id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 3671 Crash during geometry change lynnettj@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: Darwin-19.5.0-x86_64-i386-64bit ChimeraX Version: 1.0 (2020-06-04 23:15:07 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. Process: ChimeraX [50133] Path: /Applications/ChimeraX-1.0.app/Contents/MacOS/ChimeraX Identifier: ChimeraX Version: 1.0.0 (1.0.0.0) Code Type: X86-64 (Native) Parent Process: ??? [1] Responsible: ChimeraX [50133] User ID: 501 Date/Time: 2020-08-29 08:59:40.771 -0700 OS Version: Mac OS X 10.15.5 (19F101) Report Version: 12 Bridge OS Version: 4.5 (17P5300) Anonymous UUID: 19B202EA-2AEA-B7E4-0983-A274FDA27900 Sleep/Wake UUID: A684E888-88D2-45B0-AE2A-BC81608C78CC Time Awake Since Boot: 330000 seconds Time Since Wake: 2100 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 0x0000000000000008 Exception Note: EXC_CORPSE_NOTIFY VM Regions Near 0x8: --> __TEXT 00000001012dc000-00000001012dd000 [ 4K] r-x/r-x SM=COW /Applications/ChimeraX-1.0.app/Contents/MacOS/ChimeraX Thread 0 Crashed:: CrBrowserMain Dispatch queue: com.apple.main-thread 0 libsystem_kernel.dylib 0x00007fff68f6c33a __pthread_kill + 10 1 libsystem_pthread.dylib 0x00007fff69028e60 pthread_kill + 430 2 libsystem_c.dylib 0x00007fff68e8393e raise + 26 3 libsystem_platform.dylib 0x00007fff6901d5fd _sigtramp + 29 4 ??? 000000000000000000 0 + 0 5 QtGui 0x000000010ec1b14d 0x10e8ec000 + 3338573 6 QtGui 0x000000010ec1a570 QOpenGLFunctions::initializeOpenGLFunctions() + 16 7 QtGui 0x000000010ec1ba96 0x10e8ec000 + 3340950 8 QtGui 0x000000010ec1cb86 QOpenGLFramebufferObject::QOpenGLFramebufferObject(QSize const&, QOpenGLFramebufferObjectFormat const&) + 230 9 QtQuickWidgets 0x0000000118c1eb0a QQuickWidget::createFramebufferObject() + 1338 10 QtQuickWidgets 0x0000000118c1f2af QQuickWidget::resizeEvent(QResizeEvent*) + 735 11 QtWebEngineWidgets 0x00000001117d6bfe 0x1117bc000 + 109566 12 QtWidgets 0x000000010e3876ff QWidget::event(QEvent*) + 1135 13 QtQuickWidgets 0x0000000118c202ce QQuickWidget::event(QEvent*) + 782 14 QtWebEngineWidgets 0x00000001117d70e7 0x1117bc000 + 110823 15 QtWidgets 0x000000010e34b70d QApplicationPrivate::notify_helper(QObject*, QEvent*) + 269 16 QtWidgets 0x000000010e34cb12 QApplication::notify(QObject*, QEvent*) + 594 17 QtWidgets.so 0x000000010df0b3ca sipQApplication::notify(QObject*, QEvent*) + 234 18 QtCore 0x000000010f0374c4 QCoreApplication::notifyInternal2(QObject*, QEvent*) + 212 19 QtWidgets 0x000000010e383c66 QWidgetPrivate::setGeometry_sys(int, int, int, int, bool) + 2230 20 QtWidgets 0x000000010e383f00 QWidget::setGeometry(QRect const&) + 256 21 QtWidgets 0x000000010e36b5fe QWidgetItem::setGeometry(QRect const&) + 702 22 QtWidgets 0x000000010e35e2dc QBoxLayout::setGeometry(QRect const&) + 1948 23 QtWidgets 0x000000010e367f63 QLayoutPrivate::doResize(QSize const&) + 147 24 QtWidgets 0x000000010e34b6ed QApplicationPrivate::notify_helper(QObject*, QEvent*) + 237 25 QtWidgets 0x000000010e34cb12 QApplication::notify(QObject*, QEvent*) + 594 26 QtWidgets.so 0x000000010df0b3ca sipQApplication::notify(QObject*, QEvent*) + 234 27 QtCore 0x000000010f0374c4 QCoreApplication::notifyInternal2(QObject*, QEvent*) + 212 28 QtWidgets 0x000000010e383c66 QWidgetPrivate::setGeometry_sys(int, int, int, int, bool) + 2230 29 QtWidgets 0x000000010e383f00 QWidget::setGeometry(QRect const&) + 256 30 QtWidgets 0x000000010e36b5fe QWidgetItem::setGeometry(QRect const&) + 702 31 QtWidgets 0x000000010e36446f 0x10e33b000 + 169071 32 QtWidgets 0x000000010e365cdf QGridLayout::setGeometry(QRect const&) + 207 33 QtWidgets.so 0x000000010de87120 sipQGridLayout::setGeometry(QRect const&) + 176 34 QtWidgets 0x000000010e367f63 QLayoutPrivate::doResize(QSize const&) + 147 35 QtWidgets 0x000000010e34b6ed QApplicationPrivate::notify_helper(QObject*, QEvent*) + 