mmCIF reader crashes on 4ffh

[Tom Goddard]

open mmcif:4ffh

produces the following crash.

Process: Chimera2 [27151]
Path: /Users/USER/*/Chimera2.app/Contents/MacOS/Chimera2
Identifier: edu.ucsf.cgl.Chimera2
Version: 2.0.0 (2.0.0.0)
Code Type: X86-64 (Native)
Parent Process: bash [98806]
Responsible: Emacs-10.7 [98780]
User ID: 501

Date/Time: 2015-08-10 16:58:44.449 -0700
OS Version: Mac OS X 10.10.4 (14E46)
Report Version: 11
Anonymous UUID: ADCA02F2-9A59-6574-CF8F-380125498A20

Time Awake Since Boot: 2300000 seconds

Crashed Thread: 0 Dispatch queue: com.apple.main-thread

Exception Type: EXC_BAD_ACCESS (SIGSEGV)
Exception Codes: KERN_INVALID_ADDRESS at 0x00000000000001ec

VM Regions Near 0x1ec:
-->

TEXT 0000000101b20000-0000000101b21000 [ 4K] r-x/rwx SM=COW /Users/USER/*/Chimera2.app/Contents/bin/Chimera2

Application Specific Information:
Performing @selector(controlAction:) from sender wxNSComboBox 0x7f87dd65ba70

