![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 3 years ago
Closed 3 years ago
#7256 closed defect (fixed)
Crash in swapaa
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Structure Editing | Version: | |
| Keywords: | Cc: | Tom Goddard | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.5.dev202206100131 (2022-06-10 01:31:06 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault
Thread 0x00007000130d5000 (most recent call first):
File "/Users/amandaghilardi/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 316 in wait
File "/Users/amandaghilardi/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 574 in wait
File "/Users/amandaghilardi/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 1297 in run
File "/Users/amandaghilardi/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/Users/amandaghilardi/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Current thread 0x00000001095c2600 (most recent call first):
File "/Users/amandaghilardi/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/clashes/clashes.py", line 120 in find_clashes
File "/Users/amandaghilardi/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/swap_res/swap_res.py", line 739 in process_clashes
File "/Users/amandaghilardi/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/swap_res/swap_res.py", line 97 in swap_aa
File "/Users/amandaghilardi/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/swap_res/cmd.py", line 45 in swap_aa
File "/Users/amandaghilardi/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/commands/cli.py", line 2897 in run
File "/Users/amandaghilardi/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/cmd_line/tool.py", line 319 in execute
File "/Users/amandaghilardi/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/cmd_line/tool.py", line 146 in keyPressEvent
File "/Users/amandaghilardi/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 332 in event_loop
File "/Users/amandaghilardi/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/ChimeraX_main.py", line 870 in init
File "/Users/amandaghilardi/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/ChimeraX_main.py", line 1021 in
File "/Users/amandaghilardi/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 87 in _run_code
File "/Users/amandaghilardi/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 197 in _run_module_as_main
{"app_name":"ChimeraX","timestamp":"2022-07-11 16:23:05.00 -0400","app_version":"1.5.0","slice_uuid":"9596eff5-d2be-396c-9c4e-6177235c3dae","build_version":"1.5.0.0","platform":1,"bundleID":"edu.ucsf.cgl.ChimeraX","share_with_app_devs":0,"is_first_party":0,"bug_type":"309","os_version":"macOS 12.0.1 (21A559)","incident_id":"5082318E-B788-4D55-9C10-EF9BFCCF5CA3","name":"ChimeraX"}
{
"uptime" : 1600000,
"procLaunch" : "2022-07-10 15:01:50.9925 -0400",
"procRole" : "Foreground",
"version" : 2,
"userID" : 504,
"deployVersion" : 210,
"modelCode" : "iMac20,1",
"procStartAbsTime" : 1566490417338423,
"coalitionID" : 78064,
"osVersion" : {
"train" : "macOS 12.0.1",
"build" : "21A559",
"releaseType" : "User"
},
"captureTime" : "2022-07-11 16:22:54.8263 -0400",
"incident" : "5082318E-B788-4D55-9C10-EF9BFCCF5CA3",
"bug_type" : "309",
"pid" : 65355,
"procExitAbsTime" : 1657755977135567,
"cpuType" : "X86-64",
"procName" : "ChimeraX",
"procPath" : "\/Users\/USER\/Desktop\/ChimeraX_Daily.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.5.0","CFBundleVersion":"1.5.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"31B0C3D6-302F-5CA1-AC22-678F30BF7167","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "B648F3E9-3C05-5922-1609-51E501149E1F",
"bridgeVersion" : {"build":"19P549","train":"6.0"},
"sip" : "enabled",
"vmRegionInfo" : "0 is not in any region. Bytes before following region: 4425338880\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 107c55000-107c56000 [ 4K] r-x\/r-x SM=COW ...acOS\/ChimeraX",
"isCorpse" : 1,
"exception" : {"codes":"0x0000000000000001, 0x0000000000000000","rawCodes":[1,0],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000000000000000"},
"ktriageinfo" : "VM - Fault hit memory shortage\nVM - Fault hit memory shortage\nVM - Fault hit memory shortage\nVM - Fault hit memory shortage\nVM - Fault hit memory shortage\n",
"vmregioninfo" : "0 is not in any region. Bytes before following region: 4425338880\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 107c55000-107c56000 [ 4K] r-x\/r-x SM=COW ...acOS\/ChimeraX",
"extMods" : {"caller":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"system":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"targeted":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"warnings":0},
"faultingThread" : 0,
"threads" : [{"queue":"com.apple.main-thread","instructionState":{"instructionStream":{"bytes":[243,15,126,6,102,15,46,3,73,137,217,119,3,73,137,241,72,131,195,8,76,137,206,73,57,216,117,228,76,137,248,72,193,224,4,73,139,17,73,137,84,4,16,77,57,194,116,100,72,137,254,72,141,93,136,102,15,31,132,0,0,0,0,0,243,65,15,126,2,102,15,46,6,76,137,210,119,3,72,137,242,73,131,194,8,72,137,214,77,57,208,117,227,235,60,144,72,139,7,76,137,250,72,193,226,4,76,139,101,176,235,10,72,139,7,76,137,250,72,193,226,4,73,137,68,20,16,72,139,7,76,137,250,72,193,226,4,73,137,68,20,24,76,139,117,168,235,20,72,137,250,72,141,93,136,72,139,18,73,137,84,4,24,72,133,255,116,23,72,131,193,248,15,31,64,0,72,131,193,8,117,250,72,137,125,200,232,143,127,7,0,73],"offset":96}},"frames":[{"imageOffset":28946,"symbol":"__pthread_kill","symbolLocation":10,"imageIndex":0},{"imageOffset":25139,"symbol":"pthread_kill","symbolLocation":263,"imageIndex":1},{"imageOffset":278980,"symbol":"raise","symbolLocation":26,"imageIndex":2},{"imageOffset":15917,"symbol":"_sigtramp","symbolLocation":29,"imageIndex":3},{"imageOffset":0,"imageIndex":4},{"imageOffset":661684,"symbol":"atomstruct::_Node::_Node(std::__1::vector > const&, bool, double)","symbolLocation":116,"imageIndex":5},{"imageOffset":664431,"symbol":"atomstruct::_Node::_Node(std::__1::vector > const&, bool, double)","symbolLocation":2863,"imageIndex":5},{"imageOffset":664431,"symbol":"atomstruct::_Node::_Node(std::__1::vector > const&, bool, double)","symbolLocation":2863,"imageIndex":5},{"imageOffset":664583,"symbol":"atomstruct::_Node::_Node(std::__1::vector > const&, bool, double)","symbolLocation":3015,"imageIndex":5},{"imageOffset":664431,"symbol":"atomstruct::_Node::_Node(std::__1::vector > const&, bool, double)","symbolLocation":2863,"imageIndex":5},{"imageOffset":664431,"symbol":"atomstruct::_Node::_Node(std::__1::vector > const&, bool, double)","symbolLocation":2863,"imageIndex":5},{"imageOffset":664431,"symbol":"atomstruct::_Node::_Node(std::__1::vector > const&, bool, double)","symbolLocation":2863,"imageIndex":5},{"imageOffset":664583,"symbol":"atomstruct::_Node::_Node(std::__1::vector > const&, bool, double)","symbolLocation":3015,"imageIndex":5},{"imageOffset":664431,"symbol":"atomstruct::_Node::_Node(std::__1::vector > const&, bool, double)","symbolLocation":2863,"imageIndex":5},{"imageOffset":664583,"symbol":"atomstruct::_Node::_Node(std::__1::vector > const&, bool, double)","symbolLocation":3015,"imageIndex":5},{"imageOffset":664583,"symbol":"atomstruct::_Node::_Node(std::__1::vector > const&, bool, double)","symbolLocation":3015,"imageIndex":5},{"imageOffset":664583,"symbol":"atomstruct::_Node::_Node(std::__1::vector > const&, bool, double)","symbolLocation":3015,"imageIndex":5},{"imageOffset":664583,"symbol":"atomstruct::_Node::_Node(std::__1::vector > const&, bool, double)","symbolLocation":3015,"imageIndex":5},{"imageOffset":664583,"symbol":"atomstruct::_Node::_Node(std::__1::vector > const&, bool, double)","symbolLocation":3015,"imageIndex":5},{"imageOffset":658359,"symbol":"atomstruct::AtomSearchTree::AtomSearchTree(std::__1::vector > const&, bool, double)","symbolLocation":455,"imageIndex":5},{"imageOffset":16074,"symbol":"__pyx_tp_new_8chimerax_11atom_search_3ast_CyAtomSearchTree(_typeobject*, _object*, _object*)","symbolLocation":2826,"imageIndex":6},{"imageOffset":609974,"symbol":"type_call","symbolLocation":86,"imageIndex":7},{"imageOffset":259511,"symbol":"_PyObject_MakeTpCall","symbolLocation":359,"imageIndex":7},{"imageOffset":1146524,"symbol":"call_function","symbolLocation":876,"imageIndex":7},{"imageOffset":1135592,"symbol":"_PyEval_EvalFrameDefault","symbolLocation":25880,"imageIndex":7},{"imageOffset":1149699,"symbol":"_PyEval_EvalCode","symbolLocation":2611,"imageIndex":7},{"imageOffset":261297,"symbol":"_PyFunction_Vectorcall","symbolLocation":289,"imageIndex":7},{"imageOffset":1146380,"symbol":"call_function","symbolLocation":732,"imageIndex":7},{"imageOffset":1135592,"symbol":"_PyEval_EvalFrameDefault","symbolLocation":25880,"imageIndex":7},{"imageOffset":261416,"symbol":"function_code_fastcall","symbolLocation":104,"imageIndex":7},{"imageOffset":1146380,"symbol":"call_function","symbolLocation":732,"imageIndex":7},{"imageOffset":1135435,"symbol":"_PyEval_EvalFrameDefault","symbolLocation":25723,"imageIndex":7},{"imageOffset":1149699,"symbol":"_PyEval_EvalCode","symbolLocation":2611,"imageIndex":7},{"imageOffset":261297,"symbol":"_PyFunction_Vectorcall","symbolLocation":289,"imageIndex":7},{"imageOffset":1146380,"symbol":"call_function","symbolLocation":732,"imageIndex":7},{"imageOffset":1135592,"symbol":"_PyEval_EvalFrameDefault","symbolLocation":25880,"imageIndex":7},{"imageOffset":1149699,"symbol":"_PyEval_EvalCode","symbolLocation":2611,"imageIndex":7},{"imageOffset":261297,"symbol":"_PyFunction_Vectorcall","symbolLocation":289,"imageIndex":7},{"imageOffset":260482,"symbol":"PyVectorcall_Call","symbolLocation":162,"imageIndex":7},{"imageOffset":1137033,"symbol":"_PyEval_EvalFrameDefault","symbolLocation":27321,"imageIndex":7},{"imageOffset":1149699,"symbol":"_PyEval_EvalCode","symbolLocation":2611,"imageIndex":7},{"imageOffset":261297,"symbol":"_PyFunction_Vectorcall","symbolLocation":289,"imageIndex":7},{"imageOffset":1146380,"symbol":"call_function","symbolLocation":732,"imageIndex":7},{"imageOffset":1135230,"symbol":"_PyEval_EvalFrameDefault","symbolLocation":25518,"imageIndex":7},{"imageOffset":1149699,"symbol":"_PyEval_EvalCode","symbolLocation":2611,"imageIndex":7},{"imageOffset":261297,"symbol":"_PyFunction_Vectorcall","symbolLocation":289,"imageIndex":7},{"imageOffset":269746,"symbol":"method_vectorcall","symbolLocation":274,"imageIndex":7},{"imageOffset":1259015,"symbol":"PyQtSlot::call(_object*, _object*) const","symbolLocation":39,"imageIndex":8},{"imageOffset":1258774,"symbol":"PyQtSlot::invoke(void**, _object*, void*, bool) const","symbolLocation":358,"imageIndex":8},{"imageOffset":1262661,"symbol":"PyQtSlotProxy::unislot(void**)","symbolLocation":85,"imageIndex":8},{"imageOffset":1262522,"symbol":"PyQtSlotProxy::qt_metacall(QMetaObject::Call, int, void**)","symbolLocation":58,"imageIndex":8},{"imageOffset":772583,"imageIndex":9},{"imageOffset":1691113,"imageIndex":10},{"imageOffset":773282,"imageIndex":9},{"imageOffset":1719524,"symbol":"QWidgetLineControl::processKeyEvent(QKeyEvent*)","symbolLocation":532,"imageIndex":10},{"imageOffset":1664826,"symbol":"QLineEdit::keyPressEvent(QKeyEvent*)","symbolLocation":26,"imageIndex":10},{"imageOffset":403047,"symbol":"QWidget::event(QEvent*)","symbolLocation":471,"imageIndex":10},{"imageOffset":1662428,"symbol":"QLineEdit::event(QEvent*)","symbolLocation":524,"imageIndex":10},{"imageOffset":1405644,"symbol":"QComboBox::keyPressEvent(QKeyEvent*)","symbolLocation":572,"imageIndex":10},{"imageOffset":2215321,"symbol":"meth_QComboBox_keyPressEvent(_object*, _object*)","symbolLocation":169,"imageIndex":11},{"imageOffset":517917,"symbol":"cfunction_call","symbolLocation":125,"imageIndex":7},{"imageOffset":259511,"symbol":"_PyObject_MakeTpCall","symbolLocation":359,"imageIndex":7},{"imageOffset":1146524,"symbol":"call_function","symbolLocation":876,"imageIndex":7},{"imageOffset":1135266,"symbol":"_PyEval_EvalFrameDefault","symbolLocation":25554,"imageIndex":7},{"imageOffset":1149699,"symbol":"_PyEval_EvalCode","symbolLocation":2611,"imageIndex":7},{"imageOffset":261297,"symbol":"_PyFunction_Vectorcall","symbolLocation":289,"imageIndex":7},{"imageOffset":269913,"symbol":"method_vectorcall","symbolLocation":441,"imageIndex":7},{"imageOffset":44151,"symbol":"sip_api_call_procedure_method","symbolLocation":199,"imageIndex":12},{"imageOffset":1186920,"symbol":"sipQComboBox::keyPressEvent(QKeyEvent*)","symbolLocation":104,"imageIndex":11},{"imageOffset":403047,"symbol":"QWidget::event(QEvent*)","symbolLocation":471,"imageIndex":10},{"imageOffset":1404359,"symbol":"QComboBox::event(QEvent*)","symbolLocation":311,"imageIndex":10},{"imageOffset":1184111,"symbol":"sipQComboBox::event(QEvent*)","symbolLocation":191,"imageIndex":11},{"imageOffset":57447,"symbol":"QApplicationPrivate::notify_helper(QObject*, QEvent*)","symbolLocation":247,"imageIndex":10},{"imageOffset":62018,"symbol":"QApplication::notify(QObject*, QEvent*)","symbolLocation":1042,"imageIndex":10},{"imageOffset":1300521,"symbol":"sipQApplication::notify(QObject*, QEvent*)","symbolLocation":233,"imageIndex":11},{"imageOffset":441802,"symbol":"QCoreApplication::notifyInternal2(QObject*, QEvent*)","symbolLocation":170,"imageIndex":9},{"imageOffset":492007,"imageIndex":10},{"imageOffset":57447,"symbol":"QApplicationPrivate::notify_helper(QObject*, QEvent*)","symbolLocation":247,"imageIndex":10},{"imageOffset":61475,"symbol":"QApplication::notify(QObject*, QEvent*)","symbolLocation":499,"imageIndex":10},{"imageOffset":1300521,"symbol":"sipQApplication::notify(QObject*, QEvent*)","symbolLocation":233,"imageIndex":11},{"imageOffset":441802,"symbol":"QCoreApplication::notifyInternal2(QObject*, QEvent*)","symbolLocation":170,"imageIndex":9},{"imageOffset":611684,"symbol":"QGuiApplicationPrivate::processKeyEvent(QWindowSystemInterfacePrivate::KeyEvent*)","symbolLocation":292,"imageIndex":13},{"imageOffset":918556,"symbol":"QWindowSystemInterface::sendWindowSystemEvents(QFlags)","symbolLocation":444,"imageIndex":13},{"imageOffset":917516,"symbol":"QWindowSystemInterface::flushWindowSystemEvents(QFlags)","symbolLocation":476,"imageIndex":13},{"imageOffset":465129,"imageIndex":14},{"imageOffset":2765820,"symbol":"-[NSResponder