237 36 QtWidgets 0x000000010e34cb12 QApplication::notify(QObject*, QEvent*) + 594 37 QtWidgets.so 0x000000010df0b3ca sipQApplication::notify(QObject*, QEvent*) + 234 38 QtCore 0x000000010f0374c4 QCoreApplication::notifyInternal2(QObject*, QEvent*) + 212 39 QtWidgets 0x000000010e383c66 QWidgetPrivate::setGeometry_sys(int, int, int, int, bool) + 2230 40 QtWidgets 0x000000010e383f00 QWidget::setGeometry(QRect const&) + 256 41 QtWidgets 0x000000010e36b5fe QWidgetItem::setGeometry(QRect const&) + 702 42 QtWidgets 0x000000010e35e2dc QBoxLayout::setGeometry(QRect const&) + 1948 43 QtWidgets.so 0x000000010df02780 sipQVBoxLayout::setGeometry(QRect const&) + 176 44 QtWidgets 0x000000010e367f63 QLayoutPrivate::doResize(QSize const&) + 147 45 QtWidgets 0x000000010e34b6ed QApplicationPrivate::notify_helper(QObject*, QEvent*) + 237 46 QtWidgets 0x000000010e34cb12 QApplication::notify(QObject*, QEvent*) + 594 47 QtWidgets.so 0x000000010df0b3ca sipQApplication::notify(QObject*, QEvent*) + 234 48 QtCore 0x000000010f0374c4 QCoreApplication::notifyInternal2(QObject*, QEvent*) + 212 49 QtWidgets 0x000000010e383c66 QWidgetPrivate::setGeometry_sys(int, int, int, int, bool) + 2230 50 QtWidgets 0x000000010e383f00 QWidget::setGeometry(QRect const&) + 256 51 QtWidgets 0x000000010e36b5fe QWidgetItem::setGeometry(QRect const&) + 702 52 QtWidgets 0x000000010e460ec2 QDockWidgetLayout::setGeometry(QRect const&) + 1042 53 QtWidgets 0x000000010e367f63 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thread_start + 15 Thread 17:: Chrome_ChildIOThread 0 libsystem_kernel.dylib 0x00007fff68f6a766 kevent + 10 1 QtWebEngineCore 0x0000000113c70929 0x111804000 + 38193449 2 QtWebEngineCore 0x0000000113c6dc3d 0x111804000 + 38181949 3 QtWebEngineCore 0x0000000113a24c5c 0x111804000 + 35785820 4 QtWebEngineCore 0x000000011398c005 0x111804000 + 35160069 5 QtWebEngineCore 0x00000001139de93c 0x111804000 + 35498300 6 QtWebEngineCore 0x0000000113a1e697 0x111804000 + 35759767 7 libsystem_pthread.dylib 0x00007fff69029109 _pthread_start + 148 8 libsystem_pthread.dylib 0x00007fff69024b8b thread_start + 15 Thread 18:: TaskSchedulerSingleThreadForegroundBlocking1 0 libsystem_kernel.dylib 0x00007fff68f65dfa mach_msg_trap + 10 1 libsystem_kernel.dylib 0x00007fff68f66170 mach_msg + 60 2 QtWebEngineCore 0x00000001139af2ad 0x111804000 + 35304109 3 QtWebEngineCore 0x00000001139af1af 0x111804000 + 35303855 4 QtWebEngineCore 0x00000001139c6c9a 0x111804000 + 35400858 5 QtWebEngineCore 0x00000001139c75db 0x111804000 + 35403227 6 QtWebEngineCore 0x00000001139c72a4 0x111804000 + 35402404 7 QtWebEngineCore 0x0000000113a1e697 0x111804000 + 35759767 8 libsystem_pthread.dylib 0x00007fff69029109 _pthread_start + 148 9 libsystem_pthread.dylib 0x00007fff69024b8b thread_start + 15 Thread 19:: NetworkConfigWatcher 0 libsystem_kernel.dylib 0x00007fff68f65dfa mach_msg_trap + 10 1 libsystem_kernel.dylib 0x00007fff68f66170 mach_msg + 60 2 QtWebEngineCore 0x00000001139af2ad 0x111804000 + 35304109 3 QtWebEngineCore 0x00000001139af1af 0x111804000 + 35303855 4 QtWebEngineCore 0x0000000113962fdd 0x111804000 + 34992093 5 QtWebEngineCore 0x000000011398c005 0x111804000 + 35160069 6 QtWebEngineCore 0x00000001139de93c 0x111804000 + 35498300 7 QtWebEngineCore 0x0000000113a1e697 0x111804000 + 35759767 8 libsystem_pthread.dylib 0x00007fff69029109 _pthread_start + 148 9 libsystem_pthread.dylib 0x00007fff69024b8b thread_start + 15 Thread 20:: TaskSchedulerForegroundBlockingWorker 0 libsystem_kernel.dylib 0x00007fff68f65dfa mach_msg_trap + 10 1 libsystem_kernel.dylib 0x00007fff68f66170 mach_msg + 60 2 QtWebEngineCore 0x00000001139af2ad 0x111804000 + 35304109 3 QtWebEngineCore 0x00000001139af3a1 0x111804000 + 35304353 4 QtWebEngineCore 0x00000001139c6ca8 0x111804000 + 35400872 5 QtWebEngineCore 0x00000001139c75db 0x111804000 + 35403227 6 QtWebEngineCore 0x00000001139c7244 