Thread 0 Crashed:: Dispatch queue: com.apple.main-thread
0 libsystem_kernel.dylib 0x00007fff89016c82 kill + 10
1 ??? 000000000000000000 0 + 0
2 _mmcif.so 0x000000010fc7fa87 readcif::CIFFile::internal_parse(bool) + 2727
3 _mmcif.so 0x000000010fc8194f readcif::CIFFile::process_stash() + 303
4 _mmcif.so 0x000000010fc808df readcif::CIFFile::internal_parse(bool) + 6399
5 _mmcif.so 0x000000010fc7ec7b readcif::CIFFile::parse(char const*) + 283
6 _mmcif.so 0x000000010fc7e682 readcif::CIFFile::parse_file(char const*) + 450
7 _mmcif.so 0x000000010fc6c84b mmcif::parse_mmCIF_file(char const*, _object*) + 43
8 _mmcif.so 0x000000010fc7d5b3 mmcif::_mmcif_parse_mmCIF_file(_object*, _object*, _object*) + 211
9 org.python.python 0x0000000101be5913 PyEval_EvalFrameEx + 21827 (ceval.c:4237)
10 org.python.python 0x0000000101be0267 PyEval_EvalCodeEx + 2567 (ceval.c:3588)
11 org.python.python 0x0000000101b5513d function_call + 381 (funcobject.c:632)
12 org.python.python 0x0000000101b2fbc7 PyObject_Call + 103 (abstract.c:2040)
13 org.python.python 0x0000000101be601f PyEval_EvalFrameEx + 23631 (ceval.c:4561)
14 org.python.python 0x0000000101be0267 PyEval_EvalCodeEx + 2567 (ceval.c:3588)
15 org.python.python 0x0000000101b5513d function_call + 381 (funcobject.c:632)
16 org.python.python 0x0000000101b2fbc7 PyObject_Call + 103 (abstract.c:2040)
17 org.python.python 0x0000000101be601f PyEval_EvalFrameEx + 23631 (ceval.c:4561)
18 org.python.python 0x0000000101be0267 PyEval_EvalCodeEx + 2567 (ceval.c:3588)
19 org.python.python 0x0000000101b5513d function_call + 381 (funcobject.c:632)
20 org.python.python 0x0000000101b2fbc7 PyObject_Call + 103 (abstract.c:2040)
21 org.python.python 0x0000000101be601f PyEval_EvalFrameEx + 23631 (ceval.c:4561)
22 org.python.python 0x0000000101be0267 PyEval_EvalCodeEx + 2567 (ceval.c:3588)
23 org.python.python 0x0000000101be902c fast_function + 316 (ceval.c:4348)
24 org.python.python 0x0000000101be5314 PyEval_EvalFrameEx + 20292 (ceval.c:4262)
25 org.python.python 0x0000000101be0267 PyEval_EvalCodeEx + 2567 (ceval.c:3588)
26 org.python.python 0x0000000101b5513d function_call + 381 (funcobject.c:632)
27 org.python.python 0x0000000101b2fbc7 PyObject_Call + 103 (abstract.c:2040)
28 org.python.python 0x0000000101be601f PyEval_EvalFrameEx + 23631 (ceval.c:4561)
29 org.python.python 0x0000000101be0267 PyEval_EvalCodeEx + 2567 (ceval.c:3588)
30 org.python.python 0x0000000101be902c fast_function + 316 (ceval.c:4348)
31 org.python.python 0x0000000101be5314 PyEval_EvalFrameEx + 20292 (ceval.c:4262)
32 org.python.python 0x0000000101be0267 PyEval_EvalCodeEx + 2567 (ceval.c:3588)
33 org.python.python 0x0000000101b5513d function_call + 381 (funcobject.c:632)
34 org.python.python 0x0000000101b2fbc7 PyObject_Call + 103 (abstract.c:2040)
35 org.python.python 0x0000000101b431bd method_call + 141 (classobject.c:347)
36 org.python.python 0x0000000101b2fbc7 PyObject_Call + 103 (abstract.c:2040)
37 org.python.python 0x0000000101be865d PyEval_CallObjectWithKeywords + 93 (ceval.c:4114)
38 _core.so 0x000000010413b1fc wxPyCallback::EventThunker(wxEvent&) + 284 (sip_corewxEvtHandler.cpp:70)
39 libwx_osx_cocoau-3.0.0.3.0.dylib 0x000000010517adba wxEvtHandler::SearchDynamicEventTable(wxEvent&) + 186
40 libwx_osx_cocoau-3.0.0.3.0.dylib 0x000000010517ab2b wxEvtHandler::ProcessEventLocally(wxEvent&) + 59
41 libwx_osx_cocoau-3.0.0.3.0.dylib 0x000000010517aa3e wxEvtHandler::ProcessEvent(wxEvent&) + 190
42 _core.so 0x000000010408e7ea sipwxComboBox::ProcessEvent(wxEvent&) + 154 (sip_corewxComboBox.cpp:439)
43 libwx_osx_cocoau-3.0.0.3.0.dylib 0x000000010517ae5f wxEvtHandler::SafelyProcessEvent(wxEvent&) + 15
44 libwx_osx_cocoau-3.0.0.3.0.dylib 0x000000010527df86 wxNSTextFieldControl::controlAction(NSView*, void*, void*) + 166
45 libsystem_trace.dylib 0x00007fff8c1aecd7 _os_activity_initiate + 75
46 com.apple.AppKit 0x00007fff895fdeb1 -[NSApplication sendAction:to:from:] + 452
47 com.apple.AppKit 0x00007fff89613946 -[NSControl sendAction:to:] + 86
48 com.apple.AppKit 0x00007fff896505df -[NSTextField textDidEndEditing:] + 853
49 com.apple.CoreFoundation 0x00007fff8ec6745c CFNOTIFICATIONCENTER_IS_CALLING_OUT_TO_AN_OBSERVER + 12
50 com.apple.CoreFoundation 0x00007fff8eb57634 _CFXNotificationPost + 3140
51 com.apple.Foundation 0x00007fff8f59f9d1 -[NSNotificationCenter postNotificationName:object:userInfo:] + 66
52 com.apple.AppKit 0x00007fff8975b847 -[NSTextView(NSPrivate) _giveUpFirstResponder:] + 423
53 com.apple.AppKit 0x00007fff897d7812 -[NSTextView(NSKeyBindingCommands) insertNewline:] + 239
54 com.apple.AppKit 0x00007fff896a3ef1 -[NSTextView doCommandBySelector:] + 195
55 com.apple.AppKit 0x00007fff896a3e01 -[NSTextInputContext(NSInputContext_WithCompletion) doCommandBySelector:completionHandler:] + 118
56 com.apple.AppKit 0x00007fff89689c23 -[NSKeyBindingManager(NSKeyBindingManager_MultiClients) interpretEventAsCommand:forClient:] + 1899
57 com.apple.AppKit 0x00007fff89c50272 61-[NSTextInputContext _handleEvent:options:completionHandler:]_block_invoke972 + 335
58 com.apple.AppKit 0x00007fff8968bbff -[NSTextInputContext(NSInputContext_WithCompletion) hasMarkedTextWithCompletionHandler:] + 76
59 com.apple.AppKit 0x00007fff896a3d03 61-[NSTextInputContext _handleEvent:options:completionHandler:]_block_invoke_3 + 95
60 com.apple.AppKit 0x00007fff8969ced8 -[NSTextInputContext tryHandleEvent_HasMarkedText_withDispatchCondition:dispatchWork:continuation:] + 101
61 com.apple.AppKit 0x00007fff89c50074 61-[NSTextInputContext _handleEvent:options:completionHandler:]_block_invoke960 + 321
