id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 16044 Unknown crash ruchi.sharma@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-14.6-x86_64-i386-64bit ChimeraX Version: 1.7.1 (2024-01-23 01:58:08 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. Fatal Python error: Segmentation fault Current thread 0x00007ff853245dc0 (most recent call first): File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 275 in event_loop File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 918 in init File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1069 in File """", line 88 in _run_code File """", line 198 in _run_module_as_main Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtWebChannel, PyQt6.QtNetwork, PyQt6.QtWebEngineCore, PyQt6.QtPrintSupport, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, chimerax.surface._surface, chimerax.pdb_lib._load_libs, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, numpy.linalg.lapack_lite, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.pdb._pdbio, lxml._elementpath, lxml.etree, PIL._imagingmath, chimerax.coulombic._esp (total: 61) {""app_name"":""ChimeraX"",""timestamp"":""2024-09-30 13:26:42.00 -0400"",""app_version"":""1.7.1"",""slice_uuid"":""194a3167-3db5-3029-8d22-1d742b826bb9"",""build_version"":""1.7.1.0"",""platform"":1,""bundleID"":""edu.ucsf.cgl.ChimeraX"",""share_with_app_devs"":0,""is_first_party"":0,""bug_type"":""309"",""os_version"":""macOS 14.6 (23G80)"",""roots_installed"":0,""name"":""ChimeraX"",""incident_id"":""6B9C08D8-3C20-41E3-9E64-D371AD0C8039""} { ""uptime"" : 37000, ""procRole"" : ""Foreground"", ""version"" : 2, ""userID"" : 501, ""deployVersion"" : 210, ""modelCode"" : ""MacBookPro15,4"", ""coalitionID"" : 5577, ""osVersion"" : { ""train"" : ""macOS 14.6"", ""build"" : ""23G80"", ""releaseType"" : ""User"" }, ""captureTime"" : ""2024-09-30 13:26:17.6671 -0400"", ""codeSigningMonitor"" : 0, ""incident"" : ""6B9C08D8-3C20-41E3-9E64-D371AD0C8039"", ""pid"" : 26695, ""cpuType"" : ""X86-64"", ""roots_installed"" : 0, ""bug_type"" : ""309"", ""procLaunch"" : ""2024-09-30 10:44:58.9487 -0400"", ""procStartAbsTime"" : 27808912585639, ""procExitAbsTime"" : 37487454607638, ""procName"" : ""ChimeraX"", ""procPath"" : ""\/Applications\/ChimeraX-1.7.1.app\/Contents\/MacOS\/ChimeraX"", ""bundleInfo"" : {""CFBundleShortVersionString"":""1.7.1"",""CFBundleVersion"":""1.7.1.0"",""CFBundleIdentifier"":""edu.ucsf.cgl.ChimeraX""}, ""storeInfo"" : {""deviceIdentifierForVendor"":""FAD1F7A5-AFC8-5CA0-970D-04CC3EEAC657"",""thirdParty"":true}, ""parentProc"" : ""launchd"", ""parentPid"" : 1, ""coalitionName"" : ""edu.ucsf.cgl.ChimeraX"", ""crashReporterKey"" : ""2145464F-803C-5923-4D0A-4BF9FED76F62"", ""codeSigningID"" : ""edu.ucsf.cgl.ChimeraX"", ""codeSigningTeamID"" : ""LWV8X224YF"", ""codeSigningFlags"" : 570491649, ""codeSigningValidationCategory"" : 6, ""codeSigningTrustLevel"" : 4294967295, ""wakeTime"" : 12102, ""bridgeVersion"" : {""build"":""21P6074"",""train"":""8.6""}, ""sleepWakeUUID"" : ""14E263A2-A73A-4E25-8402-F12A13CBBA69"", ""sip"" : ""enabled"", ""vmRegionInfo"" : ""0x6c is not in any region. Bytes before following region: 4403027860\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 10670e000-106712000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.7.1.app\/Contents\/MacOS\/ChimeraX"", ""exception"" : {""codes"":""0x0000000000000001, 0x000000000000006c"",""rawCodes"":[1,108],""type"":""EXC_BAD_ACCESS"",""signal"":""SIGSEGV"",""subtype"":""KERN_INVALID_ADDRESS at 0x000000000000006c""}, ""termination"" : {""flags"":0,""code"":11,""namespace"":""SIGNAL"",""indicator"":""Segmentation fault: 11"",""byProc"":""ChimeraX"",""byPid"":26695}, ""ktriageinfo"" : ""VM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\n"", ""vmregioninfo"" : ""0x6c is not in any region. Bytes before following region: 4403027860\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 10670e000-106712000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.7.1.app\/Contents\/MacOS\/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"":[198,67,48,48,76,137,255,72,137,222,76,137,242,91,65,92,65,94,65,95,93,233,94,253,255,255,73,137,198,73,139,60,36,72,133,255,116,8,76,137,230,232,42,195,44,0,72,137,223,232,210,17,46,0,76,137,247,232,10,17,46,0,102,46,15,31,132,0,0,0,0,0,85,72,137,229,93,233,38,253,255,255,102,15,31,68,0,0,85,72,137,229,72,139,71,8,72,139,64,88,72,139,64,96,93,195,102,46,15,31,132,0,0,0,0,0,15,31,64,0,85,72,137,229,72,139,127,8,93,233,50,11,0,0,102,144,85,72,137,229,72,139,63,72,133,255,116,7,72,139,7,93,255,96,8,93,195,102,46,15,31,132,0,0,0,0,0,144,85,72,137,229,72,131,199,64,93,233,50,48,1,0,102,144,85,72,137,229,65,87,65,86],""offset"":96}},""frames"":[{""imageOffset"":32182,""symbol"":""__pthread_kill"",""symbolLocation"":10,""imageIndex"":152},{""imageOffset"":24253,""symbol"":""pthread_kill"",""symbolLocation"":262,""imageIndex"":153},{""imageOffset"":282792,""symbol"":""raise"",""symbolLocation"":24,""imageIndex"":154},{""imageOffset"":2590164,""symbol"":""faulthandler_fatal_error"",""symbolLocation"":388,""imageIndex"":150},{""imageOffset"":16349,""symbol"":""_sigtramp"",""symbolLocation"":29,""imageIndex"":155},{""imageOffset"":0,""imageIndex"":156},{""imageOffset"":513151,""symbol"":""QMetaMethod::invoke(QObject*, Qt::ConnectionType, QGenericReturnArgument, QGenericArgument, QGenericArgument, QGenericArgument, QGenericArgument, QGenericArgument, QGenericArgument, QGenericArgument, QGenericArgument, QGenericArgument, QGenericArgument) const"",""symbolLocation"":879,""imageIndex"":107},{""imageOffset"":326252,""imageIndex"":83},{""imageOffset"":464639,""symbol"":""__CFNOTIFICATIONCENTER_IS_CALLING_OUT_TO_AN_OBSERVER__"",""symbolLocation"":120,""imageIndex"":157},{""imageOffset"":1057078,""symbol"":""___CFXRegistrationPost_block_invoke"",""symbolLocation"":88,""imageIndex"":157},{""imageOffset"":1056896,""symbol"":""_CFXRegistrationPost"",""symbolLocation"":532,""imageIndex"":157},{""imageOffset"":266283,""symbol"":""_CFXNotificationPost"",""symbolLocation"":682,""imageIndex"":157},{""imageOffset"":34926,""symbol"":""-[NSNotificationCenter postNotificationName:object:userInfo:]"",""symbolLocation"":82,""imageIndex"":158},{""imageOffset"":1891517,""symbol"":""-[NSWindow becomeKeyWindow]"",""symbolLocation"":1171,""imageIndex"":159},{""imageOffset"":5309322,""symbol"":""-[NSApplication _handleKeyFocusNotification:withEvent:]"",""symbolLocation"":84,""imageIndex"":159},{""imageOffset"":9773914,""symbol"":""-[NSApplication(NSEventRouting) sendEvent:]"",""symbolLocation"":1898,""imageIndex"":159},{""imageOffset"":46090,""imageIndex"":83},{""imageOffset"":5295406,""symbol"":""-[NSApplication _handleEvent:]"",""symbolLocation"":65,""imageIndex"":159},{""imageOffset"":198058,""symbol"":""-[NSApplication run]"",""symbolLocation"":640,""imageIndex"":159},{""imageOffset"":102572,""imageIndex"":83},{""imageOffset"":488230,""symbol"":""QEventLoop::exec(QFlags)"",""symbolLocation"":486,""imageIndex"":107},{""imageOffset"":451125,""symbol"":""QCoreApplication::exec()"",""symbolLocation"":133,""imageIndex"":107},{""imageOffset"":2252186,""symbol"":""meth_QApplication_exec(_object*, _object*)"",""symbolLocation"":90,""imageIndex"":101},{""imageOffset"":1095658,""symbol"":""cfunction_call"",""symbolLocation"":90,""imageIndex"":150},{""imageOffset"":680881,""symbol"":""_PyObject_MakeTpCall"",""symbolLocation"":129,""imageIndex"":150},{""imageOffset"":1917927,""symbol"":""_PyEval_EvalFrameDefault"",""symbolLocation"":60455,""imageIndex"":150},{""imageOffset"":1852538,""symbol"":""PyEval_EvalCode"",""symbolLocation"":282,""imageIndex"":150},{""imageOffset"":1830115,""symbol"":""builtin_exec"",""symbolLocation"":483,""imageIndex"":150},{""imageOffset"":1098052,""symbol"":""cfunction_vectorcall_FASTCALL_KEYWORDS"",""symbolLocation"":68,""imageIndex"":150},{""imageOffset"":1917679,""symbol"":""_PyEval_EvalFrameDefault"",""symbolLocation"":60207,""imageIndex"":150},{""imageOffset"":1942736,""symbol"":""_PyEval_Vector"",""symbolLocation"":128,""imageIndex"":150},{""imageOffset"":2561789,""symbol"":""pymain_run_module"",""symbolLocation"":253,""imageIndex"":150},{""imageOffset"":2560449,""symbol"":""Py_RunMain"",""symbolLocation"":2225,""imageIndex"":150},{""imageOffset"":2564475,""symbol"":""pymain_main"",""symbolLocation"":43,""imageIndex"":150},{""imageOffset"":2564426,""symbol"":""Py_Main"",""symbolLocation"":42,""imageIndex"":150},{""imageOffset"":15770,""symbol"":""main"",""symbolLocation"":122,""imageIndex"":151},{""imageOffset"":25413,""symbol"":""start"",""symbolLocation"":1909,""imageIndex"":160}],""id"":440338,""triggered"":true,""threadState"":{""r13"":{""value"":140701945757441},""rax"":{""value"":0},""rflags"":{""value"":582},""cpu"":{""value"":0},""r14"":{""value"":140704523509184,""symbolLocation"":0,""symbol"":""_main_thread""},""rsi"":{""value"":11},""r8"":{""value"":2},""cr2"":{""value"":0},""rdx"":{""value"":0},""r10"":{""value"":140704523509184,""symbolLocation"":0,""symbol"":""_main_thread""},""r9"":{""value"":14757395258967641293},""r15"":{""value"":22},""rbx"":{""value"":11},""trap"":{""value"":133},""err"":{""value"":33554760},""r11"":{""value"":582},""rip"":{""value"":140703393680822,""matchesCrashFrame"":1},""rbp"":{""value"":140523148794384},""rsp"":{""value"":140523148794344},""r12"":{""value"":259},""rcx"":{""value"":140523148794344},""flavor"":""x86_THREAD_STATE"",""rdi"":{""value"":259}},""name"":""CrBrowserMain""},{""id"":441054,""name"":""ThreadPoolServiceThread"",""threadState"":{""r13"":{""value"":123145501986184},""rax"":{""value"":4},""rflags"":{""value"":583},""cpu"":{""value"":0},""r14"":{""value"":140523190481464},""rsi"":{""value"":0},""r8"":{""value"":4},""cr2"":{""value"":0},""rdx"":{""value"":0},""r10"":{""value"":105553116945152},""r9"":{""value"":0},""r15"":{""value"":0},""rbx"":{""value"":0},""trap"":{""value"":133},""err"":{""value"":33554801},""r11"":{""value"":582},""rip"":{""value"":140703393692278},""rbp"":{""value"":123145501986160},""rsp"":{""value"":123145501986088},""r12"":{""value"":140523213152144},""rcx"":{""value"":123145501986088},""flavor"":""x86_THREAD_STATE"",""rdi"":{""value"":13}},""frames"":[{""imageOffset"":43638,""symbol"":""kevent64"",""symbolLocation"":10,""imageIndex"":152},{""imageOffset"":66456106,""imageIndex"":91},{""imageOffset"":66455847,""imageIndex"":91},{""imageOffset"":65919580,""imageIndex"":91},{""imageOffset"":65624472,""imageIndex"":91},{""imageOffset"":66059960,""imageIndex"":91},{""imageOffset"":65958573,""imageIndex"":91},{""imageOffset"":66060362,""imageIndex"":91},{""imageOffset"":66222344,""imageIndex"":91},{""imageOffset"":24971,""symbol"":""_pthread_start"",""symbolLocation"":99,""imageIndex"":153},{""imageOffset"":6883,""symbol"":""thread_start"",""symbolLocation"":15,""imageIndex"":153}]},{""id"":441056,""name"":""ThreadPoolBackgroundWorker"",""threadState"":{""r13"":{""value"":17179869442},""rax"":{""value"":268451845},""rflags"":{""value"":514},""cpu"":{""value"":0},""r14"":{""value"":32},""rsi"":{""value"":17179869442},""r8"":{""value"":0},""cr2"":{""value"":0},""rdx"":{""value"":0},""r10"":{""value"":188029373251584},""r9"":{""value"":188029373251584},""r15"":{""value"":188029373251584},""rbx"":{""value"":123145518788000},""trap"":{""value"":133},""err"":{""value"":16777263},""r11"":{""value"":514},""rip"":{""value"":140703393652878},""rbp"":{""value"":123145518787328},""rsp"":{""value"":123145518787224},""r12"":{""value"":33000},""rcx"":{""value"":123145518787224},""flavor"":""x86_THREAD_STATE"",""rdi"":{""value"":123145518788000}},""frames"":[{""imageOffset"":4238,""symbol"":""mach_msg2_trap"",""symbolLocation"":10,""imageIndex"":152},{""imageOffset"":63608,""symbol"":""mach_msg2_internal"",""symbolLocation"":84,""imageIndex"":152},{""imageOffset"":33144,""symbol"":""mach_msg_overwrite"",""symbolLocation"":653,""imageIndex"":152},{""imageOffset"":4989,""symbol"":""mach_msg"",""symbolLocation"":19,""imageIndex"":152},{""imageOffset"":66252326,""imageIndex"":91},{""imageOffset"":66009023,""imageIndex"":91},{""imageOffset"":66011756,""imageIndex"":91},{""imageOffset"":66010589,""imageIndex"":91},{""imageOffset"":66222344,""imageIndex"":91},{""imageOffset"":24971,""symbol"":""_pthread_start"",""symbolLocation"":99,""imageIndex"":153},{""imageOffset"":6883,""symbol"":""thread_start"",""symbolLocation"":15,""imageIndex"":153}]},{""id"":441057,""name"":""Chrome_IOThread"",""threadState"":{""r13"":{""value"":123145527188840},""rax"":{""value"":4},""rflags"":{""value"":583},""cpu"":{""value"":0},""r14"":{""value"":140523219529848},""rsi"":{""value"":0},""r8"":{""value"":3},""cr2"":{""value"":0},""rdx"":{""value"":0},""r10"":{""value"":105553132446144},""r9"":{""value"":0},""r15"":{""value"":0},""rbx"":{""value"":0},""trap"":{""value"":133},""err"":{""value"":33554801},""r11"":{""value"":582},""rip"":{""value"":140703393692278},""rbp"":{""value"":123145527188816},""rsp"":{""value"":123145527188744},""r12"":{""value"":140523220471776},""rcx"":{""value"":123145527188744},""flavor"":""x86_THREAD_STATE"",""rdi"":{""value"":14}},""frames"":[{""imageOffset"":43638,""symbol"":""kevent64"",""symbolLocation"":10,""imageIndex"":152},{""imageOffset"":66456106,""imageIndex"":91},{""imageOffset"":66455847,""imageIndex"":91},{""imageOffset"":65919580,""imageIndex"":91},{""imageOffset"":65624472,""imageIndex"":91},{""imageOffset"":66059960,""imageIndex"":91},{""imageOffset"":48386978,""imageIndex"":91},{""imageOffset"":66060362,""imageIndex"":91},{""imageOffset"":66222344,""imageIndex"":91},{""imageOffset"":24971,""symbol"":""_pthread_start"",""symbolLocation"":99,""imageIndex"":153},{""imageOffset"":6883,""symbol"":""thread_start"",""symbolLocation"":15,""imageIndex"":153}]},{""id"":441058,""name"":""NetworkConfigWatcher"",""threadState"":{""r13"":{""value"":17179869186},""rax"":{""value"":268451845},""rflags"":{""value"":514},""cpu"":{""value"":0},""r14"":{""value"":32},""rsi"":{""value"":17179869186},""r8"":{""value"":0},""cr2"":{""value"":0},""rdx"":{""value"":0},""r10"":{""value"":199024489529344},""r9"":{""value"":199024489529344},""r15"":{""value"":199024489529344},""rbx"":{""value"":123145535589520},""trap"":{""value"":133},""err"":{""value"":16777263},""r11"":{""value"":514},""rip"":{""value"":140703393652878},""rbp"":{""value"":123145535588848},""rsp"":{""value"":123145535588744},""r12"":{""value"":0},""rcx"":{""value"":123145535588744},""flavor"":""x86_THREAD_STATE"",""rdi"":{""value"":123145535589520}},""frames"":[{""imageOffset"":4238,""symbol"":""mach_msg2_trap"",""symbolLocation"":10,""imageIndex"":152},{""imageOffset"":63608,""symbol"":""mach_msg2_internal"",""symbolLocation"":84,""imageIndex"":152},{""imageOffset"":33144,""symbol"":""mach_msg_overwrite"",""symbolLocation"":653,""imageIndex"":152},{""imageOffset"":4989,""symbol"":""mach_msg"",""symbolLocation"":19,""imageIndex"":152},{""imageOffset"":66252326,""imageIndex"":91},{""imageOffset"":66251759,""imageIndex"":91},{""imageOffset"":65421769,""imageIndex"":91},{""imageOffset"":65919580,""imageIndex"":91},{""imageOffset"":65624472,""imageIndex"":91},{""imageOffset"":66059960,""imageIndex"":91},{""imageOffset"":66060362,""imageIndex"":91},{""imageOffset"":66222344,""imageIndex"":91},{""imageOffset"":24971,""symbol"":""_pthread_start"",""symbolLocation"":99,""imageIndex"":153},{""imageOffset"":6883,""symbol"":""thread_start"",""symbolLocation"":15,""imageIndex"":153}]},{""id"":441061,""name"":""CompositorTileWorker1"",""threadState"":{""r13"":{""value"":2203318223616},""rax"":{""value"":260},""rflags"":{""value"":583},""cpu"":{""value"":0},""r14"":{""value"":123145560793088},""rsi"":{""value"":2203318223616},""r8"":{""value"":0},""cr2"":{""value"":0},""rdx"":{""value"":512},""r10"":{""value"":0},""r9"":{""value"":161},""r15"":{""value"":512},""rbx"":{""value"":22},""trap"":{""value"":133},""err"":{""value"":33554737},""r11"":{""value"":582},""rip"":{""value"":140703393664058},""rbp"":{""value"":123145560792768},""rsp"":{""value"":123145560792616},""r12"":{""value"":0},""rcx"":{""value"":123145560792616},""flavor"":""x86_THREAD_STATE"",""rdi"":{""value"":140523217092472}},""frames"":[{""imageOffset"":15418,""symbol"":""__psynch_cvwait"",""symbolLocation"":10,""imageIndex"":152},{""imageOffset"":26355,""symbol"":""_pthread_cond_wait"",""symbolLocation"":1211,""imageIndex"":153},{""imageOffset"":66219291,""imageIndex"":91},{""imageOffset"":100616493,""imageIndex"":91},{""imageOffset"":66222344,""imageIndex"":91},{""imageOffset"":24971,""symbol"":""_pthread_start"",""symbolLocation"":99,""imageIndex"":153},{""imageOffset"":6883,""symbol"":""thread_start"",""symbolLocation"":15,""imageIndex"":153}]},{""id"":441063,""name"":""Chrome_InProcGpuThread"",""threadState"":{""r13"":{""value"":17179869186},""rax"":{""value"":268451845},""rflags"":{""value"":514},""cpu"":{""value"":0},""r14"":{""value"":32},""rsi"":{""value"":17179869186},""r8"":{""value"":0},""cr2"":{""value"":0},""rdx"":{""value"":0},""r10"":{""value"":215517163945984},""r9"":{""value"":215517163945984},""r15"":{""value"":215517163945984},""rbx"":{""value"":123145577594000},""trap"":{""value"":133},""err"":{""value"":16777263},""r11"":{""value"":514},""rip"":{""value"":140703393652878},""rbp"":{""value"":123145577593328},""rsp"":{""value"":123145577593224},""r12"":{""value"":0},""rcx"":{""value"":123145577593224},""flavor"":""x86_THREAD_STATE"",""rdi"":{""value"":123145577594000}},""frames"":[{""imageOffset"":4238,""symbol"":""mach_msg2_trap"",""symbolLocation"":10,""imageIndex"":152},{""imageOffset"":63608,""symbol"":""mach_msg2_internal"",""symbolLocation"":84,""imageIndex"":152},{""imageOffset"":33144,""symbol"":""mach_msg_overwrite"",""symbolLocation"":653,""imageIndex"":152},{""imageOffset"":4989,""symbol"":""mach_msg"",""symbolLocation"":19,""imageIndex"":152},{""imageOffset"":66252326,""imageIndex"":91},{""imageOffset"":66251759,""imageIndex"":91},{""imageOffset"":65421769,""imageIndex"":91},{""imageOffset"":65919580,""imageIndex"":91},{""imageOffset"":65624472,""imageIndex"":91},{""imageOffset"":66059960,""imageIndex"":91},{""imageOffset"":66060362,""imageIndex"":91},{""imageOffset"":66222344,""imageIndex"":91},{""imageOffset"":24971,""symbol"":""_pthread_start"",""symbolLocation"":99,""imageIndex"":153},{""imageOffset"":6883,""symbol"":""thread_start"",""symbolLocation"":15,""imageIndex"":153}]},{""id"":441064,""name"":""Chrome_ChildIOThread"",""threadState"":{""r13"":{""value"":123145585995176},""rax