0x111804000 + 35402308 7 QtWebEngineCore 0x0000000113a1e697 0x111804000 + 35759767 8 libsystem_pthread.dylib 0x00007fff69029109 _pthread_start + 148 9 libsystem_pthread.dylib 0x00007fff69024b8b thread_start + 15 Thread 21: 0 libsystem_pthread.dylib 0x00007fff69024b68 start_wqthread + 0 Thread 22: 0 libsystem_pthread.dylib 0x00007fff69024b68 start_wqthread + 0 Thread 23: 0 libsystem_pthread.dylib 0x00007fff69024b68 start_wqthread + 0 Thread 24: 0 libsystem_pthread.dylib 0x00007fff69024b68 start_wqthread + 0 Thread 25: 0 libsystem_pthread.dylib 0x00007fff69024b68 start_wqthread + 0 Thread 26: 0 libsystem_pthread.dylib 0x00007fff69024b68 start_wqthread + 0 Thread 27: 0 libsystem_pthread.dylib 0x00007fff69024b68 start_wqthread + 0 Thread 0 crashed with X86 Thread State (64-bit): rax: 0x0000000000000000 rbx: 0x000000010745cdc0 rcx: 0x00007fe53ee77a58 rdx: 0x0000000000000000 rdi: 0x0000000000000307 rsi: 0x000000000000000b rbp: 0x00007fe53ee77a80 rsp: 0x00007fe53ee77a58 r8: 0x00007fe53ee77f48 r9: 0xc75847065473cbb1 r10: 0x000000010745cdc0 r11: 0x0000000000000246 r12: 0x0000000000000307 r13: 0x00007ffeee91ccc0 r14: 0x000000000000000b r15: 0x0000000000000016 rip: 0x00007fff68f6c33a rfl: 0x0000000000000246 cr2: 0x00000001014df7c8 Logical CPU: 0 Error Code: 0x02000148 Trap Number: 133 Binary Images: 0x1012dc000 - 0x1012dcff3 +edu.ucsf.cgl.ChimeraX (1.0.0 - 1.0.0.0) /Applications/ChimeraX-1.0.app/Contents/MacOS/ChimeraX 0x1012e3000 - 0x1014defff +org.python.python (3.7.7, [c] 2001-2019 Python Software Foundation. - 3.7.7) 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/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/lib-dynload/_lzma.cpython-37m-darwin.so 0x1019a7000 - 0x1019a7ffb +grp.cpython-37m-darwin.so (0) /Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/lib-dynload/grp.cpython-37m-darwin.so 0x1019ef000 - 0x1019f4ffb +math.cpython-37m-darwin.so (0) /Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/lib-dynload/math.cpython-37m-darwin.so 0x101a00000 - 0x101a02ff3 +_hashlib.cpython-37m-darwin.so (0) /Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/lib-dynload/_hashlib.cpython-37m-darwin.so 0x101a0b000 - 0x101a68ff7 +libssl.1.1.dylib (0) /Applications/ChimeraX-1.0.app/Contents/lib/libssl.1.1.dylib 0x101a97000 - 0x101c5eaf3 +libcrypto.1.1.dylib (0) /Applications/ChimeraX-1.0.app/Contents/lib/libcrypto.1.1.dylib 0x101cf7000 - 0x101cfcff3 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0x101e41000 - 0x101e4eff3 +_ssl.cpython-37m-darwin.so (0) /Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/lib-dynload/_ssl.cpython-37m-darwin.so 0x101e64000 - 0x101e6dffb +_socket.cpython-37m-darwin.so (0) /Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/lib-dynload/_socket.cpython-37m-darwin.so 0x101ebf000 - 0x101ec2fff +select.cpython-37m-darwin.so (0) /Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/lib-dynload/select.cpython-37m-darwin.so 0x101ecc000 - 0x101ed0ff3 +_struct.cpython-37m-darwin.so (0) /Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/lib-dynload/_struct.cpython-37m-darwin.so 0x101ede000 - 0x101ee2ff7 +binascii.cpython-37m-darwin.so (0) /Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/lib-dynload/binascii.cpython-37m-darwin.so 0x101feb000 - 0x101ff9ff3 +_datetime.cpython-37m-darwin.so (0) /Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/lib-dynload/_datetime.cpython-37m-darwin.so 0x102049000 - 0x102049ff3 +_scproxy.cpython-37m-darwin.so (0) /Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/lib-dynload/_scproxy.cpython-37m-darwin.so 0x102051000 - 0x10208ffff +_decimal.cpython-37m-darwin.so (0) /Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/lib-dynload/_decimal.cpython-37m-darwin.so 0x1020f3000 - 0x102120ff3 +pyexpat.cpython-37m-darwin.so (0) /Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/lib-dynload/pyexpat.cpython-37m-darwin.so 