62 com.apple.HIToolbox 0x00007fff88a6fd4f TSMProcessRawKeyEventWithOptionsAndCompletionHandler_block_invoke_5 + 70
63 com.apple.HIToolbox 0x00007fff88a6ec45 _ZL23DispatchEventToHandlersP14EventTargetRecP14OpaqueEventRefP14HandlerCallRec_block_invoke + 108
64 com.apple.AppKit 0x00007fff8968c606 55-[NSTextInputContext handleTSMEvent:completionHandler:]_block_invoke174 + 2387
65 com.apple.AppKit 0x00007fff8968bbff -[NSTextInputContext(NSInputContext_WithCompletion) hasMarkedTextWithCompletionHandler:] + 76
66 com.apple.AppKit 0x00007fff8968bba0 55-[NSTextInputContext handleTSMEvent:completionHandler:]_block_invoke_2 + 95
67 com.apple.AppKit 0x00007fff8968bb18 -[NSTextInputContext tryHandleTSMEvent_HasMarkedText_withDispatchCondition:dispatchWork:continuation:] + 101
68 com.apple.AppKit 0x00007fff8968b7d5 -[NSTextInputContext handleTSMEvent:completionHandler:] + 3122
69 com.apple.AppKit 0x00007fff8968ab2e _NSTSMEventHandler + 324
70 com.apple.HIToolbox 0x00007fff88a08b6c DispatchEventToHandlers(EventTargetRec*, OpaqueEventRef*, HandlerCallRec*) + 1260
71 com.apple.HIToolbox 0x00007fff88a07fae SendEventToEventTargetInternal(OpaqueEventRef*, OpaqueEventTargetRef*, HandlerCallRec*) + 386
72 com.apple.HIToolbox 0x00007fff88a07e22 SendEventToEventTargetWithOptions + 43
73 com.apple.HIToolbox 0x00007fff88a6c26c SendTSMEvent_WithCompletionHandler + 417
74 com.apple.HIToolbox 0x00007fff88a6c76c SendUnicodeTextAEToUnicodeDoc_WithCompletionHandler_block_invoke + 400
75 com.apple.HIToolbox 0x00007fff88a6c5a6 SendFilterTextEvent_WithCompletionHandler_block_invoke + 189
76 com.apple.HIToolbox 0x00007fff88a6c2c0 SendTSMEvent_WithCompletionHandler + 501
77 com.apple.HIToolbox 0x00007fff88a6c08f SendFilterTextEvent_WithCompletionHandler + 236
78 com.apple.HIToolbox 0x00007fff88a6bd51 SendUnicodeTextAEToUnicodeDoc_WithCompletionHandler + 295
79 com.apple.HIToolbox 0x00007fff88a6bae9 utDeliverTSMEvent_WithCompletionHandler_block_invoke_2 + 296
80 com.apple.HIToolbox 0x00007fff88a6b988 utDeliverTSMEvent_WithCompletionHandler_block_invoke + 437
81 com.apple.HIToolbox 0x00007fff88a6b7cd TSMKeyEvent_WithCompletionHandler + 701
82 com.apple.HIToolbox 0x00007fff88a6b4d0 TSMProcessRawKeyEventWithOptionsAndCompletionHandler_block_invoke_4 + 251
83 com.apple.HIToolbox 0x00007fff88a6b386 TSMProcessRawKeyEventWithOptionsAndCompletionHandler_block_invoke_3 + 330
84 com.apple.HIToolbox 0x00007fff88a6b112 TSMProcessRawKeyEventWithOptionsAndCompletionHandler_block_invoke_2 + 259
85 com.apple.HIToolbox 0x00007fff88a6af25 TSMProcessRawKeyEventWithOptionsAndCompletionHandler_block_invoke + 251
86 com.apple.HIToolbox 0x00007fff88a4f76f TSMProcessRawKeyEventWithOptionsAndCompletionHandler + 3068
87 com.apple.AppKit 0x00007fff89c4fe86 61-[NSTextInputContext _handleEvent:options:completionHandler:]_block_invoke949 + 131
88 com.apple.AppKit 0x00007fff89689352 -[NSTextInputContext tryTSMProcessRawKeyEvent:dispatchCondition:setupForDispatch:furtherCondition:dispatchWork:continuation:] + 127
89 com.apple.AppKit 0x00007fff89689085 -[NSTextInputContext _handleEvent:options:completionHandler:] + 1266
90 com.apple.AppKit 0x00007fff89688b4e -[NSTextInputContext handleEvent:] + 109
91 com.apple.AppKit 0x00007fff89688a54 -[NSView interpretKeyEvents:] + 207
92 com.apple.AppKit 0x00007fff8968886a -[NSTextView keyDown:] + 695
93 libwx_osx_cocoau-3.0.0.3.0.dylib 0x000000010527aeee -[wxNSTextFieldEditor keyDown:] + 110
94 com.apple.AppKit 0x00007fff89b780fb -[NSWindow _reallySendEvent:isDelayedEvent:] + 5452
95 com.apple.AppKit 0x00007fff89509c86 -[NSWindow sendEvent:] + 470
96 libwx_osx_cocoau-3.0.0.3.0.dylib 0x00000001052737c6 -[wxNSWindow sendEvent:] + 118
97 com.apple.AppKit 0x00007fff895068b1 -[NSApplication sendEvent:] + 4199
98 libwx_osx_cocoau-3.0.0.3.0.dylib 0x0000000105188f36 -[wxNSApplication sendEvent:] + 134
99 com.apple.AppKit 0x00007fff8942fb68 -[NSApplication run] + 711
100 libwx_osx_cocoau-3.0.0.3.0.dylib 0x0000000105267ec3 wxGUIEventLoop::OSXDoRun() + 115
101 libwx_osx_cocoau-3.0.0.3.0.dylib 0x0000000105145c14 wxCFEventLoop::DoRun() + 52
102 libwx_osx_cocoau-3.0.0.3.0.dylib 0x0000000105070b45 wxEventLoopBase::Run() + 165
103 libwx_osx_cocoau-3.0.0.3.0.dylib 0x0000000105034ee1 wxAppConsoleBase::MainLoop() + 209
104 _core.so 0x00000001043b7ee5 wxPyApp::MainLoop() + 181 (sip_corewxPyApp.cpp:316)
105 _core.so 0x00000001043bb65d meth_wxPyApp_MainLoop(_object*, _object*) + 205 (sip_corewxPyApp.cpp:1794)
106 org.python.python 0x0000000101be5913 PyEval_EvalFrameEx + 21827 (ceval.c:4237)
107 org.python.python 0x0000000101be8fc2 fast_function + 210 (ceval.c:4334)
108 org.python.python 0x0000000101be5314 PyEval_EvalFrameEx + 20292 (ceval.c:4262)
109 org.python.python 0x0000000101be8fc2 fast_function + 210 (ceval.c:4334)
110 org.python.python 0x0000000101be5314 PyEval_EvalFrameEx + 20292 (ceval.c:4262)
111 org.python.python 0x0000000101be0267 PyEval_EvalCodeEx + 2567 (ceval.c:3588)
112 org.python.python 0x0000000101be902c fast_function + 316 (ceval.c:4348)
113 org.python.python 0x0000000101be5314 PyEval_EvalFrameEx + 20292 (ceval.c:4262)
114 org.python.python 0x0000000101be0267 PyEval_EvalCodeEx + 2567 (ceval.c:3588)
115 org.python.python 0x0000000101bdf84f PyEval_EvalCode + 63 (ceval.c:775)
116 org.python.python 0x0000000101bffab5 PyImport_ImportFrozenModuleObject + 469 (import.c:869)
117 org.python.python 0x0000000101bffba2 PyImport_ImportFrozenModule + 34 (import.c:1291)
118 org.python.python 0x0000000101bf945e Py_FrozenMain + 430 (frozenmain.c:84)
119 libdyld.dylib 0x00007fff831795c9 start + 1