"":{""value"":4},""rflags"":{""value"":583},""cpu"":{""value"":0},""r14"":{""value"":140523216710264},""rsi"":{""value"":0},""r8"":{""value"":1},""cr2"":{""value"":0},""rdx"":{""value"":0},""r10"":{""value"":105553179139104},""r9"":{""value"":0},""r15"":{""value"":0},""rbx"":{""value"":0},""trap"":{""value"":133},""err"":{""value"":33554801},""r11"":{""value"":582},""rip"":{""value"":140703393692278},""rbp"":{""value"":123145585995152},""rsp"":{""value"":123145585995080},""r12"":{""value"":140523225530800},""rcx"":{""value"":123145585995080},""flavor"":""x86_THREAD_STATE"",""rdi"":{""value"":23}},""frames"":[{""imageOffset"":43638,""symbol"":""kevent64"",""symbolLocation"":10,""imageIndex"":152},{""imageOffset"":66456106,""imageIndex"":91},{""imageOffset"":66455847,""imageIndex"":91},{""imageOffset"":65919580,""imageIndex"":91},{""imageOffset"":65624472,""imageIndex"":91},{""imageOffset"":66059960,""imageIndex"":91},{""imageOffset"":66060362,""imageIndex"":91},{""imageOffset"":66222344,""imageIndex"":91},{""imageOffset"":24971,""symbol"":""_pthread_start"",""symbolLocation"":99,""imageIndex"":153},{""imageOffset"":6883,""symbol"":""thread_start"",""symbolLocation"":15,""imageIndex"":153}]},{""id"":441066,""name"":""NetworkConfigWatcher"",""threadState"":{""r13"":{""value"":17179869186},""rax"":{""value"":268451845},""rflags"":{""value"":514},""cpu"":{""value"":0},""r14"":{""value"":32},""rsi"":{""value"":17179869186},""r8"":{""value"":0},""cr2"":{""value"":0},""rdx"":{""value"":0},""r10"":{""value"":372747326717952},""r9"":{""value"":372747326717952},""r15"":{""value"":372747326717952},""rbx"":{""value"":123145594395792},""trap"":{""value"":133},""err"":{""value"":16777263},""r11"":{""value"":514},""rip"":{""value"":140703393652878},""rbp"":{""value"":123145594395120},""rsp"":{""value"":123145594395016},""r12"":{""value"":0},""rcx"":{""value"":123145594395016},""flavor"":""x86_THREAD_STATE"",""rdi"":{""value"":123145594395792}},""frames"":[{""imageOffset"":4238,""symbol"":""mach_msg2_trap"",""symbolLocation"":10,""imageIndex"":152},{""imageOffset"":63608,""symbol"":""mach_msg2_internal"",""symbolLocation"":84,""imageIndex"":152},{""imageOffset"":33144,""symbol"":""mach_msg_overwrite"",""symbolLocation"":653,""imageIndex"":152},{""imageOffset"":4989,""symbol"":""mach_msg"",""symbolLocation"":19,""imageIndex"":152},{""imageOffset"":66252326,""imageIndex"":91},{""imageOffset"":66251759,""imageIndex"":91},{""imageOffset"":65421769,""imageIndex"":91},{""imageOffset"":65919580,""imageIndex"":91},{""imageOffset"":65624472,""imageIndex"":91},{""imageOffset"":66059960,""imageIndex"":91},{""imageOffset"":66060362,""imageIndex"":91},{""imageOffset"":66222344,""imageIndex"":91},{""imageOffset"":24971,""symbol"":""_pthread_start"",""symbolLocation"":99,""imageIndex"":153},{""imageOffset"":6883,""symbol"":""thread_start"",""symbolLocation"":15,""imageIndex"":153}]},{""id"":441067,""name"":""VizCompositorThread"",""threadState"":{""r13"":{""value"":17179869442},""rax"":{""value"":268451845},""rflags"":{""value"":514},""cpu"":{""value"":0},""r14"":{""value"":32},""rsi"":{""value"":17179869442},""r8"":{""value"":0},""cr2"":{""value"":0},""rdx"":{""value"":0},""r10"":{""value"":286985419751424},""r9"":{""value"":286985419751424},""r15"":{""value"":286985419751424},""rbx"":{""value"":123145602796720},""trap"":{""value"":133},""err"":{""value"":16777263},""r11"":{""value"":514},""rip"":{""value"":140703393652878},""rbp"":{""value"":123145602796048},""rsp"":{""value"":123145602795944},""r12"":{""value"":15},""rcx"":{""value"":123145602795944},""flavor"":""x86_THREAD_STATE"",""rdi"":{""value"":123145602796720}},""frames"":[{""imageOffset"":4238,""symbol"":""mach_msg2_trap"",""symbolLocation"":10,""imageIndex"":152},{""imageOffset"":63608,""symbol"":""mach_msg2_internal"",""symbolLocation"":84,""imageIndex"":152},{""imageOffset"":33144,""symbol"":""mach_msg_overwrite"",""symbolLocation"":653,""imageIndex"":152},{""imageOffset"":4989,""symbol"":""mach_msg"",""symbolLocation"":19,""imageIndex"":152},{""imageOffset"":66252326,""imageIndex"":91},{""imageOffset"":65421672,""imageIndex"":91},{""imageOffset"":65919580,""imageIndex"":91},{""imageOffset"":65624472,""imageIndex"":91},{""imageOffset"":66059960,""imageIndex"":91},{""imageOffset"":66060362,""imageIndex"":91},{""imageOffset"":66222344,""imageIndex"":91},{""imageOffset"":24971,""symbol"":""_pthread_start"",""symbolLocation"":99,""imageIndex"":153},{""imageOffset"":6883,""symbol"":""thread_start"",""symbolLocation"":15,""imageIndex"":153}]},{""id"":441080,""name"":""NetworkService"",""threadState"":{""r13"":{""value"":123145611197864},""rax"":{""value"":4},""rflags"":{""value"":583},""cpu"":{""value"":0},""r14"":{""value"":140523227091480},""rsi"":{""value"":0},""r8"":{""value"":2},""cr2"":{""value"":0},""rdx"":{""value"":0},""r10"":{""value"":105553134697088},""r9"":{""value"":0},""r15"":{""value"":0},""rbx"":{""value"":0},""trap"":{""value"":133},""err"":{""value"":33554801},""r11"":{""value"":582},""rip"":{""value"":140703393692278},""rbp"":{""value"":123145611197840},""rsp"":{""value"":123145611197768},""r12"":{""value"":140523255102048},""rcx"":{""value"":123145611197768},""flavor"":""x86_THREAD_STATE"",""rdi"":{""value"":24}},""frames"":[{""imageOffset"":43638,""symbol"":""kevent64"",""symbolLocation"":10,""imageIndex"":152},{""imageOffset"":66456106,""imageIndex"":91},{""imageOffset"":66455847,""imageIndex"":91},{""imageOffset"":65919580,""imageIndex"":91},{""imageOffset"":65624472,""imageIndex"":91},{""imageOffset"":66059960,""imageIndex"":91},{""imageOffset"":66060362,""imageIndex"":91},{""imageOffset"":66222344,""imageIndex"":91},{""imageOffset"":24971,""symbol"":""_pthread_start"",""symbolLocation"":99,""imageIndex"":153},{""imageOffset"":6883,""symbol"":""thread_start"",""symbolLocation"":15,""imageIndex"":153}]},{""id"":441081,""name"":""NetworkConfigWatcher"",""threadState"":{""r13"":{""value"":17179869186},""rax"":{""value"":268451845},""rflags"":{""value"":514},""cpu"":{""value"":0},""r14"":{""value"":32},""rsi"":{""value"":17179869186},""r8"":{""value"":0},""cr2"":{""value"":0},""rdx"":{""value"":0},""r10"":{""value"":297980536029184},""r9"":{""value"":297980536029184},""r15"":{""value"":297980536029184},""rbx"":{""value"":123145619598480},""trap"":{""value"":133},""err"":{""value"":16777263},""r11"":{""value"":514},""rip"":{""value"":140703393652878},""rbp"":{""value"":123145619597808},""rsp"":{""value"":123145619597704},""r12"":{""value"":0},""rcx"":{""value"":123145619597704},""flavor"":""x86_THREAD_STATE"",""rdi"":{""value"":123145619598480}},""frames"":[{""imageOffset"":4238,""symbol"":""mach_msg2_trap"",""symbolLocation"":10,""imageIndex"":152},{""imageOffset"":63608,""symbol"":""mach_msg2_internal"",""symbolLocation"":84,""imageIndex"":152},{""imageOffset"":33144,""symbol"":""mach_msg_overwrite"",""symbolLocation"":653,""imageIndex"":152},{""imageOffset"":4989,""symbol"":""mach_msg"",""symbolLocation"":19,""imageIndex"":152},{""imageOffset"":66252326,""imageIndex"":91},{""imageOffset"":66251759,""imageIndex"":91},{""imageOffset"":65421769,""imageIndex"":91},{""imageOffset"":65919580,""imageIndex"":91},{""imageOffset"":65624472,""imageIndex"":91},{""imageOffset"":66059960,""imageIndex"":91},{""imageOffset"":66060362,""imageIndex"":91},{""imageOffset"":66222344,""imageIndex"":91},{""imageOffset"":24971,""symbol"":""_pthread_start"",""symbolLocation"":99,""imageIndex"":153},{""imageOffset"":6883,""symbol"":""thread_start"",""symbolLocation"":15,""imageIndex"":153}]},{""id"":441082,""name"":""ThreadPoolSingleThreadForegroundBlocking0"",""threadState"":{""r13"":{""value"":17179869186},""rax"":{""value"":268451845},""rflags"":{""value"":514},""cpu"":{""value"":0},""r14"":{""value"":32},""rsi"":{""value"":17179869186},""r8"":{""value"":0},""cr2"":{""value"":0},""rdx"":{""value"":0},""r10"":{""value"":348558070906880},""r9"":{""value"":348558070906880},""r15"":{""value"":348558070906880},""rbx"":{""value"":123145627999648},""trap"":{""value"":133},""err"":{""value"":16777263},""r11"":{""value"":514},""rip"":{""value"":140703393652878},""rbp"":{""value"":123145627998976},""rsp"":{""value"":123145627998872},""r12"":{""value"":0},""rcx"":{""value"":123145627998872},""flavor"":""x86_THREAD_STATE"",""rdi"":{""value"":123145627999648}},""frames"":[{""imageOffset"":4238,""symbol"":""mach_msg2_trap"",""symbolLocation"":10,""imageIndex"":152},{""imageOffset"":63608,""symbol"":""mach_msg2_internal"",""symbolLocation"":84,""imageIndex"":152},{""imageOffset"":33144,""symbol"":""mach_msg_overwrite"",""symbolLocation"":653,""imageIndex"":152},{""imageOffset"":4989,""symbol"":""mach_msg"",""symbolLocation"":19,""imageIndex"":152},{""imageOffset"":66252326,""imageIndex"":91},{""imageOffset"":66009023,""imageIndex"":91},{""imageOffset"":66011756,""imageIndex"":91},{""imageOffset"":66010829,""imageIndex"":91},{""imageOffset"":66222344,""imageIndex"":91},{""imageOffset"":24971,""symbol"":""_pthread_start"",""symbolLocation"":99,""imageIndex"":153},{""imageOffset"":6883,""symbol"":""thread_start"",""symbolLocation"":15,""imageIndex"":153}]},{""id"":441107,""name"":""NetworkConfigWatcher"",""threadState"":{""r13"":{""value"":17179869186},""rax"":{""value"":268451845},""rflags"":{""value"":514},""cpu"":{""value"":0},""r14"":{""value"":32},""rsi"":{""value"":17179869186},""r8"":{""value"":0},""cr2"":{""value"":0},""rdx"":{""value"":0},""r10"":{""value"":561880506564608},""r9"":{""value"":561880506564608},""r15"":{""value"":561880506564608},""rbx"":{""value"":123145638546576},""trap"":{""value"":133},""err"":{""value"":16777263},""r11"":{""value"":514},""rip"":{""value"":140703393652878},""rbp"":{""value"":123145638545904},""rsp"":{""value"":123145638545800},""r12"":{""value"":0},""rcx"":{""value"":123145638545800},""flavor"":""x86_THREAD_STATE"",""rdi"":{""value"":123145638546576}},""frames"":[{""imageOffset"":4238,""symbol"":""mach_msg2_trap"",""symbolLocation"":10,""imageIndex"":152},{""imageOffset"":63608,""symbol"":""mach_msg2_internal"",""symbolLocation"":84,""imageIndex"":152},{""imageOffset"":33144,""symbol"":""mach_msg_overwrite"",""symbolLocation"":653,""imageIndex"":152},{""imageOffset"":4989,""symbol"":""mach_msg"",""symbolLocation"":19,""imageIndex"":152},{""imageOffset"":66252326,""imageIndex"":91},{""imageOffset"":66251759,""imageIndex"":91},{""imageOffset"":65421769,""imageIndex"":91},{""imageOffset"":65919580,""imageIndex"":91},{""imageOffset"":65624472,""imageIndex"":91},{""imageOffset"":66059960,""imageIndex"":91},{""imageOffset"":66060362,""imageIndex"":91},{""imageOffset"":66222344,""imageIndex"":91},{""imageOffset"":24971,""symbol"":""_pthread_start"",""symbolLocation"":99,""imageIndex"":153},{""imageOffset"":6883,""symbol"":""thread_start"",""symbolLocation"":15,""imageIndex"":153}]},{""id"":441209,""frames"":[{""imageOffset"":15418,""symbol"":""__psynch_cvwait"",""symbolLocation"":10,""imageIndex"":152},{""imageOffset"":26355,""symbol"":""_pthread_cond_wait"",""symbolLocation"":1211,""imageIndex"":153},{""imageOffset"":3466879,""symbol"":""blas_thread_server"",""symbolLocation"":207,""imageIndex"":129},{""imageOffset"":24971,""symbol"":""_pthread_start"",""symbolLocation"":99,""imageIndex"":153},{""imageOffset"":6883,""symbol"":""thread_start"",""symbolLocation"":15,""imageIndex"":153}],""threadState"":{""r13"":{""value"":206712481037568},""rax"":{""value"":260},""rflags"":{""value"":583},""cpu"":{""value"":0},""r14"":{""value"":123145489829888},""rsi"":{""value"":206712481037568},""r8"":{""value"":0},""cr2"":{""value"":0},""rdx"":{""value"":48128},""r10"":{""value"":0},""r9"":{""value"":160},""r15"":{""value"":48128},""rbx"":{""value"":22},""trap"":{""value"":133},""err"":{""value"":33554737},""r11"":{""value"":582},""rip"":{""value"":140703393664058},""rbp"":{""value"":123145489829744},""rsp"":{""value"":123145489829592},""r12"":{""value"":0},""rcx"":{""value"":123145489829592},""flavor"":""x86_THREAD_STATE"",""rdi"":{""value"":4568944720,""symbolLocation"":80,""symbol"":""thread_status""}}},{""id"":441210,""frames"":[{""imageOffset"":15418,""symbol"":""__psynch_cvwait"",""symbolLocation"":10,""imageIndex"":152},{""imageOffset"":26355,""symbol"":""_pthread_cond_wait"",""symbolLocation"":1211,""imageIndex"":153},{""imageOffset"":3466879,""symbol"":""blas_thread_server"",""symbolLocation"":207,""imageIndex"":129},{""imageOffset"":24971,""symbol"":""_pthread_start"",""symbolLocation"":99,""imageIndex"":153},{""imageOffset"":6883,""symbol"":""thread_start"",""symbolLocation"":15,""imageIndex"":153}],""threadState"":{""r13"":{""value"":206712481037568},""rax"":{""value"":260},""rflags"":{""value"":583},""cpu"":{""value"":0},""r14"":{""value"":123145490366464},""rsi"":{""value"":206712481037568},""r8"":{""value"":0},""cr2"":{""value"":0},""rdx"":{""value"":48128},""r10"":{""value"":0},""r9"":{""value"":160},""r15"":{""value"":48128},""rbx"":{""value"":22},""trap"":{""value"":133},""err"":{""value"":33554737},""r11"":{""value"":582},""rip"":{""value"":140703393664058},""rbp"":{""value"":123145490366320},""rsp"":{""value"":123145490366168},""r12"":{""value"":0},""rcx"":{""value"":123145490366168},""flavor"":""x86_THREAD_STATE"",""rdi"":{""value"":4568944848,""symbolLocation"":208,""symbol"":""thread_status""}}},{""id"":441211,""frames"":[{""imageOffset"":15418,""symbol"":""__psynch_cvwait"",""symbolLocation"":10,""imageIndex"":152},{""imageOffset"":26355,""symbol"":""_pthread_cond_wait"",""symbolLocation"":1211,""imageIndex"":153},{""imageOffset"":3466879,""symbol"":""blas_thread_server"",""symbolLocation"":207,""imageIndex"":129},{""imageOffset"":24971,""symbol"":""_pthread_start"",""symbolLocation"":99,""imageIndex"":153},{""imageOffset"":6883,""symbol"":""thread_start"",""symbolLocation"":15,""imageIndex"":153}],""threadState"":{""r13"":{""value"":4294967552},""rax"":{""value"":260},""rflags"":{""value"":583},""cpu"":{""value"":0},""r14"":{""value"":123145490903040},""rsi"":{""value"":4294967552},""r8"":{""value"":0},""cr2"":{""value"":0},""rdx"":{""value"":0},""r10"":{""value"":0},""r9"":{""value"":160},""r15"":{""value"":0},""rbx"":{""value"":22},""trap"":{""value"":133},""err"":{""value"":33554737},""r11"":{""value"":582},""rip"":{""value"":140703393664058},""rbp"":{""value"":123145490902896},""rsp"":{""value"":123145490902744},""r12"":{""value"":0},""rcx"":{""value"":123145490902744},""flavor"":""x86_THREAD_STATE"",""rdi"":{""value"":4568944976,""symbolLocation"":336,""symbol"":""thread_status""}}},{""id"":441334,""name"":""com.apple.NSEventThread"",""threadState"":{""r13"":{""value"":21592279046},""rax"":{""value"":268451845},""rflags"":{""value"":518},""cpu"":{""value"":0},""r14"":{""value"":2},""rsi"":{""value"":21592279046},""r8"":{""value"":0},""cr2"":{""value"":0},""rdx"":{""value"":8589934592},""r10"":{""value"":748797483286528},""r9"":{""value"":748797483286528},""r15"":{""value"":748797483286528},""rbx"":{""value"":123145491972192},""trap"":{""value"":133},""err"":{""value"":16777263},""r11"":{""value"":518},""rip"":{""value"":140703393652878},""rbp"":{""value"":123145491972032},""rsp"":{""value"":123145491971928},""r12"":{""value"":4294967295},""rcx"":{""value"":123145491971928},""flavor"":""x86_THREAD_STATE"",""rdi"":{""value"":123145491972192}},""frames"":[{""imageOffset"":4238,""symbol"":""mach_msg2_trap"",""symbolLocation"":10,""imageIndex"":152},{""imageOffset"":63608,""symbol"":""mach_msg2_internal"",""symbolLocation"":84,""imageIndex"":152},{""imageOffset"":33144,""symbol"":""mach_msg_overwrite"",""symbolLocation"":653,""imageIndex"":152},{""imageOffset"":4989,""symbol"":""mach_msg"",""symbolLocation"":19,""imageIndex"":152},{""imageOffset"":508357,""symbol"":""__CFRunLoopServiceMachPort"",""symbolLocation"":143,""imageIndex"":157},{""imageOffset"":502837,""symbol"":""__CFRunLoopRun"",""symbolLocation"":1371,""imageIndex"":157},{""imageOffset"":499986,""symbol"":""CFRunLoopRunSpecific"",""symbolLocation"":557,""imageIndex"":157},{""imageOffset"":1692316,""symbol"":""_NSEventThread"",""symbolLocation"":122,""imageIndex"":159},{""imageOffset"":24971,""symbol"":""_pthread_start"",""symbolLocation"":99,""imageIndex"":153},{""imageOffset"":6883,""symbol"":""thread_start"",""symbolLocation"":15,""imageIndex"":153}]},{""id"":441469,""name"":""MemoryInfra"",""threadState"":{""r13"":{""value"":17179869186},""rax"":{""value"":268451845},""rflags"":{""value"":514},""cpu"":{""value"":0},""r14"":{""value"":32},""rsi"":{""value"":17179869186},""r8"":{""value"":0},""cr2"":{""value"":0},""rdx"":{""value"":0},""r10"":{""value"":701501303422976},""r9"":{""value"":701501303422976},""r15"":{""value"":701501303422976},""rbx"":{""value"":123145716264080},""trap"":{""value"":133},""err"":{""value"":16777263},""r11"":{""value"":514},""rip"":{""value"":140703393652878},""rbp"":{""value"":123145716263408},""rsp"":{""value"":123145716263304},""r12"":{""value"":0},""rcx"":{""value"":123145716263304},""flavor"":""x86_THREAD_STATE"",""rdi"":{""value"":123145716264080}},""frames"":[{""imageOffset"":4238,""symbol"":""mach_msg2_trap"",""symbolLocation"":10,""imageIndex"":152},{""imageOffset"":63608,""symbol"":""mach_msg2_internal"",""symbolLocation"":84,""imageIndex"":152},{""imageOffset"":33144,""symbol"":""mach_msg_overwrite"",""symbolLocation"":653,""imageIndex"":152},{""imageOffset"":4989,""symbol"":""mach_msg"",""symbolLocation"":19,""imageIndex"":152},{""imageOffset"":66252326,""imageIndex"":91},{""imageOffset"":66251759,""imageIndex"":91},{""imageOffset"":65421769,""imageIndex"":91},{""imageOffset"":65919580,""imageIndex"":91},{""imageOffset"":65624472,""imageIndex"":91},{""imageOffset"":66059960,""imageIndex"":91},{""imageOffset"":66060362,""imageIndex"":91},{""imageOffset"":66222344,""imageIndex"":91},{""imageOffset"":24971,""symbol"":""_pthread_start"",""symbolLocation"":99,""imageIndex"":153},{""imageOffset"":6883,""symbol"":""thread_start"",""symbolLocation"":15,""imageIndex"":153}]},{""id"":441470,""name"":""ThreadPoolSingleThreadSharedBackgroundBlocking1"",""threadState"":{""r13"":{""value"":17179869186},""rax"":{""value"":268451845},""rflags"":{""value"":514},""cpu"":{""value"":0},""r14"":{""value"":32},""rsi"":{""value"":17179869186},""r8"":{""value"":0},""cr2"":{""value"":0},""rdx"":{""value"":0},""r10"":{""value"":611341349945344},""r9"":{""value"":611341349945344},""r15"":{""value"":611341349945344},""rbx"":{""value"":123145724665248},""trap"":{""value"":133},""err"":{""value"":16777263},""r11"":{""value"":514},""rip"":{""value