tryToPerform:with:]","symbolLocation":53,"imageIndex":15},{"imageOffset":473894,"imageIndex":14},{"imageOffset":3280315,"symbol":"-[NSTextInputContext(NSInputContext_WithCompletion) doCommandBySelector:completionHandler:]","symbolLocation":236,"imageIndex":15},{"imageOffset":2405022,"symbol":"-[NSKeyBindingManager(NSKeyBindingManager_MultiClients) interpretEventAsCommand:forClient:]","symbolLocation":2271,"imageIndex":15},{"imageOffset":2440657,"symbol":"__84-[NSTextInputContext _handleEvent:options:allowingSyntheticEvent:completionHandler:]_block_invoke_5","symbolLocation":533,"imageIndex":15},{"imageOffset":10475495,"symbol":"__84-[NSTextInputContext _handleEvent:options:allowingSyntheticEvent:completionHandler:]_block_invoke_3.843","symbolLocation":74,"imageIndex":15},{"imageOffset":2440081,"symbol":"-[NSTextInputContext tryHandleEvent_HasMarkedText_withDispatchCondition:dispatchWork:continuation:]","symbolLocation":87,"imageIndex":15},{"imageOffset":10475373,"symbol":"__84-[NSTextInputContext _handleEvent:options:allowingSyntheticEvent:completionHandler:]_block_invoke.840","symbolLocation":251,"imageIndex":15},{"imageOffset":422257,"symbol":"__TSMProcessRawKeyEventWithOptionsAndCompletionHandler_block_invoke_5","symbolLocation":70,"imageIndex":16},{"imageOffset":500862,"symbol":"invocation function for block in DispatchEventToHandlers(EventTargetRec*, OpaqueEventRef*, HandlerCallRec*)","symbolLocation":110,"imageIndex":16},{"imageOffset":10456722,"symbol":"__55-[NSTextInputContext handleTSMEvent:completionHandler:]_block_invoke.310","symbolLocation":885,"imageIndex":15},{"imageOffset":2412744,"symbol":"__55-[NSTextInputContext handleTSMEvent:completionHandler:]_block_invoke_2","symbolLocation":74,"imageIndex":15},{"imageOffset":2412622,"symbol":"-[NSTextInputContext tryHandleTSMEvent_HasMarkedText_withDispatchCondition:dispatchWork:continuation:]","symbolLocation":87,"imageIndex":15},{"imageOffset":2409897,"symbol":"-[NSTextInputContext handleTSMEvent:completionHandler:]","symbolLocation":1859,"imageIndex":15},{"imageOffset":2407928,"symbol":"_NSTSMEventHandler","symbolLocation":299,"imageIndex":15},{"imageOffset":35757,"symbol":"DispatchEventToHandlers(EventTargetRec*, OpaqueEventRef*, HandlerCallRec*)","symbolLocation":1391,"imageIndex":16},{"imageOffset":32734,"symbol":"SendEventToEventTargetInternal(OpaqueEventRef*, OpaqueEventTargetRef*, HandlerCallRec*)","symbolLocation":333,"imageIndex":16},{"imageOffset":32383,"symbol":"SendEventToEventTargetWithOptions","symbolLocation":45,"imageIndex":16},{"imageOffset":407014,"symbol":"SendTSMEvent_WithCompletionHandler","symbolLocation":381,"imageIndex":16},{"imageOffset":408209,"symbol":"__SendUnicodeTextAEToUnicodeDoc_WithCompletionHandler_block_invoke","symbolLocation":387,"imageIndex":16},{"imageOffset":407785,"symbol":"__SendFilterTextEvent_WithCompletionHandler_block_invoke","symbolLocation":182,"imageIndex":16},{"imageOffset":407092,"symbol":"SendTSMEvent_WithCompletionHandler","symbolLocation":459,"imageIndex":16},{"imageOffset":406588,"symbol":"SendFilterTextEvent_WithCompletionHandler","symbolLocation":219,"imageIndex":16},{"imageOffset":405781,"symbol":"SendUnicodeTextAEToUnicodeDoc_WithCompletionHandler","symbolLocation":274,"imageIndex":16},{"imageOffset":405189,"symbol":"__utDeliverTSMEvent_WithCompletionHandler_block_invoke_2","symbolLocation":281,"imageIndex":16},{"imageOffset":404773,"symbol":"__utDeliverTSMEvent_WithCompletionHandler_block_invoke","symbolLocation":354,"imageIndex":16},{"imageOffset":404344,"symbol":"TSMKeyEvent_WithCompletionHandler","symbolLocation":577,"imageIndex":16},{"imageOffset":403740,"symbol":"__TSMProcessRawKeyEventWithOptionsAndCompletionHandler_block_invoke_4","symbolLocation":250,"imageIndex":16},{"imageOffset":403355,"symbol":"__TSMProcessRawKeyEventWithOptionsAndCompletionHandler_block_invoke_3","symbolLocation":257,"imageIndex":16},{"imageOffset":402791,"symbol":"__TSMProcessRawKeyEventWithOptionsAndCompletionHandler_block_invoke_2","symbolLocation":282,"imageIndex":16},{"imageOffset":402202,"symbol":"__TSMProcessRawKeyEventWithOptionsAndCompletionHandler_block_invoke","symbolLocation":274,"imageIndex":16},{"imageOffset":332826,"symbol":"TSMProcessRawKeyEventWithOptionsAndCompletionHandler","symbolLocation":3490,"imageIndex":16},{"imageOffset":10475101,"symbol":"__84-[NSTextInputContext _handleEvent:options:allowingSyntheticEvent:completionHandler:]_block_invoke_3.838","symbolLocation":110,"imageIndex":15},{"imageOffset":10474423,"symbol":"__204-[NSTextInputContext tryTSMProcessRawKeyEvent_orSubstitution:dispatchCondition:setupForDispatch:furtherCondition:doubleSpaceSubstitutionCondition:doubleSpaceSubstitutionWork:dispatchTSMWork:continuation:]_block_invoke.799","symbolLocation":120,"imageIndex":15},{"imageOffset":2402403,"symbol":"-[NSTextInputContext tryTSMProcessRawKeyEvent_orSubstitution:dispatchCondition:setupForDispatch:furtherCondition:doubleSpaceSubstitutionCondition:doubleSpaceSubstitutionWork:dispatchTSMWork:continuation:]","symbolLocation":245,"imageIndex":15},{"imageOffset":2400879,"symbol":"-[NSTextInputContext _handleEvent:options:allowingSyntheticEvent:completionHandler:]","symbolLocation":1424,"imageIndex":15},{"imageOffset":2399396,"symbol":"-[NSTextInputContext _handleEvent:allowingSyntheticEvent:]","symbolLocation":105,"imageIndex":15},{"imageOffset":2399006,"symbol":"-[NSView interpretKeyEvents:]","symbolLocation":209,"imageIndex":15},{"imageOffset":455289,"imageIndex":14},{"imageOffset":459603,"imageIndex":14},{"imageOffset":1778300,"symbol":"-[NSWindow(NSEventRouting) _reallySendEvent:isDelayedEvent:]","symbolLocation":7150,"imageIndex":15},{"imageOffset":1770606,"symbol":"-[NSWindow(NSEventRouting) sendEvent:]","symbolLocation":352,"imageIndex":15},{"imageOffset":493743,"imageIndex":14},{"imageOffset":1766058,"symbol":"-[NSApplication(NSEvent) sendEvent:]","symbolLocation":3022,"imageIndex":15},{"imageOffset":46282,"imageIndex":14},{"imageOffset":4618251,"symbol":"-[NSApplication _handleEvent:]","symbolLocation":65,"imageIndex":15},{"imageOffset":193406,"symbol":"-[NSApplication run]","symbolLocation":623,"imageIndex":15},{"imageOffset":103564,"imageIndex":14},{"imageOffset":480534,"symbol":"QEventLoop::exec(QFlags)","symbolLocation":486,"imageIndex":9},{"imageOffset":443365,"symbol":"QCoreApplication::exec()","symbolLocation":133,"imageIndex":9},{"imageOffset":2271498,"symbol":"meth_QApplication_exec(_object*, _object*)","symbolLocation":90,"imageIndex":11},{"imageOffset":517917,"symbol":"cfunction_call","symbolLocation":125,"imageIndex":7},{"imageOffset":259511,"symbol":"_PyObject_MakeTpCall","symbolLocation":359,"imageIndex":7},{"imageOffset":1146524,"symbol":"call_function","symbolLocation":876,"imageIndex":7},{"imageOffset":1135266,"symbol":"_PyEval_EvalFrameDefault","symbolLocation":25554,"imageIndex":7},{"imageOffset":261416,"symbol":"function_code_fastcall","symbolLocation":104,"imageIndex":7},{"imageOffset":269674,"symbol":"method_vectorcall","symbolLocation":202,"imageIndex":7},{"imageOffset":1146380,"symbol":"call_function","symbolLocation":732,"imageIndex":7},{"imageOffset":1135266,"symbol":"_PyEval_EvalFrameDefault","symbolLocation":25554,"imageIndex":7},{"imageOffset":1149699,"symbol":"_PyEval_EvalCode","symbolLocation":2611,"imageIndex":7},{"imageOffset":261297,"symbol":"_PyFunction_Vectorcall","symbolLocation":289,"imageIndex":7},{"imageOffset":1146380,"symbol":"call_function","symbolLocation":732,"imageIndex":7},{"imageOffset":1135435,"symbol":"_PyEval_EvalFrameDefault","symbolLocation":25723,"imageIndex":7},{"imageOffset":1149699,"symbol":"_PyEval_EvalCode","symbolLocation":2611,"imageIndex":7},{"imageOffset":1109419,"symbol":"PyEval_EvalCode","symbolLocation":139,"imageIndex":7},{"imageOffset":1096722,"symbol":"builtin_exec","symbolLocation":626,"imageIndex":7},{"imageOffset":516131,"symbol":"cfunction_vectorcall_FASTCALL","symbolLocation":195,"imageIndex":7},{"imageOffset":1146380,"symbol":"call_function","symbolLocation":732,"imageIndex":7},{"imageOffset":1135435,"symbol":"_PyEval_EvalFrameDefault","symbolLocation":25723,"imageIndex":7},{"imageOffset":1149699,"symbol":"_PyEval_EvalCode","symbolLocation":2611,"imageIndex":7},{"imageOffset":261297,"symbol":"_PyFunction_Vectorcall","symbolLocation":289,"imageIndex":7},{"imageOffset":1146380,"symbol":"call_function","symbolLocation":732,"imageIndex":7},{"imageOffset":1135435,"symbol":"_PyEval_EvalFrameDefault","symbolLocation":25723,"imageIndex":7},{"imageOffset":1149699,"symbol":"_PyEval_EvalCode","symbolLocation":2611,"imageIndex":7},{"imageOffset":261297,"symbol":"_PyFunction_Vectorcall","symbolLocation":289,"imageIndex":7},{"imageOffset":1566832,"symbol":"pymain_run_module","symbolLocation":208,"imageIndex":7},{"imageOffset":1564551,"symbol":"Py_RunMain","symbolLocation":1431,"imageIndex":7},{"imageOffset":1566095,"symbol":"pymain_main","symbolLocation":223,"imageIndex":7},{"imageOffset":1565851,"symbol":"Py_Main","symbolLocation":43,"imageIndex":7},{"imageOffset":3528,"symbol":"main","symbolLocation":120,"imageIndex":17},{"imageOffset":21758,"symbol":"start","symbolLocation":462,"imageIndex":18}],"id":10927245,"triggered":true,"threadState":{"r13":{"value":0},"rax":{"value":0},"rflags":{"value":582},"cpu":{"value":0},"r14":{"value":11},"rsi":{"value":11},"r8":{"value":140516410089288},"cr2":{"value":140516413385696},"rdx":{"value":0},"r10":{"value":4452001280,"symbolLocation":0,"symbol":"_main_thread"},"r9":{"value":7653502562944420474},"r15":{"value":22},"rbx":{"value":4452001280,"symbolLocation":0,"symbol":"_main_thread"},"trap":{"value":133},"err":{"value":33554760},"r11":{"value":582},"rip":{"value":140703159841042,"matchesCrashFrame":1},"rbp":{"value":140516410088064},"rsp":{"value":140516410088024},"r12":{"value":259},"rcx":{"value":140516410088024},"flavor":"x86_THREAD_STATE","rdi":{"value":259}},"name":"CrBrowserMain"},{"id":10927505,"name":"OGL Profiler","frames":[{"imageOffset":2746,"symbol":"mach_msg_trap","symbolLocation":10,"imageIndex":0},{"imageOffset":3627,"symbol":"mach_msg","symbolLocation":59,"imageIndex":0},{"imageOffset":8670,"symbol":"glcDebugListener","symbolLocation":300,"imageIndex":19},{"imageOffset":25876,"symbol":"_pthread_start","symbolLocation":125,"imageIndex":1},{"imageOffset":8239,"symbol":"thread_start","symbolLocation":15,"imageIndex":1}]},{"id":10927687,"name":"ThreadPoolServiceThread","frames":[{"imageOffset":39366,"symbol":"kevent64","symbolLocation":10,"imageIndex":0},{"imageOffset":66463178,"imageIndex":20},{"imageOffset":66462919,"imageIndex":20},{"imageOffset":65925532,"imageIndex":20},{"imageOffset":65630200,"imageIndex":20},{"imageOffset":66065496,"imageIndex":20},{"imageOffset":65964109,"imageIndex":20},{"imageOffset":66065898,"imageIndex":20},{"imageOffset":66229416,"imageIndex":20},{"imageOffset":25876,"symbol":"_pthread_start","symbolLocation":125,"imageIndex":1},{"imageOffset":8239,"symbol":"thread_start","symbolLocation":15,"imageIndex":1}]},{"id":10927690,"name":"Chrome_IOThread","frames":[{"imageOffset":39366,"symbol":"kevent64","symbolLocation":10,"imageIndex":0},{"imageOffset":66463178,"imageIndex":20},{"imageOffset":66462919,"imageIndex":20},{"imageOffset":65925532,"imageIndex":20},{"imageOffset":65630200,"imageIndex":20},{"imageOffset":66065496,"imageIndex":20},{"imageOffset":48397874,"imageIndex":20},{"imageOffset":66065898,"imageIndex":20},{"imageOffset":66229416,"imageIndex":20},{"imageOffset":25876,"symbol":"_pthread_start","symbolLocation":125,"imageIndex":1},{"imageOffset":8239,"symbol":"thread_start","symbolLocation":15,"imageIndex":1}]},{"id":10927691,"name":"NetworkConfigWatcher","frames":[{"imageOffset":2746,"symbol":"mach_msg_trap","symbolLocation":10,"imageIndex":0},{"imageOffset":3627,"symbol":"mach_msg","symbolLocation":59,"imageIndex":0},{"imageOffset":66259398,"imageIndex":20},{"imageOffset":66258831,"imageIndex":20},{"imageOffset":65429641,"imageIndex":20},{"imageOffset":65925532,"imageIndex":20},{"imageOffset":65630200,"imageIndex":20},{"imageOffset":66065496,"imageIndex":20},{"imageOffset":66065898,"imageIndex":20},{"imageOffset":66229416,"imageIndex":20},{"imageOffset":25876,"symbol":"_pthread_start","symbolLocation":125