Thread 1:: Dispatch queue: com.apple.libdispatch-manager
0 libsystem_kernel.dylib 0x00007fff89018232 kevent64 + 10
1 libdispatch.dylib 0x00007fff87692a6a _dispatch_mgr_thread + 52

Thread 2:
0 libsystem_kernel.dylib 0x00007fff8901794a workq_kernreturn + 10
1 libsystem_pthread.dylib 0x00007fff8b89840d start_wqthread + 13

Thread 3:
0 libsystem_kernel.dylib 0x00007fff8901794a workq_kernreturn + 10
1 libsystem_pthread.dylib 0x00007fff8b89840d start_wqthread + 13

Thread 4:
0 libsystem_kernel.dylib 0x00007fff8901794a workq_kernreturn + 10
1 libsystem_pthread.dylib 0x00007fff8b89840d start_wqthread + 13

Thread 5:
0 libsystem_kernel.dylib 0x00007fff8901794a workq_kernreturn + 10
1 libsystem_pthread.dylib 0x00007fff8b89840d start_wqthread + 13

Thread 6:
0 libsystem_kernel.dylib 0x00007fff890124de mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff8901164f mach_msg + 55
2 com.apple.CoreFoundation 0x00007fff8ebb9eb4 CFRunLoopServiceMachPort + 212
3 com.apple.CoreFoundation 0x00007fff8ebb937b CFRunLoopRun + 1371
4 com.apple.CoreFoundation 0x00007fff8ebb8bd8 CFRunLoopRunSpecific + 296
5 com.apple.AppKit 0x00007fff8950256b _NSEventThread + 137
6 libsystem_pthread.dylib 0x00007fff8b89a268 _pthread_body + 131
7 libsystem_pthread.dylib 0x00007fff8b89a1e5 _pthread_start + 176
8 libsystem_pthread.dylib 0x00007fff8b89841d thread_start + 13

Thread 7:
0 libsystem_kernel.dylib 0x00007fff8901794a workq_kernreturn + 10
1 libsystem_pthread.dylib 0x00007fff8b89840d start_wqthread + 13

Thread 8:
0 libsystem_kernel.dylib 0x00007fff8901794a workq_kernreturn + 10
1 libsystem_pthread.dylib 0x00007fff8b89840d start_wqthread + 13

Thread 9:
0 libsystem_kernel.dylib 0x00007fff8901794a workq_kernreturn + 10
1 libsystem_pthread.dylib 0x00007fff8b89840d start_wqthread + 13

Thread 10:
0 libsystem_kernel.dylib 0x00007fff8901794a workq_kernreturn + 10
1 libsystem_pthread.dylib 0x00007fff8b89840d start_wqthread + 13

Thread 11:: OGL Profiler
0 libsystem_kernel.dylib 0x00007fff890124de mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff8901164f mach_msg + 55
2 com.apple.opengl 0x00007fff912a0a79 glcDebugListener + 336
3 libsystem_pthread.dylib 0x00007fff8b89a268 _pthread_body + 131
4 libsystem_pthread.dylib 0x00007fff8b89a1e5 _pthread_start + 176
5 libsystem_pthread.dylib 0x00007fff8b89841d thread_start + 13