"":140703393652878},""rbp"":{""value"":123145724664576},""rsp"":{""value"":123145724664472},""r12"":{""value"":0},""rcx"":{""value"":123145724664472},""flavor"":""x86_THREAD_STATE"",""rdi"":{""value"":123145724665248}},""frames"":[{""imageOffset"":4238,""symbol"":""mach_msg2_trap"",""symbolLocation"":10,""imageIndex"":152},{""imageOffset"":63608,""symbol"":""mach_msg2_internal"",""symbolLocation"":84,""imageIndex"":152},{""imageOffset"":33144,""symbol"":""mach_msg_overwrite"",""symbolLocation"":653,""imageIndex"":152},{""imageOffset"":4989,""symbol"":""mach_msg"",""symbolLocation"":19,""imageIndex"":152},{""imageOffset"":66252326,""imageIndex"":91},{""imageOffset"":66009023,""imageIndex"":91},{""imageOffset"":66011034,""imageIndex"":91},{""imageOffset"":66010637,""imageIndex"":91},{""imageOffset"":66222344,""imageIndex"":91},{""imageOffset"":24971,""symbol"":""_pthread_start"",""symbolLocation"":99,""imageIndex"":153},{""imageOffset"":6883,""symbol"":""thread_start"",""symbolLocation"":15,""imageIndex"":153}]},{""id"":447461,""name"":""ThreadPoolForegroundWorker"",""threadState"":{""r13"":{""value"":17179869442},""rax"":{""value"":268451845},""rflags"":{""value"":514},""cpu"":{""value"":0},""r14"":{""value"":32},""rsi"":{""value"":17179869442},""r8"":{""value"":0},""cr2"":{""value"":0},""rdx"":{""value"":0},""r10"":{""value"":679064394268672},""r9"":{""value"":679064394268672},""r15"":{""value"":679064394268672},""rbx"":{""value"":123145510387104},""trap"":{""value"":133},""err"":{""value"":16777263},""r11"":{""value"":514},""rip"":{""value"":140703393652878},""rbp"":{""value"":123145510386432},""rsp"":{""value"":123145510386328},""r12"":{""value"":33000},""rcx"":{""value"":123145510386328},""flavor"":""x86_THREAD_STATE"",""rdi"":{""value"":123145510387104}},""frames"":[{""imageOffset"":4238,""symbol"":""mach_msg2_trap"",""symbolLocation"":10,""imageIndex"":152},{""imageOffset"":63608,""symbol"":""mach_msg2_internal"",""symbolLocation"":84,""imageIndex"":152},{""imageOffset"":33144,""symbol"":""mach_msg_overwrite"",""symbolLocation"":653,""imageIndex"":152},{""imageOffset"":4989,""symbol"":""mach_msg"",""symbolLocation"":19,""imageIndex"":152},{""imageOffset"":66252326,""imageIndex"":91},{""imageOffset"":66009023,""imageIndex"":91},{""imageOffset"":66011756,""imageIndex"":91},{""imageOffset"":66010733,""imageIndex"":91},{""imageOffset"":66222344,""imageIndex"":91},{""imageOffset"":24971,""symbol"":""_pthread_start"",""symbolLocation"":99,""imageIndex"":153},{""imageOffset"":6883,""symbol"":""thread_start"",""symbolLocation"":15,""imageIndex"":153}]},{""id"":611279,""name"":""ThreadPoolForegroundWorker"",""threadState"":{""r13"":{""value"":17179869442},""rax"":{""value"":268451845},""rflags"":{""value"":514},""cpu"":{""value"":0},""r14"":{""value"":32},""rsi"":{""value"":17179869442},""r8"":{""value"":0},""cr2"":{""value"":0},""rdx"":{""value"":0},""r10"":{""value"":651009667891200},""r9"":{""value"":651009667891200},""r15"":{""value"":651009667891200},""rbx"":{""value"":123145545063840},""trap"":{""value"":133},""err"":{""value"":16777263},""r11"":{""value"":514},""rip"":{""value"":140703393652878},""rbp"":{""value"":123145545063168},""rsp"":{""value"":123145545063064},""r12"":{""value"":33000},""rcx"":{""value"":123145545063064},""flavor"":""x86_THREAD_STATE"",""rdi"":{""value"":123145545063840}},""frames"":[{""imageOffset"":4238,""symbol"":""mach_msg2_trap"",""symbolLocation"":10,""imageIndex"":152},{""imageOffset"":63608,""symbol"":""mach_msg2_internal"",""symbolLocation"":84,""imageIndex"":152},{""imageOffset"":33144,""symbol"":""mach_msg_overwrite"",""symbolLocation"":653,""imageIndex"":152},{""imageOffset"":4989,""symbol"":""mach_msg"",""symbolLocation"":19,""imageIndex"":152},{""imageOffset"":66252326,""imageIndex"":91},{""imageOffset"":66009023,""imageIndex"":91},{""imageOffset"":66011756,""imageIndex"":91},{""imageOffset"":66010733,""imageIndex"":91},{""imageOffset"":66222344,""imageIndex"":91},{""imageOffset"":24971,""symbol"":""_pthread_start"",""symbolLocation"":99,""imageIndex"":153},{""imageOffset"":6883,""symbol"":""thread_start"",""symbolLocation"":15,""imageIndex"":153}]},{""id"":611280,""name"":""ThreadPoolBackgroundWorker"",""threadState"":{""r13"":{""value"":17179869442},""rax"":{""value"":268451845},""rflags"":{""value"":514},""cpu"":{""value"":0},""r14"":{""value"":32},""rsi"":{""value"":17179869442},""r8"":{""value"":0},""cr2"":{""value"":0},""rdx"":{""value"":0},""r10"":{""value"":314043713716224},""r9"":{""value"":314043713716224},""r15"":{""value"":314043713716224},""rbx"":{""value"":123145569193376},""trap"":{""value"":133},""err"":{""value"":16777263},""r11"":{""value"":514},""rip"":{""value"":140703393652878},""rbp"":{""value"":123145569192704},""rsp"":{""value"":123145569192600},""r12"":{""value"":33000},""rcx"":{""value"":123145569192600},""flavor"":""x86_THREAD_STATE"",""rdi"":{""value"":123145569193376}},""frames"":[{""imageOffset"":4238,""symbol"":""mach_msg2_trap"",""symbolLocation"":10,""imageIndex"":152},{""imageOffset"":63608,""symbol"":""mach_msg2_internal"",""symbolLocation"":84,""imageIndex"":152},{""imageOffset"":33144,""symbol"":""mach_msg_overwrite"",""symbolLocation"":653,""imageIndex"":152},{""imageOffset"":4989,""symbol"":""mach_msg"",""symbolLocation"":19,""imageIndex"":152},{""imageOffset"":66252326,""imageIndex"":91},{""imageOffset"":66009023,""imageIndex"":91},{""imageOffset"":66011756,""imageIndex"":91},{""imageOffset"":66010589,""imageIndex"":91},{""imageOffset"":66222344,""imageIndex"":91},{""imageOffset"":24971,""symbol"":""_pthread_start"",""symbolLocation"":99,""imageIndex"":153},{""imageOffset"":6883,""symbol"":""thread_start"",""symbolLocation"":15,""imageIndex"":153}]},{""id"":612175,""frames"":[{""imageOffset"":6848,""symbol"":""start_wqthread"",""symbolLocation"":0,""imageIndex"":153}],""threadState"":{""r13"":{""value"":0},""rax"":{""value"":33554800},""rflags"":{""value"":512},""cpu"":{""value"":0},""r14"":{""value"":1},""rsi"":{""value"":154171},""r8"":{""value"":409604},""cr2"":{""value"":0},""rdx"":{""value"":123145491988480},""r10"":{""value"":0},""r9"":{""value"":18446744073709551615},""r15"":{""value"":123145492511608},""rbx"":{""value"":123145492512768},""trap"":{""value"":133},""err"":{""value"":33554800},""r11"":{""value"":582},""rip"":{""value"":140703393897152},""rbp"":{""value"":0},""rsp"":{""value"":123145492512768},""r12"":{""value"":5193734},""rcx"":{""value"":0},""flavor"":""x86_THREAD_STATE"",""rdi"":{""value"":123145492512768}}},{""id"":612188,""frames"":[{""imageOffset"":6848,""symbol"":""start_wqthread"",""symbolLocation"":0,""imageIndex"":153}],""threadState"":{""r13"":{""value"":0},""rax"":{""value"":33554800},""rflags"":{""value"":512},""cpu"":{""value"":0},""r14"":{""value"":1},""rsi"":{""value"":176415},""r8"":{""value"":409602},""cr2"":{""value"":0},""rdx"":{""value"":123145535602688},""r10"":{""value"":0},""r9"":{""value"":18446744073709551615},""r15"":{""value"":123145536125816},""rbx"":{""value"":123145536126976},""trap"":{""value"":133},""err"":{""value"":33554800},""r11"":{""value"":582},""rip"":{""value"":140703393897152},""rbp"":{""value"":0},""rsp"":{""value"":123145536126976},""r12"":{""value"":5193730},""rcx"":{""value"":0},""flavor"":""x86_THREAD_STATE"",""rdi"":{""value"":123145536126976}}},{""id"":612992,""frames"":[{""imageOffset"":6848,""symbol"":""start_wqthread"",""symbolLocation"":0,""imageIndex"":153}],""threadState"":{""r13"":{""value"":0},""rax"":{""value"":33554800},""rflags"":{""value"":512},""cpu"":{""value"":0},""r14"":{""value"":1},""rsi"":{""value"":48563},""r8"":{""value"":409604},""cr2"":{""value"":0},""rdx"":{""value"":123145490915328},""r10"":{""value"":0},""r9"":{""value"":18446744073709551615},""r15"":{""value"":123145491438464},""rbx"":{""value"":123145491439616},""trap"":{""value"":133},""err"":{""value"":33554800},""r11"":{""value"":582},""rip"":{""value"":140703393897152},""rbp"":{""value"":0},""rsp"":{""value"":123145491439616},""r12"":{""value"":1982472},""rcx"":{""value"":0},""flavor"":""x86_THREAD_STATE"",""rdi"":{""value"":123145491439616}}},{""id"":612993,""frames"":[{""imageOffset"":6848,""symbol"":""start_wqthread"",""symbolLocation"":0,""imageIndex"":153}],""threadState"":{""r13"":{""value"":0},""rax"":{""value"":33554800},""rflags"":{""value"":512},""cpu"":{""value"":0},""r14"":{""value"":1},""rsi"":{""value"":176211},""r8"":{""value"":409604},""cr2"":{""value"":0},""rdx"":{""value"":123145492525056},""r10"":{""value"":0},""r9"":{""value"":18446744073709551615},""r15"":{""value"":123145493048184},""rbx"":{""value"":123145493049344},""trap"":{""value"":133},""err"":{""value"":33554800},""r11"":{""value"":582},""rip"":{""value"":140703393897152},""rbp"":{""value"":0},""rsp"":{""value"":123145493049344},""r12"":{""value"":5193734},""rcx"":{""value"":0},""flavor"":""x86_THREAD_STATE"",""rdi"":{""value"":123145493049344}}},{""id"":612994,""frames"":[{""imageOffset"":6848,""symbol"":""start_wqthread"",""symbolLocation"":0,""imageIndex"":153}],""threadState"":{""r13"":{""value"":0},""rax"":{""value"":33554800},""rflags"":{""value"":512},""cpu"":{""value"":0},""r14"":{""value"":1},""rsi"":{""value"":114607},""r8"":{""value"":409604},""cr2"":{""value"":0},""rdx"":{""value"":123145493061632},""r10"":{""value"":0},""r9"":{""value"":18446744073709551615},""r15"":{""value"":123145493584768},""rbx"":{""value"":123145493585920},""trap"":{""value"":133},""err"":{""value"":33554800},""r11"":{""value"":582},""rip"":{""value"":140703393897152},""rbp"":{""value"":0},""rsp"":{""value"":123145493585920},""r12"":{""value"":1982472},""rcx"":{""value"":0},""flavor"":""x86_THREAD_STATE"",""rdi"":{""value"":123145493585920}}},{""id"":613348,""frames"":[{""imageOffset"":6848,""symbol"":""start_wqthread"",""symbolLocation"":0,""imageIndex"":153}],""threadState"":{""r13"":{""value"":0},""rax"":{""value"":0},""rflags"":{""value"":512},""cpu"":{""value"":0},""r14"":{""value"":0},""rsi"":{""value"":0},""r8"":{""value"":278532},""cr2"":{""value"":0},""rdx"":{""value"":123145536139264},""r10"":{""value"":0},""r9"":{""value"":18446744073709551615},""r15"":{""value"":0},""rbx"":{""value"":0},""trap"":{""value"":0},""err"":{""value"":0},""r11"":{""value"":0},""rip"":{""value"":140703393897152},""rbp"":{""value"":0},""rsp"":{""value"":123145536663552},""r12"":{""value"":0},""rcx"":{""value"":0},""flavor"":""x86_THREAD_STATE"",""rdi"":{""value"":123145536663552}}}], ""usedImages"" : [ [deleted to fit within ticket size limits] ], ""sharedCache"" : { ""base"" : 140703389474816, ""size"" : 25769803776, ""uuid"" : ""693edd13-ec80-3b3f-b8f3-15340ec37b23"" }, ""vmSummary"" : ""ReadOnly portion of Libraries: Total=1.3G resident=0K(0%) swapped_out_or_unallocated=1.3G(100%)\nWritable regions: Total=3.7G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=3.7G(100%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 128K 1 \nActivity Tracing 256K 1 \nCG image 12.0M 30 \nColorSync 268K 35 \nCoreAnimation 2052K 168 \nCoreGraphics 12K 2 \nCoreUI image data 4984K 38 \nFoundation 16K 1 \nKernel Alloc Once 8K 1 \nMALLOC 3.1G 555 \nMALLOC guard page 32K 8 \nMALLOC_LARGE (reserved) 256K 1 reserved VM address space (unallocated)\nMach message 16K 3 \nOpenGL GLSL 384K 4 \nSTACK GUARD 112K 28 \nStack 157.2M 29 \nStack Guard 56.0M 1 \nVM_ALLOCATE 432.4M 296 \nVM_ALLOCATE (reserved) 32.0M 1 reserved VM address space (unallocated)\n__CTF 824 1 \n__DATA 56.0M 806 \n__DATA_CONST 47.4M 438 \n__DATA_DIRTY 1698K 225 \n__FONT_DATA 2352 1 \n__GLSLBUILTINS 5174K 1 \n__LINKEDIT 213.2M 154 \n__OBJC_RO 71.9M 1 \n__OBJC_RW 2201K 2 \n__TEXT 1.0G 812 \ndyld private memory 160K 2 \nmapped file 227.6M 62 \nshared memory 3532K 35 \n=========== ======= ======= \nTOTAL 5.4G 3743 \nTOTAL, minus reserved VM space 5.4G 3743 \n"", ""legacyInfo"" : { ""threadTriggered"" : { ""name"" : ""CrBrowserMain"", ""queue"" : ""com.apple.main-thread"" } }, ""logWritingSignature"" : ""643fef17dd0c2a14b8744c0f9e24095d235fd781"", ""trialInfo"" : { ""rollouts"" : [ { ""rolloutId"" : ""62745b8e85854550ad70b6e4"", ""factorPackIds"" : { }, ""deploymentId"" : 240000073 }, { ""rolloutId"" : ""645197bf528fbf3c3af54105"", ""factorPackIds"" : { ""SIRI_VALUE_INFERENCE_PERVASIVE_ENTITY_RESOLUTION"" : ""663e65b4a1526e1ca0e288a1"" }, ""deploymentId"" : 240000002 } ], ""experiments"" : [ { ""treatmentId"" : ""c47ab4cc-c9c3-4b5d-a87c-e2433ce02597"", ""experimentId"" : ""6639bc6ba73d460582162323"", ""deploymentId"" : 400000006 }, { ""treatmentId"" : ""45f4e2a5-551b-4bc2-a2dc-19c244dda8f8"", ""experimentId"" : ""6643969b3099cf28e049862f"", ""deploymentId"" : 400000007 } ] } } ===== Log before crash start ===== UCSF ChimeraX version: 1.7.1 (2024-01-23) © 2016-2023 Regents of the University of California. All rights reserved. > open /Users/ruchigautamsharma/Desktop/25HepE525K/25HepE525KwithMava_4.cxs Opened cryosparc_P30_J279_map.mrc as #4, grid size 300,300,300, pixel 0.83, shown at level 0.047, step 1, values float32 Opened cryosparc_P30_J280_class_05_00027_volume.mrc z flip as #10, grid size 180,180,180, pixel 1.38, shown at level 0.0748, step 1, values float32 Opened cryosparc_P30_J276_map_sharp.mrc z flip as #7, grid size 300,300,300, pixel 0.83, shown at level 0.00111, step 1, values float32 Opened cryosparc_P30_J366_003_volume_map_sharp.mrc z flip as #9, grid size 300,300,300, pixel 0.83, shown at level 0.0455, step 1, values float32 Log from Fri Sep 27 17:28:16 2024UCSF ChimeraX version: 1.7.1 (2024-01-23) © 2016-2023 Regents of the University of California. All rights reserved. > open > /Users/ruchigautamsharma/Desktop/25HepE525K/25HepE525KwithMava_Interaction.cxs Opened cryosparc_P30_J279_map.mrc as #4, grid size 300,300,300, pixel 0.83, shown at level 0.047, step 1, values float32 Opened cryosparc_P30_J280_class_05_00027_volume.mrc z flip as #10, grid size 180,180,180, pixel 1.38, shown at level 0.0971, step 1, values float32 Log from Thu Sep 26 13:21:30 2024UCSF ChimeraX version: 1.7.1 (2024-01-23) © 2016-2023 Regents of the University of California. All rights reserved. > open > /Users/ruchigautamsharma/Desktop/25HepE525K/25HepE525KwithMava_Interaction.cxs Opened cryosparc_P30_J279_map.mrc as #4, grid size 300,300,300, pixel 0.83, shown at level 0.047, step 1, values float32 Opened cryosparc_P30_J280_class_00_00027_volume (1).mrc z flip as #6, grid size 180,180,180, pixel 1.38, shown at level 0.0903, step 1, values float32 Opened cryosparc_P30_J280_class_01_00027_volume.mrc z flip as #7, grid size 180,180,180, pixel 1.38, shown at level 0.0709, step 1, values float32 Opened cryosparc_P30_J280_class_02_00027_volume.mrc z flip as #8, grid size 180,180,180, pixel 1.38, shown at level 0.0781, step 1, values float32 Opened cryosparc_P30_J280_class_04_00027_volume.mrc z flip as #9, grid size 180,180,180, pixel 1.38, shown at level 0.0892, step 1, values float32 Opened cryosparc_P30_J280_class_05_00027_volume.mrc z flip as #10, grid size 180,180,180, pixel 1.38, shown at level 0.0971, step 1, values float32 Opened cryosparc_P30_J280_class_08_00027_volume.mrc z flip as #11, grid size 180,180,180, pixel 1.38, shown at level 0.0708, step 1, values float32 Log from Thu Sep 26 13:06:28 2024UCSF ChimeraX version: 1.7.1 (2024-01-23) © 2016-2023 Regents of the University of California. All rights reserved. > open ""/Users/ruchigautamsharma/Desktop/25HepE525K/interaction > 25HepE525K.cxs"" Opened cryosparc_P30_J279_map.mrc as #4, grid size 300,300,300, pixel 0.83, shown at level 0.047, step 1, values float32 Opened cryosparc_P30_J280_class_00_00027_volume (1).mrc z flip as #6, grid size 180,180,180, pixel 1.38, shown at level 0.0903, step 1, values float32 Opened cryosparc_P30_J280_class_01_00027_volume.mrc z flip as #7, grid size 180,180,180, pixel 1.38, shown at level 0.0709, step 1, values float32 Opened cryosparc_P30_J280_class_02_00027_volume.mrc z flip as #8, grid size 180,180,180, pixel 1.38, shown at level 0.0781, step 1, values float32 Opened cryosparc_P30_J280_class_04_00027_volume.mrc z flip as #9, grid size 180,180,180, pixel 1.38, shown at level 0.0892, step 1, values float32 Opened cryosparc_P30_J280_class_05_00027_volume.mrc z flip as #10, grid size 180,180,180, pixel 1.38, shown at level 0.0971, step 1, values float32 Opened cryosparc_P30_J280_class_08_00027_volume.mrc z flip as #11, grid size 180,180,180, pixel 1.38, shown at level 0.0708, step 1, values float32 Log from Wed Sep 25 04:14:14 2024UCSF ChimeraX version: 1.7.1 (2024-01-23) © 2016-2023 Regents of the University of California. All rights reserved. > open > /Users/ruchigautamsharma/Desktop/25HepE525K/25HepE525KwithMava_20240903.cxs Opened cryosparc_P30_J279_map.mrc as #4, grid size 300,300,300, pixel 0.83, shown at level 0.033, step 1, values float32 Opened cryosparc_P30_J280_class_00_00027_volume (1).mrc z flip as #6, grid size 180,180,180, pixel 1.38, shown at level 0.0903, step 1, values float32 Opened cryosparc_P30_J280_class_01_00027_volume.mrc z flip as #7, grid size 180,180,180, pixel 1.38, shown at level 0.0709, step 1, values float32 Opened cryosparc_P30_J280_class_02_00027_volume.mrc z flip as #8, grid size 180,180,180, pixel 1.38, shown at level 0.0781, step 1, values float32 Opened cryosparc_P30_J280_class_04_00027_volume.mrc z flip as #9, grid size 180,180,180, pixel 1.38, shown at level 0.0892, step 1, values float32 Opened cryosparc_P30_J280_class_05_00027_volume.mrc z flip as #10, grid size 180,180,180, pixel 1.38, shown at level 0.0971, step 1, values float32 Opened cryosparc_P30_J280_class_08_00027_volume.mrc z flip as #11, grid size 180,180,180, pixel 1.38, shown at level 0.0708, step 1, values float32 Log from Tue Sep 3 19:15:56 2024 Startup Messages --- warnings | Replacing fetcher for 'ngff' and format OME-Zarr from OME-Zarr bundle with that from OME-Zarr bundle Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR bundle with that from NMRSTAR bundle UCSF ChimeraX version: 1.7.1 (2024-01-23) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open > /Users/ruchigautamsharma/Downloads/cryosparc_P30_J277_005_volume_map_sharp.mrc Opened cryosparc_P30_J277_005_volume_map_sharp.mrc as #1, grid size 300,300,300, pixel 0.83, shown at level 0.061, step 2, values float32 > set bgColor white > color #1 #699dbfff models > color #1 #6b98bfff models > surface dust #1 size 8.3 > transparency 50 > volume #1 level 0.04162 > volume #1 step 1 > volume #1 level 0.04802 > open /Users/ruchigautamsharma/Desktop/pdbs/8g4l.pdb Summary of feedback from opening /Users/ruchigautamsharma/Desktop/pdbs/8g4l.pdb --- warning | Ignored bad PDB record found on line 1 HEADER CONTRACTILE PROTEIN 2023-02-10 XXXX Chain information for 8g4l.pdb #2 --- Chain | Description A B | No description available C D | No description available E F | No description available G H | No description available I J | No description available K L | No description available M N | No description available > ui mousemode right select Drag select of 62714 atoms, 4 pseudobonds > ui mousemode right translate > select /E 5809 atoms, 5816 bonds, 355 residues, 1 model selected > hide sel atoms > select /F 5809 atoms, 5816 bonds, 355 residues, 1 model selected > hide sel atoms > select /G 5820 atoms, 5829 bonds, 357 residues, 1 model selected > hide sel atoms > select /H 5820 atoms, 5829 bonds, 357 residues, 1 model selected > hide sel atoms > select /I 5683 atoms, 5699 bonds, 350 residues, 1 model selected > hide sel atoms > select /J 5683 atoms, 5699 bonds, 350 residues, 1 model selected > hide sel atoms > select /K 5823 atoms, 5842 bonds, 359 residues, 1 model selected > hide sel atoms > select /L 5823 atoms, 5842 bonds, 359 residues, 1 model selected > hide sel atoms > select /L 5823 atoms, 5842 bonds, 359 residues, 1 model selected > select /M 5809 atoms, 5829 bonds, 358 residues, 1 model selected > hide sel atoms > select /M 5809 atoms, 5829 bonds, 358 residues, 1 model selected > select /N 5809 atoms, 5829 bonds, 358 residues, 1 model selected > hide sel atoms > ui mousemode right select Drag select of 39683 atoms, 4 pseudobonds > select clear Drag select of 31714 atoms, 4 pseudobonds > select clear Drag select of 41883 atoms, 4 pseudobonds > show sel cartoons > hide sel atoms > ui mousemode right ""translate selected models"" > select add #2 99840 atoms, 100312 bonds, 4 pseudobonds, 6146 residues, 2 models selected > view matrix models #2,1,0,0,-145.97,0,1,0,-273.41,0,0,1,-71.128 > ui mousemode right ""rotate selected models"" > view matrix models > #2,-0.33201,0.77488,0.53789,-305.02,0.61793,-0.25218,0.7447,-219.31,0.7127,0.57962,-0.39509,36.051 > view matrix models > #2,0.68978,-0.71496,0.11413,226.44,-0.050952,0.10931,0.9927,-277.33,-0.72222,-0.69057,0.038968,877.43 > ui mousemode right translate > ui mousemode right ""translate selected models"" > view matrix models > #2,0.68978,-0.71496,0.11413,251.77,-0.050952,0.10931,0.9927,-152.19,-0.72222,-0.69057,0.038968,779.18 > ui mousemode right ""rotate selected models"" > view matrix models > #2,0.78513,-0.60169,0.14676,156.66,0.1682,0.43522,0.88447,-322.45,-0.59606,-0.66974,0.44291,558.11 > view matrix models > #2,-0.50413,0.63042,0.59027,-182.3,0.83794,0.19158,0.51104,-264.56,0.20909,0.75224,-0.62484,116.61 > ui mousemode right ""translate selected models"" > view matrix models > #2,-0.50413,0.63042,0.59027,-238.07,0.83794,0.19158,0.51104,-324.86,0.20909,0.75224,-0.62484,-90.886 > view matrix models > #2,-0.50413,0.63042,0.59027,-157.14,0.83794,0.19158,0.51104,-349.51,0.20909,0.75224,-0.62484,-89.187 > ui mousemode right ""rotate selected models"" > view matrix models > #2,-0.64055,0.44273,0.62745,-45.163,0.76397,0.28458,0.57911,-397.18,0.077832,0.8503,-0.52052,-136.51 > view matrix models > #2,-0.53777,0.61178,0.58011,-133.79,0.81962,0.21814,0.52975,-363.7,0.19755,0.76035,-0.61874,-91.81 > ui mousemode right select Drag select of 57 atoms, 260 residues > hide sel cartoons > hide sel atoms Drag select of 68 residues Drag select of 120 residues > hide sel cartoons > select add #2 99840 atoms, 100312 bonds, 4 pseudobonds, 6146 residues, 2 models selected > ui mousemode right ""translate selected models"" > view matrix models > #2,-0.53777,0.61178,0.58011,-133.74,0.81962,0.21814,0.52975,-360.37,0.19755,0.76035,-0.61874,-108 > ui mousemode right ""rotate selected models"" > view matrix models > #2,-0.82313,0.40245,0.40062,100.33,0.56745,0.60968,0.55344,-466.49,-0.021518,0.68288,-0.73021,26.515 > open /Users/ruchigautamsharma/Desktop/pdbs/8act.pdb 8act.pdb title: Structure of the human β-cardiac myosin folded-back off state [more info...] Chain information for 8act.pdb #3 --- Chain | Description | UniProt A B | myosin-7 | MYH7_HUMAN 3-906 C D | myosin light chain 3 | MYL3_HUMAN 39-195 E F | myosin regulatory light chain 2, ventricular/cardiac muscle isoform | MLRV_HUMAN 20-163 Non-standard residues in 8act.pdb #3 --- ADP — adenosine-5'-diphosphate MG — magnesium ion PO4 — phosphate ion > select add #3 118674 atoms, 119507 bonds, 23 pseudobonds, 8474 residues, 5 models selected > select subtract #2 18834 atoms, 19195 bonds, 19 pseudobonds, 2328 residues, 3 models selected > show sel cartoons > hide sel atoms > ui mousemode right ""translate selected models"" > view matrix models #3,1,0,0,4.2373,0,1,0,-97.37,0,0,1,-63.243 > view matrix models #3,1,0,0,2.676,0,1,0,-7.5822,0,0,1,-6.9289 > view matrix models #3,1,0,0,-28.537,0,1,0,-116.48,0,0,1,-73.257 > view matrix models #3,1,0,0,-74.431,0,1,0,-86.716,0,0,1,-91.941 > view matrix models #3,1,0,0,-77.549,0,1,0,-89.295,0,0,1,-82.343 > hide #!1 models > open /Users/ruchigautamsharma/Desktop/25HepE525K/cryosparc_P30_J279_map.mrc Opened cryosparc_P30_J279_map.mrc as #4, grid size 300,300,300, pixel 0.83, shown at level 0.0557, step 2, values float32 > select subtract #3 Nothing selected > select add #4 2 models selected > view matrix models #4,1,0,0,-3.5551,0,1,0,1.2444,0,0,1,9.7098 > view matrix models #4,1,0,0,-29.5,0,1,0,31.846,0,0,1,74.225 > volume #4 level 0.03328 > ui mousemode right ""rotate selected models"" > view matrix models > #4,-0.91868,-0.12918,-0.37327,255.55,-0.23246,-0.5872,0.77534,174.17,-0.31934,0.79907,0.50942,65.389 > view matrix models > #4,-0.91602,-0.1276,-0.38031,255.91,-0.21581,-0.6424,0.73535,184.54,-0.33814,0.75567,0.56091,66.973 > view matrix models > #4,-0.8978,-0.097493,-0.42947,255.87,-0.045054,-0.94974,0.30978,258.35,-0.43809,0.29747,0.84829,104 > view matrix models > #4,0.93714,0.02002,0.34839,-67.977,0.070672,-0.98855,-0.1333,304.93,0.34173,0.14954,-0.92782,253.19 > transparency sel 50 > view matrix models > #4,0.98946,0.13009,0.063575,-53.463,0.13724,-0.98257,-0.1254,295.46,0.046154,0.13281,-0.99007,297.27 > surface dust #4 size 8.3 > ui mousemode right ""translate selected models"" > view matrix models > #4,0.98946,0.13009,0.063575,-55.693,0.13724,-0.98257,-0.1254,243.61,0.046154,0.13281,-0.99007,230.84 > select subtract #4 Nothing selected > select add #4 2 models selected > hide #!2 models > view matrix models > #4,0.98946,0.13009,0.063575,-17.14,0.13724,-0.98257,-0.1254,238.58,0.046154,0.13281,-0.99007,218.87 > view matrix models > #4,0.98946,0.13009,0.063575,-14.137,0.13724,-0.98257,-0.1254,247.93,0.046154,0.13281,-0.99007,226.91 > fitmap #3 inMap #4 Fit molecule 8act.pdb (#3) to map cryosparc_P30_J279_map.mrc (#4) using 18834 atoms average map value = 0.06921, steps = 132 shifted from previous position = 3.77 rotated from previous position = 11.1 degrees atoms outside contour = 3445, contour level = 0.033285 Position of 8act.pdb (#3) relative to cryosparc_P30_J279_map.mrc (#4) coordinates: Matrix rotation and translation 0.99530642 -0.04985030 0.08294620 -93.88397645 -0.05708112 -0.99455248 0.08721873 330.44446938 0.07814647 -0.09154402 -0.99272998 332.89917405 Axis -0.99882356 0.02681814 -0.04040165 Axis point 0.00000000 171.51399022 160.98585768 Rotation angle (degrees) 174.86592494 Shift along axis 89.18575633 > color #4 #a1d7ff80 models > color #4 #76ffcf80 models > view matrix models > #4,0.98946,0.13009,0.063575,-14.422,0.13724,-0.98257,-0.1254,247.38,0.046154,0.13281,-0.99007,228.5 > fitmap #3 inMap #4 Fit molecule 8act.pdb (#3) to map cryosparc_P30_J279_map.mrc (#4) using 18834 atoms average map value = 0.06921, steps = 72 shifted from previous position = 1.7 rotated from previous position = 0.0115 degrees atoms outside contour = 3448, contour level = 0.033285 Position of 8act.pdb (#3) relative to cryosparc_P30_J279_map.mrc (#4) coordinates: Matrix rotation and translation 0.99528837 -0.04999379 0.08307632 -93.87652160 -0.05723957 -0.99453995 0.08725781 330.47220450 0.07826037 -0.09160194 -0.99271567 332.89509969 Axis -0.99881903 0.02689404 -0.04046312 Axis point 0.00000000 171.52859786 160.98201658 Rotation angle (degrees) 174.86310814 Shift along axis 89.18341503 > ui mousemode right translate > show #!2 models > hide #!3 models > select add #2 99840 atoms, 100312 bonds, 4 pseudobonds, 6146 residues, 4 models selected > select subtract #2 2 models selected > select add #2 99840 atoms, 100312 bonds, 4 pseudobonds, 6146 residues, 4 models selected > select subtract #4 99840 atoms, 100312 bonds, 4 pseudobonds, 6146 residues, 2 models selected > ui mousemode right ""translate selected models"" > view matrix models > #2,-0.82313,0.40245,0.40062,100.26,0.56745,0.60968,0.55344,-467.99,-0.021518,0.68288,-0.73021,28.334 > ui mousemode right ""rotate selected models"" > view matrix models > #2,-0.98302,0.15318,0.10103,348.35,0.18276,0.76793,0.61391,-438.53,0.016457,0.62195,-0.78289,59.345 > view matrix models > #2,-0.8026,0.36897,0.46871,89.465,0.5558,0.74787,0.36301,-472.01,-0.2166,0.55187,-0.80531,169.18 > fitmap #2 inMap #4 Fit molecule 8g4l.pdb (#2) to map cryosparc_P30_J279_map.mrc (#4) using 99840 atoms average map value = 0.03324, steps = 1916 shifted from previous position = 40 rotated from previous position = 19.9 degrees atoms outside contour = 75314, contour level = 0.033285 Position of 8g4l.pdb (#2) relative to cryosparc_P30_J279_map.mrc (#4) coordinates: Matrix rotation and translation -0.89768062 0.39496708 0.19537273 171.38448995 -0.43446605 -0.71933681 -0.54202750 713.12497930 -0.07354423 -0.57145040 0.81733450 187.01973679 Axis -0.03372507 0.30823754 -0.95071144 Axis point 167.14028490 366.03689970 0.00000000 Rotation angle (degrees) 154.13723635 Shift along axis 36.23013114 > volume #4 step 1 > select subtract #2 Nothing selected > color #4 #7cc1f980 models > show #!3 models > save /Users/ruchigautamsharma/Desktop/image5.png supersample 3 > movie record > turn y 2 180 > wait 180 > movie encode /Users/ruchigautamsharma/Desktop/movie4.mp4 Movie saved to /Users/ruchigautamsharma/Desktop/movie4.mp4 > ui tool show ""Show Sequence Viewer"" > sequence chain #2/A Alignment identifier is 2/A > select #2/A:524-525 34 atoms, 33 bonds, 2 residues, 1 model selected > select #2/A:524-526 56 atoms, 55 bonds, 3 residues, 1 model selected > show sel atoms > style sel ball Changed 56 atom styles > rainbow sel > select #2/A:940 22 atoms, 21 bonds, 1 residue, 1 model selected > select #2/A:939-940 44 atoms, 43 bonds, 2 residues, 1 model selected > select > #2/A:10-16,20-27,82-84,90-92,98-111,136-142,154-168,184-199,216-231,271-273,284-291,295-301,307-309,311-314,325-338,343-359,379-388,393-400,417-447,473-504,518-524,530-539,545-555,604-611,615-618,647-662,686-696,698-707,715-723,738-748,753-755,769-826,829-836,842-919,922-1171 11821 atoms, 11850 bonds, 720 residues, 1 model selected > ui mousemode right translate > select #2/A:903 15 atoms, 14 bonds, 1 residue, 1 model selected > select #2/A:903-904 39 atoms, 38 bonds, 2 residues, 1 model selected > ui tool show ""Show Sequence Viewer"" > sequence chain #2/B Alignment identifier is 2/B > select #2/B:903 15 atoms, 14 bonds, 1 residue, 1 model selected > select #2/B:903-904 39 atoms, 38 bonds, 2 residues, 1 model selected > show sel atoms > style sel ball Changed 39 atom styles > rainbow sel > close #1 > volume #4 level 0.04236 > ui mousemode right distance > distance #2/B:903@OE2 #2/A:525@CD Distance between 8g4l.pdb #2/B GLU 903 OE2 and /A GLU 525 CD: 7.678Å > save /Users/ruchigautamsharma/Desktop/image6.png supersample 3 > open > ""/Users/ruchigautamsharma/Desktop/25HepE525K/cryosparc_P30_J280_class_00_00027_volume > (1).mrc"" Opened cryosparc_P30_J280_class_00_00027_volume (1).mrc as #5, grid size 180,180,180, pixel 1.38, shown at level 0.123, step 1, values float32 > flip volume #5 Unknown command: flip volume #5 > volume flip #5 Opened cryosparc_P30_J280_class_00_00027_volume (1).mrc z flip as #6, grid size 180,180,180, pixel 1.38, shown at step 1, values float32 > select add #6 39 atoms, 38 bonds, 2 residues, 3 models selected > select add #2 99840 atoms, 100312 bonds, 5 pseudobonds, 6146 residues, 5 models selected > select subtract #2 2 models selected > ui mousemode right ""translate selected models"" > view matrix models #6,1,0,0,-12.543,0,1,0,-4.9141,0,0,1,-59.886 > ui mousemode right ""rotate selected models"" > view matrix models > #6,0.97719,-0.1898,-0.095255,24.452,0.21213,0.85157,0.47941,-74.838,-0.0098755,-0.48869,0.8724,14.37 > view matrix models > #6,0.9436,-0.26902,-0.193,50.243,0.32425,0.63294,0.70303,-91.715,-0.066973,-0.72595,0.68448,72.907 > view matrix models > #6,0.94098,-0.27295,-0.20014,51.932,0.33074,0.6159,0.71504,-92.063,-0.071902,-0.73903,0.66983,76.899 > view matrix models > #6,-0.96802,-0.2488,0.032094,272.71,-0.24873,0.93529,-0.25172,66.645,0.032612,-0.25166,-0.96727,208.41 > ui mousemode right ""translate selected models"" > view matrix models > #6,-0.96802,-0.2488,0.032094,298.35,-0.24873,0.93529,-0.25172,67.863,0.032612,-0.25166,-0.96727,270.44 > view matrix models > #6,-0.96802,-0.2488,0.032094,280.09,-0.24873,0.93529,-0.25172,73.622,0.032612,-0.25166,-0.96727,274.5 > view matrix models > #6,-0.96802,-0.2488,0.032094,279.77,-0.24873,0.93529,-0.25172,74.716,0.032612,-0.25166,-0.96727,273.45 > close #5 > hide #!2 models > hide #!3 models > hide #!4 models > volume #6 level 0.09029 > surface dust #6 size 13.8 > ui mousemode right translate > select subtract #6 Nothing selected > save /Users/ruchigautamsharma/Desktop/image7.png supersample 3 > movie record > turn y 2 180 > wait 180 > movie encode /Users/ruchigautamsharma/Desktop/movie5.mp4 Movie saved to /Users/ruchigautamsharma/Desktop/movie5.mp4 > show #!2 models > show #!3 models > show #!4 models > hide #!2 models > hide #!3 models > fitmap #4 inMap #6 Fit map cryosparc_P30_J279_map.mrc in map cryosparc_P30_J280_class_00_00027_volume (1).mrc z flip using 398148 points correlation = 0.9513, correlation about mean = 0.6514, overlap = 4478 steps = 120, shift = 2.21, angle = 10.5 degrees Position of cryosparc_P30_J279_map.mrc (#4) relative to cryosparc_P30_J280_class_00_00027_volume (1).mrc z flip (#6) coordinates: Matrix rotation and translation -0.99999913 -0.00034252 -0.00127077 249.21336620 0.00034239 -0.99999993 0.00010594 248.98589046 -0.00127081 0.00010551 0.99999919 -1.22511845 Axis -0.00063596 0.00005334 0.99999980 Axis point 124.58497705 124.51431379 0.00000000 Rotation angle (degrees) 179.98037890 Shift along axis -1.37032688 > show #!2 models > show #!3 models > undo [Repeated 3 time(s)] > select add #6 2 models selected > hide #!3 models > hide #!2 models > ui mousemode right ""translate selected models"" > fitmap #6 inMap #4 Fit map cryosparc_P30_J280_class_00_00027_volume (1).mrc z flip in map cryosparc_P30_J279_map.mrc using 102014 points correlation = 0.9277, correlation about mean = 0.6892, overlap = 1011 steps = 48, shift = 0.0317, angle = 0.033 degrees Position of cryosparc_P30_J280_class_00_00027_volume (1).mrc z flip (#6) relative to cryosparc_P30_J279_map.mrc (#4) coordinates: Matrix rotation and translation -0.99999934 -0.00020646 -0.00113078 249.17086350 0.00020623 -0.99999996 0.00020732 248.95988727 -0.00113082 0.00020709 0.99999934 1.49527864 Axis -0.00056633 0.00010440 0.99999983 Axis point 124.57301229 124.49271938 0.00000000 Rotation angle (degrees) 179.98817733 Shift along axis 1.38015468 > select subtract #6 Nothing selected > show #!2 models > hide #!6 models > fitmap #2 inMap #4 Fit molecule 8g4l.pdb (#2) to map cryosparc_P30_J279_map.mrc (#4) using 99840 atoms average map value = 0.03324, steps = 796 shifted from previous position = 21.2 rotated from previous position = 10.5 degrees atoms outside contour = 78980, contour level = 0.04236 Position of 8g4l.pdb (#2) relative to cryosparc_P30_J279_map.mrc (#4) coordinates: Matrix rotation and translation -0.89772325 0.39491741 0.19527728 171.44427967 -0.43436867 -0.71936134 -0.54207299 713.11865308 -0.07359913 -0.57145385 0.81732715 187.04031769 Axis -0.03368282 0.30824538 -0.95071039 Axis point 167.15705533 366.03494475 0.00000000 Rotation angle (degrees) 154.14213016 Shift along axis 36.21962762 > show #!3 models > hide #!2 models > fitmap #3 inMap #4 Fit molecule 8act.pdb (#3) to map cryosparc_P30_J279_map.mrc (#4) using 18834 atoms average map value = 0.06921, steps = 156 shifted from previous position = 2.77 rotated from previous position = 10.5 degrees atoms outside contour = 5343, contour level = 0.04236 Position of 8act.pdb (#3) relative to cryosparc_P30_J279_map.mrc (#4) coordinates: Matrix rotation and translation 0.99530058 -0.04986346 0.08300844 -93.89354486 -0.05710589 -0.99454449 0.08729358 330.43411156 0.07820282 -0.09162362 -0.99271820 332.90953349 Axis -0.99882208 0.02682778 -0.04043159 Axis point 0.00000000 171.51509590 160.98648532 Rotation angle (degrees) 174.86146946 Shift along axis 89.18769933 > show #!2 models > show #!6 models > hide #!6 models > open > /Users/ruchigautamsharma/Desktop/25HepE525K/cryosparc_P30_J280_class_01_00027_volume.mrc Opened cryosparc_P30_J280_class_01_00027_volume.mrc as #5, grid size 180,180,180, pixel 1.38, shown at level 0.12, step 1, values float32 > volume flip #6 Opened cryosparc_P30_J280_class_00_00027_volume (1).mrc z flip z flip as #7, grid size 180,180,180, pixel 1.38, shown at step 1, values float32 > undo > hide #!6 models > show #!6 models > hide #!7 models > close #7 > volume flip #5 Opened cryosparc_P30_J280_class_01_00027_volume.mrc z flip as #7, grid size 180,180,180, pixel 1.38, shown at step 1, values float32 > hide #!6 models > close #5 > select add #7 2 models selected > hide #!3 models > hide #!2 models > show #!2 models > hide #!2 models > ui mousemode right ""rotate selected models"" > view matrix models > #7,0.84223,-0.48294,-0.23962,106.87,0.48671,0.48999,0.7232,-95.43,-0.23185,-0.72572,0.64774,158.93 > ui mousemode right ""translate selected models"" > view matrix models > #7,0.84223,-0.48294,-0.23962,105.38,0.48671,0.48999,0.7232,-78.575,-0.23185,-0.72572,0.64774,170.33 > ui mousemode right ""rotate selected models"" > view matrix models > #7,-0.95159,-0.22068,-0.21396,309.08,-0.18623,0.96771,-0.16985,66.446,0.24453,-0.12179,-0.96196,238.05 > ui mousemode right ""translate selected models"" > view matrix models > #7,-0.95159,-0.22068,-0.21396,310.5,-0.18623,0.96771,-0.16985,52.678,0.24453,-0.12179,-0.96196,229.62 > volume #7 level 0.07479 > surface dust #7 size 13.8 > fitmap #7 inMap #4 Fit map cryosparc_P30_J280_class_01_00027_volume.mrc z flip in map cryosparc_P30_J279_map.mrc using 113502 points correlation = 0.9643, correlation about mean = 0.8414, overlap = 1130 steps = 208, shift = 5.04, angle = 14.9 degrees Position of cryosparc_P30_J280_class_01_00027_volume.mrc z flip (#7) relative to cryosparc_P30_J279_map.mrc (#4) coordinates: Matrix rotation and translation -0.99999966 -0.00026364 -0.00078820 249.12543022 0.00026376 -0.99999995 -0.00015099 248.98160004 -0.00078816 -0.00015120 0.99999968 1.49763888 Axis -0.00039360 -0.00007449 0.99999992 Axis point 124.54659569 124.50727948 0.00000000 Rotation angle (degrees) 179.98489106 Shift along axis 1.38103566 > show #!3 models > show #!2 models > hide #!2 models > hide #!3 models > hide #!4 models > select subtract #7 Nothing selected > volume #7 level 0.0619 > volume #7 level 0.07092 > save /Users/ruchigautamsharma/Desktop/image7.png supersample 3 > movie record > turn y 2 180 > wait 180 > movie encode /Users/ruchigautamsharma/Desktop/movie5.mp4 Movie saved to /Users/ruchigautamsharma/Desktop/movie5.mp4 > show #!6 models > show #!4 models > show #!3 models > show #!2 models > save > /Users/ruchigautamsharma/Desktop/25HepE525K/25HepE525KwithMava_classes.cxs > open > /Users/ruchigautamsharma/Desktop/25HepE525K/cryosparc_P30_J280_class_02_00027_volume.mrc Opened cryosparc_P30_J280_class_02_00027_volume.mrc as #5, grid size 180,180,180, pixel 1.38, shown at level 0.119, step 1, values float32 > volume flip #5 Opened cryosparc_P30_J280_class_02_00027_volume.mrc z flip as #8, grid size 180,180,180, pixel 1.38, shown at step 1, values float32 > close #5 > select add #8 2 models selected > hide #!3 models > hide #!2 models > hide #!6 models > hide #!7 models > view matrix models #8,1,0,0,2.8324,0,1,0,-4.8659,0,0,1,8.6713 > ui mousemode right ""rotate selected models"" > view matrix models > #8,-0.96696,-0.17515,-0.18521,304.59,-0.10484,0.93554,-0.33731,57.912,0.23235,-0.30675,-0.92299,250.36 > ui mousemode right ""translate selected models"" > view matrix models > #8,-0.96696,-0.17515,-0.18521,302.83,-0.10484,0.93554,-0.33731,66.738,0.23235,-0.30675,-0.92299,248.15 > surface dust #8 size 13.8 > fitmap #8 inMap #4 Fit map cryosparc_P30_J280_class_02_00027_volume.mrc z flip in map cryosparc_P30_J279_map.mrc using 58302 points correlation = 0.9609, correlation about mean = 0.7291, overlap = 874.3 steps = 144, shift = 5.03, angle = 14.4 degrees Position of cryosparc_P30_J280_class_02_00027_volume.mrc z flip (#8) relative to cryosparc_P30_J279_map.mrc (#4) coordinates: Matrix rotation and translation -0.99999916 0.00002492 -0.00129399 249.16805302 -0.00002528 -0.99999996 0.00027762 248.99198953 -0.00129399 0.00027765 0.99999912 1.50291671 Axis 0.00064340 -0.00013133 -0.99999978 Axis point 124.58607228 124.49433268 0.00000000 Rotation angle (degrees) 179.99856201 Shift along axis -1.37530370 > show #!7 models > show #!6 models > hide #!6 models > hide #!7 models > select subtract #8 Nothing selected > hide #!4 models > volume #8 level 0.07811 > surface dust #8 size 13.8 > save /Users/ruchigautamsharma/Desktop/image7.png supersample 3 > movie record > turn y 2 180 > wait 180 > movie encode /Users/ruchigautamsharma/Desktop/movie5.mp4 Movie saved to /Users/ruchigautamsharma/Desktop/movie5.mp4 > show #!4 models > show #!3 models > show #!2 models > hide #!8 models > open > /Users/ruchigautamsharma/Desktop/25HepE525K/cryosparc_P30_J280_class_04_00027_volume.mrc Opened cryosparc_P30_J280_class_04_00027_volume.mrc as #5, grid size 180,180,180, pixel 1.38, shown at level 0.122, step 1, values float32 > volume flip #5 Opened cryosparc_P30_J280_class_04_00027_volume.mrc z flip as #9, grid size 180,180,180, pixel 1.38, shown at step 1, values float32 > close #5 > select add #9 2 models selected > hide #!2 models > hide #!3 models > hide #!4 models > show #!4 models > ui mousemode right ""rotate selected models"" > view matrix models > #9,-0.94987,-0.3125,-0.0095436,296.08,-0.29326,0.90112,-0.31935,89.841,0.1084,-0.30054,-0.94759,261.2 > ui mousemode right ""translate selected models"" > view matrix models > #9,-0.94987,-0.3125,-0.0095436,296.29,-0.29326,0.90112,-0.31935,94.465,0.1084,-0.30054,-0.94759,265.66 > surface dust #9 size 13.8 > fitmap #9 inMap #4 Fit map cryosparc_P30_J280_class_04_00027_volume.mrc z flip in map cryosparc_P30_J279_map.mrc using 58281 points correlation = 0.9434, correlation about mean = 0.6496, overlap = 833.5 steps = 116, shift = 5.59, angle = 6.08 degrees Position of cryosparc_P30_J280_class_04_00027_volume.mrc z flip (#9) relative to cryosparc_P30_J279_map.mrc (#4) coordinates: Matrix rotation and translation -0.99999961 -0.00086803 -0.00014872 249.12096554 0.00086814 -0.99999934 -0.00074800 249.01468160 -0.00014807 -0.00074812 0.99999971 1.52412702 Axis -0.00007408 -0.00037371 0.99999993 Axis point 124.50649781 124.56168997 0.00000000 Rotation angle (degrees) 179.95026257 Shift along axis 1.41261188 > hide #!4 models > select subtract #9 Nothing selected > volume #9 level 0.07975 > show #!4 models > hide #!4 models > volume #9 level 0.08919 > save /Users/ruchigautamsharma/Desktop/image7.png supersample 3 > movie record > turn y 2 180 > wait 180 > movie encode /Users/ruchigautamsharma/Desktop/movie5.mp4 Movie saved to /Users/ruchigautamsharma/Desktop/movie5.mp4 > show #!4 models > show #!3 models > show #!2 models > open > /Users/ruchigautamsharma/Desktop/25HepE525K/cryosparc_P30_J280_class_05_00027_volume.mrc Opened cryosparc_P30_J280_class_05_00027_volume.mrc as #5, grid size 180,180,180, pixel 1.38, shown at level 0.125, step 1, values float32 > volume flip #5 Opened cryosparc_P30_J280_class_05_00027_volume.mrc z flip as #10, grid size 180,180,180, pixel 1.38, shown at step 1, values float32 > close #5 > color #10 #4ab7ffff models > color #10 #fbd6ffff models > color #10 #ffb5b1ff models > color #10 #f7b45cff models > color #10 #30bdf7ff models > hide #!9 models > hide #!2 models > hide #!3 models > volume #10 level 0.09708 > select add #10 2 models selected > view matrix models #10,1,0,0,3.1115,0,1,0,-2.0096,0,0,1,8.118 > ui mousemode right ""rotate selected models"" > view matrix models > #10,-0.79927,-0.55558,-0.2291,334.52,-0.51624,0.8299,-0.21156,112.19,0.30768,-0.050826,-0.95013,212.13 > ui mousemode right ""translate selected models"" > view matrix models > #10,-0.79927,-0.55558,-0.2291,333.19,-0.51624,0.8299,-0.21156,115.1,0.30768,-0.050826,-0.95013,210.7 > surface dust #10 size 13.8 > fitmap #10 inMap #4 Fit map cryosparc_P30_J280_class_05_00027_volume.mrc z flip in map cryosparc_P30_J279_map.mrc using 84424 points correlation = 0.9741, correlation about mean = 0.8468, overlap = 1111 steps = 276, shift = 5.07, angle = 25.6 degrees Position of cryosparc_P30_J280_class_05_00027_volume.mrc z flip (#10) relative to cryosparc_P30_J279_map.mrc (#4) coordinates: Matrix rotation and translation -0.99999922 0.00035517 0.00119687 248.79666503 -0.00035522 -0.99999994 -0.00003695 249.05630070 0.00119686 -0.00003738 0.99999928 1.23988110 Axis -0.00059829 0.00001925 -0.99999982 Axis point 124.42007755 124.50606948 0.00000000 Rotation angle (degrees) 179.97964879 Shift along axis -1.38393827 > hide #!4 models > save /Users/ruchigautamsharma/Desktop/image7.png supersample 3 > movie record > turn y 2 180 > wait 180 > movie encode /Users/ruchigautamsharma/Desktop/movie5.mp4 Movie saved to /Users/ruchigautamsharma/Desktop/movie5.mp4 > show #!4 models > show #!2 models > show #!3 models > select subtract #10 Nothing selected > hide #!10 models > open > /Users/ruchigautamsharma/Desktop/25HepE525K/cryosparc_P30_J280_class_08_00027_volume.mrc Opened cryosparc_P30_J280_class_08_00027_volume.mrc as #5, grid size 180,180,180, pixel 1.38, shown at level 0.121, step 1, values float32 > volume flip #5 Opened cryosparc_P30_J280_class_08_00027_volume.mrc z flip as #11, grid size 180,180,180, pixel 1.38, shown at step 1, values float32 > close #5 > volume #11 level 0.08441 > hide #!3 models > hide #!2 models > select add #11 2 models selected > view matrix models #11,1,0,0,1.1155,0,1,0,-3.8677,0,0,1,5.8448 > ui mousemode right ""rotate selected models"" > view matrix models > #11,0.99209,-0.0053981,-0.12542,17.552,0.081093,0.7902,0.60746,-62.634,0.095827,-0.61282,0.78439,87.413 > view matrix models > #11,0.99729,-0.013338,-0.072294,11.493,0.039229,0.92824,0.36991,-44.599,0.062172,-0.37174,0.92625,48.066 > view matrix models > #11,0.96616,0.092495,-0.24077,23.583,0.23126,0.10267,0.96746,-47.711,0.1142,-0.99041,0.077802,210.68 > view matrix models > #11,-0.87555,-0.41067,0.25448,270.56,-0.45727,0.87442,-0.16216,91.081,-0.15593,-0.25834,-0.95338,285.91 > ui mousemode right ""translate selected models"" > view matrix models > #11,-0.87555,-0.41067,0.25448,270.16,-0.45727,0.87442,-0.16216,97.04,-0.15593,-0.25834,-0.95338,295.44 > surface dust #11 size 13.8 > fitmap #11 inMap #4 Fit map cryosparc_P30_J280_class_08_00027_volume.mrc z flip in map cryosparc_P30_J279_map.mrc using 102298 points correlation = 0.8925, correlation about mean = 0.5767, overlap = 958.6 steps = 172, shift = 10.7, angle = 16.9 degrees Position of cryosparc_P30_J280_class_08_00027_volume.mrc z flip (#11) relative to cryosparc_P30_J279_map.mrc (#4) coordinates: Matrix rotation and translation -0.99999904 -0.00116328 0.00074464 249.06176278 0.00116310 -0.99999929 -0.00024302 248.90777913 0.00074493 -0.00024215 0.99999969 1.24883054 Axis 0.00037212 -0.00012116 0.99999992 Axis point 124.45826735 124.52639149 0.00000000 Rotation angle (degrees) 179.93335425 Shift along axis 1.31135186 > volume #11 level 0.05725 > volume #11 level 0.06342 > volume #11 level 0.07083 > select subtract #11 Nothing selected > hide #!4 models > save /Users/ruchigautamsharma/Desktop/image7.png supersample 3 > movie record > turn y 2 180 > wait 180 > movie encode /Users/ruchigautamsharma/Desktop/movie5.mp4 Movie saved to /Users/ruchigautamsharma/Desktop/movie5.mp4 > show #!4 models > show #!3 models > show #!2 models > show #!6 models > show #!7 models > show #!8 models > show #!9 models > show #!10 models > hide #!11 models > hide #!10 models > hide #!9 models > hide #!8 models > hide #!7 models > hide #!6 models > hide #!2 models > hide #!3 models > open /Users/ruchigautamsharma/Desktop/25HepE525K/8qyq.pdb 8qyq.pdb title: Beta-cardiac myosin S1 fragment In the pre-powerstroke state complexed to mavacamten [more info...] Chain information for 8qyq.pdb #5 --- Chain | Description | UniProt A B | myosin-7 | MYH7_BOVIN 1-807 C | myosin light chain 3 | MYL3_BOVIN 1-199 D | myosin light chain 3 | MYL3_BOVIN 1-199 Non-standard residues in 8qyq.pdb #5 --- ADP — adenosine-5'-diphosphate BEF — beryllium trifluoride ion FMT — formic acid GOL — glycerol (glycerin; propane-1,2,3-triol) MG — magnesium ion XB2 — 6-[[(1~{S})-1-phenylethyl]amino]-3-propan-2-yl-1~{H}-pyrimidine-2,4-dione > select #5/B 6497 atoms, 6383 bonds, 8 pseudobonds, 1018 residues, 3 models selected > hide sel cartoons > hide sel atoms > select #5/D 602 atoms, 605 bonds, 3 pseudobonds, 86 residues, 2 models selected > hide sel cartoons > select add #5 14943 atoms, 14737 bonds, 20 pseudobonds, 2292 residues, 3 models selected > ui mousemode right ""rotate selected models"" > view matrix models > #5,0.99553,0.05401,0.077471,-2.8146,-0.030633,0.96065,-0.27608,6.0307,-0.089333,0.27247,0.95801,-6.3562 > view matrix models > #5,0.99476,0.059463,0.083204,-3.0609,-0.032039,0.95383,-0.29862,6.6171,-0.097119,0.29439,0.95074,-6.797 > view matrix models > #5,0.84862,0.26572,-0.45743,1.348,0.52607,-0.33296,0.78255,20.637,0.05564,-0.90473,-0.42234,49.406 > view matrix models > #5,-0.20948,0.94179,-0.26296,-32.356,0.63406,0.33555,0.69669,9.3355,0.74437,-0.020792,-0.66744,44.88 > view matrix models > #5,-0.26135,0.93427,-0.24258,-33.342,0.74088,0.35525,0.57,12.994,0.61871,-0.030752,-0.78502,45.702 > view matrix models > #5,-0.27941,0.93151,-0.23283,-33.736,0.77438,0.36199,0.51894,14.36,0.56769,-0.035305,-0.82249,45.838 > view matrix models > #5,-0.37124,0.91598,-0.15218,-36.338,0.9014,0.39485,0.17771,22.376,0.22287,-0.071201,-0.97224,44.77 > view matrix models > #5,-0.41927,0.90453,-0.077722,-38.282,0.90689,0.41333,-0.08192,27.324,-0.041974,-0.10483,-0.9936,42.18 > view matrix models > #5,-0.44992,0.89092,0.061874,-41.255,0.77059,0.4223,-0.47733,33.225,-0.4514,-0.16708,-0.87654,35.351 > view matrix models > #5,-0.31556,0.89055,0.32762,-44.738,0.035597,0.35613,-0.93376,33.51,-0.94824,-0.28299,-0.14408,15.954 > view matrix models > #5,-0.16915,0.90579,0.3885,-44.23,-0.41809,0.29101,-0.86053,27.006,-0.89252,-0.30799,0.32948,7.6715 > view matrix models > #5,-0.31793,0.89036,0.32585,-44.732,0.044144,0.35721,-0.93298,33.592,-0.94709,-0.28224,-0.15287,16.132 > view matrix models > #5,-0.16449,0.90636,0.38916,-44.19,-0.4306,0.28897,-0.85503,26.761,-0.88742,-0.30822,0.34275,7.4794 > view matrix models > #5,0.9568,-0.19924,0.21174,-0.56848,0.28104,0.4472,-0.84914,33.288,0.074496,0.87196,0.48387,-7.475 > view matrix models > #5,0.93545,-0.26582,0.23296,0.14939,0.35203,0.64149,-0.68159,26.655,0.031741,0.71961,0.69366,-9.0199 > view matrix models > #5,0.91741,-0.3204,0.23603,1.0211,0.39769,0.75969,-0.51451,21.332,-0.014464,0.56588,0.82436,-8.9778 > view matrix models > #5,0.95721,-0.19796,0.21112,-0.57814,0.27948,0.44284,-0.85193,33.417,0.075155,0.87447,0.47922,-7.4258 > view matrix models > #5,0.97238,-0.14881,0.17983,-0.79935,0.21341,0.25467,-0.94319,38.437,0.094555,0.95551,0.27939,-4.8593 > view matrix models > #5,0.98941,-0.090123,0.11382,-0.49676,0.10944,-0.052142,-0.99262,44.656,0.095393,0.99456,-0.041726,0.82277 > view matrix models > #5,-0.35779,-0.60534,0.71102,-20.504,0.19127,-0.79279,-0.57871,53.561,0.914,-0.07106,0.39943,26.714 > view matrix models > #5,-0.60867,0.67803,0.41206,-45.977,-0.79266,-0.54248,-0.27823,28.041,0.034888,-0.49597,0.86764,13.998 > ui mousemode right ""translate selected models"" > view matrix models > #5,-0.60867,0.67803,0.41206,-23.555,-0.79266,-0.54248,-0.27823,128.79,0.034888,-0.49597,0.86764,182.06 > view matrix models > #5,-0.60867,0.67803,0.41206,37.381,-0.79266,-0.54248,-0.27823,174.2,0.034888,-0.49597,0.86764,205.17 > view matrix models > #5,-0.60867,0.67803,0.41206,99.031,-0.79266,-0.54248,-0.27823,162.54,0.034888,-0.49597,0.86764,155.36 > view matrix models > #5,-0.60867,0.67803,0.41206,98.801,-0.79266,-0.54248,-0.27823,159.71,0.034888,-0.49597,0.86764,149.89 > view matrix models > #5,-0.60867,0.67803,0.41206,105.09,-0.79266,-0.54248,-0.27823,156.53,0.034888,-0.49597,0.86764,147.11 > ui mousemode right ""rotate selected models"" > view matrix models > #5,-0.23298,0.92288,0.30662,107.22,-0.95501,-0.15762,-0.25124,145.28,-0.18353,-0.35136,0.91808,139.83 > view matrix models > #5,-0.098877,0.94921,0.29871,108.71,-0.97369,-0.030362,-0.22583,141.73,-0.20529,-0.31318,0.92724,138.51 > ui mousemode right ""translate selected models"" > view matrix models > #5,-0.098877,0.94921,0.29871,108.51,-0.97369,-0.030362,-0.22583,147.51,-0.20529,-0.31318,0.92724,141.89 > fitmap #5 inMap #4 Fit molecule 8qyq.pdb (#5) to map cryosparc_P30_J279_map.mrc (#4) using 14943 atoms average map value = 0.04173, steps = 400 shifted from previous position = 15.1 rotated from previous position = 20 degrees atoms outside contour = 9505, contour level = 0.04236 Position of 8qyq.pdb (#5) relative to cryosparc_P30_J279_map.mrc (#4) coordinates: Matrix rotation and translation -0.58239663 0.81290458 -0.00055383 102.85355786 0.70719581 0.50699846 0.49277443 96.93889710 0.40085939 0.28659850 -0.87015691 105.31002093 Axis -0.44484143 -0.86608184 -0.22807532 Axis point 21.76765973 0.00000000 42.22852380 Rotation angle (degrees) 166.60041068 Shift along axis -153.72915848 > ui mousemode right ""rotate selected models"" > view matrix models > #5,-0.37977,0.92425,0.039174,104.73,-0.87919,-0.37378,0.29547,144.57,0.28774,0.077772,0.95455,140.89 > view matrix models > #5,0.32827,-0.92374,-0.19734,159.88,0.44949,0.33651,-0.82748,170.74,0.83078,0.18294,0.52568,155.01 > ui mousemode right ""translate selected models"" > view matrix models > #5,0.32827,-0.92374,-0.19734,161.33,0.44949,0.33651,-0.82748,156.99,0.83078,0.18294,0.52568,143.67 > ui mousemode right ""rotate selected models"" > view matrix models > #5,0.52982,-0.80788,-0.25811,162.9,0.69083,0.58764,-0.42123,146.68,0.49198,0.044868,0.86945,134.89 > ui mousemode right ""translate selected models"" > view matrix models > #5,0.52982,-0.80788,-0.25811,162.52,0.69083,0.58764,-0.42123,163.45,0.49198,0.044868,0.86945,142.3 > ui mousemode right ""rotate selected models"" > view matrix models > #5,-0.72386,-0.68979,0.014695,136.61,0.19093,-0.22074,-0.95646,184.86,0.66301,-0.68954,0.29149,172.48 > view matrix models > #5,0.50281,-0.86437,-0.0066101,158.26,0.47814,0.28449,-0.83093,175.36,0.72011,0.41464,0.55634,143.83 > ui mousemode right ""translate selected models"" > view matrix models > #5,0.50281,-0.86437,-0.0066101,160.27,0.47814,0.28449,-0.83093,157.85,0.72011,0.41464,0.55634,140.82 > view matrix models > #5,0.50281,-0.86437,-0.0066101,169.69,0.47814,0.28449,-0.83093,74.983,0.72011,0.41464,0.55634,59.074 > view matrix models > #5,0.50281,-0.86437,-0.0066101,164.23,0.47814,0.28449,-0.83093,100.24,0.72011,0.41464,0.55634,83.15 > ui mousemode right ""rotate selected models"" > view matrix models > #5,0.35446,-0.92893,-0.10696,165.58,0.84213,0.36685,-0.39528,94.756,0.40642,0.050033,0.91231,79.421 > ui mousemode right ""translate selected models"" > view matrix models > #5,0.35446,-0.92893,-0.10696,172.36,0.84213,0.36685,-0.39528,136.98,0.40642,0.050033,0.91231,91.143 > ui mousemode right ""rotate selected models"" > view matrix models > #5,-0.56298,-0.74543,0.35692,145.92,0.33568,-0.60087,-0.72544,157.6,0.75523,-0.2886,0.58851,110.05 > ui mousemode right ""translate selected models"" > view matrix models > #5,-0.56298,-0.74543,0.35692,130.04,0.33568,-0.60087,-0.72544,145.96,0.75523,-0.2886,0.58851,88.151 > ui mousemode right ""rotate selected models"" > view matrix models > #5,-0.082785,-0.99082,0.10686,147.28,0.60357,-0.13517,-0.78577,140.83,0.793,-0.00055352,0.60922,81.985 > ui mousemode right ""translate selected models"" > view matrix models > #5,-0.082785,-0.99082,0.10686,146.82,0.60357,-0.13517,-0.78577,138.38,0.793,-0.00055352,0.60922,93.162 > ui mousemode right ""rotate selected models"" > view matrix models > #5,-0.3921,-0.86583,0.3108,135.56,0.71686,-0.49931,-0.48661,141.85,0.57651,0.032004,0.81646,85.171 > ui mousemode right ""translate selected models"" > view matrix models > #5,-0.3921,-0.86583,0.3108,138.82,0.71686,-0.49931,-0.48661,142.44,0.57651,0.032004,0.81646,82.838 > fitmap #5 inMap #4 Fit molecule 8qyq.pdb (#5) to map cryosparc_P30_J279_map.mrc (#4) using 14943 atoms average map value = 0.07346, steps = 220 shifted from previous position = 13.1 rotated from previous position = 20.7 degrees atoms outside contour = 3995, contour level = 0.04236 Position of 8qyq.pdb (#5) relative to cryosparc_P30_J279_map.mrc (#4) coordinates: Matrix rotation and translation -0.48628488 -0.87349851 -0.02296421 131.98115481 -0.50944434 0.26206455 0.81962712 104.75313384 -0.70992497 0.41027126 -0.57243691 157.52284441 Axis -0.46589276 0.78183820 0.41433437 Axis point 115.26114932 0.00000000 25.56332067 Rotation angle (degrees) 153.93923432 Shift along axis 85.67806483 > select ::name=""XB2"" 40 atoms, 42 bonds, 2 residues, 1 model selected > show sel atoms > style sel ball Changed 40 atom styles > rainbow sel > select add #5 14943 atoms, 14737 bonds, 20 pseudobonds, 2292 residues, 3 models selected > select subtract #5 Nothing selected > hide #!5 models > select ::name=""XB2"" 40 atoms, 42 bonds, 2 residues, 1 model selected > show #!5 models > select #5/A 6584 atoms, 6484 bonds, 9 pseudobonds, 1016 residues, 3 models selected > hide sel cartoons > hide sel atoms > select #5/C 1260 atoms, 1265 bonds, 172 residues, 1 model selected > hide sel cartoons > hide sel atoms > select ::name=""XB2"" 40 atoms, 42 bonds, 2 residues, 1 model selected > hide sel atoms > select ::name=""XB2"" 40 atoms, 42 bonds, 2 residues, 1 model selected > select #5/A 6584 atoms, 6484 bonds, 9 pseudobonds, 1016 residues, 3 models selected > select ::name=""XB2"" 40 atoms, 42 bonds, 2 residues, 1 model selected > style sel ball Changed 40 atom styles > show sel cartoons > select #5/A 6584 atoms, 6484 bonds, 9 pseudobonds, 1016 residues, 3 models selected > show sel cartoons > select ::name=""XB2"" 40 atoms, 42 bonds, 2 residues, 1 model selected > style sel ball Changed 40 atom styles > select add #5 14943 atoms, 14737 bonds, 20 pseudobonds, 2292 residues, 3 models selected > select ::name=""XB2"" 40 atoms, 42 bonds, 2 residues, 1 model selected > style sel ball Changed 40 atom styles > select add #5 14943 atoms, 14737 bonds, 20 pseudobonds, 2292 residues, 3 models selected > show sel atoms > show sel cartoons > hide sel atoms > select ::name=""XB2"" 40 atoms, 42 bonds, 2 residues, 1 model selected > style sel ball Changed 40 atom styles > select ::name=""ADP"" 108 atoms, 116 bonds, 4 residues, 2 models selected > style sel & #!5 ball Changed 54 atom styles > rainbow sel & #!5 > select add #5 14997 atoms, 14795 bonds, 20 pseudobonds, 2294 residues, 4 models selected > select add #3 33777 atoms, 33932 bonds, 39 pseudobonds, 4620 residues, 6 models selected > select subtract #3 14943 atoms, 14737 bonds, 20 pseudobonds, 2292 residues, 3 models selected > select ::name=""ADP"" 108 atoms, 116 bonds, 4 residues, 2 models selected > select add #5 14997 atoms, 14795 bonds, 20 pseudobonds, 2294 residues, 4 models selected > select subtract #5 54 atoms, 58 bonds, 2 residues, 1 model selected > select ::name=""ADP"" 108 atoms, 116 bonds, 4 residues, 2 models selected > style sel & #!5 ball Changed 54 atom styles > rainbow sel & #!5 > select #5/A 6584 atoms, 6484 bonds, 9 pseudobonds, 1016 residues, 3 models selected > select ::name=""XB2"" 40 atoms, 42 bonds, 2 residues, 1 model selected > color sel byhetero > show #!3 models > show #!2 models > hide #!5 models > select add #5 14943 atoms, 14737 bonds, 20 pseudobonds, 2292 residues, 3 models selected > select subtract #5 Nothing selected > hide #!3 models > fitmap #2 inMap #4 Fit molecule 8g4l.pdb (#2) to map cryosparc_P30_J279_map.mrc (#4) using 99840 atoms average map value = 0.03324, steps = 212 shifted from previous position = 0.00596 rotated from previous position = 0.00292 degrees atoms outside contour = 78983, contour level = 0.04236 Position of 8g4l.pdb (#2) relative to cryosparc_P30_J279_map.mrc (#4) coordinates: Matrix rotation and translation -0.89771304 0.39493434 0.19528995 171.43072531 -0.43439308 -0.71937790 -0.54203144 713.12426462 -0.07357955 -0.57142130 0.81735167 187.01292814 Axis -0.03369168 0.30822422 -0.95071694 Axis point 167.15376056 366.03172418 0.00000000 Rotation angle (degrees) 154.14093715 Shift along axis 36.23002059 > hide #!2 models > show #!3 models > fitmap #3 inMap #4 Fit molecule 8act.pdb (#3) to map cryosparc_P30_J279_map.mrc (#4) using 18834 atoms average map value = 0.06921, steps = 64 shifted from previous position = 0.0125 rotated from previous position = 0.00171 degrees atoms outside contour = 5339, contour level = 0.04236 Position of 8act.pdb (#3) relative to cryosparc_P30_J279_map.mrc (#4) coordinates: Matrix rotation and translation 0.99529777 -0.04988324 0.08303014 -93.89145014 -0.05712784 -0.99454304 0.08729576 330.45021647 0.07822245 -0.09162861 -0.99271620 332.90769160 Axis -0.99882138 0.02683827 -0.04044199 Axis point 0.00000000 171.52297541 160.98536353 Rotation angle (degrees) 174.86125937 Shift along axis 89.18605104 > show #!2 models > show #!5 models > hide #!4 models > hide #!3 models > show #!4 models > hide #!2 models > fitmap #5 inMap #4 Fit molecule 8qyq.pdb (#5) to map cryosparc_P30_J279_map.mrc (#4) using 14943 atoms average map value = 0.07346, steps = 28 shifted from previous position = 0.026 rotated from previous position = 0.0648 degrees atoms outside contour = 4000, contour level = 0.04236 Position of 8qyq.pdb (#5) relative to cryosparc_P30_J279_map.mrc (#4) coordinates: Matrix rotation and translation -0.48597381 -0.87364307 -0.02402555 131.99331828 -0.50982761 0.26105496 0.81971099 104.73346858 -0.70986284 0.41060696 -0.57227324 157.51977670 Axis -0.46618686 0.78153309 0.41457912 Axis point 115.27505316 0.00000000 25.56334997 Rotation angle (degrees) 153.97413268 Shift along axis 85.62353087 > show #!3 models > show #!2 models > hide #!5 models > hide #!2 models > select add #3 18834 atoms, 19195 bonds, 19 pseudobonds, 2328 residues, 3 models selected > view matrix models > #3,0.95172,-0.29911,0.069057,-20.803,0.28197,0.94071,0.18854,-169,-0.12136,-0.15997,0.97963,-13.019 > fitmap #3 inMap #4 Fit molecule 8act.pdb (#3) to map cryosparc_P30_J279_map.mrc (#4) using 18834 atoms average map value = 0.06921, steps = 76 shifted from previous position = 3.09 rotated from previous position = 0.00809 degrees atoms outside contour = 5343, contour level = 0.04236 Position of 8act.pdb (#3) relative to cryosparc_P30_J279_map.mrc (#4) coordinates: Matrix rotation and translation 0.99529429 -0.04999011 0.08300768 -93.86164081 -0.05722488 -0.99454601 0.08719835 330.49357732 0.07819590 -0.09153812 -0.99272664 332.89632413 Axis -0.99882051 0.02688932 -0.04042956 Axis point 0.00000000 171.53441271 160.98537615 Rotation angle (degrees) 174.86666587 Shift along axis 89.17882775 > select subtract #3 Nothing selected > show #!2 models > select add #2 99840 atoms, 100312 bonds, 5 pseudobonds, 6146 residues, 3 models selected > hide #!3 models > view matrix models > #2,-0.97957,0.18401,0.081197,326.1,0.20088,0.91487,0.35022,-426.82,-0.0098435,0.35937,-0.93314,214.54,#1,1,0,0,0,0,1,0,0,0,0,1,0 > fitmap #2 inMap #4 Fit molecule 8g4l.pdb (#2) to map cryosparc_P30_J279_map.mrc (#4) using 99840 atoms average map value = 0.03324, steps = 224 shifted from previous position = 2.05 rotated from previous position = 0.0135 degrees atoms outside contour = 78989, contour level = 0.04236 Position of 8g4l.pdb (#2) relative to cryosparc_P30_J279_map.mrc (#4) coordinates: Matrix rotation and translation -0.89780391 0.39481948 0.19510437 171.55908545 -0.43419345 -0.71946808 -0.54207170 713.11615692 -0.07364910 -0.57138713 0.81736929 187.01348437 Axis -0.03361936 0.30821036 -0.95072399 Axis point 167.18733995 366.02013285 0.00000000 Rotation angle (degrees) 154.15167345 Shift along axis 36.22387450 > show #!3 models > select subtract #2 Nothing selected > volume #4 level 0.03302 > hide #!3 models > hide #!2 models > show #!5 models > select add #5 14943 atoms, 14737 bonds, 20 pseudobonds, 2292 residues, 3 models selected > select ::name=""XB2"" 40 atoms, 42 bonds, 2 residues, 1 model selected > color sel byhetero > select ::name=""XB2"" 40 atoms, 42 bonds, 2 residues, 1 model selected > show sel atoms > hide #!5 models > show #!5 models > select add #5 14943 atoms, 14737 bonds, 20 pseudobonds, 2292 residues, 3 models selected > hide sel cartoons > ui mousemode right translate > volume #4 level 0.04236 > volume #4 level 0.08254 > show sel cartoons > hide sel cartoons > show sel cartoons > fitmap #5 inMap #4 Fit molecule 8qyq.pdb (#5) to map cryosparc_P30_J279_map.mrc (#4) using 14943 atoms average map value = 0.07346, steps = 28 shifted from previous position = 0.0249 rotated from previous position = 0.0574 degrees atoms outside contour = 9432, contour level = 0.082538 Position of 8qyq.pdb (#5) relative to cryosparc_P30_J279_map.mrc (#4) coordinates: Matrix rotation and translation -0.48625976 -0.87350889 -0.02310098 131.98359794 -0.50952602 0.26196441 0.81960836 104.75385886 -0.70988356 0.41031312 -0.57245827 157.52305140 Axis -0.46592829 0.78181077 0.41434616 Axis point 115.26244630 0.00000000 25.56654333 Rotation angle (degrees) 153.94551965 Shift along axis 85.67187553 > volume #4 level 0.06852 > ui mousemode right ""rotate selected models"" > view matrix models > #5,-0.68456,-0.70867,0.17078,136.17,0.45982,-0.60159,-0.65319,142.81,0.56564,-0.36862,0.73768,90.628 > view matrix models > #5,-0.67257,-0.72389,0.15376,136.39,0.47921,-0.58434,-0.6549,142.55,0.56392,-0.36678,0.7399,90.602 > fitmap #5 inMap #4 Fit molecule 8qyq.pdb (#5) to map cryosparc_P30_J279_map.mrc (#4) using 14943 atoms average map value = 0.07346, steps = 84 shifted from previous position = 0.173 rotated from previous position = 4.64 degrees atoms outside contour = 7674, contour level = 0.068522 Position of 8qyq.pdb (#5) relative to cryosparc_P30_J279_map.mrc (#4) coordinates: Matrix rotation and translation -0.48604532 -0.87361366 -0.02364530 131.98433118 -0.50971212 0.26139904 0.81967316 104.73161110 -0.70989682 0.41045061 -0.57234325 157.51876880 Axis -0.46610167 0.78163575 0.41448135 Axis point 115.26785562 0.00000000 25.56530335 Rotation angle (degrees) 153.96091166 Shift along axis 85.63244638 > ui mousemode right translate > volume #4 level 0.05824 > hide sel cartoons > show #!3 models > show #!2 models > volume #4 level 0.03582 > select subtract #5 Nothing selected > select add #5 14943 atoms, 14737 bonds, 20 pseudobonds, 2292 residues, 3 models selected > save /Users/ruchigautamsharma/Desktop/25HepE525K/25HepE525KwithMava_3.cxs > volume #4 level 0.04703 > volume #4 level 0.03302 > show #!6 models > show #!7 models > show #!8 models > show #!9 models > show #!10 models > show #!11 models > hide #!11 models > hide #!10 models > hide #!9 models > hide #!8 models > hide #!7 models > hide #!6 models > save > /Users/ruchigautamsharma/Desktop/25HepE525K/25HepE525KwithMava_20240903.cxs > includeMaps true ——— End of log from Tue Sep 3 19:15:56 2024 ——— opened ChimeraX session > volume #4 level 0.04423 > select > #2/B:12-16,20-28,99-111,136-142,154-166,184-199,216-222,224-231,271-274,284-291,295-301,311-315,326-337,343-360,378-388,393-400,417-447,473-503,518-525,530-538,545-555,593-597,604-611,615-619,647-664,686-696,698-707,715-722,727-729,738-748,753-755,767-824,828-832,837-965,968-995,998-1165,1168-1171 11706 atoms, 11732 bonds, 715 residues, 1 model selected > hide #!4 models > show #!4 models > hide #!3 models > hide #!2 models > volume #4 level 0.06198 > volume #4 level 0.05357 > volume #4 level 0.04703 > show #!3 models > show #!2 models > hide #!3 models > select add #2 99840 atoms, 100312 bonds, 5 pseudobonds, 6146 residues, 3 models selected > select subtract #2 Nothing selected > hide #!2 models > show #!2 models > show #!3 models > show #!10 models > transparency #4.1#10.1 0 > hide #!4 models > transparency #10.1 50 > ui mousemode right select > hide #!10 models Drag select of 18 residues Drag select of 24 residues > style sel ball Changed 309 atom styles > show sel atoms > coulombic sel Using Amber 20 recommended default charges and atom types for standard residues Assigning partial charges to residue M3L (net charge +1) with am1-bcc method Running ANTECHAMBER command: /Applications/ChimeraX-1.7.1.app/Contents/bin/amber20/bin/antechamber -ek qm_theory='AM1', -i /var/folders/1r/q7x50qrs79s_c_5jlk649y5m0000gn/T/tmpytfstoqe/ante.in.mol2 -fi mol2 -o /var/folders/1r/q7x50qrs79s_c_5jlk649y5m0000gn/T/tmpytfstoqe/ante.out.mol2 -fo mol2 -c bcc -nc 1 -j 5 -s 2 -dr n (M3L) `` (M3L) `Welcome to antechamber 20.0: molecular input file processor.` (M3L) `` (M3L) `Info: Finished reading file (/var/folders/1r/q7x50qrs79s_c_5jlk649y5m0000gn/T/tmpytfstoqe/ante.in.mol2); atoms read (43), bonds read (42).` (M3L) `Info: Determining atomic numbers from atomic symbols which are case sensitive.` (M3L) `Running: /Applications/ChimeraX-1.7.1.app/Contents/bin/amber20/bin/bondtype -j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac` (M3L) `` (M3L) `` (M3L) `Running: /Applications/ChimeraX-1.7.1.app/Contents/bin/amber20/bin/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff` (M3L) `Info: Total number of electrons: 134; net charge: 1` (M3L) `` (M3L) `Running: /Applications/ChimeraX-1.7.1.app/Contents/bin/amber20/bin/sqm -O -i sqm.in -o sqm.out` (M3L) `` (M3L) `Running: /Applications/ChimeraX-1.7.1.app/Contents/bin/amber20/bin/am1bcc -i ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p /Applications/ChimeraX-1.7.1.app/Contents/bin/amber20/dat/antechamber/BCCPARM.DAT -s 2 -j 1` (M3L) `` (M3L) `Running: /Applications/ChimeraX-1.7.1.app/Contents/bin/amber20/bin/atomtype -f ac -p bcc -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC` (M3L) `` Charges for residue M3L determined Using Amber 20 recommended default charges and atom types for standard residues Coulombic values for 8g4l.pdb_A SES surface #2.2: minimum, -21.91, mean -0.65, maximum 19.75 Coulombic values for 8g4l.pdb_B SES surface #2.3: minimum, -23.19, mean -0.75, maximum 24.96 Coulombic values for 8act.pdb_A SES surface #3.3: minimum, -23.72, mean -1.16, maximum 15.27 Coulombic values for 8act.pdb_B SES surface #3.4: minimum, -25.84, mean -0.34, maximum 15.00 To also show corresponding color key, enter the above coulombic command and add key true > ui mousemode right translate Drag select of 8g4l.pdb_B SES surface, 200 of 1516366 triangles, 8act.pdb_A SES surface, 14 of 807322 triangles, 1 atoms, 12 residues > select add #3 18867 atoms, 19195 bonds, 19 pseudobonds, 2331 residues, 7 models selected > select add #2 118674 atoms, 119507 bonds, 24 pseudobonds, 8474 residues, 10 models selected > select subtract #3 99840 atoms, 100312 bonds, 5 pseudobonds, 6146 residues, 7 models selected > select subtract #2 2 models selected > save /Users/ruchigautamsharma/Desktop/image1.png supersample 3 > show #!10 models > hide #!3 models > hide #!2 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!10 models > show #!10 models > hide #!10 models > show #!10 models > hide #!10 models > ui mousemode right select > ui mousemode right translate > ui mousemode right select > show #!10 models > hide #!10 models Drag select of 42 residues > select add #3 18834 atoms, 19195 bonds, 19 pseudobonds, 2328 residues, 5 models selected > select subtract #3 2 models selected Drag select of 25 residues > style sel ball Changed 204 atom styles > show sel atoms > coulombic sel Coulombic values for 8act.pdb_A SES surface #3.3: minimum, -23.72, mean -1.16, maximum 15.27 Coulombic values for 8act.pdb_B SES surface #3.4: minimum, -25.84, mean -0.34, maximum 15.00 To also show corresponding color key, enter the above coulombic command and add key true Drag select of 8act.pdb_B SES surface, 36 of 774284 triangles, 13 residues Drag select of 8act.pdb_B SES surface, 335 of 774284 triangles, 1 atoms, 32 residues, 1 bonds > style sel ball Changed 263 atom styles > show sel atoms > coulombic sel Coulombic values for 8act.pdb_A SES surface #3.3: minimum, -23.72, mean -1.16, maximum 15.27 Coulombic values for 8act.pdb_B SES surface #3.4: minimum, -25.84, mean -0.34, maximum 15.00 To also show corresponding color key, enter the above coulombic command and add key true Drag select of 20 atoms, 46 residues, 17 bonds Drag select of 8act.pdb_A SES surface, 1775 of 807322 triangles, 8act.pdb_B SES surface, 1980 of 774284 triangles, 44 atoms, 78 residues, 37 bonds Drag select of 8act.pdb_B SES surface, 1283 of 774284 triangles, 62 atoms, 33 residues, 49 bonds > coulombic sel Coulombic values for 8act.pdb_A SES surface #3.3: minimum, -23.72, mean -1.16, maximum 15.27 Coulombic values for 8act.pdb_B SES surface #3.4: minimum, -25.84, mean -0.34, maximum 15.00 To also show corresponding color key, enter the above coulombic command and add key true > show #!10 models > select add #3 18834 atoms, 19195 bonds, 19 pseudobonds, 2328 residues, 5 models selected > select subtract #3 2 models selected > hide #!3 models > show #!3 models > hide #!10 models > save /Users/ruchigautamsharma/Desktop/image2.png supersample 3 > hide #!3 models > show #!2 models > show #!10 models > hide #!5 models > ui mousemode right translate > hide #!10 models > ui mousemode right select Drag select of 40 atoms, 31 residues, 37 bonds, 1 pseudobonds > style sel ball Changed 477 atom styles > show sel atoms > coulombic sel Coulombic values for 8g4l.pdb_A SES surface #2.2: minimum, -21.91, mean -0.65, maximum 19.75 Coulombic values for 8g4l.pdb_B SES surface #2.3: minimum, -23.19, mean -0.75, maximum 24.96 To also show corresponding color key, enter the above coulombic command and add key true > ui mousemode right translate > show #!10 models > hide #!2 models > show #!3 models > show #!2 models > hide #!10 models > save /Users/ruchigautamsharma/Desktop/image3.png supersample 3 > save ""/Users/ruchigautamsharma/Desktop/25HepE525K/interaction > 25HepE525K.cxs"" includeMaps true ——— End of log from Wed Sep 25 04:14:14 2024 ——— opened ChimeraX session > select add #2 99840 atoms, 100312 bonds, 5 pseudobonds, 6146 residues, 3 models selected > select subtract #2 2 models selected > hide #!2 models > ui mousemode right select Drag select of 50 atoms, 26 residues, 42 bonds Drag select of 8act.pdb_A SES surface, 9674 of 807322 triangles, 8act.pdb_B SES surface, 2496 of 774284 triangles, 48 atoms, 91 residues, 38 bonds Drag select of 8act.pdb_A SES surface, 5160 of 807322 triangles, 8act.pdb_B SES