,"imageIndex":1},{"imageOffset":8239,"symbol":"thread_start","symbolLocation":15,"imageIndex":1}]},{"id":10927695,"name":"CompositorTileWorker1","frames":[{"imageOffset":13574,"symbol":"__psynch_cvwait","symbolLocation":10,"imageIndex":0},{"imageOffset":27273,"symbol":"_pthread_cond_wait","symbolLocation":1224,"imageIndex":1},{"imageOffset":66226363,"imageIndex":20},{"imageOffset":100635997,"imageIndex":20},{"imageOffset":66229416,"imageIndex":20},{"imageOffset":25876,"symbol":"_pthread_start","symbolLocation":125,"imageIndex":1},{"imageOffset":8239,"symbol":"thread_start","symbolLocation":15,"imageIndex":1}]},{"id":10927696,"name":"Chrome_InProcGpuThread","frames":[{"imageOffset":2746,"symbol":"mach_msg_trap","symbolLocation":10,"imageIndex":0},{"imageOffset":3627,"symbol":"mach_msg","symbolLocation":59,"imageIndex":0},{"imageOffset":66259398,"imageIndex":20},{"imageOffset":66258831,"imageIndex":20},{"imageOffset":65429641,"imageIndex":20},{"imageOffset":65925532,"imageIndex":20},{"imageOffset":65630200,"imageIndex":20},{"imageOffset":66065496,"imageIndex":20},{"imageOffset":66065898,"imageIndex":20},{"imageOffset":66229416,"imageIndex":20},{"imageOffset":25876,"symbol":"_pthread_start","symbolLocation":125,"imageIndex":1},{"imageOffset":8239,"symbol":"thread_start","symbolLocation":15,"imageIndex":1}]},{"id":10927697,"name":"Chrome_ChildIOThread","frames":[{"imageOffset":39366,"symbol":"kevent64","symbolLocation":10,"imageIndex":0},{"imageOffset":66463178,"imageIndex":20},{"imageOffset":66462919,"imageIndex":20},{"imageOffset":65925532,"imageIndex":20},{"imageOffset":65630200,"imageIndex":20},{"imageOffset":66065496,"imageIndex":20},{"imageOffset":66065898,"imageIndex":20},{"imageOffset":66229416,"imageIndex":20},{"imageOffset":25876,"symbol":"_pthread_start","symbolLocation":125,"imageIndex":1},{"imageOffset":8239,"symbol":"thread_start","symbolLocation":15,"imageIndex":1}]},{"id":10927698,"name":"NetworkConfigWatcher","frames":[{"imageOffset":2746,"symbol":"mach_msg_trap","symbolLocation":10,"imageIndex":0},{"imageOffset":3627,"symbol":"mach_msg","symbolLocation":59,"imageIndex":0},{"imageOffset":66259398,"imageIndex":20},{"imageOffset":66258831,"imageIndex":20},{"imageOffset":65429641,"imageIndex":20},{"imageOffset":65925532,"imageIndex":20},{"imageOffset":65630200,"imageIndex":20},{"imageOffset":66065496,"imageIndex":20},{"imageOffset":66065898,"imageIndex":20},{"imageOffset":66229416,"imageIndex":20},{"imageOffset":25876,"symbol":"_pthread_start","symbolLocation":125,"imageIndex":1},{"imageOffset":8239,"symbol":"thread_start","symbolLocation":15,"imageIndex":1}]},{"id":10927699,"name":"VizCompositorThread","frames":[{"imageOffset":2746,"symbol":"mach_msg_trap","symbolLocation":10,"imageIndex":0},{"imageOffset":3627,"symbol":"mach_msg","symbolLocation":59,"imageIndex":0},{"imageOffset":66259398,"imageIndex":20},{"imageOffset":66258831,"imageIndex":20},{"imageOffset":65429641,"imageIndex":20},{"imageOffset":65925532,"imageIndex":20},{"imageOffset":65630200,"imageIndex":20},{"imageOffset":66065496,"imageIndex":20},{"imageOffset":66065898,"imageIndex":20},{"imageOffset":66229416,"imageIndex":20},{"imageOffset":25876,"symbol":"_pthread_start","symbolLocation":125,"imageIndex":1},{"imageOffset":8239,"symbol":"thread_start","symbolLocation":15,"imageIndex":1}]},{"id":10927708,"name":"NetworkService","frames":[{"imageOffset":39366,"symbol":"kevent64","symbolLocation":10,"imageIndex":0},{"imageOffset":66463178,"imageIndex":20},{"imageOffset":66462919,"imageIndex":20},{"imageOffset":65925532,"imageIndex":20},{"imageOffset":65630200,"imageIndex":20},{"imageOffset":66065496,"imageIndex":20},{"imageOffset":66065898,"imageIndex":20},{"imageOffset":66229416,"imageIndex":20},{"imageOffset":25876,"symbol":"_pthread_start","symbolLocation":125,"imageIndex":1},{"imageOffset":8239,"symbol":"thread_start","symbolLocation":15,"imageIndex":1}]},{"id":10927709,"name":"NetworkConfigWatcher","frames":[{"imageOffset":2746,"symbol":"mach_msg_trap","symbolLocation":10,"imageIndex":0},{"imageOffset":3627,"symbol":"mach_msg","symbolLocation":59,"imageIndex":0},{"imageOffset":66259398,"imageIndex":20},{"imageOffset":66258831,"imageIndex":20},{"imageOffset":65429641,"imageIndex":20},{"imageOffset":65925532,"imageIndex":20},{"imageOffset":65630200,"imageIndex":20},{"imageOffset":66065496,"imageIndex":20},{"imageOffset":66065898,"imageIndex":20},{"imageOffset":66229416,"imageIndex":20},{"imageOffset":25876,"symbol":"_pthread_start","symbolLocation":125,"imageIndex":1},{"imageOffset":8239,"symbol":"thread_start","symbolLocation":15,"imageIndex":1}]},{"id":10927710,"name":"ThreadPoolSingleThreadForegroundBlocking0","frames":[{"imageOffset":2746,"symbol":"mach_msg_trap","symbolLocation":10,"imageIndex":0},{"imageOffset":3627,"symbol":"mach_msg","symbolLocation":59,"imageIndex":0},{"imageOffset":66259398,"imageIndex":20},{"imageOffset":66014559,"imageIndex":20},{"imageOffset":66017292,"imageIndex":20},{"imageOffset":66016365,"imageIndex":20},{"imageOffset":66229416,"imageIndex":20},{"imageOffset":25876,"symbol":"_pthread_start","symbolLocation":125,"imageIndex":1},{"imageOffset":8239,"symbol":"thread_start","symbolLocation":15,"imageIndex":1}]},{"id":10927773,"name":"NetworkConfigWatcher","frames":[{"imageOffset":2746,"symbol":"mach_msg_trap","symbolLocation":10,"imageIndex":0},{"imageOffset":3627,"symbol":"mach_msg","symbolLocation":59,"imageIndex":0},{"imageOffset":66259398,"imageIndex":20},{"imageOffset":66258831,"imageIndex":20},{"imageOffset":65429641,"imageIndex":20},{"imageOffset":65925532,"imageIndex":20},{"imageOffset":65630200,"imageIndex":20},{"imageOffset":66065496,"imageIndex":20},{"imageOffset":66065898,"imageIndex":20},{"imageOffset":66229416,"imageIndex":20},{"imageOffset":25876,"symbol":"_pthread_start","symbolLocation":125,"imageIndex":1},{"imageOffset":8239,"symbol":"thread_start","symbolLocation":15,"imageIndex":1}]},{"id":10927917,"name":"com.apple.NSEventThread","frames":[{"imageOffset":2746,"symbol":"mach_msg_trap","symbolLocation":10,"imageIndex":0},{"imageOffset":3627,"symbol":"mach_msg","symbolLocation":59,"imageIndex":0},{"imageOffset":526914,"symbol":"__CFRunLoopServiceMachPort","symbolLocation":319,"imageIndex":21},{"imageOffset":520475,"symbol":"__CFRunLoopRun","symbolLocation":1325,"imageIndex":21},{"imageOffset":517421,"symbol":"CFRunLoopRunSpecific","symbolLocation":563,"imageIndex":21},{"imageOffset":1756396,"symbol":"_NSEventThread","symbolLocation":132,"imageIndex":15},{"imageOffset":25876,"symbol":"_pthread_start","symbolLocation":125,"imageIndex":1},{"imageOffset":8239,"symbol":"thread_start","symbolLocation":15,"imageIndex":1}]},{"id":10927923,"name":"MemoryInfra","frames":[{"imageOffset":2746,"symbol":"mach_msg_trap","symbolLocation":10,"imageIndex":0},{"imageOffset":3627,"symbol":"mach_msg","symbolLocation":59,"imageIndex":0},{"imageOffset":66259398,"imageIndex":20},{"imageOffset":66258831,"imageIndex":20},{"imageOffset":65429641,"imageIndex":20},{"imageOffset":65925532,"imageIndex":20},{"imageOffset":65630200,"imageIndex":20},{"imageOffset":66065496,"imageIndex":20},{"imageOffset":66065898,"imageIndex":20},{"imageOffset":66229416,"imageIndex":20},{"imageOffset":25876,"symbol":"_pthread_start","symbolLocation":125,"imageIndex":1},{"imageOffset":8239,"symbol":"thread_start","symbolLocation":15,"imageIndex":1}]},{"id":10927924,"name":"ThreadPoolSingleThreadSharedBackgroundBlocking1","frames":[{"imageOffset":2746,"symbol":"mach_msg_trap","symbolLocation":10,"imageIndex":0},{"imageOffset":3627,"symbol":"mach_msg","symbolLocation":59,"imageIndex":0},{"imageOffset":66259398,"imageIndex":20},{"imageOffset":66014559,"imageIndex":20},{"imageOffset":66016570,"imageIndex":20},{"imageOffset":66016173,"imageIndex":20},{"imageOffset":66229416,"imageIndex":20},{"imageOffset":25876,"symbol":"_pthread_start","symbolLocation":125,"imageIndex":1},{"imageOffset":8239,"symbol":"thread_start","symbolLocation":15,"imageIndex":1}]},{"id":11436300,"name":"NetworkConfigWatcher","frames":[{"imageOffset":2746,"symbol":"mach_msg_trap","symbolLocation":10,"imageIndex":0},{"imageOffset":3627,"symbol":"mach_msg","symbolLocation":59,"imageIndex":0},{"imageOffset":66259398,"imageIndex":20},{"imageOffset":66258831,"imageIndex":20},{"imageOffset":65429641,"imageIndex":20},{"imageOffset":65925532,"imageIndex":20},{"imageOffset":65630200,"imageIndex":20},{"imageOffset":66065496,"imageIndex":20},{"imageOffset":66065898,"imageIndex":20},{"imageOffset":66229416,"imageIndex":20},{"imageOffset":25876,"symbol":"_pthread_start","symbolLocation":125,"imageIndex":1},{"imageOffset":8239,"symbol":"thread_start","symbolLocation":15,"imageIndex":1}]},{"id":11436303,"name":"ThreadPoolBackgroundWorker","frames":[{"imageOffset":2746,"symbol":"mach_msg_trap","symbolLocation":10,"imageIndex":0},{"imageOffset":3627,"symbol":"mach_msg","symbolLocation":59,"imageIndex":0},{"imageOffset":66259398,"imageIndex":20},{"imageOffset":66014559,"imageIndex":20},{"imageOffset":66017292,"imageIndex":20},{"imageOffset":66016125,"imageIndex":20},{"imageOffset":66229416,"imageIndex":20},{"imageOffset":25876,"symbol":"_pthread_start","symbolLocation":125,"imageIndex":1},{"imageOffset":8239,"symbol":"thread_start","symbolLocation":15,"imageIndex":1}]},{"id":11490578,"frames":[{"imageOffset":13574,"symbol":"__psynch_cvwait","symbolLocation":10,"imageIndex":0},{"imageOffset":27273,"symbol":"_pthread_cond_wait","symbolLocation":1224,"imageIndex":1},{"imageOffset":3347615,"symbol":"blas_thread_server","symbolLocation":207,"imageIndex":22},{"imageOffset":25876,"symbol":"_pthread_start","symbolLocation":125,"imageIndex":1},{"imageOffset":8239,"symbol":"thread_start","symbolLocation":15,"imageIndex":1}]},{"id":11490579,"frames":[{"imageOffset":13574,"symbol":"__psynch_cvwait","symbolLocation":10,"imageIndex":0},{"imageOffset":27273,"symbol":"_pthread_cond_wait","symbolLocation":1224,"imageIndex":1},{"imageOffset":3347615,"symbol":"blas_thread_server","symbolLocation":207,"imageIndex":22},{"imageOffset":25876,"symbol":"_pthread_start","symbolLocation":125,"imageIndex":1},{"imageOffset":8239,"symbol":"thread_start","symbolLocation":15,"imageIndex":1}]},{"id":11490580,"frames":[{"imageOffset":13574,"symbol":"__psynch_cvwait","symbolLocation":10,"imageIndex":0},{"imageOffset":27273,"symbol":"_pthread_cond_wait","symbolLocation":1224,"imageIndex":1},{"imageOffset":3347615,"symbol":"blas_thread_server","symbolLocation":207,"imageIndex":22},{"imageOffset":25876,"symbol":"_pthread_start","symbolLocation":125,"imageIndex":1},{"imageOffset":8239,"symbol":"thread_start","symbolLocation":15,"imageIndex":1}]},{"id":11490581,"frames":[{"imageOffset":13574,"symbol":"__psynch_cvwait","symbolLocation":10,"imageIndex":0},{"imageOffset":27273,"symbol":"_pthread_cond_wait","symbolLocation":1224,"imageIndex":1},{"imageOffset":3347615,"symbol":"blas_thread_server","symbolLocation":207,"imageIndex":22},{"imageOffset":25876,"symbol":"_pthread_start","symbolLocation":125,"imageIndex":1},{"imageOffset":8239,"symbol":"thread_start","symbolLocation":15,"imageIndex":1}]},{"id":11490582,"frames":[{"imageOffset":13574,"symbol":"__psynch_cvwait","symbolLocation":10,"imageIndex":0},{"imageOffset":27273,"symbol":"_pthread_cond_wait","symbolLocation":1224,"imageIndex":1},{"imageOffset":3347615,"symbol":"blas_thread_server","symbolLocation":207,"imageIndex":22},{"imageOffset":25876,"symbol":"_pthread_start","symbolLocation":125,"imageIndex":1},{"imageOffset":8239,"symbol":"thread_start","symbolLocation":15,"imageIndex":1}]},{"id":11490583,"frames":[{"imageOffset":13574,"symbol":"__psynch_cvwait","symbolLocation":10,"imageIndex":0},{"imageOffset":27273,"symbol":"_pthread_cond_wait","symbolLocation":1224,"imageIndex":1},{"imageOffset":3347615,"symbol":"blas_thread_server","symbolLocation":207,"imageIndex":22},{"imageOffset":25876,"symbol":"_pthread_start","symbolLocation":125,"imageIndex":1},{"imageOffset":8239,"symbol":"thread_start","symbolLocation":15,"imageIndex":1}]},{"id":11490584,"frames":[{"imageOffset":13574,"symbol":"__psynch_cvwait","symbolLocation":10,"imageIndex":0},{"imageOffset":27273,"symbol":"_pthread_cond_wait","symbolLocation":1224,"imageIndex":1},{"imageOffset":3347615,"symbol":"blas_thread_server","symbolLocation":207,"imageIndex":22},{"imageOffset":25876,"symbol":"_pthread_start","symbolLocation":125,"imageIndex":1},{"imageOffset":8239,"symbol":"thread_start","symbolLocation":15,"imageIndex":1}]},{"id":11495446,"name":"ThreadPoolForegroundWorker","frames":[{"imageOffset":2746,"symbol":"mach_msg_trap","symbolLocation":10,"imageIndex":0},{"imageOffset":3627,"symbol":"mach_msg","symbolLocation":59,"imageIndex":0},{"imageOffset":66259398,"imageIndex":20},{"imageOffset":66014559,"imageIndex":20},{"imageOffset":66017292,"imageIndex":20},{"imageOffset":66016269,"imageIndex":20},{"imageOffset":66229416,"imageIndex":20},{"imageOffset":25876,"symbol":"_pthread_start","symbolLocation":125,"imageIndex":1},{"imageOffset":8239,"symbol":"thread_start","symbolLocation":15,"imageIndex":1}]},{"id":11553910,"frames":[{"imageOffset":8204,"symbol":"start_wqthread","symbolLocation":0,"imageIndex":1}]},{"id":11553912,"frames":[{"imageOffset":8204,"symbol":"start_wqthread","symbolLocation":0,"imageIndex":1}]},{"id":11554190,"frames":[{"imageOffset":13574,"symbol":"__psynch_cvwait","symbolLocation":10,"imageIndex":0},{"imageOffset":27273,"symbol":"_pthread_cond_wait","symbolLocation":1224,"imageIndex":1},{"imageOffset":1501084,"symbol":"PyThread_acquire_lock_timed","symbolLocation":700,"imageIndex":7},{"imageOffset":1824415,"symbol":"acquire_timed","symbolLocation":111,"imageIndex":7},{"imageOffset":1824688,"symbol":"lock_PyThread_acquire_lock","symbolLocation":48,"imageIndex":7},{"imageOffset":295246,"symbol":"method_vectorcall_VARARGS_KEYWORDS","symbolLocation":350,"imageIndex":7},{"imageOffset":1146380,"symbol":"call_function","symbolLocation":732,"imageIndex":7},{"imageOffset":1135230,"symbol":"_PyEval_EvalFrameDefault","symbolLocation":25518,"imageIndex":7},{"imageOffset":1149699,"symbol":"_PyEval_EvalCode","symbolLocation":2611,"imageIndex":7},{"imageOffset":261297,"symbol":"_PyFunction_Vectorcall","symbolLocation":289,"imageIndex":7},{"imageOffset":1146380,"symbol":"call_function","symbolLocation":732,"imageIndex":7},{"imageOffset":1135230,"symbol":"_PyEval_EvalFrameDefault","symbolLocation":25518,"imageIndex":7},{"imageOffset":1149699,"symbol":"_PyEval_EvalCode","symbolLocation":2611,"imageIndex":7},{"imageOffset":261297,"symbol":"_PyFunction_Vectorcall","symbolLocation":289,"imageIndex":7},{"imageOffset":1146380,"symbol":"call_function","symbolLocation":732,"imageIndex":7},{"imageOffset":1135230,"symbol":"_PyEval_EvalFrameDefault","symbolLocation":25518,"imageIndex":7},{"imageOffset":261416,"symbol":"function_code_fastcall","symbolLocation":104,"imageIndex":7},{"imageOffset":1146380,"symbol":"call_function","symbolLocation":732,"imageIndex":7},{"imageOffset":1135230,"symbol":"_PyEval_EvalFrameDefault","symbolLocation":25518,"imageIndex":7},{"imageOffset":261416,"symbol":"function_code_fastcall","symbolLocation":104,"imageIndex":7},{"imageOffset":1146380,"symbol":"call_function","symbolLocation":732,"imageIndex":7},{"imageOffset":1135230,"symbol":"_PyEval_EvalFrameDefault","symbolLocation":25518,"imageIndex":7},{"imageOffset":261416,"symbol":"function_code_fastcall","symbolLocation":104,"imageIndex":7},{"imageOffset":269746,"symbol":"method_vectorcall","symbolLocation":274,"imageIndex":7},{"imageOffset":1822790,"symbol":"t_bootstrap","symbolLocation":70,"imageIndex":7},{"imageOffset":1499897,"symbol":"pythread_wrapper","symbolLocation":25,"imageIndex":7},{"imageOffset":25876,"symbol":"_pthread_start","symbolLocation":125,"imageIndex":1},{"imageOffset":8239,"symbol":"thread_start","symbolLocation":15,"imageIndex":1}]}],
"usedImages" : [
{
"source" : "P",
"arch" : "x86_64",
"base" : 140703159812096,
"size" : 225280,
"uuid" : "12bd6f13-c452-35ee-9069-51befef29f1a",
"path" : "\/usr\/lib\/system\/libsystem_kernel.dylib",
"name" : "libsystem_kernel.dylib"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 140703160037376,
"size" : 49152,
"uuid" : "29a2750e-f31b-3630-8761-242a6bc3e99e",
"path" : "\/usr\/lib\/system\/libsystem_pthread.dylib",
"name" : "libsystem_pthread.dylib"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 140703158796288,
"size" : 561152,
"uuid" : "991f58b7-b4c0-3c3a-84a8-c9c571de5a27",
"path" : "\/usr\/lib\/system\/libsystem_c.dylib",
"name" : "libsystem_c.dylib"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 140703160135680,
"size" : 40960,
"uuid" : "e443252e-7302-3580-b8c8-9dacd0be818d",
"path" : "\/usr\/lib\/system\/libsystem_platform.dylib",
"name" : "libsystem_platform.dylib"
},
{
"size" : 0,
"source" : "A",
"base" : 0,
"uuid" : "00000000-0000-0000-0000-000000000000"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4913164288,
"size" : 1249280,
"uuid" : "6f61e4c7-0cb1-3ddd-bb43-974036ffd107",
"path" : "\/Users\/USER\/Desktop\/ChimeraX_Daily.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/chimerax\/atomic_lib\/lib\/libatomstruct.dylib",
"name" : "libatomstruct.dylib"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4983296000,
"size" : 36864,
"uuid" : "177f3b07-c786-3f8a-bef6-22bc20b6b3d0",
"path" : "\/Users\/USER\/Desktop\/ChimeraX_Daily.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/chimerax\/atom_search\/ast.cpython-39-darwin.so",
"name" : "ast.cpython-39-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4430159872,
"CFBundleShortVersionString" : "3.9.11, (c) 2001-2021 Python Software Foundation.",
"CFBundleIdentifier" : "org.python.python",
"size" : 2527232,
"uuid" : "ef9cc1f4-5991-3213-9a9e-e68c578b6c1b",
"path" : "\/Users\/USER\/Desktop\/ChimeraX_Daily.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/Python",
"name" : "Python",
"CFBundleVersion" : "3.9.11"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4493275136,
"size" : 1589248,
"uuid" : "e1eca899-9707-3319-ac6c-d8028378fb9a",
"path" : "\/Users\/USER\/Desktop\/ChimeraX_Daily.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/PyQt6\/QtCore.abi3.so",
"name" : "QtCore.abi3.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4496982016,
"size" : 5226496,
"uuid" : "97d356c9-7652-3ff7-be10-198e30670243",
"path" : "\/Users\/USER\/Desktop\/ChimeraX_Daily.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/PyQt6\/Qt6\/lib\/QtCore.framework\/Versions\/A\/QtCore",
"name" : "QtCore"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4509364224,
"size" : 4997120,
"uuid" : "4969d1ff-28d9-3632-9358-784c5dec38c8",
"path" : "\/Users\/USER\/Desktop\/ChimeraX_Daily.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/PyQt6\/Qt6\/lib\/QtWidgets.framework\/Versions\/A\/QtWidgets",
"name" : "QtWidgets"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4485783552,
"size" : 2818048,
"uuid" : "0a164d84-8b44-3f10-9065-1d0486c25a4b",
"path" : "\/Users\/USER\/Desktop\/ChimeraX_Daily.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/PyQt6\/QtWidgets.abi3.so",
"name" : "QtWidgets.abi3.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4445601792,
"size" : 98304,
"uuid" : "34b1db54-21e7-38de-825b-bf145e2aae42",
"path" : "\/Users\/USER\/Desktop\/ChimeraX_Daily.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/PyQt6\/sip.cpython-39-darwin.so",
"name" : "sip.cpython-39-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4857380864,
"size" : 6815744,
"uuid" : "1d3e67c7-22f9-33ac-a03a-446da81fdc43",
"path" : "\/Users\/USER\/Desktop\/ChimeraX_Daily.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/PyQt6\/Qt6\/lib\/QtGui.framework\/Versions\/A\/QtGui",
"name" : "QtGui"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4517048320,
"size" : 655360,
"uuid" : "009cdea9-f1bc-35e0-bf0e-099d3df37399",
"path" : "\/Users\/USER\/Desktop\/ChimeraX_Daily.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/PyQt6\/Qt6\/plugins\/platforms\/libqcocoa.dylib",
"name" : "libqcocoa.dylib"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 140703204831232,
"CFBundleShortVersionString" : "6.9",
"CFBundleIdentifier" : "com.apple.AppKit",
"size" : 15257600,
"uuid" : "dd0028a3-78e3-3a8a-a51b-ddd68123adef",
"path" : "\/System\/Library\/Frameworks\/AppKit.framework\/Versions\/C\/AppKit",
"name" : "AppKit",
"CFBundleVersion" : "2113"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 140703307599872,
"CFBundleShortVersionString" : "2.1.1",
"CFBundleIdentifier" : "com.apple.HIToolbox",
"size" : 3112960,
"uuid" : "4163a93f-bf71-3219-80ed-6f65e9266b81",
"path" : "\/System\/Library\/Frameworks\/Carbon.framework\/Versions\/A\/Frameworks\/HIToolbox.framework\/Versions\/A\/HIToolbox",
"name" : "HIToolbox"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4425338880,
"CFBundleShortVersionString" : "1.5.0",
"CFBundleIdentifier" : "edu.ucsf.cgl.ChimeraX",
"size" : 4096,
"uuid" : "9596eff5-d2be-396c-9c4e-6177235c3dae",
"path" : "\/Users\/USER\/Desktop\/ChimeraX_Daily.app\/Contents\/MacOS\/ChimeraX",
"name" : "ChimeraX",
"CFBundleVersion" : "1.5.0.0"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4451508224,
"size" : 442368,
"uuid" : "1a6ae033-9438-33c0-8077-988fd885250a",
"path" : "\/usr\/lib\/dyld",
"name" : "dyld"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 140712146579456,
"CFBundleShortVersionString" : "19.1.1",
"CFBundleIdentifier" : "com.apple.opengl",
"size" : 65536,
"uuid" : "478396c4-b9a8-3a73-9475-32b5cdfffeaa",
"path" : "\/System\/Library\/Frameworks\/OpenGL.framework\/Versions\/A\/OpenGL",
"name" : "OpenGL",
"CFBundleVersion" : "19.1.1"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5040402432,
"size" : 165068800,
"uuid" : "c9795830-14cd-3b40-983d-a3143cd9cbd9",
"path" : "\/Users\/USER\/Desktop\/ChimeraX_Daily.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/PyQt6\/Qt6\/lib\/QtWebEngineCore.framework\/Versions\/A\/QtWebEngineCore",
"name" : "QtWebEngineCore"
},
{
"source" : "P",
"arch" : "x86_64h",
"base" : 140703160352768,
"CFBundleShortVersionString" : "6.9",
"CFBundleIdentifier" : "com.apple.CoreFoundation",
"size" : 5255168,
"uuid" : "3002b545-6841-3fc8-91a2-bcfbe5872465",
"path" : "\/System\/Library\/Frameworks\/CoreFoundation.framework\/Versions\/A\/CoreFoundation",
"name" : "CoreFoundation",
"CFBundleVersion" : "1855.105"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4518522880,
"size" : 63488000,
"uuid" : "10431d8f-5e3b-3bbc-abd5-81f6a73a5269",
"path" : "\/Users\/USER\/Desktop\/ChimeraX_Daily.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/numpy\/.dylibs\/libopenblas64_.0.dylib",
"name" : "libopenblas64_.0.dylib"
}
],
"sharedCache" : {
"base" : 140703156809728,
"size" : 15213641728,
"uuid" : "3d05845f-3f65-358f-9ebf-2236e772ac01"
},
"vmSummary" : "ReadOnly portion of Libraries: Total=1.5G resident=0K(0%) swapped_out_or_unallocated=1.5G(100%)\nWritable regions: Total=2.4G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=2.4G(100%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 640K 5 \nActivity Tracing 256K 1 \nCG backing stores 3840K 4 \nCG image 1708K 69 \nColorSync 244K 29 \nCoreAnimation 7288K 102 \nCoreGraphics 12K 2 \nCoreUI image data 5240K 38 \nFoundation 36K 2 \nKernel Alloc Once 12K 2 \nMALLOC 1.5G 6548 \nMALLOC guard page 32K 8 \nMALLOC_LARGE (reserved) 384K 1 reserved VM address space (unallocated)\nMALLOC_NANO (reserved) 128.0M 1 reserved VM address space (unallocated)\nMach message 32K 6 \nOpenGL GLSL 384K 4 \nSTACK GUARD 116K 29 \nStack 165.7M 30 \nStack Guard 56.0M 1 \nVM_ALLOCATE 262.1M 354 \nVM_ALLOCATE (reserved) 320.0M 4 reserved VM address space (unallocated)\n__DATA 58.1M 736 \n__DATA_CONST 30.3M 350 \n__DATA_DIRTY 1639K 219 \n__FONT_DATA 4K 1 \n__GLSLBUILTINS 5176K 1 \n__LINKEDIT 675.4M 206 \n__OBJC_RO 81.5M 1 \n__OBJC_RW 3120K 2 \n__TEXT 856.3M 733 \n__UNICODE 588K 1 \ndyld private memory 1280K 3 \nmapped file 556.6M 78 \nshared memory 2976K 25 \n=========== ======= ======= \nTOTAL 4.7G 9596 \nTOTAL, minus reserved VM space 4.2G 9596 \n",
"legacyInfo" : {
"threadTriggered" : {
"name" : "CrBrowserMain",
"queue" : "com.apple.main-thread"
}
},
"trialInfo" : {
"rollouts" : [
{
"rolloutId" : "5fb4245a1bbfe8005e33a1e1",
"factorPackIds" : {
},
"deploymentId" : 240000015
},
{
"rolloutId" : "601d9415f79519000ccd4b69",
"factorPackIds" : {
"SIRI_TEXT_TO_SPEECH" : "61ef3bd729647d394933a0a6"
},
"deploymentId" : 240000416
},
{
"rolloutId" : "602ad4dac86151000cf27e46",
"factorPackIds" : {
"SIRI_DICTATION_ASSETS" : "614a34c5eae97a2111628dc5"
},
"deploymentId" : 240000305
},
{
"rolloutId" : "60da5e84ab0ca017dace9abf",
"factorPackIds" : {
},
"deploymentId" : 240000008
},
{
"rolloutId" : "607844aa04477260f58a8077",
"factorPackIds" : {
"SIRI_MORPHUN_ASSETS" : "6103050cbfe6dc472e1c982a"
},
"deploymentId" : 240000066
},
{
"rolloutId" : "5ffde50ce2aacd000d47a95f",
"factorPackIds" : {
},
"deploymentId" : 240000167
},
{
"rolloutId" : "60186475825c62000ccf5450",
"factorPackIds" : {
},
"deploymentId" : 240000022
},
{
"rolloutId" : "5fc94383418129005b4e9ae0",
"factorPackIds" : {
},
"deploymentId" : 240000401
}
],
"experiments" : [
]
}
}
===== Log before crash start =====
UCSF ChimeraX version: 1.5.dev202206100131 (2022-06-10)
© 2016-2022 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/amandaghilardi/Desktop/sdf/py145.sdf format sdf
> close session
> open /Users/amandaghilardi/Desktop/Docking/AHR/py108/py108_test1.pdbqt
Summary of feedback from opening
/Users/amandaghilardi/Desktop/Docking/AHR/py108/py108_test1.pdbqt
---
warnings | Ignored bad PDB record found on line 2
REMARK VINA RESULT: -10.445 0.000 0.000
Ignored bad PDB record found on line 3
REMARK INTER + INTRA: -11.764
Ignored bad PDB record found on line 4
REMARK INTER: -11.390
Ignored bad PDB record found on line 5
REMARK INTRA: -0.375
Ignored bad PDB record found on line 6
REMARK UNBOUND: -0.098
139 messages similar to the above omitted
Opened py108_test1.pdbqt containing 9 structures (180 atoms, 198 bonds)
> open /Users/amandaghilardi/Desktop/Docking/AHR/py108/hAhR_49.pdbqt
Chain information for hAhR_49.pdb #2
---
Chain | Description
? | No description available
Opened hAhR_49.pdbqt containing 1 structures (1146 atoms, 1165 bonds)
> hide #1.9 models
> hide #1.8 models
> hide #1.7 models
> hide #1.6 models
> hide #1.5 models
> hide #1.4 models
> hide #1.3 models
> hide #1.2 models
> select ::name="UNL"
180 atoms, 198 bonds, 9 residues, 9 models selected
Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps,
got 2 atomic models, 0 maps.