Thread 12:: JavaScriptCore::BlockFree
0 libsystem_kernel.dylib 0x00007fff89017136 psynch_cvwait + 10
1 libc++.1.dylib 0x00007fff91715c95 std::1::condition_variable::wait(std::1::unique_lock<std::__1::mutex>&) + 47
2 com.apple.JavaScriptCore 0x00007fff8d64d544 JSC::BlockAllocator::blockFreeingThreadMain() + 228
3 com.apple.JavaScriptCore 0x00007fff8d642cff WTF::wtfThreadEntryPoint(void*) + 15
4 libsystem_pthread.dylib 0x00007fff8b89a268 _pthread_body + 131
5 libsystem_pthread.dylib 0x00007fff8b89a1e5 _pthread_start + 176
6 libsystem_pthread.dylib 0x00007fff8b89841d thread_start + 13

Thread 13:: JavaScriptCore::Marking
0 libsystem_kernel.dylib 0x00007fff89017136 psynch_cvwait + 10
1 libc++.1.dylib 0x00007fff91715c95 std::1::condition_variable::wait(std::1::unique_lock<std::__1::mutex>&) + 47
2 com.apple.JavaScriptCore 0x00007fff8d64dadb JSC::GCThread::waitForNextPhase() + 171
3 com.apple.JavaScriptCore 0x00007fff8d64d938 JSC::GCThread::gcThreadMain() + 88
4 com.apple.JavaScriptCore 0x00007fff8d642cff WTF::wtfThreadEntryPoint(void*) + 15
5 libsystem_pthread.dylib 0x00007fff8b89a268 _pthread_body + 131
6 libsystem_pthread.dylib 0x00007fff8b89a1e5 _pthread_start + 176
7 libsystem_pthread.dylib 0x00007fff8b89841d thread_start + 13

Thread 14:: JavaScriptCore::Marking
0 libsystem_kernel.dylib 0x00007fff89017136 psynch_cvwait + 10
1 libc++.1.dylib 0x00007fff91715c95 std::1::condition_variable::wait(std::1::unique_lock<std::__1::mutex>&) + 47
2 com.apple.JavaScriptCore 0x00007fff8d64dadb JSC::GCThread::waitForNextPhase() + 171
3 com.apple.JavaScriptCore 0x00007fff8d64d938 JSC::GCThread::gcThreadMain() + 88
4 com.apple.JavaScriptCore 0x00007fff8d642cff WTF::wtfThreadEntryPoint(void*) + 15
5 libsystem_pthread.dylib 0x00007fff8b89a268 _pthread_body + 131
6 libsystem_pthread.dylib 0x00007fff8b89a1e5 _pthread_start + 176
7 libsystem_pthread.dylib 0x00007fff8b89841d thread_start + 13

Thread 15:: JavaScriptCore::Marking
0 libsystem_kernel.dylib 0x00007fff89017136 psynch_cvwait + 10
1 libc++.1.dylib 0x00007fff91715c95 std::1::condition_variable::wait(std::1::unique_lock<std::__1::mutex>&) + 47
2 com.apple.JavaScriptCore 0x00007fff8d64dadb JSC::GCThread::waitForNextPhase() + 171
3 com.apple.JavaScriptCore 0x00007fff8d64d938 JSC::GCThread::gcThreadMain() + 88
4 com.apple.JavaScriptCore 0x00007fff8d642cff WTF::wtfThreadEntryPoint(void*) + 15
5 libsystem_pthread.dylib 0x00007fff8b89a268 _pthread_body + 131
6 libsystem_pthread.dylib 0x00007fff8b89a1e5 _pthread_start + 176
7 libsystem_pthread.dylib 0x00007fff8b89841d thread_start + 13

Thread 16:: JavaScriptCore::Marking
0 libsystem_kernel.dylib 0x00007fff89017136 psynch_cvwait + 10
1 libc++.1.dylib 0x00007fff91715c95 std::1::condition_variable::wait(std::1::unique_lock<std::__1::mutex>&) + 47
2 com.apple.JavaScriptCore 0x00007fff8d64dadb JSC::GCThread::waitForNextPhase() + 171
3 com.apple.JavaScriptCore 0x00007fff8d64d938 JSC::GCThread::gcThreadMain() + 88
4 com.apple.JavaScriptCore 0x00007fff8d642cff WTF::wtfThreadEntryPoint(void*) + 15
5 libsystem_pthread.dylib 0x00007fff8b89a268 _pthread_body + 131
6 libsystem_pthread.dylib 0x00007fff8b89a1e5 _pthread_start + 176
7 libsystem_pthread.dylib 0x00007fff8b89841d thread_start + 13

Thread 17:: JavaScriptCore::Marking
0 libsystem_kernel.dylib 0x00007fff89017136 psynch_cvwait + 10
1 libc++.1.dylib 0x00007fff91715c95 std::1::condition_variable::wait(std::1::unique_lock<std::__1::mutex>&) + 47
2 com.apple.JavaScriptCore 0x00007fff8d64dadb JSC::GCThread::waitForNextPhase() + 171
3 com.apple.JavaScriptCore 0x00007fff8d64d938 JSC::GCThread::gcThreadMain() + 88
4 com.apple.JavaScriptCore 0x00007fff8d642cff WTF::wtfThreadEntryPoint(void*) + 15
5 libsystem_pthread.dylib 0x00007fff8b89a268 _pthread_body + 131
6 libsystem_pthread.dylib 0x00007fff8b89a1e5 _pthread_start + 176
7 libsystem_pthread.dylib 0x00007fff8b89841d thread_start + 13