surface, 2203 of 774284 triangles, 69 atoms, 95 residues, 57 bonds > coulombic sel Coulombic values for 8act.pdb_A SES surface #3.3: minimum, -23.72, mean -1.16, maximum 15.27 Coulombic values for 8act.pdb_B SES surface #3.4: minimum, -25.84, mean -0.34, maximum 15.00 To also show corresponding color key, enter the above coulombic command and add key true Drag select of 8act.pdb_A SES surface, 1211 of 807322 triangles, 8act.pdb_B SES surface, 784 of 774284 triangles, 4 atoms, 22 residues, 4 bonds > ui mousemode right translate > ui mousemode right select Drag select of 8act.pdb_A SES surface, 9181 of 807322 triangles, 8act.pdb_B SES surface, 7593 of 774284 triangles, 46 atoms, 34 residues, 39 bonds > select add #3 18834 atoms, 19195 bonds, 19 pseudobonds, 2328 residues, 5 models selected > select subtract #3 2 models selected Drag select of 8act.pdb_A SES surface, 45732 of 807322 triangles, 8act.pdb_B SES surface, 16784 of 774284 triangles, 242 atoms, 415 residues, 1 pseudobonds, 201 bonds > select add #3 18834 atoms, 19195 bonds, 19 pseudobonds, 2328 residues, 5 models selected > select subtract #3 2 models selected Drag select of 8act.pdb_A SES surface, 170 of 807322 triangles, 8act.pdb_B SES surface, 459 of 774284 triangles > ui mousemode right translate > ui mousemode right select Drag select of 8act.pdb_A SES surface, 40121 of 807322 triangles, 8act.pdb_B SES surface, 13087 of 774284 triangles, 153 atoms, 281 residues, 127 bonds > select add #3 18834 atoms, 19195 bonds, 19 pseudobonds, 2328 residues, 5 models selected > coulombic sel The following heavy (non-hydrogen) atoms are missing, which may result in inaccurate electrostatics: 8act.pdb #3/D SER 195 OXT 8act.pdb #3/C SER 195 OXT 8act.pdb #3/E GLU 163 OXT Using Amber 20 recommended default charges and atom types for standard residues Coulombic values for 8act.pdb_A SES surface #3.3: minimum, -23.72, mean -1.16, maximum 15.27 Coulombic values for 8act.pdb_B SES surface #3.4: minimum, -25.84, mean -0.34, maximum 15.00 Coulombic values for 8act.pdb_C SES surface #3.5: minimum, -22.56, mean -3.87, maximum 14.68 Coulombic values for 8act.pdb_D SES surface #3.6: minimum, -19.82, mean -3.44, maximum 15.48 Coulombic values for 8act.pdb_E SES surface #3.7: minimum, -20.97, mean -5.04, maximum 8.16 Coulombic values for 8act.pdb_F SES surface #3.8: minimum, -22.95, mean -4.14, maximum 7.43 To also show corresponding color key, enter the above coulombic command and add key true > ui mousemode right translate > show #!10 models > show #!4 models > hide #!10 models > select subtract #3 6 models selected > hide #!3 models > show #!10 models > hide #!4 models > show #!3 models > save > /Users/ruchigautamsharma/Desktop/25HepE525K/25HepE525KwithMava_Interaction.cxs ——— End of log from Thu Sep 26 13:06:28 2024 ——— opened ChimeraX session > show #!2 models > close #6 > close #7 > close #8 > close #9 > close #11 > save > /Users/ruchigautamsharma/Desktop/25HepE525K/25HepE525KwithMava_Interaction.cxs ——— End of log from Thu Sep 26 13:21:30 2024 ——— opened ChimeraX session > hide #!3 models > hide #!2 models > show #!2 models > hide #!2 models > volume #10 level 0.07481 > show #!3 models > show #!2 models > hide #!2 models > open > /Users/ruchigautamsharma/Desktop/25HepE525K/cryosparc_P30_J276_map_sharp.mrc Opened cryosparc_P30_J276_map_sharp.mrc as #6, grid size 300,300,300, pixel 0.83, shown at level 0.0289, step 2, values float32 > hide #!3 models > select add #6 2 models selected > ui mousemode right ""translate selected models"" > view matrix models #6,1,0,0,-13.259,0,1,0,-59.644,0,0,1,-60.922 > ui mousemode right ""rotate selected models"" > view matrix models > #6,0.97989,-0.19467,-0.043828,17.497,0.19799,0.97586,0.092126,-93.748,0.024836,-0.09895,0.99478,-51.92 > undo [Repeated 1 time(s)] > volumeflip #6 Unknown command: volumeflip #6 > volume flip #6 Opened cryosparc_P30_J276_map_sharp.mrc z flip as #7, grid size 300,300,300, pixel 0.83, shown at step 1, values float32 > select subtract #6 Nothing selected > select add #7 2 models selected > view matrix models > #7,0.96691,0.024547,-0.25392,32.662,0.2299,0.34752,0.90905,-65.44,0.11056,-0.93735,0.33038,177.52 > view matrix models > #7,-0.99755,-0.034454,-0.060947,267.99,-0.00070731,0.87544,-0.48332,74.136,0.070008,-0.48209,-0.87332,277.93 > ui mousemode right ""translate selected models"" > view matrix models > #7,-0.99755,-0.034454,-0.060947,269.51,-0.00070731,0.87544,-0.48332,81.793,0.070008,-0.48209,-0.87332,283.92 > fitmap #7 inMap #10 Fit map cryosparc_P30_J276_map_sharp.mrc z flip in map cryosparc_P30_J280_class_05_00027_volume.mrc z flip using 270132 points correlation = 0.765, correlation about mean = 0.4371, overlap = 1.18e+04 steps = 156, shift = 3.04, angle = 18.9 degrees Position of cryosparc_P30_J276_map_sharp.mrc z flip (#7) relative to cryosparc_P30_J280_class_05_00027_volume.mrc z flip (#10) coordinates: Matrix rotation and translation 0.99868521 -0.01194978 0.04985040 -4.14668671 0.01153380 0.99989629 0.00862389 -2.79643992 -0.04994828 -0.00803759 0.99871946 7.43685902 Axis -0.16040788 0.96080890 0.22608753 Axis point 148.17070643 0.00000000 88.18561170 Rotation angle (degrees) 2.97697945 Shift along axis -0.34030206 > ui mousemode right translate > hide #!10 models > volume #7 level 0.009114 > transparency sel 50 > show #!2 models > volume #7 level 0.00811 > volume #7 level 0.00611 > volume #7 level 0.00111 > surface dust #7 size 8.3 > fitmap #2 inMap #7 Fit molecule 8g4l.pdb (#2) to map cryosparc_P30_J276_map_sharp.mrc z flip (#7) using 99840 atoms average map value = 0.07007, steps = 304 shifted from previous position = 0.129 rotated from previous position = 0.285 degrees atoms outside contour = 75934, contour level = 0.00111 Position of 8g4l.pdb (#2) relative to cryosparc_P30_J276_map_sharp.mrc z flip (#7) coordinates: Matrix rotation and translation 0.90356614 -0.36251243 -0.22837025 69.94133890 0.42750669 0.72750591 0.53663133 -463.88516185 -0.02839482 -0.58251171 0.81232619 178.12186061 Axis -0.80838767 -0.14444773 0.57065245 Axis point 0.00000000 -62.59090162 802.47834953 Rotation angle (degrees) 43.80505846 Shift along axis 112.11311861 > show #!3 models > select subtract #7 Nothing selected > hide #!2 models > show #!2 models > hide #!3 models > hide #!2 models > show #!2 models > open > /Users/ruchigautamsharma/Desktop/25HepE525K/cryosparc_P30_J366_003_volume_map_sharp.mrc Opened cryosparc_P30_J366_003_volume_map_sharp.mrc as #8, grid size 300,300,300, pixel 0.83, shown at level 0.0628, step 2, values float32 > volume flip #8 Opened cryosparc_P30_J366_003_volume_map_sharp.mrc z flip as #9, grid size 300,300,300, pixel 0.83, shown at step 1, values float32 > close #8 > close #6 > select add #9 2 models selected > ui mousemode right ""translate selected models"" > ui mousemode right ""rotate selected models"" > view matrix models > #9,0.72491,0.12345,-0.6777,107.22,-0.31498,0.93434,-0.16672,71.607,0.61261,0.33432,0.71619,-88.209 > view matrix models > #9,-0.78393,-0.37061,0.49809,227.29,-0.46679,0.88081,-0.079276,87.942,-0.40935,-0.29465,-0.86349,320.77 > view matrix models > #9,-0.9341,-0.13426,0.33081,241.15,-0.20068,0.96381,-0.17551,53.522,-0.29528,-0.23033,-0.92723,305.45 > ui mousemode right ""translate selected models"" > view matrix models > #9,-0.9341,-0.13426,0.33081,237.7,-0.20068,0.96381,-0.17551,58.891,-0.29528,-0.23033,-0.92723,312.4 > select subtract #9 Nothing selected > hide #!9 models > hide #!7 models > show #!10 models > show #!9 models Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps, got 1 atomic models, 2 maps. > hide #!2 models > fitmap #10 inMap #9 Fit map cryosparc_P30_J280_class_05_00027_volume.mrc z flip in map cryosparc_P30_J366_003_volume_map_sharp.mrc z flip using 110989 points correlation = 0.8661, correlation about mean = 0.6378, overlap = 1281 steps = 248, shift = 14.1, angle = 17.3 degrees Position of cryosparc_P30_J280_class_05_00027_volume.mrc z flip (#10) relative to cryosparc_P30_J366_003_volume_map_sharp.mrc z flip (#9) coordinates: Matrix rotation and translation 0.99912867 0.03701040 0.01929050 -6.45856044 -0.03695133 0.99931125 -0.00340957 4.82258956 -0.01940341 0.00269379 0.99980811 2.58781556 Axis 0.07292398 0.46232197 -0.88370838 Axis point 133.82942588 176.61647977 0.00000000 Rotation angle (degrees) 2.39837754 Shift along axis -0.52826911 > show #!2 models > hide #!9 models > fitmap #2 inMap #10 Fit molecule 8g4l.pdb (#2) to map cryosparc_P30_J280_class_05_00027_volume.mrc z flip (#10) using 99840 atoms average map value = 0.0705, steps = 2000 shifted from previous position = 42.4 rotated from previous position = 17.7 degrees atoms outside contour = 75484, contour level = 0.074814 Position of 8g4l.pdb (#2) relative to cryosparc_P30_J280_class_05_00027_volume.mrc z flip (#10) coordinates: Matrix rotation and translation 0.89869523 -0.39132784 -0.19801364 76.37796838 0.43305938 0.72042893 0.54170263 -464.23480660 -0.06932856 -0.57257723 0.81691423 184.96627548 Axis -0.80046161 -0.09244309 0.59221237 Axis point 0.00000000 -34.72317143 823.48795667 Rotation angle (degrees) 44.10881728 Shift along axis 91.31698418 > show #!9 models > hide #!10 models > surface dust #9 size 8.3 > volume #9 level 0.04335 > transparency #2.2-3#9.1 50 > volume #9 level 0.04552 > show #!3 models > hide #!2 models > fitmap #3 inMap #9 Fit molecule 8act.pdb (#3) to map cryosparc_P30_J366_003_volume_map_sharp.mrc z flip (#9) using 18834 atoms average map value = 0.07945, steps = 224 shifted from previous position = 13.7 rotated from previous position = 17.3 degrees atoms outside contour = 5855, contour level = 0.045517 Position of 8act.pdb (#3) relative to cryosparc_P30_J366_003_volume_map_sharp.mrc z flip (#9) coordinates: Matrix rotation and translation -0.99082281 0.08342546 -0.10635013 340.09974533 0.09230379 0.99239110 -0.08148569 -89.94149170 0.09874294 -0.09055440 -0.99098422 327.06025206 Axis -0.04413312 -0.99809091 0.04320662 Axis point 163.69830978 0.00000000 170.46022157 Rotation angle (degrees) 174.10287196 Shift along axis 88.89128906 > hide #!3 models > show #!3 models > save /Users/ruchigautamsharma/Desktop/25HepE525K/25HepE525KwithMava_4.cxs ——— End of log from Fri Sep 27 17:28:16 2024 ——— opened ChimeraX session > show #!2 models > hide #!3 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > color #9 #78c1fe80 models > select > #2/A:10-16,20-27,82-84,90-92,98-111,136-142,154-168,184-199,216-231,271-273,284-291,295-301,307-309,311-314,325-338,343-359,379-388,393-400,417-447,473-504,518-524,530-539,545-555,604-611,615-618,647-662,686-696,698-707,715-723,738-748,753-755,769-826,829-836,842-919,922-1171 11821 atoms, 11850 bonds, 720 residues, 1 model selected > select add #2 99840 atoms, 100312 bonds, 5 pseudobonds, 6146 residues, 4 models selected > select subtract #2 2 models selected > select #2/A:483-484 37 atoms, 36 bonds, 2 residues, 1 model selected > select #2/A:483-485 56 atoms, 55 bonds, 3 residues, 1 model selected > style sel ball Changed 56 atom styles > show sel atoms > rainbow sel > hide #!9 models > show #!9 models > hide #!9 models > show #!9 models > coulombic sel Coulombic values for 8g4l.pdb_A SES surface #2.2: minimum, -21.91, mean -0.65, maximum 19.75 To also show corresponding color key, enter the above coulombic command and add key true > hide #!9 models > show #!9 models ===== Log before crash end ===== Log: UCSF ChimeraX version: 1.7.1 (2024-01-23) © 2016-2023 Regents of the University of California. All rights reserved. > open /Users/ruchigautamsharma/Desktop/25HepE525K/25HepE525KwithMava_4.cxs Opened cryosparc_P30_J279_map.mrc as #4, grid size 300,300,300, pixel 0.83, shown at level 0.047, step 1, values float32 Opened cryosparc_P30_J280_class_05_00027_volume.mrc z flip as #10, grid size 180,180,180, pixel 1.38, shown at level 0.0748, step 1, values float32 Opened cryosparc_P30_J276_map_sharp.mrc z flip as #7, grid size 300,300,300, pixel 0.83, shown at level 0.00111, step 1, values float32 Opened cryosparc_P30_J366_003_volume_map_sharp.mrc z flip as #9, grid size 300,300,300, pixel 0.83, shown at level 0.0455, step 1, values float32 Log from Fri Sep 27 17:28:16 2024UCSF ChimeraX version: 1.7.1 (2024-01-23) © 2016-2023 Regents of the University of California. All rights reserved. > open > /Users/ruchigautamsharma/Desktop/25HepE525K/25HepE525KwithMava_Interaction.cxs Opened cryosparc_P30_J279_map.mrc as #4, grid size 300,300,300, pixel 0.83, shown at level 0.047, step 1, values float32 Opened cryosparc_P30_J280_class_05_00027_volume.mrc z flip as #10, grid size 180,180,180, pixel 1.38, shown at level 0.0971, step 1, values float32 Log from Thu Sep 26 13:21:30 2024UCSF ChimeraX version: 1.7.1 (2024-01-23) © 2016-2023 Regents of the University of California. All rights reserved. > open > /Users/ruchigautamsharma/Desktop/25HepE525K/25HepE525KwithMava_Interaction.cxs Opened cryosparc_P30_J279_map.mrc as #4, grid size 300,300,300, pixel 0.83, shown at level 0.047, step 1, values float32 Opened cryosparc_P30_J280_class_00_00027_volume (1).mrc z flip as #6, grid size 180,180,180, pixel 1.38, shown at level 0.0903, step 1, values float32 Opened cryosparc_P30_J280_class_01_00027_volume.mrc z flip as #7, grid size 180,180,180, pixel 1.38, shown at level 0.0709, step 1, values float32 Opened cryosparc_P30_J280_class_02_00027_volume.mrc z flip as #8, grid size 180,180,180, pixel 1.38, shown at level 0.0781, step 1, values float32 Opened cryosparc_P30_J280_class_04_00027_volume.mrc z flip as #9, grid size 180,180,180, pixel 1.38, shown at level 0.0892, step 1, values float32 Opened cryosparc_P30_J280_class_05_00027_volume.mrc z flip as #10, grid size 180,180,180, pixel 1.38, shown at level 0.0971, step 1, values float32 Opened cryosparc_P30_J280_class_08_00027_volume.mrc z flip as #11, grid size 180,180,180, pixel 1.38, shown at level 0.0708, step 1, values float32 Log from Thu Sep 26 13:06:28 2024UCSF ChimeraX version: 1.7.1 (2024-01-23) © 2016-2023 Regents of the University of California. All rights reserved. > open ""/Users/ruchigautamsharma/Desktop/25HepE525K/interaction > 25HepE525K.cxs"" Opened cryosparc_P30_J279_map.mrc as #4, grid size 300,300,300, pixel 0.83, shown at level 0.047, step 1, values float32 Opened cryosparc_P30_J280_class_00_00027_volume (1).mrc z flip as #6, grid size 180,180,180, pixel 1.38, shown at level 0.0903, step 1, values float32 Opened cryosparc_P30_J280_class_01_00027_volume.mrc z flip as #7, grid size 180,180,180, pixel 1.38, shown at level 0.0709, step 1, values float32 Opened cryosparc_P30_J280_class_02_00027_volume.mrc z flip as #8, grid size 180,180,180, pixel 1.38, shown at level 0.0781, step 1, values float32 Opened cryosparc_P30_J280_class_04_00027_volume.mrc z flip as #9, grid size 180,180,180, pixel 1.38, shown at level 0.0892, step 1, values float32 Opened cryosparc_P30_J280_class_05_00027_volume.mrc z flip as #10, grid size 180,180,180, pixel 1.38, shown at level 0.0971, step 1, values float32 Opened cryosparc_P30_J280_class_08_00027_volume.mrc z flip as #11, grid size 180,180,180, pixel 1.38, shown at level 0.0708, step 1, values float32 Log from Wed Sep 25 04:14:14 2024UCSF ChimeraX version: 1.7.1 (2024-01-23) © 2016-2023 Regents of the University of California. All rights reserved. > open > /Users/ruchigautamsharma/Desktop/25HepE525K/25HepE525KwithMava_20240903.cxs Opened cryosparc_P30_J279_map.mrc as #4, grid size 300,300,300, pixel 0.83, shown at level 0.033, step 1, values float32 Opened cryosparc_P30_J280_class_00_00027_volume (1).mrc z flip as #6, grid size 180,180,180, pixel 1.38, shown at level 0.0903, step 1, values float32 Opened cryosparc_P30_J280_class_01_00027_volume.mrc z flip as #7, grid size 180,180,180, pixel 1.38, shown at level 0.0709, step 1, values float32 Opened cryosparc_P30_J280_class_02_00027_volume.mrc z flip as #8, grid size 180,180,180, pixel 1.38, shown at level 0.0781, step 1, values float32 Opened cryosparc_P30_J280_class_04_00027_volume.mrc z flip as #9, grid size 180,180,180, pixel 1.38, shown at level 0.0892, step 1, values float32 Opened cryosparc_P30_J280_class_05_00027_volume.mrc z flip as #10, grid size 180,180,180, pixel 1.38, shown at level 0.0971, step 1, values float32 Opened cryosparc_P30_J280_class_08_00027_volume.mrc z flip as #11, grid size 180,180,180, pixel 1.38, shown at level 0.0708, step 1, values float32 Log from Tue Sep 3 19:15:56 2024 Startup Messages --- warnings | Replacing fetcher for 'ngff' and format OME-Zarr from OME-Zarr bundle with that from OME-Zarr bundle Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR bundle with that from NMRSTAR bundle UCSF ChimeraX version: 1.7.1 (2024-01-23) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open > /Users/ruchigautamsharma/Downloads/cryosparc_P30_J277_005_volume_map_sharp.mrc Opened cryosparc_P30_J277_005_volume_map_sharp.mrc as #1, grid size 300,300,300, pixel 0.83, shown at level 0.061, step 2, values float32 > set bgColor white > color #1 #699dbfff models > color #1 #6b98bfff models > surface dust #1 size 8.3 > transparency 50 > volume #1 level 0.04162 > volume #1 step 1 > volume #1 level 0.04802 > open /Users/ruchigautamsharma/Desktop/pdbs/8g4l.pdb Summary of feedback from opening /Users/ruchigautamsharma/Desktop/pdbs/8g4l.pdb --- warning | Ignored bad PDB record found on line 1 HEADER CONTRACTILE PROTEIN 2023-02-10 XXXX Chain information for 8g4l.pdb #2 --- Chain | Description A B | No description available C D | No description available E F | No description available G H | No description available I J | No description available K L | No description available M N | No description available > ui mousemode right select Drag select of 62714 atoms, 4 pseudobonds > ui mousemode right translate > select /E 5809 atoms, 5816 bonds, 355 residues, 1 model selected > hide sel atoms > select /F 5809 atoms, 5816 bonds, 355 residues, 1 model selected > hide sel atoms > select /G 5820 atoms, 5829 bonds, 357 residues, 1 model selected > hide sel atoms > select /H 5820 atoms, 5829 bonds, 357 residues, 1 model selected > hide sel atoms > select /I 5683 atoms, 5699 bonds, 350 residues, 1 model selected > hide sel atoms > select /J 5683 atoms, 5699 bonds, 350 residues, 1 model selected > hide sel atoms > select /K 5823 atoms, 5842 bonds, 359 residues, 1 model selected > hide sel atoms > select /L 5823 atoms, 5842 bonds, 359 residues, 1 model selected > hide sel atoms > select /L 5823 atoms, 5842 bonds, 359 residues, 1 model selected > select /M 5809 atoms, 5829 bonds, 