> select clear
Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps,
got 2 atomic models, 0 maps.
> ui tool show ViewDockX
> open https://www.rbvi.ucsf.edu/chimerax/tutorials.html
Opened https://www.rbvi.ucsf.edu/chimerax/tutorials.html
> ZOOM
Unknown command: ZOOM
> zoom
Pixel size at center of rotation is 0.0695
> zoom
Pixel size at center of rotation is 0.0695
> zoom
Pixel size at center of rotation is 0.0695
> color bfactor #2#1.1
1166 atoms, 114 residues, atom bfactor range 0 to 0
> color bfactor #2#1.1
1166 atoms, 114 residues, atom bfactor range 0 to 0
> select
> ::name="ALA"::name="ARG"::name="ASN"::name="ASP"::name="CYS"::name="GLN"::name="GLU"::name="GLY"::name="HIS"::name="ILE"::name="LEU"::name="LYS"::name="MET"::name="PHE"::name="PRO"::name="SER"::name="THR"::name="TRP"::name="TYR"::name="VAL"
1146 atoms, 1165 bonds, 113 residues, 1 model selected
> color bfactor sel
1146 atoms, 113 residues, atom bfactor range 0 to 0
> color bfactor sel
1146 atoms, 113 residues, atom bfactor range 0 to 0
> mlp sel
Map values for surface "hAhR_49.pdb_ SES surface": minimum -25.13, mean
-2.884, maximum 26.25
To also show corresponding color key, enter the above mlp command and add key
true
> mlp sel
Map values for surface "hAhR_49.pdb_ SES surface": minimum -25.13, mean
-2.884, maximum 26.25
To also show corresponding color key, enter the above mlp command and add key
true
> select clear
> mlp #1.1#!2
Map values for surface "hAhR_49.pdb_ SES surface": minimum -25.13, mean
-2.884, maximum 26.25
To also show corresponding color key, enter the above mlp command and add key
true
> mlp #1.1#!2
Map values for surface "hAhR_49.pdb_ SES surface": minimum -25.13, mean
-2.884, maximum 26.25
To also show corresponding color key, enter the above mlp command and add key
true
> select
> ::name="ALA"::name="ARG"::name="ASN"::name="ASP"::name="CYS"::name="GLN"::name="GLU"::name="GLY"::name="HIS"::name="ILE"::name="LEU"::name="LYS"::name="MET"::name="PHE"::name="PRO"::name="SER"::name="THR"::name="TRP"::name="TYR"::name="VAL"
1146 atoms, 1165 bonds, 113 residues, 1 model selected
> mlp sel
Map values for surface "hAhR_49.pdb_ SES surface": minimum -25.13, mean
-2.884, maximum 26.25
To also show corresponding color key, enter the above mlp command and add key
true
> rainbow sel
> color sel bypolymer
> color sel byhetero
> nucleotides sel atoms
> style nucleic & sel stick
Changed 0 atom styles
> style sel stick
Changed 1146 atom styles
> style sel sphere
Changed 1146 atom styles
> hide sel surfaces
> show sel cartoons
> show sel atoms
> hide sel atoms
> close session
> open /Users/amandaghilardi/Desktop/Docking/AHR/py108/complex.pdb
Chain information for complex.pdb #1
---
Chain | Description
? | No description available
> color bfactor
1166 atoms, 114 residues, atom bfactor range 0 to 0
> close session
> open /Users/amandaghilardi/Desktop/Docking/AHR/py108/hAhR_49.pdb
Chain information for hAhR_49.pdb #1
---
Chain | Description
? | No description available
> close session
> open
> /Users/amandaghilardi/Desktop/Docking/Practice/practice-2_basic/1iep.pdb
1iep.pdb title:
Crystal structure of the C-abl kinase domain In complex with sti-571. [more
info...]
Chain information for 1iep.pdb #1
---
Chain | Description | UniProt
A B | proto-oncogene tyrosine-protein kinase abl | ABL1_MOUSE
Non-standard residues in 1iep.pdb #1
---
CL — chloride ion
STI — 4-(4-methyl-piperazin-1-ylmethyl)-N-[4-methyl-3-(4-pyridin-3-yl-
pyrimidin-2-ylamino)-phenyl]-benzamide (sti-571;imatinib)
> color bfactor
4710 atoms, 728 residues, atom bfactor range 23.6 to 114
> select ::name="STI"
74 atoms, 82 bonds, 2 residues, 1 model selected
> mlp sel
mlp: no amino acids specified
> mlp sel
mlp: no amino acids specified
> mlp sel
mlp: no amino acids specified
> style sel sphere
Changed 74 atom styles
> select /B:225-498
2229 atoms, 2288 bonds, 274 residues, 1 model selected
> select /B:225-498
2229 atoms, 2288 bonds, 274 residues, 1 model selected
> select clear
> color bfactor
4710 atoms, 728 residues, atom bfactor range 23.6 to 114
> ui tool show "Side View"
> coulombic
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for 1iep.pdb_A SES surface #1.1: minimum, -17.03, mean -2.62,
maximum 9.00
Coulombic values for 1iep.pdb_B SES surface #1.2: minimum, -16.91, mean -2.57,
maximum 11.58
To also show corresponding color key, enter the above coulombic command and
add key true
> undo
> coulombic
Coulombic values for 1iep.pdb_A SES surface #1.1: minimum, -17.03, mean -2.62,
maximum 9.00
Coulombic values for 1iep.pdb_B SES surface #1.2: minimum, -16.91, mean -2.57,
maximum 11.58
To also show corresponding color key, enter the above coulombic command and
add key true
> coulombic
Coulombic values for 1iep.pdb_A SES surface #1.1: minimum, -17.03, mean -2.62,
maximum 9.00
Coulombic values for 1iep.pdb_B SES surface #1.2: minimum, -16.91, mean -2.57,
maximum 11.58
To also show corresponding color key, enter the above coulombic command and
add key true
> coulombic
Coulombic values for 1iep.pdb_A SES surface #1.1: minimum, -17.03, mean -2.62,
maximum 9.00
Coulombic values for 1iep.pdb_B SES surface #1.2: minimum, -16.91, mean -2.57,
maximum 11.58
To also show corresponding color key, enter the above coulombic command and
add key true
> coulombic
Coulombic values for 1iep.pdb_A SES surface #1.1: minimum, -17.03, mean -2.62,
maximum 9.00
Coulombic values for 1iep.pdb_B SES surface #1.2: minimum, -16.91, mean -2.57,
maximum 11.58
To also show corresponding color key, enter the above coulombic command and
add key true
> coulombic
Coulombic values for 1iep.pdb_A SES surface #1.1: minimum, -17.03, mean -2.62,
maximum 9.00
Coulombic values for 1iep.pdb_B SES surface #1.2: minimum, -16.91, mean -2.57,
maximum 11.58
To also show corresponding color key, enter the above coulombic command and
add key true
> close session
> open
> /Users/amandaghilardi/Desktop/Docking/Practice/practice-2_basic/1iep.pdb
1iep.pdb title:
Crystal structure of the C-abl kinase domain In complex with sti-571. [more
info...]
Chain information for 1iep.pdb #1
---
Chain | Description | UniProt
A B | proto-oncogene tyrosine-protein kinase abl | ABL1_MOUSE
Non-standard residues in 1iep.pdb #1
---
CL — chloride ion
STI — 4-(4-methyl-piperazin-1-ylmethyl)-N-[4-methyl-3-(4-pyridin-3-yl-
pyrimidin-2-ylamino)-phenyl]-benzamide (sti-571;imatinib)
> select :CL
6 atoms, 6 residues, 1 model selected
> delete
Missing or invalid "atoms" argument: empty atom specifier
> delete CL
Missing or invalid "atoms" argument: invalid atoms specifier
> delete 'CL'
Missing or invalid "atoms" argument: invalid atoms specifier
> delete "CL"
Missing or invalid "atoms" argument: invalid atoms specifier
> select :CL
6 atoms, 6 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> color bfactor
4704 atoms, 722 residues, atom bfactor range 23.6 to 114
> open 1iep fromDatabase Database eds
Invalid "fromDatabase" argument: Should be one of 'alphafold', 'ccd',
'cellpack', 'eds', 'edsdiff', 'emdb', 'emdb_china', 'emdb_europe',
'emdb_japan', 'emdb_us', 'ftp', 'help', 'http', 'https', 'pdb', 'pdbdev',
'pdbe', 'pdbe_bio', 'pdbj', 'pubchem', 'rcsb_bio', 'smiles', or 'uniprot'
> ui tool show "Side View"
> ui tool show "Volume Viewer"
> modelcol white
Unknown command: modelcol white
> open 1iep fromDatabse eds
'fromDatabse' has no suffix
> open 1iep fromDatabase eds
Summary of feedback from opening 1iep fetched from eds
---
note | Fetching map 1iep from
http://www.ebi.ac.uk/pdbe/coordinates/files/1iep.ccp4
Opened eds 1iep as #2, grid size 93,142,147, pixel 0.706,0.709,0.697, shown at
level 0.514, step 1, values float32
> volume #2 level 0.4502
> volume #2 level 0.3734
> volume #2 color #2700d7
> undo
> volume #2 color #d77692
> color bfactor
4704 atoms, 722 residues, atom bfactor range 23.6 to 114
> preset "initial styles" "original look"
Using preset: Initial Styles / Original Look
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> volume #2 level 0.5849
> hide #!2 models
> delete /A
> combine #1
> rename #ligand
Missing or invalid "models" argument: invalid models specifier
> rename #1 ligand
> hide #3 models
> select
> ::name="ALA"::name="ARG"::name="ASN"::name="ASP"::name="CYS"::name="GLN"::name="GLU"::name="GLY"::name="HIS"::name="ILE"::name="LEU"::name="LYS"::name="MET"::name="PHE"::name="PRO"::name="SER"::name="THR"::name="TRP"::name="TYR"::name="VAL"
4458 atoms, 4576 bonds, 548 residues, 2 models selected
> delete atoms (#1 & sel)
> delete bonds (#1 & sel)
> select ::name="HOH"
146 atoms, 146 residues, 2 models selected
> delete atoms (#1 & sel)
> delete bonds (#1 & sel)
> show #3 models
> hide #1 models
> select
> ::name="ALA"::name="ARG"::name="ASN"::name="ASP"::name="CYS"::name="GLN"::name="GLU"::name="GLY"::name="HIS"::name="ILE"::name="LEU"::name="LYS"::name="MET"::name="PHE"::name="PRO"::name="SER"::name="THR"::name="TRP"::name="TYR"::name="VAL"
2229 atoms, 2288 bonds, 274 residues, 1 model selected
> select ~sel
147 atoms, 82 bonds, 75 residues, 4 models selected
> delete atoms (#3 & sel)
> delete bonds (#3 & sel)
> show #1 models
> select ::name="STI"
37 atoms, 41 bonds, 1 residue, 1 model selected
> color sel magenta
> color sel byhetero
> select clear
> select ligand
37 atoms, 41 bonds, 1 residue, 1 model selected
> select zone
Missing or invalid "near" argument: empty atom specifier
> select Zone...
Expected an objects specifier or a keyword
> select sel @ show sel atoms
> hbonds sel reveal true
16 hydrogen bonds found
> select clear
> hbonds reveal true
251 hydrogen bonds found
> hide #4 models
> ui tool show H-Bonds
> hbonds intraModel false intraMol false intraRes false select true reveal
> true
5 hydrogen bonds found
> show #4 models
> select clear
> select ligand
37 atoms, 41 bonds, 1 residue, 1 model selected
> select invert
Expected an objects specifier or a keyword
> invert
Unknown command: invert
> select ~sel
2229 atoms, 2288 bonds, 274 residues, 3 models selected
> show sel surfaces
> select clear
> mlp
Map values for surface "copy of 1iep.pdb_B SES surface": minimum -26.69, mean
-3.94, maximum 23.19
To also show corresponding color key, enter the above mlp command and add key
true
> select ::name="STI"
37 atoms, 41 bonds, 1 residue, 1 model selected
> mlp sel
mlp: no amino acids specified
> ui tool show "Surface Color"
> transparency sel 50
> select
> ::name="ALA"::name="ARG"::name="ASN"::name="ASP"::name="CYS"::name="GLN"::name="GLU"::name="GLY"::name="HIS"::name="ILE"::name="LEU"::name="LYS"::name="MET"::name="PHE"::name="PRO"::name="SER"::name="THR"::name="TRP"::name="TYR"::name="VAL"
2229 atoms, 2288 bonds, 274 residues, 1 model selected
> transparency (#!3 & sel) 60
> select clear
Alignment identifier is 3/B
> select
> #3/B:238-240,249-252,263-265,279-291,322-330,336-357,365-367,373-375,383-387,402-414,417-434,444-454,465-476,479-483,485-496
1099 atoms, 1109 bonds, 136 residues, 1 model selected
> select clear
> select #3/B:302-303
12 atoms, 11 bonds, 2 residues, 1 model selected
> select #3/B:302-303
12 atoms, 11 bonds, 2 residues, 1 model selected
> select clear
> select ::name="STI"
37 atoms, 41 bonds, 1 residue, 1 model selected
> style sel ball
Changed 37 atom styles
> style sel sphere
Changed 37 atom styles
> style sel ball
Changed 37 atom styles
> show sel surfaces
> hide sel surfaces
Color zone shortcut requires 1 displayed atomic model and 1 map, got 2 atomic
models, 0 maps.
Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps,
got 2 atomic models, 0 maps.
> volume show
> volume hide
> ui mousemode right "mark surface"
> ui mousemode right "mark point"
> ui mousemode right "link markers"
> ui mousemode right distance
> show sel surfaces
> interfaces select & ~solvent
Missing or invalid "atoms" argument: invalid atoms specifier
> view sel
> side view
Unknown command: side view
> sideview
Unknown command: sideview
> ui tool show "Side View"
> distance #3/B:326@CA #3/B:260@CB
Distance between copy of 1iep.pdb #3/B TYR 326 CA and VAL 260 CB: 23.969Å
> distance #3/B:317@CE2 #3/B:258@OE1
Distance between copy of 1iep.pdb #3/B PHE 317 CE2 and GLU 258 OE1: 6.675Å
> distance #3/B:258@CG #3/B:312@OH
Distance between copy of 1iep.pdb #3/B GLU 258 CG and TYR 312 OH: 12.629Å
> distance #3/B:250@CA #3/B:266@CD2
Distance between copy of 1iep.pdb #3/B GLY 250 CA and LEU 266 CD2: 19.784Å
> distance #3/B:317@CZ #3/B:258@CD
Distance between copy of 1iep.pdb #3/B PHE 317 CZ and GLU 258 CD: 4.712Å
> slect ligand
Unknown command: slect ligand
> hide sel surfaces
> hide #!5 models
> hide #4 models
> hide #!3 models
> ui mousemode right "translate selected models"
> view matrix models #1,1,0,0,-3.1412,0,1,0,0.85101,0,0,1,0.10614
> view matrix models #1,1,0,0,-5.6603,0,1,0,1.7873,0,0,1,-0.10158
> view matrix models #1,1,0,0,-8.7063,0,1,0,1.4387,0,0,1,-1.8774
> view matrix models #1,1,0,0,-6.0654,0,1,0,-0.87088,0,0,1,-3.027
> view matrix models #1,1,0,0,-6.1034,0,1,0,-1.4409,0,0,1,-3.9743
> show #!3 models
> slect ligand
Unknown command: slect ligand
> slect clear
Unknown command: slect clear
> mlp sel
mlp: no amino acids specified
> hide sel surfaces
> select ligand
37 atoms, 41 bonds, 1 residue, 1 model selected
> select ~sel
2229 atoms, 2288 bonds, 5 pseudobonds, 274 residues, 7 models selected
> mlp sel
Map values for surface "copy of 1iep.pdb_B SES surface": minimum -26.69, mean
-3.94, maximum 23.19
To also show corresponding color key, enter the above mlp command and add key
true
> hide sel surfaces
> view matrix models
> #2,1,0,0,0.16969,0,1,0,2.5458,0,0,1,4.112,#3,1,0,0,0.16969,0,1,0,2.5458,0,0,1,4.112,#1.1.1,1,0,0,0.16969,0,1,0,2.5458,0,0,1,4.112,#5,1,0,0,0,0,1,0,0,0,0,1,0
> undo
> select clear
> preset "initial styles" "original look"
Using preset: Initial Styles / Original Look
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> close session
> open
> /Users/amandaghilardi/Desktop/Docking/Practice/practice-2_basic/1iep.pdb
> format pdb
1iep.pdb title:
Crystal structure of the C-abl kinase domain In complex with sti-571. [more
info...]
Chain information for 1iep.pdb #1
---
Chain | Description | UniProt
A B | proto-oncogene tyrosine-protein kinase abl | ABL1_MOUSE
Non-standard residues in 1iep.pdb #1
---
CL — chloride ion
STI — 4-(4-methyl-piperazin-1-ylmethyl)-N-[4-methyl-3-(4-pyridin-3-yl-
pyrimidin-2-ylamino)-phenyl]-benzamide (sti-571;imatinib)
> select ::name="CL"
6 atoms, 6 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select ::name="HOH"
172 atoms, 172 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> delecte /B
Unknown command: delecte /B
> delete /B
> combina #1
Unknown command: combina #1
> combine #1
> rename #2 ligand
> hide #2 models
> select ::name="STI"
74 atoms, 82 bonds, 2 residues, 2 models selected
> delete atoms (#1 & sel)
> delete bonds (#1 & sel)
> show #2 models
> hide #1 models
> select
> ::name="ALA"::name="ARG"::name="ASN"::name="ASP"::name="CYS"::name="GLN"::name="GLU"::name="GLY"::name="HIS"::name="ILE"::name="LEU"::name="LYS"::name="MET"::name="PHE"::name="PRO"::name="SER"::name="THR"::name="TRP"::name="TYR"::name="VAL"
4458 atoms, 4576 bonds, 548 residues, 2 models selected
> delete atoms (#2 & sel)
> delete bonds (#2 & sel)
> show #1 models
> select clear
> select ligand
Nothing selected
> style ball
Changed 2266 atom styles
> color light sea green
> undo
> select ligand
Nothing selected
> color cyan
> select clear
> select ::name="STI"
37 atoms, 41 bonds, 1 residue, 1 model selected
> color sel light sea green
> color sel byhetero
> select clear
> select ::name="STI"
37 atoms, 41 bonds, 1 residue, 1 model selected
> select sel @ show sel atoms
> style sel stick
Changed 149 atom styles
> color sel byhetero
> select clear
> ui tool show H-Bonds
> hbonds intraModel false intraMol false intraRes false select true reveal
> true
5 hydrogen bonds found
> hbonds intraModel false intraMol false intraRes false select true reveal
> true
5 hydrogen bonds found
> view matrix models
> #1,1,0,0,-3.6848,0,1,0,0.023014,0,0,1,1.3471,#2,1,0,0,-3.6848,0,1,0,0.023014,0,0,1,1.3471
> view matrix models
> #1,1,0,0,-4.5413,0,1,0,-0.011304,0,0,1,1.7374,#2,1,0,0,-4.5413,0,1,0,-0.011304,0,0,1,1.7374
> close session
> open /Users/amandaghilardi/Desktop/Docking/AHR/py108/py108_test1.pdbqt
Summary of feedback from opening
/Users/amandaghilardi/Desktop/Docking/AHR/py108/py108_test1.pdbqt
---
warnings | Ignored bad PDB record found on line 2
REMARK VINA RESULT: -10.445 0.000 0.000
Ignored bad PDB record found on line 3
REMARK INTER + INTRA: -11.764
Ignored bad PDB record found on line 4
REMARK INTER: -11.390
Ignored bad PDB record found on line 5
REMARK INTRA: -0.375
Ignored bad PDB record found on line 6
REMARK UNBOUND: -0.098
139 messages similar to the above omitted
Opened py108_test1.pdbqt containing 9 structures (180 atoms, 198 bonds)
> open /Users/amandaghilardi/Desktop/Docking/AHR/py108/hAhR_49.pdbqt
Chain information for hAhR_49.pdb #2
---
Chain | Description
? | No description available
Opened hAhR_49.pdbqt containing 1 structures (1146 atoms, 1165 bonds)
> hide #1.9 models
> hide #1.8 models
> hide #1.7 models
> hide #1.6 models
> hide #1.5 models
> hide #1.4 models
> hide #1.3 models
> hide #1.2 models
> hide #2 models
> show #2 models
> ui tool show ViewDockX
> select down
Nothing selected
> select down
Nothing selected
> select down
Nothing selected
> select down
Nothing selected
> select down
Nothing selected
> select down
Nothing selected
> select down
Nothing selected
> select down
Nothing selected
> hide #1.1 models
> show #1.1 models
> hide #1.1 models
> show #1.2 models
> hide #1.2 models
> show #1.1 models
> hide #1.1 models
> show #1.2 models
> hide #1.2 models
> show #1.3 models
> hide #1.3 models
> show #1.4 models
> hide #1.4 models
> show #1.5 models
> hide #1.5 models
> show #1.6 models
> hide #1.6 models
> show #1.7 models
> hide #1.7 models
> show #1.8 models
> hide #1.8 models
> show #1.9 models
> hide #1.9 models
> show #1.8 models
> hide #1.8 models
> show #1.7 models
> hide #1.7 models
> show #1.6 models
> hide #1.6 models
> show #1.5 models
> hide #1.5 models
> show #1.4 models
> hide #1.4 models
> show #1.3 models
> hide #1.3 models
> show #1.2 models
> hide #1.2 models
> show #1.1 models
> Add H
Unknown command: Add H
> hide #2 models
> select ::name="UNL"
180 atoms, 198 bonds, 9 residues, 9 models selected
> addh
Summary of feedback from adding hydrogens to multiple structures
---
notes | Chain-initial residues that are actual N termini:
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini:
Chain-final residues that are not actual C termini:
0 hydrogen bonds
Chain-initial residues that are actual N termini:
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini:
Chain-final residues that are not actual C termini:
0 hydrogen bonds
Chain-initial residues that are actual N termini:
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini:
Chain-final residues that are not actual C termini:
0 hydrogen bonds
Chain-initial residues that are actual N termini:
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini:
Chain-final residues that are not actual C termini:
0 hydrogen bonds
Chain-initial residues that are actual N termini:
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini:
Chain-final residues that are not actual C termini:
0 hydrogen bonds
Chain-initial residues that are actual N termini:
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini:
Chain-final residues that are not actual C termini:
0 hydrogen bonds
Chain-initial residues that are actual N termini:
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini:
Chain-final residues that are not actual C termini:
0 hydrogen bonds
Chain-initial residues that are actual N termini:
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini:
Chain-final residues that are not actual C termini:
0 hydrogen bonds
Chain-initial residues that are actual N termini:
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini:
Chain-final residues that are not actual C termini:
0 hydrogen bonds
No usable SEQRES records for hAhR_49.pdb (#2) chain (blank); guessing termini
instead
Chain-initial residues that are actual N termini: hAhR_49.pdb #2/? GLU 1
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini: hAhR_49.pdb #2/? GLY 113
Chain-final residues that are not actual C termini:
80 hydrogen bonds
774 hydrogens added
> open https://www.rbvi.ucsf.edu/chimerax/tutorials.html
Opened https://www.rbvi.ucsf.edu/chimerax/tutorials.html
> close session
> open help:user/tutorial/binding-sites.html
Opened help:user/tutorial/binding-sites.html
No help found for 'help:user/tutorial/binding-sites.html'
> open help:user/tutorials/binding-sites.html
Opened help:user/tutorials/binding-sites.html
> open help:user/tutorials/binding-sites.html
Opened help:user/tutorials/binding-sites.html
> open help:user/tutorials/binding-sites.html
Opened help:user/tutorials/binding-sites.html
> open help:user/tutorials/binding-sites.html
Opened help:user/tutorials/binding-sites.html
> open help:user/tutorials/binding-sites.html
Opened help:user/tutorials/binding-sites.html
> open help:user/tutorials/binding-sites.html
Opened help:user/tutorials/binding-sites.html
> open 2hyy
Summary of feedback from opening 2hyy fetched from pdb
---
notes | Fetching compressed mmCIF 2hyy from
http://files.rcsb.org/download/2hyy.cif
Fetching CCD STI from http://ligand-expo.rcsb.org/reports/S/STI/STI.cif
2hyy title:
Human Abl kinase domain in complex with imatinib (STI571, Glivec) [more
info...]
Chain information for 2hyy #1
---
Chain | Description | UniProt
A B C D | Proto-oncogene tyrosine-protein kinase ABL1 | ABL1_HUMAN
Non-standard residues in 2hyy #1
---
STI — 4-(4-methyl-piperazin-1-ylmethyl)-N-[4-methyl-3-(4-pyridin-3-yl-
pyrimidin-2-ylamino)-phenyl]-benzamide (sti-571;imatinib)
2hyy mmCIF Assemblies
---
1| author_defined_assembly
2| author_defined_assembly
3| author_defined_assembly
4| author_defined_assembly
> panel
Unknown command: modeller panel
> close session
> log clear
> open 1fpp
Summary of feedback from opening 1fpp fetched from pdb
---
notes | Fetching compressed mmCIF 1fpp from
http://files.rcsb.org/download/1fpp.cif
Fetching CCD ZN from http://ligand-expo.rcsb.org/reports/Z/ZN/ZN.cif
Fetching CCD PO4 from http://ligand-expo.rcsb.org/reports/P/PO4/PO4.cif
Fetching CCD FPP from http://ligand-expo.rcsb.org/reports/F/FPP/FPP.cif
1fpp title:
Protein farnesyltransferase complex with farnesyl diphosphate [more info...]
Chain information for 1fpp #1
---
Chain | Description | UniProt
A | protein farnesyltransferase | PFTA_RAT
B | protein farnesyltransferase | PFTB_RAT
Non-standard residues in 1fpp #1
---
FPP — farnesyl diphosphate
PO4 — phosphate ion
ZN — zinc ion
> mlp
Map values for surface "1fpp_A SES surface": minimum -28.46, mean -4.976,
maximum 24.73
Map values for surface "1fpp_B SES surface": minimum -27.83, mean -4.111,
maximum 22.2
> surface zone #1 nearAtoms :fpp distance 8 maxComponents 1
> hide ~:fpp target ar
> close
> open 4xt3
Summary of feedback from opening 4xt3 fetched from pdb
---
notes | Fetching compressed mmCIF 4xt3 from
http://files.rcsb.org/download/4xt3.cif
Fetching CCD NAG from http://ligand-expo.rcsb.org/reports/N/NAG/NAG.cif
Fetching CCD PCA from http://ligand-expo.rcsb.org/reports/P/PCA/PCA.cif
4xt3 title:
Structure of a viral GPCR bound to human chemokine CX3CL1 [more info...]
Chain information for 4xt3 #1
---
Chain | Description | UniProt
A | G-protein coupled receptor homolog US28 | US28_HCMVA
B | Fractalkine | X3CL1_HUMAN
Non-standard residues in 4xt3 #1
---
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose
PO4 — phosphate ion
UNL — unknown ligand
> mlp
Map values for surface "4xt3_A SES surface": minimum -28.71, mean 1.122,
maximum 23.28
Map values for surface "4xt3_B SES surface": minimum -25.15, mean -4.785,
maximum 22.04
> close
> open 1g74
Summary of feedback from opening 1g74 fetched from pdb
---
notes | Fetching compressed mmCIF 1g74 from
http://files.rcsb.org/download/1g74.cif
Fetching CCD OLA from http://ligand-expo.rcsb.org/reports/O/OLA/OLA.cif
1g74 title:
Toward changing specificity: adipocyte lipid binding protein mutant, oleic
acid bound form [more info...]