Thread 18:: JavaScriptCore::Marking
0 libsystem_kernel.dylib 0x00007fff89017136 psynch_cvwait + 10
1 libc++.1.dylib 0x00007fff91715c95 std::1::condition_variable::wait(std::1::unique_lock<std::__1::mutex>&) + 47
2 com.apple.JavaScriptCore 0x00007fff8d64dadb JSC::GCThread::waitForNextPhase() + 171
3 com.apple.JavaScriptCore 0x00007fff8d64d938 JSC::GCThread::gcThreadMain() + 88
4 com.apple.JavaScriptCore 0x00007fff8d642cff WTF::wtfThreadEntryPoint(void*) + 15
5 libsystem_pthread.dylib 0x00007fff8b89a268 _pthread_body + 131
6 libsystem_pthread.dylib 0x00007fff8b89a1e5 _pthread_start + 176
7 libsystem_pthread.dylib 0x00007fff8b89841d thread_start + 13

Thread 0 crashed with X86 Thread State (64-bit):

rax: 0x0000000000000000 rbx: 0x0000000101ed4f48 rcx: 0x0000000101ed4aa8 rdx: 0x0000000000000000
rdi: 0x0000000000006a0f rsi: 0x000000000000000b rbp: 0x0000000101ed4ab0 rsp: 0x0000000101ed4aa8

r8: 0x0000000101ed4f48 r9: 0x00007f87e0837710 r10: 0x00007fff89018c22 r11: 0x0000000000000202

r12: 0x0000000000000023 r13: 0x0000000000000000 r14: 0x00000000000001ec r15: 0x00007fff5e0da008
rip: 0x00007fff89016c82 rfl: 0x0000000000000202 cr2: 0x0000000104315000

Logical CPU: 0
Error Code: 0x02000025
Trap Number: 133

Binary Images:

