id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 2107 save mmCIF crashes ChimeraX Elaine Meng Greg Couch "I was testing the new mmCIF save option ""relModel"" and both times using different structures it crashed ChimeraX. Then I tried simply saving mmCIF without even using the ""relModel"" option and it crashed again. E.g. open 1gcn save test.cif Fortunately, this is in the daily build (2019-06-24) and not in the 0.9 release. Process: ChimeraX [29453] Path: /Users/USER/*/ChimeraX_Daily.app/Contents/MacOS/ChimeraX Identifier: edu.ucsf.cgl.ChimeraX Version: 0.91.0 (0.91.0.0) Code Type: X86-64 (Native) Parent Process: ??? [1] Responsible: ChimeraX [29453] User ID: 501 Date/Time: 2019-06-24 10:53:34.142 -0700 OS Version: Mac OS X 10.13.6 (17G7024) Report Version: 12 Anonymous UUID: 6CE578F8-EF60-FDA6-D943-AB5EC3429D70 Time Awake Since Boot: 2700000 seconds System Integrity Protection: enabled Crashed Thread: 0 CrBrowserMain Dispatch queue: com.apple.main-thread Exception Type: EXC_CRASH (SIGABRT) Exception Codes: 0x0000000000000000, 0x0000000000000000 Exception Note: EXC_CORPSE_NOTIFY Application Specific Information: abort() called terminating with uncaught exception of type std::invalid_argument: set_alt_loc(): atom N in residue ARG /A:1 does not have an alt loc '.' Thread 0 Crashed:: CrBrowserMain Dispatch queue: com.apple.main-thread 0 libsystem_kernel.dylib 0x00007fff52b18b66 __pthread_kill + 10 1 libsystem_pthread.dylib 0x00007fff52ce3080 pthread_kill + 333 2 libsystem_c.dylib 0x00007fff52a266fe raise + 26 3 libsystem_platform.dylib 0x00007fff52cd6f5a _sigtramp + 26 4 ??? 000000000000000000 0 + 0 5 libsystem_c.dylib 0x00007fff52a741ae abort + 127 6 libc++abi.dylib 0x00007fff50971f8f abort_message + 245 7 libc++abi.dylib 0x00007fff50972113 default_terminate_handler() + 241 8 libobjc.A.dylib 0x00007fff51db3a4f _objc_terminate() + 105 9 libc++abi.dylib 0x00007fff5098d7c9 std::__terminate(void (*)()) + 8 10 libc++abi.dylib 0x00007fff5098d26f __cxa_throw + 121 11 libatomstruct.dylib 0x000000012c6d7180 atomstruct::Atom::set_alt_loc(char, bool, bool) + 1232 12 cymol.so 0x000000012c8469ed __pyx_pw_8chimerax_6atomic_5cymol_6CyAtom_33set_alt_loc(_object*, _object*, _object*) + 509 13 org.python.python 0x0000000109fcc59a _PyMethodDef_RawFastCallKeywords 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0x0000000116c60992 QLineEdit::keyPressEvent(QKeyEvent*) + 34 56 QtWidgets 0x0000000116b5b9ef QWidget::event(QEvent*) + 527 57 QtWidgets 0x0000000116c5fcf7 QLineEdit::event(QEvent*) + 727 58 QtWidgets 0x0000000116c24940 QComboBox::keyPressEvent(QKeyEvent*) + 784 59 QtWidgets.so 0x00000001167d023b meth_QComboBox_keyPressEvent(_object*, _object*) + 139 60 org.python.python 0x0000000109fcc3ab _PyMethodDef_RawFastCallKeywords + 251 61 org.python.python 0x0000000109fcb93c _PyCFunction_FastCallKeywords + 44 62 org.python.python 0x000000010a095209 call_function + 617 63 org.python.python 0x000000010a08d8da _PyEval_EvalFrameDefault + 5562 64 org.python.python 0x000000010a095e81 _PyEval_EvalCodeWithName + 2721 65 org.python.python 0x0000000109fcb3d2 _PyFunction_FastCallDict + 450 66 org.python.python 0x0000000109fcc886 _PyObject_Call_Prepend + 150 67 org.python.python 0x0000000109fcba58 PyObject_Call + 136 68 sip.so 0x0000000117bf5f6e call_method + 76 69 sip.so 0x0000000117bf1d6b 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QEvent*) + 234 83 QtCore 0x00000001177e76e4 QCoreApplication::notifyInternal2(QObject*, QEvent*) + 212 84 QtGui 0x00000001170e46b8 QGuiApplicationPrivate::processKeyEvent(QWindowSystemInterfacePrivate::KeyEvent*) + 152 85 QtGui 0x00000001170cb50b QWindowSystemInterface::sendWindowSystemEvents(QFlags) + 219 86 QtGui 0x00000001170c6565 QWindowSystemInterface::flushWindowSystemEvents(QFlags) + 581 87 libqcocoa.dylib 0x0000000121306cf8 0x1212d9000 + 187640 88 libqcocoa.dylib 0x0000000121306ec8 0x1212d9000 + 188104 89 com.apple.AppKit 0x00007fff288c843d -[NSWindow(NSEventRouting) _reallySendEvent:isDelayedEvent:] + 5040 90 com.apple.AppKit 0x00007fff288c6c70 -[NSWindow(NSEventRouting) sendEvent:] + 497 91 libqcocoa.dylib 0x000000012130a2d5 0x1212d9000 + 201429 92 com.apple.AppKit 0x00007fff28728236 -[NSApplication(NSEvent) sendEvent:] + 2462 93 libqcocoa.dylib 0x000000012131129a 0x1212d9000 + 230042 94 com.apple.AppKit 0x00007fff27f888b5 -[NSApplication run] + 812 95 libqcocoa.dylib 0x000000012130db7b 0x1212d9000 + 215931 96 QtCore 0x00000001177e2cff QEventLoop::exec(QFlags) + 431 97 QtCore 0x00000001177e7cf2 QCoreApplication::exec() + 130 98 QtWidgets.so 0x00000001167dd7d2 meth_QApplication_exec_(_object*, _object*) + 82 99 org.python.python 0x0000000109fcc3ab _PyMethodDef_RawFastCallKeywords + 251 100 org.python.python 0x0000000109fcb93c _PyCFunction_FastCallKeywords + 44 101 org.python.python 0x000000010a095209 call_function + 617 102 org.python.python 0x000000010a08d8da _PyEval_EvalFrameDefault + 5562 103 org.python.python 0x0000000109fcbdf3 function_code_fastcall + 195 104 org.python.python 0x000000010a095271 call_function + 721 105 org.python.python 0x000000010a08d8da _PyEval_EvalFrameDefault + 5562 106 org.python.python 0x000000010a095e81 _PyEval_EvalCodeWithName + 2721 107 org.python.python 0x0000000109fcb8f6 _PyFunction_FastCallKeywords + 230 108 org.python.python 0x000000010a095271 call_function + 721 109 org.python.python 0x000000010a08d96b 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mach_msg_trap + 10 1 libsystem_kernel.dylib 0x00007fff52b0e724 mach_msg + 60 2 QtWebEngineCore 0x000000011a5a53ad 0x1183fc000 + 35296173 3 QtWebEngineCore 0x000000011a5a52af 0x1183fc000 + 35295919 4 QtWebEngineCore 0x000000011a5590dd 0x1183fc000 + 34984157 5 