Chain information for 1g74 #1
---
Chain | Description | UniProt
A | adipocyte lipid-binding protein | FABPA_MOUSE
Non-standard residues in 1g74 #1
---
OLA — oleic acid
PO4 — phosphate ion
> surface
> cliup
Unknown command: cliup
> clip
> volume planes z style image imageMode "full region"
No volumes specified
> ui mousemode right clip
> ui mousemode right "clip rotate"
> ui mousemode right translate
> ui mousemode right rotate
> ui mousemode right "clip rotate"
> ui mousemode right clip
> ui mousemode right "clip rotate"
> ui mousemode right translate
> clip model #!1 false
> hide ~:ola target ar
> color :ola & C green
> mlp
Map values for surface "1g74_A SES surface": minimum -27.91, mean -5.662,
maximum 22.39
> mlp protein surfaces #1.1.1
Map values for surface "cap front": minimum -53.62, mean 0.8646, maximum 49.31
> transparency #1.1.1 30
> coulombic protein
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for 1g74_A SES surface #1.1: minimum, -11.34, mean -0.02,
maximum 10.80
> coulombic protein surfaces #1.1.1 offset 0
Coulombic values for cap front #1.1.1: minimum, -2199.36, mean 4.92, maximum
1486.74
> close session
> open 3d6y fromDatabase rcsb_bio maxAssemblies 1
Summary of feedback from opening 3d6y fetched from rcsb_bio
---
notes | Fetching compressed 3d6y bioassembly 1 from
https://files.rcsb.org/download/3d6y-assembly1.cif
Fetching CCD BER from http://ligand-expo.rcsb.org/reports/B/BER/BER.cif
Fetching CCD GOL from http://ligand-expo.rcsb.org/reports/G/GOL/GOL.cif
3d6y bioassembly 1 title:
Crystal structure of R275E mutant of BMRR bound to DNA and berberine [more
info...]
Chain information for 3d6y bioassembly 1 #1
---
Chain | Description
A A-2 | Multidrug-efflux transporter 1 regulator
B B-2 | BMR promoter DNA
Non-standard residues in 3d6y bioassembly 1 #1
---
BER — berberine
GOL — glycerol (glycerin; propane-1,2,3-triol)
Opened 1 biological assemblies for 3d6y
> select :BER
50 atoms, 58 bonds, 2 residues, 1 model selected
> select :BER
50 atoms, 58 bonds, 2 residues, 1 model selected
> select :BER
50 atoms, 58 bonds, 2 residues, 1 model selected
> select :BER
50 atoms, 58 bonds, 2 residues, 1 model selected
> select :GOL
24 atoms, 20 bonds, 4 residues, 1 model selected
> hide :gol
> hide solvent
> hide protein
> select clear
> coulombic protein
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for 3d6y bioassembly 1_A SES surface #1.1: minimum, -16.84,
mean -2.11, maximum 14.59
Coulombic values for 3d6y bioassembly 1_A-2 SES surface #1.2: minimum, -16.17,
mean -2.12, maximum 15.04
> color nucleic tan
> cartoon style nucleic xsection round width 1.5 thickness 1.5
> nucleotides tubs
Missing or invalid "representation" argument: Should be one of 'atoms',
'fill', 'ladder', 'slab', 'stubs', or 'tube/slab'
> nucleotides stubs
> nucleotides tube/slab shape muffler
> nucleotides tube/slab shape ellipsoid
> nucleotides tube/slab shape box
> nucleotides slab
> style nucleic stick
Changed 976 atom styles
> nucleotides fill
> style nucleic stick
Changed 976 atom styles
> nucleotides atoms
> style nucleic stick
Changed 976 atom styles
> nucleotides stubs
> size :ber stickRadius .7
Changed 58 bond radii
> color C & :ber limegreen
> set bgColor white
> set bgColor gray
> set bgColor black
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> lighting shadows true
> lighting flat
> lighting full
> lighting soft
> lighting simple
> lighting shadows true
> lighting full
> lighting soft
> lighting simple
> graphics silhouettes false
> coulombic protein key true
Coulombic values for 3d6y bioassembly 1_A SES surface #1.1: minimum, -16.84,
mean -2.11, maximum 14.59
Coulombic values for 3d6y bioassembly 1_A-2 SES surface #1.2: minimum, -16.17,
mean -2.12, maximum 15.04
> key red-white-blue :-10 :0 :10 showTool true
> ui mousemode right "color key"
> ui mousemode right translate
> 2dlabels text "electrostatic potential"
> hide #!3 models
> hide #2 models
> show #!3 models
> show #2 models
> set bgColor white
> ui mousemode right label
> label delete residues
> select clear
> label delete residues
> select clear
> label delete residues
> ui mousemode right label
> ui mousemode right select
> select //chain_id='A-2':20@NZ
1 atom, 1 residue, 1 model selected
> select //chain_id='B-2':-5
19 atoms, 20 bonds, 1 residue, 1 model selected
> select /A:26@O
1 atom, 1 residue, 1 model selected
> select /A:32@CB
1 atom, 1 residue, 1 model selected
> slect clear
Unknown command: slect clear
> ui mousemode right label
> ui mousemode right "move label"
> 2dlabels #3.1 xpos 0.658 ypos 0.140
> ui mousemode right translate
> close session
> open https://www.rbvi.ucsf.edu/chimerax/data/conservation-
> coloring/conservation-coloring.html
Opened https://www.rbvi.ucsf.edu/chimerax/data/conservation-
coloring/conservation-coloring.html
> open 121p
Summary of feedback from opening 121p fetched from pdb
---
notes | Fetching compressed mmCIF 121p from
http://files.rcsb.org/download/121p.cif
Fetching CCD MG from http://ligand-expo.rcsb.org/reports/M/MG/MG.cif
Fetching CCD GCP from http://ligand-expo.rcsb.org/reports/G/GCP/GCP.cif
121p title:
Struktur und guanosintriphosphat-hydrolysemechanismus des C-terminal
verkuerzten menschlichen krebsproteins P21-H-ras [more info...]
Chain information for 121p #1
---
Chain | Description | UniProt
A | H-ras P21 protein | RASH_HUMAN
Non-standard residues in 121p #1
---
GCP — phosphomethylphosphonic acid guanylate ester
MG — magnesium ion
121p mmCIF Assemblies
---
1| author_defined_assembly
> hide solvent
> style ligand ball
Changed 32 atom styles
> open https://www.rbvi.ucsf.edu/chimerax/data/conservation-
> coloring/121p-consurf.aln
Summary of feedback from opening
//www.rbvi.ucsf.edu/chimerax/data/conservation-coloring/121p-consurf.aln
fetched from https
---
notes | Fetching 121p-consurf.aln from
https://www.rbvi.ucsf.edu/chimerax/data/conservation-coloring/121p-consurf.aln
Downloaded 121p-consurf.aln to
/Users/amandaghilardi/Downloads/121p-consurf.aln
Alignment identifier is 121p-consurf.aln
Associated 121p chain A to Input_pdb_SEQRES_A with 0 mismatches
Showing conservation header ("seq_conservation" residue attribute) for
alignment 121p-consurf.aln
Opened 150 sequences from 121p-consurf.aln
> color byattr_conservation
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random'
or a keyword
> color byattribute seq_conservation
1550 atoms, 363 residues, atom seq_conservation range -1.47 to 2.83
> color byattribute seq_conservation palette cyanmaroon range -1.4,1.4
1550 atoms, 363 residues, atom seq_conservation range -1.47 to 2.83
> color byattribute seq_conservation palette blue:red:yellow
1550 atoms, 363 residues, atom seq_conservation range -1.47 to 2.83
> color byattribute seq_conservation palette cyanmaroon
1550 atoms, 363 residues, atom seq_conservation range -1.47 to 2.83
> color byattribute seq_conservation palette cyanmaroon range -1.4,1.4
1550 atoms, 363 residues, atom seq_conservation range -1.47 to 2.83
> open https://www.rbvi.ucsf.edu/chimerax/data/conservation-
> coloring/conservation-coloring.html
Opened https://www.rbvi.ucsf.edu/chimerax/data/conservation-
coloring/conservation-coloring.html
> hide protein
> show ::seq_conservation>1.8
> label ::seq_conservation>1.8
> label height 1.3
> preset pub
Multiple preset names match 'pub': publication 1 (silhouettes); publication 2
(depth-cued)
> preset "overall look" "publication 1 (silhouettes)"
Using preset: Overall Look / Publication 1 (Silhouettes)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes t
lighting depthCue f
> preset "overall look" "publication 2 (depth-cued)"
Using preset: Overall Look / Publication 2 (Depth-Cued)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes f
lighting depthCue t
> preset "overall look" "publication 2 (depth-cued)"
Using preset: Overall Look / Publication 2 (Depth-Cued)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes f
lighting depthCue t
> preset "overall look" "publication 1 (silhouettes)"
Using preset: Overall Look / Publication 1 (Silhouettes)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes t
lighting depthCue f
> label delete
> surface
> color fromatoms
> preset inter
Using preset: Overall Look / Interactive
Preset expands to these ChimeraX commands:
~set bg
graphics silhouettes f
lighting depthCue t
> close session
> open 3sn6
Summary of feedback from opening 3sn6 fetched from pdb
---
notes | Fetching compressed mmCIF 3sn6 from
http://files.rcsb.org/download/3sn6.cif
Fetching CCD P0G from http://ligand-expo.rcsb.org/reports/P/P0G/P0G.cif
3sn6 title:
Crystal structure of the beta2 adrenergic receptor-Gs protein complex [more
info...]
Chain information for 3sn6 #1
---
Chain | Description | UniProt
A | Guanine nucleotide-binding protein G(s) subunit α isoforms short |
GNAS2_BOVIN
B | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 |
GBB1_RAT
G | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 |
GBG2_BOVIN
N | Camelid antibody VHH fragment |
R | Endolysin,Beta-2 adrenergic receptor | ADRB2_HUMAN
Non-standard residues in 3sn6 #1
---
P0G —
8-[(1R)-2-{[1,1-dimethyl-2-(2-methylphenyl)ethyl]amino}-1-hydroxyethyl]-5-hydroxy-2H-1,4-benzoxazin-3(4H)-one
> preset cylinders
Using preset: Cartoons/Nucleotides / Cylinders/Stubs
Changed 10247 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
cartoon style protein modeh tube rad 2 sides 24 thick 0.6
cartoon style nucleic x round width 1.6 thick 1.6
nucleotides stubs
> preset cylinders
Using preset: Cartoons/Nucleotides / Cylinders/Stubs
Changed 0 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
cartoon style protein modeh tube rad 2 sides 24 thick 0.6
cartoon style nucleic x round width 1.6 thick 1.6
nucleotides stubs
> color /R yellow
> hide /N cartoons
> open /Users/amandaghilardi/Desktop/81321.ali.rtf
Unrecognized file suffix '.rtf'
> open https://www.rbvi.ucsf.edu/chimerax/data/conservation-coloring/81321.ali
Summary of feedback from opening
//www.rbvi.ucsf.edu/chimerax/data/conservation-coloring/81321.ali fetched from
https
---
notes | Fetching 81321.ali from
https://www.rbvi.ucsf.edu/chimerax/data/conservation-coloring/81321.ali
Downloaded 81321.ali to /Users/amandaghilardi/Downloads/81321.ali
Alignment identifier is 81321.ali
Showing conservation header ("seq_conservation" residue attribute) for
alignment 81321.ali
Opened 10 sequences from 81321.ali
> sequence associate /N 81321.ali
Associated 3sn6 chain N to d1m0ka- with 128 mismatches and/or gaps
> sequence associate /R 81321.ali
Associated 3sn6 chain R to d2rh1a1 with 2 mismatches and/or gaps
> sequence associate /R 81321.ali
Disassociated 3sn6 chain R from d2rh1a1
Associated 3sn6 chain R to d2rh1a1 with 2 mismatches and/or gaps
> color byattribute seq_conservation /R & protein range -1.5,3 noValueColor
> gray
3433 atoms, 443 residues, atom seq_conservation range -1.76 to 4.75
> show :: seq_conversation>2
> size stickRadius .5
Changed 10478 bond radii
> color ligand byhetero
> lighting soft
> color ligand byhetero
> lighting soft
> lighting simple
> close session
> open 1kmo
Summary of feedback from opening 1kmo fetched from pdb
---
notes | Fetching compressed mmCIF 1kmo from
http://files.rcsb.org/download/1kmo.cif
Fetching CCD LDA from http://ligand-expo.rcsb.org/reports/L/LDA/LDA.cif
Fetching CCD HTO from http://ligand-expo.rcsb.org/reports/H/HTO/HTO.cif
1kmo title:
Crystal structure of the Outer Membrane Transporter FecA [more info...]
Chain information for 1kmo #1
---
Chain | Description | UniProt
A | Iron(III) dicitrate transport protein fecA | FECA_ECOLI
Non-standard residues in 1kmo #1
---
HTO — heptane-1,2,3-triol
LDA — lauryl dimethylamine-N-oxide
> hide
> open https://www.rbvi.ucsf.edu/chimerax/data/conservation-coloring/56935.ali
Summary of feedback from opening
//www.rbvi.ucsf.edu/chimerax/data/conservation-coloring/56935.ali fetched from
https
---
notes | Fetching 56935.ali from
https://www.rbvi.ucsf.edu/chimerax/data/conservation-coloring/56935.ali
Downloaded 56935.ali to /Users/amandaghilardi/Downloads/56935.ali
Alignment identifier is 56935.ali
Associated 1kmo chain A to d1kmoa- with 0 mismatches
Showing conservation header ("seq_conservation" residue attribute) for
alignment 56935.ali
Opened 13 sequences from 56935.ali
> color byattribute attr seq_conservation
Expected a collection of one of 'atoms', 'cartoons', 'ribbons', or 'surfaces'
or a keyword
> color byattribute seq_conservation
5862 atoms, 1066 residues, atom seq_conservation range -2.29 to 4.37
> select ~::seq_conservation
2540 atoms, 2148 bonds, 653 residues, 1 model selected
> sequence header conservation setting al2co_gap 0.51
> sequence header conservation setting al2co_gap 0.52
> sequence header conservation setting al2co_gap 0.6
> select ~::seq_conservation
1364 atoms, 946 bonds, 496 residues, 1 model selected
> select clear
> color byattrseq_convservation
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random'
or a keyword
> color byattribute seq_convservation
No known/registered numeric attribute seq_convservation
> color byattribute seq_conservation
5862 atoms, 1066 residues, atom seq_conservation range -1.92 to 4.18
> color byattribute seq_conservation palette cyanmaroon range -2,3
> noValueColor silver key true
> key cyan-white-maroon :-2.0 :0.5 :3.0 showTool true
> ui mousemode right "color key"
5862 atoms, 1066 residues, atom seq_conservation range -1.92 to 4.18
> ui mousemode right translate
> windowsize 600 600
> preset pub
Multiple preset names match 'pub': publication 1 (silhouettes); publication 2
(depth-cued)
> ui windowfill toggle
> preset "overall look" "publication 2 (depth-cued)"
Using preset: Overall Look / Publication 2 (Depth-Cued)
> set bgColor #ffffff00
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes f
lighting depthCue t
> preset "overall look" "publication 1 (silhouettes)"
Using preset: Overall Look / Publication 1 (Silhouettes)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes t
lighting depthCue f
> set bgColor steelblue
> set bgColor #4682b400
> lighting flat
> graphics silhouettes depthJump 0.003
> graphics silhouettes depthJump 0.03
> 2dlabels text "Conservation (AL2CO entropy measure)"
> ui mousemode right "move label"
> 2dlabels #3.1 xpos 0.406 ypos 0.157
> 2dlabels #3.1 xpos 0.349 ypos 0.141
> 2dlabels #3.1 xpos 0.354 ypos 0.018
> key labelSide left/top
> key pos 0.06,0.1 size 0.3,0.04
> 2dlabels xpos 0.021 ypos 0.021
> close session
> open 6ddf
Summary of feedback from opening 6ddf fetched from pdb
---
notes | Fetching compressed mmCIF 6ddf from
http://files.rcsb.org/download/6ddf.cif
Fetching CCD DAL from http://ligand-expo.rcsb.org/reports/D/DAL/DAL.cif
Fetching CCD MEA from http://ligand-expo.rcsb.org/reports/M/MEA/MEA.cif
Fetching CCD ETA from http://ligand-expo.rcsb.org/reports/E/ETA/ETA.cif
6ddf title:
μ Opioid Receptor-Gi Protein Complex [more info...]