0x101b20000 - 0x101b20ff7 +edu.ucsf.cgl.Chimera2 (2.0.0 - 2.0.0.0) <73F8A8A6-F58F-3A9D-8AD0-972177C7A943> /Users/USER/*/Chimera2.app/Contents/MacOS/Chimera2
0x101b23000 - 0x101cb2ff7 +org.python.python (3.4.3, [c] 2001-2015 Python Software Foundation. - 3.4.3) <B05216B6-F925-3443-8EDD-E303D42E94A4> /Users/USER/*/Chimera2.app/Contents/Library/Frameworks/Python.framework/Versions/3.4/Python
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0x7fff8eb12000 - 0x7fff8eb16fff libpam.2.dylib (20) <E805398D-9A92-31F8-8005-8DC188BD8B6E> /usr/lib/libpam.2.dylib
0x7fff8eb47000 - 0x7fff8eedfff7 com.apple.CoreFoundation (6.9 - 1153.18) <5C0892B8-9691-341F-9279-CA3A74D59AA0> /System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation
0x7fff8eef3000 - 0x7fff8f0d8ff7 libicucore.A.dylib (531.48) <3CD34752-B1F9-31D2-865D-B5B0F0BE3111> /usr/lib/libicucore.A.dylib
0x7fff8f0d9000 - 0x7fff8f0eafff libcmph.dylib (1) <46EC3997-DB5E-38AE-BBBB-A035A54AD3C0> /usr/lib/libcmph.dylib
0x7fff8f0eb000 - 0x7fff8f0ecfff com.apple.TrustEvaluationAgent (2.0 - 25) <2D61A2C3-C83E-3A3F-8EC1-736DBEC250AB> /System/Library/PrivateFrameworks/TrustEvaluationAgent.framework/Versions/A/TrustEvaluationAgent
0x7fff8f0ed000 - 0x7fff8f106ff3 com.apple.openscripting (1.6.4 - 162.2) <BF79207B-C762-346D-8FF0-3DDCECC9E9E2> /System/Library/Frameworks/Carbon.framework/Versions/A/Frameworks/OpenScripting.framework/Versions/A/OpenScripting
0x7fff8f107000 - 0x7fff8f142fff com.apple.Symbolication (1.4 - 56045) <D64571B1-4483-3FE2-BD67-A91360F79727> /System/Library/PrivateFrameworks/Symbolication.framework/Versions/A/Symbolication
0x7fff8f17d000 - 0x7fff8f195ff7 libexpat.1.dylib (12) <C5FE8836-E277-3162-9D15-6735321CB2C6> /usr/lib/libexpat.1.dylib
0x7fff8f211000 - 0x7fff8f4f8ffb com.apple.CoreServices.CarbonCore (1108.6 - 1108.6) <8953580E-7857-33B2-AA64-98296830D3A8> /System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/CarbonCore.framework/Versions/A/CarbonCore
0x7fff8f4f9000 - 0x7fff8f4f9ff7 libunc.dylib (29) <5676F7EA-C1DF-329F-B006-D2C3022B7D70> /usr/lib/system/libunc.dylib
0x7fff8f518000 - 0x7fff8f58afff com.apple.framework.IOKit (2.0.2 - 1050.20.2) <09C0518C-90DF-3FC3-96D6-34D35F72C8EF> /System/Library/Frameworks/IOKit.framework/Versions/A/IOKit
0x7fff8f598000 - 0x7fff8f8c9fff com.apple.Foundation (6.9 - 1153.20) <F0FF3A5D-C5B7-34A1-9319-DE1EF928E58E> /System/Library/Frameworks/Foundation.framework/Versions/C/Foundation
0x7fff8f9e9000 - 0x7fff8fa02ff7 com.apple.CFOpenDirectory (10.10 - 187) <2BF2705E-2CC6-37E7-BD49-D4B4E01591E3> /System/Library/Frameworks/OpenDirectory.framework/Versions/A/Frameworks/CFOpenDirectory.framework/Versions/A/CFOpenDirectory
0x7fff8fa28000 - 0x7fff8fcf7ff3 com.apple.CoreImage (10.3.4) <C1AE8252-A95D-3BF4-83B8-BE85E979F2CB> /System/Library/Frameworks/QuartzCore.framework/Versions/A/Frameworks/CoreImage.framework/Versions/A/CoreImage
0x7fff8fd01000 - 0x7fff90cc3ffb com.apple.WebCore (10600 - 10600.7.11) <930FAFBB-C906-3017-A62B-5AE3B404A168> /System/Library/Frameworks/WebKit.framework/Versions/A/Frameworks/WebCore.framework/Versions/A/WebCore
0x7fff90cc4000 - 0x7fff9109bfe7 com.apple.CoreAUC (211.1.0 - 211.1.0) <12645629-E065-388E-A6B5-094A240578CE> /System/Library/PrivateFrameworks/CoreAUC.framework/Versions/A/CoreAUC
0x7fff9109c000 - 0x7fff9118fff7 libJP2.dylib (1238) <008AE93E-FB7F-3217-8220-0C1A6BEBFE0F> /System/Library/Frameworks/ImageIO.framework/Versions/A/Resources/libJP2.dylib
0x7fff91190000 - 0x7fff91282fff libxml2.2.dylib (26) <B834E7C8-EC3E-3382-BC5A-DA38DC4D720C> /usr/lib/libxml2.2.dylib
0x7fff9129f000 - 0x7fff912adff7 com.apple.opengl (11.1.2 - 11.1.2) <5F355713-4637-33CD-9CBA-4B4CA43FB0FE> /System/Library/Frameworks/OpenGL.framework/Versions/A/OpenGL
0x7fff91422000 - 0x7fff9142afff libMatch.1.dylib (24) <C917279D-33C2-38A8-9BDD-18F3B24E6FBD> /usr/lib/libMatch.1.dylib
0x7fff9142b000 - 0x7fff91465ffb com.apple.DebugSymbols (115 - 115) <6F03761D-7C3A-3C80-8031-AA1C1AD7C706> /System/Library/PrivateFrameworks/DebugSymbols.framework/Versions/A/DebugSymbols
0x7fff91466000 - 0x7fff914a7fff libGLU.dylib (11.1.2) <2BA52A8D-ED35-3D86-B2D6-41479969C96D> /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGLU.dylib
0x7fff914a8000 - 0x7fff914b0fe7 libcldcpuengine.dylib (2.4.5) <6CC680F9-0D13-333B-B151-F0D9C631A1E5> /System/Library/Frameworks/OpenCL.framework/Versions/A/Libraries/libcldcpuengine.dylib
0x7fff914b1000 - 0x7fff914ddfff libsandbox.1.dylib (358.20.5) <931BB6B5-F207-344A-8596-F1D0BB910C9A> /usr/lib/libsandbox.1.dylib
0x7fff9150c000 - 0x7fff91598ff7 libsystem_c.dylib (1044.10.1) <86FBED7A-F2C8-3591-AD6F-486DD57E6B6A> /usr/lib/system/libsystem_c.dylib
0x7fff915c6000 - 0x7fff915ceffb libcopyfile.dylib (118.1.2) <0C68D3A6-ACDD-3EF3-991A-CC82C32AB836> /usr/lib/system/libcopyfile.dylib
0x7fff916ea000 - 0x7fff916efffb libheimdal-asn1.dylib (398.10.1) <D362D79B-CC4F-3E62-9BC7-9B645BEBBF4E> /usr/lib/libheimdal-asn1.dylib
0x7fff916f0000 - 0x7fff9170bff7 libCRFSuite.dylib (34) <D64842BE-7BD4-3D0C-9842-1D202F7C2A51> /usr/lib/libCRFSuite.dylib
0x7fff9170c000 - 0x7fff9170dfff libDiagnosticMessagesClient.dylib (100) <2EE8E436-5CDC-34C5-9959-5BA218D507FB> /usr/lib/libDiagnosticMessagesClient.dylib
0x7fff9170e000 - 0x7fff91762fff libc++.1.dylib (120) <1B9530FD-989B-3174-BB1C-BDC159501710> /usr/lib/libc++.1.dylib
0x7fff9179d000 - 0x7fff917c1ff7 com.apple.Sharing (328.17 - 328.17) <AD5E243A-B79F-3D7B-800B-A2C99A1CFEF1> /System/Library/PrivateFrameworks/Sharing.framework/Versions/A/Sharing
0x7fff917eb000 - 0x7fff91838ff7 com.apple.print.framework.PrintCore (10.3 - 451.1) <DE992474-0841-38A1-B4F6-46D653E454D5> /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/PrintCore.framework/Versions/A/PrintCore
0x7fff91839000 - 0x7fff91839fff libOpenScriptingUtil.dylib (162.2) <D6A2216D-ADB2-3F24-AD30-F6D00829F545> /usr/lib/libOpenScriptingUtil.dylib
0x7fff9183a000 - 0x7fff9195eff7 com.apple.LaunchServices (644.56 - 644.56) <20AABB1C-9319-3E4D-A024-51B0DD5FCD3B> /System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/LaunchServices.framework/Versions/A/LaunchServices
0x7fff9195f000 - 0x7fff919cbff3 com.apple.MMCS (1.3 - 327.5) <FC998246-ED60-334D-9E94-453F35EF9C78> /System/Library/PrivateFrameworks/MMCS.framework/Versions/A/MMCS
0x7fff919f4000 - 0x7fff91e47fc7 com.apple.vImage (8.0 - 8.0) <33BE7B31-72DB-3364-B37E-C322A32748C5> /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vImage.framework/Versions/A/vImage