0x102138000 - 0x102139ff3 +_queue.cpython-37m-darwin.so (0) /Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/lib-dynload/_queue.cpython-37m-darwin.so 0x102202000 - 0x102203fff +_posixsubprocess.cpython-37m-darwin.so (0) /Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/lib-dynload/_posixsubprocess.cpython-37m-darwin.so 0x10224b000 - 0x10225dfff +_pickle.cpython-37m-darwin.so (0) /Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/lib-dynload/_pickle.cpython-37m-darwin.so 0x1022ae000 - 0x1022b1ffb +_csv.cpython-37m-darwin.so (0) /Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/lib-dynload/_csv.cpython-37m-darwin.so 0x10243c000 - 0x10279ffe7 +_multiarray_umath.cpython-37m-darwin.so (0) /Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/numpy/core/_multiarray_umath.cpython-37m-darwin.so 0x1028c5000 - 0x106330ae7 +libopenblasp-r0.3.7.dylib (0) /Applications/ChimeraX-1.0.app/Contents/lib/python3.7/site-packages/numpy/.dylibs/libopenblasp-r0.3.7.dylib 0x106639000 - 0x106750ff7 +libgfortran.3.dylib (0) /Applications/ChimeraX-1.0.app/Contents/lib/python3.7/site-packages/numpy/.dylibs/libgfortran.3.dylib 0x1067be000 - 0x1067f4fff +libquadmath.0.dylib (0) /Applications/ChimeraX-1.0.app/Contents/lib/python3.7/site-packages/numpy/.dylibs/libquadmath.0.dylib 0x106808000 - 0x10681dff7 +libgcc_s.1.dylib (0) /Applications/ChimeraX-1.0.app/Contents/lib/python3.7/site-packages/numpy/.dylibs/libgcc_s.1.dylib 0x1069ad000 - 0x1069baff3 +_multiarray_tests.cpython-37m-darwin.so (0) /Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/numpy/core/_multiarray_tests.cpython-37m-darwin.so 0x1069d0000 - 0x1069e2ff7 +_ctypes.cpython-37m-darwin.so (0) /Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/lib-dynload/_ctypes.cpython-37m-darwin.so 0x106a79000 - 0x106a7afff +lapack_lite.cpython-37m-darwin.so (0) /Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/numpy/linalg/lapack_lite.cpython-37m-darwin.so 0x106a82000 - 0x106a9bffb +_umath_linalg.cpython-37m-darwin.so (0) /Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/numpy/linalg/_umath_linalg.cpython-37m-darwin.so 0x106b6f000 - 0x106b80ffb +_pocketfft_internal.cpython-37m-darwin.so (0) /Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/numpy/fft/_pocketfft_internal.cpython-37m-darwin.so 0x106bc9000 - 0x106c35fff +mtrand.cpython-37m-darwin.so (0) /Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/numpy/random/mtrand.cpython-37m-darwin.so 0x106c90000 - 0x106caffff +_bit_generator.cpython-37m-darwin.so (0) /Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/numpy/random/_bit_generator.cpython-37m-darwin.so 0x106d10000 - 0x106d41ff3 +_common.cpython-37m-darwin.so (0) /Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/numpy/random/_common.cpython-37m-darwin.so 0x106d5c000 - 0x106db0ffb +_bounded_integers.cpython-37m-darwin.so (0) /Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/numpy/random/_bounded_integers.cpython-37m-darwin.so 0x106dd9000 - 0x106decffb +_mt19937.cpython-37m-darwin.so (0) /Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/numpy/random/_mt19937.cpython-37m-darwin.so 0x106dfd000 - 0x106e0aff7 +_philox.cpython-37m-darwin.so (0) /Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/numpy/random/_philox.cpython-37m-darwin.so 0x106e1a000 - 0x106e24ffb +_pcg64.cpython-37m-darwin.so (0) /Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/numpy/random/_pcg64.cpython-37m-darwin.so 0x106e34000 - 0x106e3cffb +_sfc64.cpython-37m-darwin.so (0) /Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/numpy/random/_sfc64.cpython-37m-darwin.so 0x106e4b000 - 0x106eceff7 +_generator.cpython-37m-darwin.so (0) /Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/numpy/random/_generator.cpython-37m-darwin.so 0x10702e000 - 0x10702fff7 +_appdirs.so (0) /Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/core/_appdirs.so 0x107037000 - 0x107038ffb +libappdirs.dylib (0) /Applications/ChimeraX-1.0.app/Contents/lib/libappdirs.dylib 0x107040000 - 0x107062ff7 +_serialize.cpython-37m-darwin.so (0) /Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/core/_serialize.cpython-37m-darwin.so 0x107082000 - 0x10709affb +_cmsgpack.cpython-37m-darwin.so (0) 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(1.0 - 662) /System/Library/PrivateFrameworks/UIFoundation.framework/Versions/A/UIFoundation 0x7fff60114000 - 0x7fff6011affe com.apple.URLFormatting (119 - 119.18) /System/Library/PrivateFrameworks/URLFormatting.framework/Versions/A/URLFormatting 0x7fff60cf0000 - 0x7fff60d10ffc com.apple.UserManagement (1.0 - 1) /System/Library/PrivateFrameworks/UserManagement.framework/Versions/A/UserManagement 0x7fff61abc000 - 0x7fff61ba6ff8 com.apple.ViewBridge (464.1 - 464.1) /System/Library/PrivateFrameworks/ViewBridge.framework/Versions/A/ViewBridge 0x7fff61d4c000 - 0x7fff61d4dfff com.apple.WatchdogClient.framework (1.0 - 67.120.2) /System/Library/PrivateFrameworks/WatchdogClient.framework/Versions/A/WatchdogClient 0x7fff6297a000 - 0x7fff6297dffa com.apple.dt.XCTTargetBootstrap (1.0 - 16091) /System/Library/PrivateFrameworks/XCTTargetBootstrap.framework/Versions/A/XCTTargetBootstrap 0x7fff629f7000 - 0x7fff62a05ff5 com.apple.audio.caulk (1.0 - 32.3) /System/Library/PrivateFrameworks/caulk.framework/Versions/A/caulk 0x7fff62d47000 - 0x7fff62d49ff3 com.apple.loginsupport (1.0 - 1) /System/Library/PrivateFrameworks/login.framework/Versions/A/Frameworks/loginsupport.framework/Versions/A/loginsupport 0x7fff62d4a000 - 0x7fff62d5dffd com.apple.login (3.0 - 3.0) /System/Library/PrivateFrameworks/login.framework/Versions/A/login 0x7fff62d8f000 - 0x7fff62d9bffd com.apple.perfdata (1.0 - 51.100.6) /System/Library/PrivateFrameworks/perfdata.framework/Versions/A/perfdata 0x7fff65820000 - 0x7fff6582cff9 libAudioStatistics.dylib (1104.84) /usr/lib/libAudioStatistics.dylib 0x7fff6582d000 - 0x7fff65860ffa libAudioToolboxUtility.dylib (1104.84) /usr/lib/libAudioToolboxUtility.dylib 0x7fff65867000 - 0x7fff6589bfff libCRFSuite.dylib (48) /usr/lib/libCRFSuite.dylib 0x7fff6589e000 - 0x7fff658a8fff libChineseTokenizer.dylib (34) /usr/lib/libChineseTokenizer.dylib 0x7fff658a9000 - 0x7fff65931fff libCoreStorage.dylib (551) /usr/lib/libCoreStorage.dylib 0x7fff65934000 - 0x7fff65936ff7 libDiagnosticMessagesClient.dylib (112) /usr/lib/libDiagnosticMessagesClient.dylib 0x7fff6597c000 - 0x7fff65b33ffb libFosl_dynamic.dylib (100.4) /usr/lib/libFosl_dynamic.dylib 0x7fff65b5a000 - 0x7fff65b60ff3 libIOReport.dylib (54) /usr/lib/libIOReport.dylib 0x7fff65c42000 - 0x7fff65c49fff libMatch.1.dylib (36) /usr/lib/libMatch.1.dylib 0x7fff65c78000 - 0x7fff65c98fff libMobileGestalt.dylib (826.120.5) /usr/lib/libMobileGestalt.dylib 0x7fff65d18000 - 0x7fff65df5ff7 libSMC.dylib (20) /usr/lib/libSMC.dylib 0x7fff65e0a000 - 0x7fff65e0bfff libSystem.B.dylib (1281.100.1) /usr/lib/libSystem.B.dylib 0x7fff65e0c000 - 0x7fff65e97ff7 libTelephonyUtilDynamic.dylib (5017.1) /usr/lib/libTelephonyUtilDynamic.dylib 0x7fff65e98000 - 0x7fff65e99fff libThaiTokenizer.dylib (3) /usr/lib/libThaiTokenizer.dylib 0x7fff65eb1000 - 0x7fff65ec7fff libapple_nghttp2.dylib (1.39.2) /usr/lib/libapple_nghttp2.dylib 0x7fff65efc000 - 0x7fff65f6eff7 libarchive.2.dylib (72.100.1) /usr/lib/libarchive.2.dylib 0x7fff65f6f000 - 0x7fff66008fe5 libate.dylib (3.0.1) /usr/lib/libate.dylib 0x7fff6600c000 - 0x7fff6600cff3 libauto.dylib (187) /usr/lib/libauto.dylib 0x7fff6600d000 - 0x7fff660d1ffe libboringssl.dylib (283.120.1) /usr/lib/libboringssl.dylib 0x7fff660d2000 - 0x7fff660e2ffb libbsm.0.dylib (60.100.1) /usr/lib/libbsm.0.dylib 0x7fff660e3000 - 0x7fff660effff libbz2.1.0.dylib (44) /usr/lib/libbz2.1.0.dylib 0x7fff660f0000 - 0x7fff66142fff