QtWebEngineCore 0x000000011a582105 0x1183fc000 + 35152133 6 QtWebEngineCore 0x000000011a5d4a3c 0x1183fc000 + 35490364 7 QtWebEngineCore 0x000000011a614787 0x1183fc000 + 35751815 8 libsystem_pthread.dylib 0x00007fff52ce0661 _pthread_body + 340 9 libsystem_pthread.dylib 0x00007fff52ce050d _pthread_start + 377 10 libsystem_pthread.dylib 0x00007fff52cdfbf9 thread_start + 13 Thread 7:: DnsConfigService 0 libsystem_kernel.dylib 0x00007fff52b19bea kevent + 10 1 QtWebEngineCore 0x000000011a866a19 0x1183fc000 + 38185497 2 QtWebEngineCore 0x000000011a863d2d 0x1183fc000 + 38173997 3 QtWebEngineCore 0x000000011a61ad4c 0x1183fc000 + 35777868 4 QtWebEngineCore 0x000000011a582105 0x1183fc000 + 35152133 5 QtWebEngineCore 0x000000011a5d4a3c 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0x00007fff52ce050d _pthread_start + 377 5 libsystem_pthread.dylib 0x00007fff52cdfbf9 thread_start + 13 Thread 0 crashed with X86 Thread State (64-bit): rax: 0x0000000000000000 rbx: 0x00007fff8b0ea380 rcx: 0x000000010a3fda48 rdx: 0x0000000000000000 rdi: 0x0000000000000307 rsi: 0x0000000000000006 rbp: 0x000000010a3fda80 rsp: 0x000000010a3fda48 r8: 0x000000010a3fdf48 r9: 0x0000000000000010 r10: 0x00007fff8b0ea3c8 r11: 0x0000000000000206 r12: 0x0000000000000307 r13: 0x0000000000000030 r14: 0x0000000000000006 r15: 0x000000000000002d rip: 0x00007fff52b18b66 rfl: 0x0000000000000206 cr2: 0x000000010a1f425c Logical CPU: 0 Error Code: 0x02000148 Trap Number: 133 Binary Images: 0x109fa6000 - 0x109fa6ff3 +edu.ucsf.cgl.ChimeraX (0.91.0 - 0.91.0.0) <9286D94B-829A-322C-8B23-1CEE205A97DB> /Users/USER/*/ChimeraX_Daily.app/Contents/MacOS/ChimeraX 0x109fab000 - 0x10a190fff +org.python.python (3.7.2, [c] 2001-2018 Python Software Foundation. - 3.7.2) 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/usr/lib/system/libcommonCrypto.dylib 0x7fff5286e000 - 0x7fff52875fff libcompiler_rt.dylib (62) <968B8E3F-3681-3230-9D78-BB8732024F6E> /usr/lib/system/libcompiler_rt.dylib 0x7fff52876000 - 0x7fff5287fffb libcopyfile.dylib (146.50.5) <3885083D-50D8-3EEC-B481-B2E605180D7F> /usr/lib/system/libcopyfile.dylib 0x7fff52880000 - 0x7fff52905ffb libcorecrypto.dylib (562.70.3) <37AF8EC6-BF34-3D15-BC3A-A9B98F2427D4> /usr/lib/system/libcorecrypto.dylib 0x7fff5298d000 - 0x7fff529c6ff7 libdispatch.dylib (913.60.3) /usr/lib/system/libdispatch.dylib 0x7fff529c7000 - 0x7fff529e4ff7 libdyld.dylib (551.5) <49BF9E96-8297-30CF-8AA6-128CC14054B2> /usr/lib/system/libdyld.dylib 0x7fff529e5000 - 0x7fff529e5ffb libkeymgr.dylib (28) /usr/lib/system/libkeymgr.dylib 0x7fff529e6000 - 0x7fff529f2ff3 libkxld.dylib (4570.71.45) <03FEE7FE-74F1-3EAE-99AE-DEB3EC414AEF> /usr/lib/system/libkxld.dylib 0x7fff529f3000 - 0x7fff529f3ff7 liblaunch.dylib (1205.70.12) <4950A0B3-5EE1-3F9A-8B1A-94FB85FCCA2C> /usr/lib/system/liblaunch.dylib 0x7fff529f4000 - 0x7fff529f8ffb libmacho.dylib (906) <1902A611-081A-3452-B11E-EBD1B166E831> /usr/lib/system/libmacho.dylib 0x7fff529f9000 - 0x7fff529fbff3 libquarantine.dylib (86) <26C0BA22-8F93-3A07-9A4E-C8D53D2CE42E> /usr/lib/system/libquarantine.dylib 0x7fff529fc000 - 0x7fff529fdff3 libremovefile.dylib (45) <711E18B2-5BBE-3211-A916-56740C27D17A> /usr/lib/system/libremovefile.dylib 0x7fff529fe000 - 0x7fff52a15fff libsystem_asl.dylib (356.70.1) <39E46A6F-B228-3E78-B83E-1779F9707A39> /usr/lib/system/libsystem_asl.dylib 0x7fff52a16000 - 0x7fff52a16fff libsystem_blocks.dylib (67) <17303FDF-0D2D-3963-B05E-B4DF63052D47> /usr/lib/system/libsystem_blocks.dylib 0x7fff52a17000 - 0x7fff52aa0ff7 libsystem_c.dylib (1244.50.9) <1187BFE8-4576-3247-8177-481554E1F9E7> /usr/lib/system/libsystem_c.dylib 0x7fff52aa1000 - 0x7fff52aa4ffb libsystem_configuration.dylib (963.50.9) /usr/lib/system/libsystem_configuration.dylib 0x7fff52aa5000 - 0x7fff52aa8ffb libsystem_coreservices.dylib (51) <486000D3-D8CB-3BE7-8EE5-8BF380DE6DF7> /usr/lib/system/libsystem_coreservices.dylib 0x7fff52aa9000 - 0x7fff52aaafff libsystem_darwin.dylib (1244.50.9) <09C21A4A-9EE0-388B-A9D9-DFF8F6758791> /usr/lib/system/libsystem_darwin.dylib 0x7fff52aab000 - 0x7fff52ab1ff7 libsystem_dnssd.dylib (878.70.3) /usr/lib/system/libsystem_dnssd.dylib 0x7fff52ab2000 - 0x7fff52afbff7 libsystem_info.dylib (517.30.1) /usr/lib/system/libsystem_info.dylib 0x7fff52afc000 - 0x7fff52b22ff7 libsystem_kernel.dylib (4570.71.45) <939FEA3D-15A3-33E5-9476-789AF120C330> /usr/lib/system/libsystem_kernel.dylib 0x7fff52b23000 - 0x7fff52b6efcb libsystem_m.dylib (3147.50.1) <17570F46-566C-39FC-BEF6-635A355DD549> /usr/lib/system/libsystem_m.dylib 0x7fff52b6f000 - 0x7fff52b8eff7 libsystem_malloc.dylib (140.50.7) /usr/lib/system/libsystem_malloc.dylib 0x7fff52b8f000 - 0x7fff52cbfff7 libsystem_network.dylib (1229.70.2) <5E86B2DE-9E15-3354-8714-4094ED5F698D> /usr/lib/system/libsystem_network.dylib 0x7fff52cc0000 - 0x7fff52ccaffb libsystem_networkextension.dylib (767.70.2) <9DC03712-552D-3AEE-9519-B5ED70980B70> /usr/lib/system/libsystem_networkextension.dylib 0x7fff52ccb000 - 0x7fff52cd4ff3 libsystem_notify.dylib (172) <08012EC0-2CD2-34BE-BF93-E7F56491299A> /usr/lib/system/libsystem_notify.dylib 0x7fff52cd5000 - 0x7fff52cdcff7 libsystem_platform.dylib (161.50.1) <6355EE2D-5456-3CA8-A227-B96E8F1E2AF8> /usr/lib/system/libsystem_platform.dylib 0x7fff52cdd000 - 0x7fff52ce8fff libsystem_pthread.dylib (301.50.1) <0E51CCBA-91F2-34E1-BF2A-FEEFD3D321E4> /usr/lib/system/libsystem_pthread.dylib 0x7fff52ce9000 - 0x7fff52cecfff libsystem_sandbox.dylib (765.70.1) <553DFCC6-9D31-3B9C-AB7C-30F6F265786D> /usr/lib/system/libsystem_sandbox.dylib 0x7fff52ced000 - 0x7fff52ceeff3 libsystem_secinit.dylib (30) /usr/lib/system/libsystem_secinit.dylib 0x7fff52cef000 - 0x7fff52cf6ff7 libsystem_symptoms.dylib (820.60.3) <70753784-099A-3E44-9E80-7364C9901CDA> /usr/lib/system/libsystem_symptoms.dylib 0x7fff52cf7000 - 0x7fff52d0afff libsystem_trace.dylib (829.70.1) <3A6CB706-8CA6-3616-8AFC-14AAD7FAF187> /usr/lib/system/libsystem_trace.dylib 0x7fff52d0c000 - 0x7fff52d11ff7 libunwind.dylib (35.3) /usr/lib/system/libunwind.dylib 0x7fff52d12000 - 0x7fff52d3fff7 libxpc.dylib (1205.70.12) <7B82608D-ED82-35C1-B13F-99855E25D6DC> /usr/lib/system/libxpc.dylib External Modification Summary: Calls made by other processes targeting this process: task_for_pid: 0 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: 923820 thread_create: 0 thread_set_state: 0 VM Region Summary: ReadOnly portion of Libraries: Total=633.2M resident=0K(0%) swapped_out_or_unallocated=633.2M(100%) Writable regions: Total=946.0M written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=946.0M(100%) VIRTUAL REGION REGION TYPE SIZE COUNT (non-coalesced) =========== ======= ======= Accelerate framework 128K 2 Activity Tracing 256K 2 CG backing stores 3752K 5 CG image 60K 10 CoreAnimation 44K 8 CoreGraphics 8K 2 CoreImage 8K 3 CoreUI image data 1528K 21 CoreUI image file 180K 3 Foundation 4K 2 Kernel Alloc Once 8K 2 MALLOC 608.8M 109 MALLOC guard page 48K 13 MALLOC_LARGE (reserved) 1664K 10 reserved VM address space (unallocated) Memory Tag 242 12K 2 OpenGL GLSL 512K 7 PROTECTED_MEMORY 4K 2 STACK GUARD 112K 29 Stack 164.7M 30 Stack Guard 56.0M 2 VM_ALLOCATE 131.3M 102 VM_ALLOCATE (reserved) 32.0M 2 reserved VM address space (unallocated) __DATA 49.2M 429 __FONT_DATA 4K 2 __GLSLBUILTINS 2588K 2 __LINKEDIT 211.8M 122 __TEXT 421.5M 409 __UNICODE 560K 2 mapped file 72.4M 37 shared memory 708K 16 =========== ======= ======= TOTAL 1.7G 1357 TOTAL, minus reserved VM space 1.7G 1357 Model: iMac13,2, BootROM 285.0.0.0.0, 4 processors, Intel Core i5, 3.2 GHz, 8 GB, SMC 2.11f16 Graphics: NVIDIA GeForce GTX 675MX, NVIDIA GeForce GTX 675MX, PCIe Memory Module: BANK 0/DIMM0, 4 GB, DDR3, 1600 MHz, 0x80AD, 0x484D54333531533643465238432D50422020 Memory Module: BANK 1/DIMM0, 4 GB, DDR3, 1600 MHz, 0x80AD, 0x484D54333531533643465238432D50422020 AirPort: spairport_wireless_card_type_airport_extreme (0x14E4, 0xF4), Broadcom BCM43xx 1.0 (7.21.190.19.1a4) Bluetooth: Version 6.0.7f13, 3 services, 27 devices, 1 incoming serial ports Network Service: Ethernet, Ethernet, en0 Serial ATA Device: APPLE HDD ST1000DM003, 1 TB Serial ATA Device: APPLE SSD SM128E, 121.33 GB USB Device: USB 2.0 Bus USB Device: Hub USB Device: Keyboard Hub USB Device: HP USB Laser Mouse USB Device: Apple Keyboard USB Device: FaceTime HD Camera (Built-in) USB Device: USB 2.0 Bus USB Device: Hub USB Device: Hub USB Device: BRCM20702 Hub USB Device: Bluetooth USB Host Controller USB Device: USB 3.0 Bus USB Device: MT1887 Thunderbolt Bus: iMac, Apple Inc., 23.4 " defect closed blocker Input/Output fixed chimera-programmers all ChimeraX