Chain information for 6ddf #1
---
Chain | Description | UniProt
A | Guanine nucleotide-binding protein G(i) subunit alpha-1 | GNAI1_HUMAN
B | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 |
GBB1_HUMAN
C | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 |
GBG2_HUMAN
D | DAMGO |
R | Mu-type opioid receptor | OPRM_MOUSE
Non-standard residues in 6ddf #1
---
ETA — ethanolamine
> set bgColor black
> set bgColor transparent
> close
> open 4n6h
Summary of feedback from opening 4n6h fetched from pdb
---
notes | Fetching compressed mmCIF 4n6h from
http://files.rcsb.org/download/4n6h.cif
Fetching CCD OLC from http://ligand-expo.rcsb.org/reports/O/OLC/OLC.cif
Fetching CCD PGE from http://ligand-expo.rcsb.org/reports/P/PGE/PGE.cif
Fetching CCD TLA from http://ligand-expo.rcsb.org/reports/T/TLA/TLA.cif
Fetching CCD EJ4 from http://ligand-expo.rcsb.org/reports/E/EJ4/EJ4.cif
Fetching CCD NA from http://ligand-expo.rcsb.org/reports/N/NA/NA.cif
4n6h title:
1.8 A Structure of the human δ opioid 7TM receptor (PSI Community Target)
[more info...]
Chain information for 4n6h #1
---
Chain | Description | UniProt
A | Soluble cytochrome b562, Delta-type opioid receptor chimeric protein |
OPRD_HUMAN
Non-standard residues in 4n6h #1
---
EJ4 —
(4bS,8R,8aS,14bR)-7-(cyclopropylmethyl)-5,6,7,8,14,14b-hexahydro-4,8-methano[1]benzofuro[2,3-a]pyrido[4,3-b]carbazole-1,8a(9H)-diol
(Naltrindole)
NA — sodium ion
OLA — oleic acid
OLC — (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate (1-Oleoyl-R-glycerol)
PGE — triethylene glycol
TLA — L(+)-tartaric acid
> surface
> mlp
Map values for surface "4n6h_A SES surface": minimum -26.77, mean -0.8566,
maximum 23.81
> hide solvent
> hide
> show
> lighting soft
> lighting simple
> hide surfaces
> delete :1002-1106
> hbonds
582 hydrogen bonds found
> hide solvent
> select protein
2314 atoms, 2370 bonds, 327 pseudobonds, 303 residues, 2 models selected
> hide
> hide sel atoms
> select clear
> hbonds :EH4
Atom specifier selects no atoms
> hbonds :EJ4
10 hydrogen bonds found
> select ::name="EJ4"
31 atoms, 38 bonds, 1 residue, 1 model selected
> select sel @ show sel atoms
> select clear
> color :EJ orange
> color :EJ4 orange
> color byhetero
> hide cartoons
> clip off
> hide atoms
> show :EJ4 : addh
Summary of feedback from adding hydrogens to 4n6h #1
---
warnings | Not adding hydrogens to /A ARG 41 CD because it is missing heavy-
atom bond partners
Not adding hydrogens to /A VAL 154 CB because it is missing heavy-atom bond
partners
Not adding hydrogens to /A LEU 157 CG because it is missing heavy-atom bond
partners
Not adding hydrogens to /A LYS 166 CE because it is missing heavy-atom bond
partners
Not adding hydrogens to /A ARG 192 CD because it is missing heavy-atom bond
partners
10 messages similar to the above omitted
notes | Termini for 4n6h (#1) chain A determined from SEQRES records
Chain-initial residues that are actual N termini:
Chain-initial residues that are not actual N termini: /A GLY 36
Chain-final residues that are actual C termini: /A GLY 338
Chain-final residues that are not actual C termini:
Missing OXT added to C-terminal residue /A GLY 338
581 hydrogen bonds
Adding 'H' to /A GLY 36
3076 hydrogens added
> open 4n6h fromDatabase eds
Summary of feedback from opening 4n6h fetched from eds
---
note | Fetching map 4n6h from
http://www.ebi.ac.uk/pdbe/coordinates/files/4n6h.ccp4
Opened eds 4n6h as #2, grid size 114,100,190, pixel 0.599,0.607,0.603, shown
at level 0.799, step 1, values float32
> volume #2 level 1.201
> volume zone #2 nearAtoms :EJ4 range 6 newMap false
> volume #2 level 0.7072
> delete H
> volume level .5
> close #2
> style :EJ4 sphere
Changed 31 atom styles
> surface :EJ4 : ui mousemode right translate
> transparency 50
> close session
> open 6pt2
Summary of feedback from opening 6pt2 fetched from pdb
---
notes | Fetching compressed mmCIF 6pt2 from
http://files.rcsb.org/download/6pt2.cif
Fetching CCD CLR from http://ligand-expo.rcsb.org/reports/C/CLR/CLR.cif
Fetching CCD DI7 from http://ligand-expo.rcsb.org/reports/D/DI7/DI7.cif
Fetching CCD DAR from http://ligand-expo.rcsb.org/reports/D/DAR/DAR.cif
Fetching CCD SAR from http://ligand-expo.rcsb.org/reports/S/SAR/SAR.cif
Fetching CCD OXJ from http://ligand-expo.rcsb.org/reports/O/OXJ/OXJ.cif
6pt2 title:
Crystal structure of the active δ opioid receptor in complex with the peptide
agonist KGCHM07 [more info...]
Chain information for 6pt2 #1
---
Chain | Description
A B | δ opioid receptor
C D | Peptide agonist KGCHM07
Non-standard residues in 6pt2 #1
---
CLR — cholesterol
OLA — oleic acid
OLC — (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate (1-Oleoyl-R-glycerol)
OXJ — 1-[3,5-bis(trifluoromethyl)phenyl]-N-methylmethanamine
> hide #1 models
> view
> open 4n6h
4n6h title:
1.8 A Structure of the human δ opioid 7TM receptor (PSI Community Target)
[more info...]
Chain information for 4n6h #2
---
Chain | Description | UniProt
A | Soluble cytochrome b562, Delta-type opioid receptor chimeric protein |
OPRD_HUMAN
Non-standard residues in 4n6h #2
---
EJ4 —
(4bS,8R,8aS,14bR)-7-(cyclopropylmethyl)-5,6,7,8,14,14b-hexahydro-4,8-methano[1]benzofuro[2,3-a]pyrido[4,3-b]carbazole-1,8a(9H)-diol
(Naltrindole)
NA — sodium ion
OLA — oleic acid
OLC — (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate (1-Oleoyl-R-glycerol)
PGE — triethylene glycol
TLA — L(+)-tartaric acid
> open 4pt2
Summary of feedback from opening 4pt2 fetched from pdb
---
note | Fetching compressed mmCIF 4pt2 from
http://files.rcsb.org/download/4pt2.cif
4pt2 title:
Myxococcus xanthus encapsulin protein (EncA) [more info...]
Chain information for 4pt2 #3
---
Chain | Description | UniProt
A B P | Encapsulin protein | Q1D6H4_MYXXD
4pt2 mmCIF Assemblies
---
1| complete icosahedral assembly
2| icosahedral asymmetric unit
3| icosahedral pentamer
4| icosahedral 23 hexamer
5| icosahedral asymmetric unit, std point frame
> hide #1 models
> hide #!2 models
> view
> delete /B,D
> delete :999-1106
> color #2:73,90,95,108,131,143,268,309,323 red
> show #1 models
> matchmaker #1 to #2
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 4n6h, chain A (#2) with 6pt2, chain A (#1), sequence alignment
score = 1850
RMSD between 198 pruned atom pairs is 1.026 angstroms; (across all 289 pairs:
3.234)
> show #!2 models
> hide #3 models
> show #1 cartoons
> style stick
Changed 9427 atom styles
> hide surfaces
> morph #1,2 same true
Computed 51 frame morph #4
> coordset #4 1,51
> morph #1,2 same true
Computed 51 frame morph #5
> coordset #5 1,51
> morph #1,2 same true
Computed 51 frame morph #6
> coordset #6 1,51
> hide #3
> hide #3 models
> show #2 models
> show :128
> color :128 & C yellow
> color /C & C pink
> hbonds /C distSlop 0.6
47 hydrogen bonds found
> swapaa #2:128 ASN
Using Dunbrack library
4n6h #2/A ASP 128: phi -58.3, psi -44.7 trans
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.5.dev202206100131 (2022-06-10)
© 2016-2022 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 ATI-4.7.29
OpenGL renderer: AMD Radeon Pro 5500 XT OpenGL Engine
OpenGL vendor: ATI Technologies Inc.
Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.3.0, Qt 6.3.0
Qt runtime version: 6.3.0
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: iMac
Model Identifier: iMac20,1
Processor Name: 8-Core Intel Core i7
Processor Speed: 3.8 GHz
Number of Processors: 1
Total Number of Cores: 8
L2 Cache (per Core): 256 KB
L3 Cache: 16 MB
Hyper-Threading Technology: Enabled
Memory: 8 GB
System Firmware Version: 1715.40.15.0.0 (iBridge: 19.16.10549.0.0,0)
OS Loader Version: 540.40.4~45
Software:
System Software Overview:
System Version: macOS 12.0.1 (21A559)
Kernel Version: Darwin 21.1.0
Time since boot: 19 days 4:30
Graphics/Displays:
AMD Radeon Pro 5500 XT:
Chipset Model: AMD Radeon Pro 5500 XT
Type: GPU
Bus: PCIe
PCIe Lane Width: x16
VRAM (Total): 8 GB
Vendor: AMD (0x1002)
Device ID: 0x7340
Revision ID: 0x0041
ROM Revision: 113-D3220I-231
VBIOS Version: 113-D322A1XT-011
Option ROM Version: 113-D322A1XT-011
EFI Driver Version: 01.01.231
Metal Family: Supported, Metal GPUFamily macOS 2
Displays:
iMac:
Display Type: Built-In Retina LCD
Resolution: Retina 5K (5120 x 2880)
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
appnope: 0.1.3
Babel: 2.10.1
backcall: 0.2.0
blockdiag: 3.0.0
build: 0.7.0
certifi: 2021.10.8
cftime: 1.6.0
charset-normalizer: 2.0.12
ChimeraX-AddCharge: 1.2.3
ChimeraX-AddH: 2.1.11
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2.1
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.4.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.39.2
ChimeraX-AtomicLibrary: 7.0
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.1
ChimeraX-BasicActions: 1.1
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.1
ChimeraX-BondRot: 2.0
ChimeraX-BugReporter: 1.0
ChimeraX-BuildStructure: 2.7
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2
ChimeraX-ButtonPanel: 1.0
ChimeraX-CageBuilder: 1.0
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.2
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.2
ChimeraX-CommandLine: 1.2.3
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0
ChimeraX-Core: 1.5.dev202206100131
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.3.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0
ChimeraX-DataFormats: 1.2.2
ChimeraX-Dicom: 1.1
ChimeraX-DistMonitor: 1.1.6
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0
ChimeraX-FunctionKey: 1.0
ChimeraX-Geometry: 1.2
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1
ChimeraX-Hbonds: 2.2
ChimeraX-Help: 1.2
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
ChimeraX-Label: 1.1.1
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.5
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.1
ChimeraX-Map: 1.1
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1
ChimeraX-Markers: 1.0
ChimeraX-Mask: 1.0
ChimeraX-MatchMaker: 2.0.6
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.1
ChimeraX-Meeting: 1.0
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.7
ChimeraX-MMTF: 2.1
ChimeraX-Modeller: 1.5.5
ChimeraX-ModelPanel: 1.3.2
ChimeraX-ModelSeries: 1.0
ChimeraX-Mol2: 2.0
ChimeraX-Morph: 1.0
ChimeraX-MouseModes: 1.1
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0.2
ChimeraX-OpenCommand: 1.9
ChimeraX-PDB: 2.6.6
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-RenumberResidues: 1.0
ChimeraX-ResidueFit: 1.0
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0.1
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
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.6.2
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0
ChimeraX-Shortcuts: 1.1
ChimeraX-ShowAttr: 1.0
ChimeraX-ShowSequences: 1.0
ChimeraX-SideView: 1.0
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.8
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.0.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0
ChimeraX-SwapRes: 2.1.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.1
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Tug: 1.0
ChimeraX-UI: 1.20.4
ChimeraX-uniprot: 2.2
ChimeraX-UnitCell: 1.0
ChimeraX-ViewDockX: 1.1.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0
ChimeraX-WebServices: 1.1.0
ChimeraX-Zone: 1.0
colorama: 0.4.4
cxservices: 1.2
cycler: 0.11.0
Cython: 0.29.26
debugpy: 1.6.0
decorator: 5.1.1
docutils: 0.17.1
entrypoints: 0.4
filelock: 3.4.2
fonttools: 4.33.3
funcparserlib: 1.0.0
grako: 3.16.5
h5py: 3.7.0
html2text: 2020.1.16
idna: 3.3
ihm: 0.27
imagecodecs: 2021.11.20
imagesize: 1.3.0
ipykernel: 6.6.1
ipython: 7.31.1
ipython-genutils: 0.2.0
jedi: 0.18.1
Jinja2: 3.0.3
jupyter-client: 7.1.0
jupyter-core: 4.10.0
kiwisolver: 1.4.2
line-profiler: 3.4.0
lxml: 4.7.1
lz4: 3.1.10
MarkupSafe: 2.1.1
matplotlib: 3.5.1
matplotlib-inline: 0.1.3
MolecularDynamicsViewer: 1.4
msgpack: 1.0.3
nest-asyncio: 1.5.5
netCDF4: 1.5.8
networkx: 2.6.3
numexpr: 2.8.1
numpy: 1.22.1
openvr: 1.16.802
packaging: 21.0
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.12.0
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 9.0.1
pip: 21.3.1
pkginfo: 1.8.2
prompt-toolkit: 3.0.29
psutil: 5.9.0
ptyprocess: 0.7.0
pycollada: 0.7.2
pydicom: 2.2.2
Pygments: 2.11.2
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.9
PyQt6-commercial: 6.3.0
PyQt6-Qt6: 6.3.0
PyQt6-sip: 13.3.1
PyQt6-WebEngine-commercial: 6.3.0
PyQt6-WebEngine-Qt6: 6.3.0
python-dateutil: 2.8.2
pytz: 2022.1
pyzmq: 23.1.0
qtconsole: 5.3.0
QtPy: 2.1.0
RandomWords: 0.3.0
requests: 2.27.1
scipy: 1.7.3
setuptools: 59.8.0
sfftk-rw: 0.7.2
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
Sphinx: 4.3.2
sphinx-autodoc-typehints: 1.15.2
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
suds-community: 1.0.0
tables: 3.7.0
tifffile: 2021.11.2
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.1
traitlets: 5.1.1
urllib3: 1.26.9
wcwidth: 0.2.5
webcolors: 1.11.1
wheel: 0.37.1
wheel-filename: 1.3.0
Attachments (1)
Change History (3)
comment:1 by , 3 years ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Structure Editing |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Crash in swapaa |
comment:2 by , 3 years ago
| Resolution: | → fixed |
|---|---|
| Status: | accepted → closed |
Hi Amanda,
I have committed a fix for this and the fix will be in the next daily build:
--Eric
fix: https://github.com/RBVI/ChimeraX/commit/ab113bb8f8bfb588e217670b7d8160800e81a0a1
Note:
See TracTickets
for help on using tickets.
Hi Amanda,
--Eric