libc++.1.dylib (902.1) /usr/lib/libc++.1.dylib 0x7fff66143000 - 0x7fff66158ffb libc++abi.dylib (902) /usr/lib/libc++abi.dylib 0x7fff66159000 - 0x7fff66159fff libcharset.1.dylib (59) /usr/lib/libcharset.1.dylib 0x7fff6615a000 - 0x7fff6616bfff libcmph.dylib (8) /usr/lib/libcmph.dylib 0x7fff6616c000 - 0x7fff66183fd7 libcompression.dylib (87) /usr/lib/libcompression.dylib 0x7fff6645d000 - 0x7fff66473ff7 libcoretls.dylib (167) /usr/lib/libcoretls.dylib 0x7fff66474000 - 0x7fff66475fff libcoretls_cfhelpers.dylib (167) /usr/lib/libcoretls_cfhelpers.dylib 0x7fff66918000 - 0x7fff66a1cfef libcrypto.44.dylib (47.120.1) /usr/lib/libcrypto.44.dylib 0x7fff66a1f000 - 0x7fff66a2afff libcsfde.dylib (551) /usr/lib/libcsfde.dylib 0x7fff66a32000 - 0x7fff66a91ff7 libcups.2.dylib (483.6) /usr/lib/libcups.2.dylib 0x7fff66a93000 - 0x7fff66af8ff7 libcurl.4.dylib (118.120.2) /usr/lib/libcurl.4.dylib 0x7fff66b9b000 - 0x7fff66b9bfff libenergytrace.dylib (21) /usr/lib/libenergytrace.dylib 0x7fff66b9c000 - 0x7fff66bb4fff libexpat.1.dylib (19.60.2) /usr/lib/libexpat.1.dylib 0x7fff66bc2000 - 0x7fff66bc4fff libfakelink.dylib (149.1) /usr/lib/libfakelink.dylib 0x7fff66bd3000 - 0x7fff66bd8fff libgermantok.dylib (24) /usr/lib/libgermantok.dylib 0x7fff66bd9000 - 0x7fff66be2ff7 libheimdal-asn1.dylib (564.100.1) /usr/lib/libheimdal-asn1.dylib 0x7fff66be3000 - 0x7fff66cd3fff libiconv.2.dylib (59) /usr/lib/libiconv.2.dylib 0x7fff66cd4000 - 0x7fff66f2bfff libicucore.A.dylib (64260.0.1) /usr/lib/libicucore.A.dylib 0x7fff66f45000 - 0x7fff66f46fff liblangid.dylib (133) /usr/lib/liblangid.dylib 0x7fff66f47000 - 0x7fff66f5fff3 liblzma.5.dylib (16) /usr/lib/liblzma.5.dylib 0x7fff66f77000 - 0x7fff6701eff7 libmecab.dylib (883.11) /usr/lib/libmecab.dylib 0x7fff6701f000 - 0x7fff67281ff1 libmecabra.dylib (883.11) /usr/lib/libmecabra.dylib 0x7fff675ee000 - 0x7fff6761dfff libncurses.5.4.dylib (57) /usr/lib/libncurses.5.4.dylib 0x7fff6774d000 - 0x7fff67bc9ff5 libnetwork.dylib (1880.120.4) /usr/lib/libnetwork.dylib 0x7fff67bca000 - 0x7fff67be1fff libnetworkextension.dylib (1095.120.6) /usr/lib/libnetworkextension.dylib 0x7fff67c6a000 - 0x7fff67c9dfde libobjc.A.dylib (787.1) /usr/lib/libobjc.A.dylib 0x7fff67c9e000 - 0x7fff67c9fff7 libodfde.dylib (26) /usr/lib/libodfde.dylib 0x7fff67cb0000 - 0x7fff67cb4fff libpam.2.dylib (25.100.1) /usr/lib/libpam.2.dylib 0x7fff67cb7000 - 0x7fff67cedff7 libpcap.A.dylib (89.120.1) /usr/lib/libpcap.A.dylib 0x7fff67d2d000 - 0x7fff67d3bff9 libperfcheck.dylib (37.100.2) /usr/lib/libperfcheck.dylib 0x7fff67d71000 - 0x7fff67d89fff libresolv.9.dylib (67.40.1) /usr/lib/libresolv.9.dylib 0x7fff67d8b000 - 0x7fff67dcfff7 libsandbox.1.dylib (1217.120.7) /usr/lib/libsandbox.1.dylib 0x7fff67dd0000 - 0x7fff67de2ff7 libsasl2.2.dylib (213.120.1) /usr/lib/libsasl2.2.dylib 0x7fff67de3000 - 0x7fff67de4ff7 libspindump.dylib (281.3) /usr/lib/libspindump.dylib 0x7fff67de5000 - 0x7fff67fcfff7 libsqlite3.dylib (308.5) /usr/lib/libsqlite3.dylib 0x7fff680c3000 - 0x7fff680f0ffb libssl.46.dylib (47.120.1) /usr/lib/libssl.46.dylib 0x7fff681c5000 - 0x7fff6821fff8 libusrtcp.dylib (1880.120.4) /usr/lib/libusrtcp.dylib 0x7fff68220000 - 0x7fff68223ffb libutil.dylib (57) /usr/lib/libutil.dylib 0x7fff68224000 - 0x7fff68231ff7 libxar.1.dylib (425.2) /usr/lib/libxar.1.dylib 0x7fff68237000 - 0x7fff68319ff7 libxml2.2.dylib (33.3) /usr/lib/libxml2.2.dylib 0x7fff6831d000 - 0x7fff68345fff libxslt.1.dylib (16.9) /usr/lib/libxslt.1.dylib 0x7fff68346000 - 0x7fff68358ff3 libz.1.dylib (76) /usr/lib/libz.1.dylib 0x7fff68c06000 - 0x7fff68c0bff3 libcache.dylib (83) /usr/lib/system/libcache.dylib 0x7fff68c0c000 - 0x7fff68c17fff libcommonCrypto.dylib (60165.120.1) /usr/lib/system/libcommonCrypto.dylib 0x7fff68c18000 - 0x7fff68c1ffff libcompiler_rt.dylib (101.2) /usr/lib/system/libcompiler_rt.dylib 0x7fff68c20000 - 0x7fff68c29ff7 libcopyfile.dylib (166.40.1) /usr/lib/system/libcopyfile.dylib 0x7fff68c2a000 - 0x7fff68cbcfe3 libcorecrypto.dylib (866.120.3) /usr/lib/system/libcorecrypto.dylib 0x7fff68dc9000 - 0x7fff68e09ff0 libdispatch.dylib (1173.100.2) /usr/lib/system/libdispatch.dylib 0x7fff68e0a000 - 0x7fff68e40fff libdyld.dylib (750.5) /usr/lib/system/libdyld.dylib 0x7fff68e41000 - 0x7fff68e41ffb libkeymgr.dylib (30) /usr/lib/system/libkeymgr.dylib 0x7fff68e42000 - 0x7fff68e4eff3 libkxld.dylib (6153.121.2) /usr/lib/system/libkxld.dylib 0x7fff68e4f000 - 0x7fff68e4fff7 liblaunch.dylib (1738.120.8) /usr/lib/system/liblaunch.dylib 0x7fff68e50000 - 0x7fff68e55ff7 libmacho.dylib (959.0.1) /usr/lib/system/libmacho.dylib 0x7fff68e56000 - 0x7fff68e58ff3 libquarantine.dylib (110.40.3) /usr/lib/system/libquarantine.dylib 0x7fff68e59000 - 0x7fff68e5aff7 libremovefile.dylib (48) /usr/lib/system/libremovefile.dylib 0x7fff68e5b000 - 0x7fff68e72ff3 libsystem_asl.dylib (377.60.2) /usr/lib/system/libsystem_asl.dylib 0x7fff68e73000 - 0x7fff68e73ff7 libsystem_blocks.dylib (74) /usr/lib/system/libsystem_blocks.dylib 0x7fff68e74000 - 0x7fff68efbfff libsystem_c.dylib (1353.100.2) /usr/lib/system/libsystem_c.dylib 0x7fff68efc000 - 0x7fff68effffb libsystem_configuration.dylib (1061.120.2) /usr/lib/system/libsystem_configuration.dylib 0x7fff68f00000 - 0x7fff68f03fff libsystem_coreservices.dylib (114) /usr/lib/system/libsystem_coreservices.dylib 0x7fff68f04000 - 0x7fff68f0cfff libsystem_darwin.dylib (1353.100.2) /usr/lib/system/libsystem_darwin.dylib 0x7fff68f0d000 - 0x7fff68f14fff libsystem_dnssd.dylib (1096.100.3) /usr/lib/system/libsystem_dnssd.dylib 0x7fff68f15000 - 0x7fff68f16ffb libsystem_featureflags.dylib (17) /usr/lib/system/libsystem_featureflags.dylib 0x7fff68f17000 - 0x7fff68f64ff7 libsystem_info.dylib (538) /usr/lib/system/libsystem_info.dylib 0x7fff68f65000 - 0x7fff68f91ff7 libsystem_kernel.dylib (6153.121.2) /usr/lib/system/libsystem_kernel.dylib 0x7fff68f92000 - 0x7fff68fd9fff libsystem_m.dylib (3178) /usr/lib/system/libsystem_m.dylib 0x7fff68fda000 - 0x7fff69001fff libsystem_malloc.dylib (283.100.6) /usr/lib/system/libsystem_malloc.dylib 0x7fff69002000 - 0x7fff6900fffb libsystem_networkextension.dylib (1095.120.6) /usr/lib/system/libsystem_networkextension.dylib 0x7fff69010000 - 0x7fff69019ff7 libsystem_notify.dylib (241.100.2) /usr/lib/system/libsystem_notify.dylib 0x7fff6901a000 - 0x7fff69022fef libsystem_platform.dylib (220.100.1) /usr/lib/system/libsystem_platform.dylib 0x7fff69023000 - 0x7fff6902dfff libsystem_pthread.dylib (416.100.3) /usr/lib/system/libsystem_pthread.dylib 0x7fff6902e000 - 0x7fff69032ff3 libsystem_sandbox.dylib (1217.120.7) /usr/lib/system/libsystem_sandbox.dylib 0x7fff69033000 - 0x7fff69035fff libsystem_secinit.dylib (62.100.2) /usr/lib/system/libsystem_secinit.dylib 0x7fff69036000 - 0x7fff6903dffb libsystem_symptoms.dylib (1238.120.1) /usr/lib/system/libsystem_symptoms.dylib 0x7fff6903e000 - 0x7fff69054ff2 libsystem_trace.dylib (1147.120) /usr/lib/system/libsystem_trace.dylib 0x7fff69056000 - 0x7fff6905bff7 libunwind.dylib (35.4) /usr/lib/system/libunwind.dylib 0x7fff6905c000 - 0x7fff69091ffe libxpc.dylib (1738.120.8) /usr/lib/system/libxpc.dylib External Modification Summary: Calls made by other processes targeting this process: task_for_pid: 117 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: 207889 thread_create: 0 thread_set_state: 0 VM Region Summary: ReadOnly portion of Libraries: Total=938.3M resident=0K(0%) swapped_out_or_unallocated=938.3M(100%) Writable regions: Total=1.2G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=1.2G(100%) VIRTUAL REGION REGION TYPE SIZE COUNT (non-coalesced) =========== ======= ======= Accelerate framework 512K 4 Activity Tracing 256K 1 CG backing stores 7100K 8 CG image 188K 21 CoreAnimation 732K 80 CoreGraphics 8K 1 CoreImage 44K 6 CoreUI image data 84K 