External Modification Summary:

Calls made by other processes targeting this process:

task_for_pid: 2
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: 2894104
thread_create: 0
thread_set_state: 0

VM Region Summary:
ReadOnly portion of Libraries: Total=295.2M resident=158.8M(54%) swapped_out_or_unallocated=136.4M(46%)
Writable regions: Total=1.2G written=51.6M(4%) resident=85.0M(7%) swapped_out=0K(0%) unallocated=1.1G(93%)

REGION TYPE VIRTUAL
=========== =======
Activity Tracing 2048K
CG backing stores 5684K
CG image 236K
CG raster data 1872K
CG shared images 368K
CoreAnimation 52K
CoreImage 8K
CoreServices 1092K
CoreUI image data 104K
Dispatch continuations 16.0M
Foundation 4K
IOKit 10.4M
JS JIT generated code 128.0M
JS JIT generated code (reserved) 896.0M reserved VM address space (unallocated)
JS garbage collector 1216K
Kernel Alloc Once 8K
MALLOC 124.8M
MALLOC (admin) 32K
MALLOC_LARGE (reserved) 256K reserved VM address space (unallocated)
Memory Tag 242 12K
OpenCL 16K
STACK GUARD 72K
Stack 72.7M
VM_ALLOCATE 17.2M
WebKit Malloc 1296K
DATA 34.6M
GLSLBUILTINS 2588K
IMAGE 528K
LINKEDIT 86.1M
TEXT 209.1M
UNICODE 552K
mapped file 75.1M
shared memory 4K
=========== =======
TOTAL 1.6G
TOTAL, minus reserved VM space 791.3M

Model: iMac13,2, BootROM IM131.010A.B08, 4 processors, Intel Core i7, 3.4 GHz, 32 GB, SMC 2.11f16
Graphics: NVIDIA GeForce GTX 680MX, NVIDIA GeForce GTX 680MX, PCIe, 2048 MB
Memory Module: BANK 0/DIMM0, 8 GB, DDR3, 1600 MHz, 0x85F7, 0x483634314755363747313630304700000000
Memory Module: BANK 1/DIMM0, 8 GB, DDR3, 1600 MHz, 0x85F7, 0x483634314755363747313630304700000000
Memory Module: BANK 0/DIMM1, 8 GB, DDR3, 1600 MHz, 0x85F7, 0x483634314755363747313630304700000000
Memory Module: BANK 1/DIMM1, 8 GB, DDR3, 1600 MHz, 0x85F7, 0x483634314755363747313630304700000000
AirPort: spairport_wireless_card_type_airport_extreme (0x14E4, 0xF4), Broadcom BCM43xx 1.0 (7.15.166.24.3)
Bluetooth: Version 4.3.5f8 15969, 3 services, 27 devices, 1 incoming serial ports
Network Service: Ethernet, Ethernet, en0
Network Service: Wi-Fi, AirPort, en1
Serial ATA Device: APPLE HDD ST3000DM001, 3 TB
Serial ATA Device: APPLE SSD SM128E, 121.33 GB
USB Device: SpaceNavigator
USB Device: Kinesis Keyboard Hub
USB Device: Composite Device
USB Device: Composite Device
USB Device: Hub
USB Device: FaceTime HD Camera (Built-in)
USB Device: Hub
USB Device: Hub
USB Device: BRCM20702 Hub
USB Device: Bluetooth USB Host Controller
Thunderbolt Bus: iMac, Apple Inc., 23.4

[Greg Couch]

Fixed. Was problem with sheet ranges where the end residue was before the start residue.

[Tom Goddard]

mmCIF 4a6s also has this problem.

[Eric Pettersen]

reducing # of categories, so lumping into I/O category