 645 Type: GPU Bus: Built-In VRAM (Dynamic, Max): 1536 MB Vendor: Intel Device ID: 0x3ea6 Revision ID: 0x0001 Metal: Supported, feature set macOS GPUFamily2 v1 Displays: Color LCD: Display Type: Built-In Retina LCD Resolution: 2560 x 1600 Retina Framebuffer Depth: 24-Bit Color (ARGB8888) Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: No Connection Type: Internal Installed Packages: alabaster: 0.7.16 appdirs: 1.4.4 appnope: 0.1.3 asttokens: 2.4.1 Babel: 2.14.0 backcall: 0.2.0 beautifulsoup4: 4.11.2 blockdiag: 3.0.0 blosc2: 2.0.0 build: 0.10.0 certifi: 2022.12.7 cftime: 1.6.3 charset-normalizer: 3.3.2 ChimeraX-AddCharge: 1.5.13 ChimeraX-AddH: 2.2.5 ChimeraX-AlignmentAlgorithms: 2.0.1 ChimeraX-AlignmentHdrs: 3.4.1 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.12.2 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.1.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.49.1 ChimeraX-AtomicLibrary: 12.1.5 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.3.2 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.1.2 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.10.5 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2.2 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.3.2 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.3.2 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.2.4 ChimeraX-ColorActions: 1.0.3 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.5 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.7.1 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.2 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2 ChimeraX-DistMonitor: 1.4 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: 1.1.1 ChimeraX-Hbonds: 2.4 ChimeraX-Help: 1.2.2 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-Label: 1.1.8 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.1.6 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 ChimeraX-Map: 1.1.4 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: 2.1.2 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.6.1 ChimeraX-MedicalToolbar: 1.0.2 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.12.1 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.14 ChimeraX-ModelPanel: 1.4 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-Neuron: 1.0 ChimeraX-Nifti: 1.1 ChimeraX-NRRD: 1.1 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.13.1 ChimeraX-PDB: 2.7.3 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 ChimeraX-PubChem: 2.1 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.1 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.2 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-SelInspector: 1.0 ChimeraX-SeqView: 2.11 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.2 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.12.4 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.1.2 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.2.2 ChimeraX-TapeMeasure: 1.0 ChimeraX-TaskManager: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1.2 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.33.3 ChimeraX-uniprot: 2.3 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.3.2 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: 1.1.3 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.2.1 contourpy: 1.2.0 cxservices: 1.2.2 cycler: 0.12.1 Cython: 0.29.33 debugpy: 1.8.0 decorator: 5.1.1 docutils: 0.19 executing: 2.0.1 filelock: 3.9.0 fonttools: 4.47.2 funcparserlib: 2.0.0a0 glfw: 2.6.4 grako: 3.16.5 h5py: 3.10.0 html2text: 2020.1.16 idna: 3.6 ihm: 0.38 imagecodecs: 2023.9.18 imagesize: 1.4.1 ipykernel: 6.23.2 ipython: 8.14.0 ipython-genutils: 0.2.0 ipywidgets: 8.1.1 jedi: 0.18.2 Jinja2: 3.1.2 jupyter-client: 8.2.0 jupyter-core: 5.7.1 jupyterlab-widgets: 3.0.9 kiwisolver: 1.4.5 line-profiler: 4.0.2 lxml: 4.9.2 lz4: 4.3.2 MarkupSafe: 2.1.4 matplotlib: 3.7.2 matplotlib-inline: 0.1.6 msgpack: 1.0.4 nest-asyncio: 1.6.0 netCDF4: 1.6.2 networkx: 3.1 nibabel: 5.0.1 nptyping: 2.5.0 numexpr: 2.8.8 numpy: 1.25.1 openvr: 1.23.701 packaging: 21.3 ParmEd: 3.4.3 parso: 0.8.3 pep517: 0.13.0 pexpect: 4.9.0 pickleshare: 0.7.5 pillow: 10.2.0 pip: 23.0 pkginfo: 1.9.6 platformdirs: 4.1.0 prompt-toolkit: 3.0.43 psutil: 5.9.5 ptyprocess: 0.7.0 pure-eval: 0.2.2 py-cpuinfo: 9.0.0 pycollada: 0.7.2 pydicom: 2.3.0 Pygments: 2.16.1 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.2801 pyparsing: 3.0.9 pyproject-hooks: 1.0.0 PyQt6-commercial: 6.3.1 PyQt6-Qt6: 6.3.2 PyQt6-sip: 13.4.0 PyQt6-WebEngine-commercial: 6.3.1 PyQt6-WebEngine-Qt6: 6.3.2 python-dateutil: 2.8.2 pytz: 2023.3.post1 pyzmq: 25.1.2 qtconsole: 5.4.3 QtPy: 2.4.1 RandomWords: 0.4.0 requests: 2.31.0 scipy: 1.11.1 setuptools: 67.4.0 setuptools-scm: 7.0.5 sfftk-rw: 0.7.3 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.5 sphinx: 6.1.3 sphinx-autodoc-typehints: 1.22 sphinxcontrib-applehelp: 1.0.8 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.6 sphinxcontrib-htmlhelp: 2.0.5 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.7 sphinxcontrib-serializinghtml: 1.1.10 stack-data: 0.6.3 superqt: 0.5.0 tables: 3.8.0 tcia-utils: 1.5.1 tifffile: 2023.7.18 tinyarray: 1.2.4 tomli: 2.0.1 tornado: 6.4 traitlets: 5.9.0 typing-extensions: 4.9.0 tzdata: 2023.4 urllib3: 2.1.0 wcwidth: 0.2.13 webcolors: 1.12 wheel: 0.38.4 wheel-filename: 1.4.1 widgetsnbextension: 4.0.9 }}} " defect closed normal Core can't reproduce Tom Goddard all ChimeraX