2 Foundation 24K 2 Kernel Alloc Once 8K 1 MALLOC 806.0M 572 MALLOC guard page 32K 8 MALLOC_LARGE (reserved) 384K 1 reserved VM address space (unallocated) Memory Tag 242 12K 1 OpenGL GLSL 512K 6 PROTECTED_MEMORY 4K 1 STACK GUARD 108K 27 Stack 141.7M 28 Stack Guard 56.0M 1 VM_ALLOCATE 201.3M 434 VM_ALLOCATE (reserved) 32.0M 1 reserved VM address space (unallocated) __DATA 51.5M 547 __DATA_CONST 44K 4 __FONT_DATA 4K 1 __GLSLBUILTINS 5176K 1 __LINKEDIT 412.3M 141 __OBJC_RO 32.2M 1 __OBJC_RW 1892K 2 __TEXT 526.0M 513 __UNICODE 564K 1 mapped file 75.5M 40 shared memory 668K 20 =========== ======= ======= TOTAL 2.3G 2477 TOTAL, minus reserved VM space 2.3G 2477 System Profile: Network Service: Wi-Fi, AirPort, en0 bridge_os_version: Bridge OS 4.5 (17P5300) Boot Volume File System Type: apfs bridge_model: iBridge2,4 Memory Module: BANK 0/ChannelA-DIMM0, 4 GB, LPDDR3, 2133 MHz, Micron, - Memory Module: BANK 2/ChannelB-DIMM0, 4 GB, LPDDR3, 2133 MHz, Micron, - USB Device: USB3.1 Hub USB Device: USB 3.1 Bus USB Device: USB2.0 Hub USB Device: USB-C Digital AV Multiport Adapter USB Device: Apple T2 Bus USB Device: Touch Bar Backlight USB Device: Touch Bar Display USB Device: Apple Internal Keyboard / Trackpad USB Device: Headset USB Device: Ambient Light Sensor USB Device: FaceTime HD Camera (Built-in) USB Device: Apple T2 Controller Thunderbolt Bus: MacBook Pro, Apple Inc., 47.4 Thunderbolt Bus: MacBook Pro, Apple Inc., 47.4 Model: MacBookPro15,2, BootROM 1037.120.87.0.0 (iBridge: 17.16.15300.0.0,0), 4 processors, Quad-Core Intel Core i5, 2.3 GHz, 8 GB, SMC Graphics: kHW_IntelIrisGraphics655Item, Intel Iris Plus Graphics 655, spdisplays_builtin AirPort: spairport_wireless_card_type_airport_extreme (0x14E4, 0x7BF), wl0: Feb 28 2020 15:24:56 version 9.30.357.35.32.5.47 FWID 01-9ce4adf3 Bluetooth: Version 7.0.5f6, 3 services, 27 devices, 1 incoming serial ports Log: UCSF ChimeraX version: 1.0 (2020-06-04) © 2016-2020 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open ""/Users/lynnettj/Documents/Grad School/Research/PyMOL and Chimera > sessions/1hvn.pdb"" 1hvn.pdb title: Zinc-and sequence-dependent binding to nucleic acids by the N-terminal zinc finger domain of the hiv-1 nucleocapsid protein: NMR structure of the complex with the ψ-site analog, D/acgcc [more info...] Chain information for 1hvn.pdb --- Chain | Description 1.1/D 1.2/D 1.3/D 1.4/D 1.5/D 1.6/D 1.7/D 1.8/D 1.9/D 1.10/D 1.11/D 1.12/D 1.13/D 1.14/D 1.15/D | DNA (5'-D(P*ap*CP*GP*CP*C)-3') 1.1/E 1.2/E 1.3/E 1.4/E 1.5/E 1.6/E 1.7/E 1.8/E 1.9/E 1.10/E 1.11/E 1.12/E 1.13/E 1.14/E 1.15/E | hiv-1 nucleocapsid zinc finger OpenGL version: 4.1 INTEL-14.6.18 OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 655 OpenGL vendor: Intel Inc.Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro15,2 Processor Name: Quad-Core Intel Core i5 Processor Speed: 2.3 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: 1037.120.87.0.0 (iBridge: 17.16.15300.0.0,0) Software: System Software Overview: System Version: macOS 10.15.5 (19F101) Kernel Version: Darwin 19.5.0 Time since boot: 11 days 9:52 Graphics/Displays: Intel Iris Plus Graphics 655: Chipset Model: Intel Iris Plus Graphics 655 Type: GPU Bus: Built-In VRAM (Dynamic, Max): 1536 MB Vendor: Intel Device ID: 0x3ea5 Revision ID: 0x0001 Metal: Supported, feature set macOS GPUFamily2 v1 Displays: HP VH240a: Resolution: 1920 x 1080 (1080p FHD - Full High Definition) UI Looks like: 1920 x 1080 @ 60 Hz Framebuffer Depth: 30-Bit Color (ARGB2101010) Display Serial Number: 6CM0191ZGD Main Display: Yes Mirror: Off Online: Yes Rotation: Supported Adapter Type: DVI or HDMI Automatically Adjust Brightness: No Adapter Firmware Version: ff.c1 PyQt version: 5.12.3 Compiled Qt version: 5.12.4 Runtime Qt version: 5.12.8 }}} " defect closed normal Window Toolkit can't reproduce Tom Goddard all ChimeraX