358 residues, 1 model selected > hide sel atoms > select /M 5809 atoms, 5829 bonds, 358 residues, 1 model selected > select /N 5809 atoms, 5829 bonds, 358 residues, 1 model selected > hide sel atoms > ui mousemode right select Drag select of 39683 atoms, 4 pseudobonds > select clear Drag select of 31714 atoms, 4 pseudobonds > select clear Drag select of 41883 atoms, 4 pseudobonds > show sel cartoons > hide sel atoms > ui mousemode right ""translate selected models"" > select add #2 99840 atoms, 100312 bonds, 4 pseudobonds, 6146 residues, 2 models selected > view matrix models #2,1,0,0,-145.97,0,1,0,-273.41,0,0,1,-71.128 > ui mousemode right ""rotate selected models"" > view matrix models > #2,-0.33201,0.77488,0.53789,-305.02,0.61793,-0.25218,0.7447,-219.31,0.7127,0.57962,-0.39509,36.051 > view matrix models > #2,0.68978,-0.71496,0.11413,226.44,-0.050952,0.10931,0.9927,-277.33,-0.72222,-0.69057,0.038968,877.43 > ui mousemode right translate > ui mousemode right ""translate selected models"" > view matrix models > #2,0.68978,-0.71496,0.11413,251.77,-0.050952,0.10931,0.9927,-152.19,-0.72222,-0.69057,0.038968,779.18 > ui mousemode right ""rotate selected models"" > view matrix models > #2,0.78513,-0.60169,0.14676,156.66,0.1682,0.43522,0.88447,-322.45,-0.59606,-0.66974,0.44291,558.11 > view matrix models > #2,-0.50413,0.63042,0.59027,-182.3,0.83794,0.19158,0.51104,-264.56,0.20909,0.75224,-0.62484,116.61 > ui mousemode right ""translate selected models"" > view matrix models > #2,-0.50413,0.63042,0.59027,-238.07,0.83794,0.19158,0.51104,-324.86,0.20909,0.75224,-0.62484,-90.886 > view matrix models > #2,-0.50413,0.63042,0.59027,-157.14,0.83794,0.19158,0.51104,-349.51,0.20909,0.75224,-0.62484,-89.187 > ui mousemode right ""rotate selected models"" > view matrix models > #2,-0.64055,0.44273,0.62745,-45.163,0.76397,0.28458,0.57911,-397.18,0.077832,0.8503,-0.52052,-136.51 > view matrix models > #2,-0.53777,0.61178,0.58011,-133.79,0.81962,0.21814,0.52975,-363.7,0.19755,0.76035,-0.61874,-91.81 > ui mousemode right select Drag select of 57 atoms, 260 residues > hide sel cartoons > hide sel atoms Drag select of 68 residues Drag select of 120 residues > hide sel cartoons > select add #2 99840 atoms, 100312 bonds, 4 pseudobonds, 6146 residues, 2 models selected > ui mousemode right ""translate selected models"" > view matrix models > #2,-0.53777,0.61178,0.58011,-133.74,0.81962,0.21814,0.52975,-360.37,0.19755,0.76035,-0.61874,-108 > ui mousemode right ""rotate selected models"" > view matrix models > #2,-0.82313,0.40245,0.40062,100.33,0.56745,0.60968,0.55344,-466.49,-0.021518,0.68288,-0.73021,26.515 > open /Users/ruchigautamsharma/Desktop/pdbs/8act.pdb 8act.pdb title: Structure of the human β-cardiac myosin folded-back off state [more info...] Chain information for 8act.pdb #3 --- Chain | Description | UniProt A B | myosin-7 | MYH7_HUMAN 3-906 C D | myosin light chain 3 | MYL3_HUMAN 39-195 E F | myosin regulatory light chain 2, ventricular/cardiac muscle isoform | MLRV_HUMAN 20-163 Non-standard residues in 8act.pdb #3 --- ADP — adenosine-5'-diphosphate MG — magnesium ion PO4 — phosphate ion > select add #3 118674 atoms, 119507 bonds, 23 pseudobonds, 8474 residues, 5 models selected > select subtract #2 18834 atoms, 19195 bonds, 19 pseudobonds, 2328 residues, 3 models selected > show sel cartoons > hide sel atoms > ui mousemode right ""translate selected models"" > view matrix models #3,1,0,0,4.2373,0,1,0,-97.37,0,0,1,-63.243 > view matrix models #3,1,0,0,2.676,0,1,0,-7.5822,0,0,1,-6.9289 > view matrix models #3,1,0,0,-28.537,0,1,0,-116.48,0,0,1,-73.257 > view matrix models #3,1,0,0,-74.431,0,1,0,-86.716,0,0,1,-91.941 > view matrix models #3,1,0,0,-77.549,0,1,0,-89.295,0,0,1,-82.343 > hide #!1 models > open /Users/ruchigautamsharma/Desktop/25HepE525K/cryosparc_P30_J279_map.mrc Opened cryosparc_P30_J279_map.mrc as #4, grid size 300,300,300, pixel 0.83, shown at level 0.0557, step 2, values float32 > select subtract #3 Nothing selected > select add #4 2 models selected > view matrix models #4,1,0,0,-3.5551,0,1,0,1.2444,0,0,1,9.7098 > view matrix models #4,1,0,0,-29.5,0,1,0,31.846,0,0,1,74.225 > volume #4 level 0.03328 > ui mousemode right ""rotate selected models"" > view matrix models > #4,-0.91868,-0.12918,-0.37327,255.55,-0.23246,-0.5872,0.77534,174.17,-0.31934,0.79907,0.50942,65.389 > view matrix models > #4,-0.91602,-0.1276,-0.38031,255.91,-0.21581,-0.6424,0.73535,184.54,-0.33814,0.75567,0.56091,66.973 > view matrix models > #4,-0.8978,-0.097493,-0.42947,255.87,-0.045054,-0.94974,0.30978,258.35,-0.43809,0.29747,0.84829,104 > view matrix models > #4,0.93714,0.02002,0.34839,-67.977,0.070672,-0.98855,-0.1333,304.93,0.34173,0.14954,-0.92782,253.19 > transparency sel 50 > view matrix models > #4,0.98946,0.13009,0.063575,-53.463,0.13724,-0.98257,-0.1254,295.46,0.046154,0.13281,-0.99007,297.27 > surface dust #4 size 8.3 > ui mousemode right ""translate selected models"" > view matrix models > #4,0.98946,0.13009,0.063575,-55.693,0.13724,-0.98257,-0.1254,243.61,0.046154,0.13281,-0.99007,230.84 > select subtract #4 Nothing selected > select add #4 2 models selected > hide #!2 models > view matrix models > #4,0.98946,0.13009,0.063575,-17.14,0.13724,-0.98257,-0.1254,238.58,0.046154,0.13281,-0.99007,218.87 > view matrix models > #4,0.98946,0.13009,0.063575,-14.137,0.13724,-0.98257,-0.1254,247.93,0.046154,0.13281,-0.99007,226.91 > fitmap #3 inMap #4 Fit molecule 8act.pdb (#3) to map cryosparc_P30_J279_map.mrc (#4) using 18834 atoms average map value = 0.06921, steps = 132 shifted from previous position = 3.77 rotated from previous position = 11.1 degrees atoms outside contour = 3445, contour level = 0.033285 Position of 8act.pdb (#3) relative to cryosparc_P30_J279_map.mrc (#4) coordinates: Matrix rotation and translation 0.99530642 -0.04985030 0.08294620 -93.88397645 -0.05708112 -0.99455248 0.08721873 330.44446938 0.07814647 -0.09154402 -0.99272998 332.89917405 Axis -0.99882356 0.02681814 -0.04040165 Axis point 0.00000000 171.51399022 160.98585768 Rotation angle (degrees) 174.86592494 Shift along axis 89.18575633 > color #4 #a1d7ff80 models > color #4 #76ffcf80 models > view matrix models > #4,0.98946,0.13009,0.063575,-14.422,0.13724,-0.98257,-0.1254,247.38,0.046154,0.13281,-0.99007,228.5 > fitmap #3 inMap #4 Fit molecule 8act.pdb (#3) to map cryosparc_P30_J279_map.mrc (#4) using 18834 atoms average map value = 0.06921, steps = 72 shifted from previous position = 1.7 rotated from previous position = 0.0115 degrees atoms outside contour = 3448, contour level = 0.033285 Position of 8act.pdb (#3) relative to cryosparc_P30_J279_map.mrc (#4) coordinates: Matrix rotation and translation 0.99528837 -0.04999379 0.08307632 -93.87652160 -0.05723957 -0.99453995 0.08725781 330.47220450 0.07826037 -0.09160194 -0.99271567 332.89509969 Axis -0.99881903 0.02689404 -0.04046312 Axis point 0.00000000 171.52859786 160.98201658 Rotation angle (degrees) 174.86310814 Shift along axis 89.18341503 > ui mousemode right translate > show #!2 models > hide #!3 models > select add #2 99840 atoms, 100312 bonds, 4 pseudobonds, 6146 residues, 4 models selected > select subtract #2 2 models selected > select add #2 99840 atoms, 100312 bonds, 4 pseudobonds, 6146 residues, 4 models selected > select subtract #4 99840 atoms, 100312 bonds, 4 pseudobonds, 6146 residues, 2 models selected > ui mousemode right ""translate selected models"" > view matrix models > #2,-0.82313,0.40245,0.40062,100.26,0.56745,0.60968,0.55344,-467.99,-0.021518,0.68288,-0.73021,28.334 > ui mousemode right ""rotate selected models"" > view matrix models > #2,-0.98302,0.15318,0.10103,348.35,0.18276,0.76793,0.61391,-438.53,0.016457,0.62195,-0.78289,59.345 > view matrix models > #2,-0.8026,0.36897,0.46871,89.465,0.5558,0.74787,0.36301,-472.01,-0.2166,0.55187,-0.80531,169.18 > fitmap #2 inMap #4 Fit molecule 8g4l.pdb (#2) to map cryosparc_P30_J279_map.mrc (#4) using 99840 atoms average map value = 0.03324, steps = 1916 shifted from previous position = 40 rotated from previous position = 19.9 degrees atoms outside contour = 75314, contour level = 0.033285 Position of 8g4l.pdb (#2) relative to cryosparc_P30_J279_map.mrc (#4) coordinates: Matrix rotation and translation -0.89768062 0.39496708 0.19537273 171.38448995 -0.43446605 -0.71933681 -0.54202750 713.12497930 -0.07354423 -0.57145040 0.81733450 187.01973679 Axis -0.03372507 0.30823754 -0.95071144 Axis point 167.14028490 366.03689970 0.00000000 Rotation angle (degrees) 154.13723635 Shift along axis 36.23013114 > volume #4 step 1 > select subtract #2 Nothing selected > color #4 #7cc1f980 models > show #!3 models > save /Users/ruchigautamsharma/Desktop/image5.png supersample 3 > movie record > turn y 2 180 > wait 180 > movie encode /Users/ruchigautamsharma/Desktop/movie4.mp4 Movie saved to /Users/ruchigautamsharma/Desktop/movie4.mp4 > ui tool show ""Show Sequence Viewer"" > sequence chain #2/A Alignment identifier is 2/A > select #2/A:524-525 34 atoms, 33 bonds, 2 residues, 1 model selected > select #2/A:524-526 56 atoms, 55 bonds, 3 residues, 1 model selected > show sel atoms > style sel ball Changed 56 atom styles > rainbow sel > select #2/A:940 22 atoms, 21 bonds, 1 residue, 1 model selected > select #2/A:939-940 44 atoms, 43 bonds, 2 residues, 1 model selected > select > #2/A:10-16,20-27,82-84,90-92,98-111,136-142,154-168,184-199,216-231,271-273,284-291,295-301,307-309,311-314,325-338,343-359,379-388,393-400,417-447,473-504,518-524,530-539,545-555,604-611,615-618,647-662,686-696,698-707,715-723,738-748,753-755,769-826,829-836,842-919,922-1171 11821 atoms, 11850 bonds, 720 residues, 1 model selected > ui mousemode right translate > select #2/A:903 15 atoms, 14 bonds, 1 residue, 1 model selected > select #2/A:903-904 39 atoms, 38 bonds, 2 residues, 1 model selected > ui tool show ""Show Sequence Viewer"" > sequence chain #2/B Alignment identifier is 2/B > select #2/B:903 15 atoms, 14 bonds, 1 residue, 1 model selected > select #2/B:903-904 39 atoms, 38 bonds, 2 residues, 1 model selected > show sel atoms > style sel ball Changed 39 atom styles > rainbow sel > close #1 > volume #4 level 0.04236 > ui mousemode right distance > distance #2/B:903@OE2 #2/A:525@CD Distance between 8g4l.pdb #2/B GLU 903 OE2 and /A GLU 525 CD: 7.678Å > save /Users/ruchigautamsharma/Desktop/image6.png supersample 3 > open > ""/Users/ruchigautamsharma/Desktop/25HepE525K/cryosparc_P30_J280_class_00_00027_volume > (1).mrc"" Opened cryosparc_P30_J280_class_00_00027_volume (1).mrc as #5, grid size 180,180,180, pixel 1.38, shown at level 0.123, step 1, values float32 > flip volume #5 Unknown command: flip volume #5 > volume flip #5 Opened cryosparc_P30_J280_class_00_00027_volume (1).mrc z flip as #6, grid size 180,180,180, pixel 1.38, shown at step 1, values float32 > select add #6 39 atoms, 38 bonds, 2 residues, 3 models selected > select add #2 99840 atoms, 100312 bonds, 5 pseudobonds, 6146 residues, 5 models selected > select subtract #2 2 models selected > ui mousemode right ""translate selected models"" > view matrix models #6,1,0,0,-12.543,0,1,0,-4.9141,0,0,1,-59.886 > ui mousemode right ""rotate selected models"" > view matrix models > #6,0.97719,-0.1898,-0.095255,24.452,0.21213,0.85157,0.47941,-74.838,-0.0098755,-0.48869,0.8724,14.37 > view matrix models > #6,0.9436,-0.26902,-0.193,50.243,0.32425,0.63294,0.70303,-91.715,-0.066973,-0.72595,0.68448,72.907 > view matrix models > #6,0.94098,-0.27295,-0.20014,51.932,0.33074,0.6159,0.71504,-92.063,-0.071902,-0.73903,0.66983,76.899 > view matrix models > #6,-0.96802,-0.2488,0.032094,272.71,-0.24873,0.93529,-0.25172,66.645,0.032612,-0.25166,-0.96727,208.41 > ui mousemode right ""translate selected models"" > view matrix models > #6,-0.96802,-0.2488,0.032094,298.35,-0.24873,0.93529,-0.25172,67.863,0.032612,-0.25166,-0.96727,270.44 > view matrix models > #6,-0.96802,-0.2488,0.032094,280.09,-0.24873,0.93529,-0.25172,73.622,0.032612,-0.25166,-0.96727,274.5 > view matrix models > #6,-0.96802,-0.2488,0.032094,279.77,-0.24873,0.93529,-0.25172,74.716,0.032612,-0.25166,-0.96727,273.45 > close #5 > hide #!2 models > hide #!3 models > hide #!4 models > volume #6 level 0.09029 > surface dust #6 size 13.8 > ui mousemode right translate > select subtract #6 Nothing selected > save /Users/ruchigautamsharma/Desktop/image7.png supersample 3 > movie record > turn y 2 180 > wait 180 > movie encode /Users/ruchigautamsharma/Desktop/movie5.mp4 Movie saved to /Users/ruchigautamsharma/Desktop/movie5.mp4 > show #!2 models > show #!3 models > show #!4 models > hide #!2 models > hide #!3 models > fitmap #4 inMap #6 Fit map cryosparc_P30_J279_map.mrc in map cryosparc_P30_J280_class_00_00027_volume (1).mrc z flip using 398148 points correlation = 0.9513, correlation about mean = 0.6514, overlap = 4478 steps = 120, shift = 2.21, angle = 10.5 degrees Position of cryosparc_P30_J279_map.mrc (#4) relative to cryosparc_P30_J280_class_00_00027_volume (1).mrc z flip (#6) coordinates: Matrix rotation and translation -0.99999913 -0.00034252 -0.00127077 249.21336620 0.00034239 -0.99999993 0.00010594 248.98589046 -0.00127081 0.00010551 0.99999919 -1.22511845 Axis -0.00063596 0.00005334 0.99999980 Axis point 124.58497705 124.51431379 0.00000000 Rotation angle (degrees) 179.98037890 Shift along axis -1.37032688 > show #!2 models > show #!3 models > undo [Repeated 3 time(s)] > select add #6 2 models selected > hide #!3 models > hide #!2 models > ui mousemode right ""translate selected models"" > fitmap #6 inMap #4 Fit map cryosparc_P30_J280_class_00_00027_volume (1).mrc z flip in map cryosparc_P30_J279_map.mrc using 102014 points correlation = 0.9277, correlation about mean = 0.6892, overlap = 1011 steps = 48, shift = 0.0317, angle = 0.033 degrees Position of cryosparc_P30_J280_class_00_00027_volume (1).mrc z flip (#6) relative to cryosparc_P30_J279_map.mrc (#4) coordinates: Matrix rotation and translation -0.99999934 -0.00020646 -0.00113078 249.17086350 0.00020623 -0.99999996 0.00020732 248.95988727 -0.00113082 0.00020709 0.99999934 1.49527864 Axis -0.00056633 0.00010440 0.99999983 Axis point 124.57301229 124.49271938 0.00000000 Rotation angle (degrees) 179.98817733 Shift along axis 1.38015468 > select subtract #6 Nothing selected > show #!2 models > hide #!6 models > fitmap #2 inMap #4 Fit molecule 8g4l.pdb (#2) to map cryosparc_P30_J279_map.mrc (#4) using 99840 atoms average map value = 0.03324, steps = 796 shifted from previous position = 21.2 rotated from previous position = 10.5 degrees atoms outside contour = 78980, contour level = 0.04236 Position of 8g4l.pdb (#2) relative to cryosparc_P30_J279_map.mrc (#4) coordinates: Matrix rotation and translation -0.89772325 0.39491741 0.19527728 171.44427967 -0.43436867 -0.71936134 -0.54207299 713.11865308 -0.07359913 -0.57145385 0.81732715 187.04031769 Axis -0.03368282 0.30824538 -0.95071039 Axis point 167.15705533 366.03494475 0.00000000 Rotation angle (degrees) 154.14213016 Shift along axis 36.21962762 > show #!3 models > hide #!2 models > fitmap #3 inMap #4 Fit molecule 8act.pdb (#3) to map cryosparc_P30_J279_map.mrc (#4) using 18834 atoms average map value = 0.06921, steps = 156 shifted from previous position = 2.77 rotated from previous position = 10.5 degrees atoms outside contour = 5343, contour level = 0.04236 Position of 8act.pdb (#3) relative to cryosparc_P30_J279_map.mrc (#4) coordinates: Matrix rotation and translation 0.99530058 -0.04986346 0.08300844 -93.89354486 -0.05710589 -0.99454449 0.08729358 330.43411156 0.07820282 -0.09162362 -0.99271820 332.90953349 Axis -0.99882208 0.02682778 -0.04043159 Axis point 0.00000000 171.51509590 160.98648532 Rotation angle (degrees) 174.86146946 Shift along axis 89.18769933 > show #!2 models > show #!6 models > hide #!6 models > open > /Users/ruchigautamsharma/Desktop/25HepE525K/cryosparc_P30_J280_class_01_00027_volume.mrc Opened cryosparc_P30_J280_class_01_00027_volume.mrc as #5, grid size 180,180,180, pixel 1.38, shown at level 0.12, step 1, values float32 > volume flip #6 Opened cryosparc_P30_J280_class_00_00027_volume (1).mrc z flip z flip as #7, grid size 180,180,180, pixel 1.38, shown at step 1, values float32 > undo > hide #!6 models > show #!6 models > hide #!7 models > close #7 > volume flip #5 Opened cryosparc_P30_J280_class_01_00027_volume.mrc z flip as #7, grid size 180,180,180, pixel 1.38, shown at step 1, values float32 > hide #!6 models > close #5 > select add #7 2 models selected > hide #!3 models > hide #!2 models > show #!2 models > hide #!2 models > ui mousemode right ""rotate selected models"" > view matrix models > #7,0.84223,-0.48294,-0.23962,106.87,0.48671,0.48999,0.7232,-95.43,-0.23185,-0.72572,0.64774,158.93 > ui mousemode right ""translate selected models"" > view matrix models > #7,0.84223,-0.48294,-0.23962,105.38,0.48671,0.48999,0.7232,-78.575,-0.23185,-0.72572,0.64774,170.33 > ui mousemode right ""rotate selected models"" > view matrix models > #7,-0.95159,-0.22068,-0.21396,309.08,-0.18623,0.96771,-0.16985,66.446,0.24453,-0.12179,-0.96196,238.05 > ui mousemode right ""translate selected models"" > view matrix models > #7,-0.95159,-0.22068,-0.21396,310.5,-0.18623,0.96771,-0.16985,52.678,0.24453,-0.12179,-0.96196,229.62 > volume #7 level 0.07479 > surface dust #7 size 13.8 > fitmap #7 inMap #4 Fit map cryosparc_P30_J280_class_01_00027_volume.mrc z flip in map cryosparc_P30_J279_map.mrc using 113502 points correlation = 0.9643, correlation about mean = 0.8414, overlap = 1130 steps = 208, shift = 5.04, angle = 14.9 degrees Position of cryosparc_P30_J280_class_01_00027_volume.mrc z flip (#7) relative to cryosparc_P30_J279_map.mrc (#4) coordinates: Matrix rotation and translation -0.99999966 -0.00026364 -0.00078820 249.12543022 0.00026376 -0.99999995 -0.00015099 248.98160004 -0.00078816 -0.00015120 0.99999968 1.49763888 Axis -0.00039360 -0.00007449 0.99999992 Axis point 124.54659569 124.50727948 0.00000000 Rotation angle (degrees) 179.98489106 Shift along axis 1.38103566 > show #!3 models > show #!2 models > hide #!2 models > hide #!3 models > hide #!4 models > select subtract #7 Nothing selected > volume #7 level 0.0619 > volume #7 level 0.07092 > save /Users/ruchigautamsharma/Desktop/image7.png supersample 3 > movie record > turn y 2 180 > wait 180 > movie encode /Users/ruchigautamsharma/Desktop/movie5.mp4 Movie saved to /Users/ruchigautamsharma/Desktop/movie5.mp4 > show #!6 models > show #!4 models > show #!3 models > show #!2 models > save > /Users/ruchigautamsharma/Desktop/25HepE525K/25HepE525KwithMava_classes.cxs > open > /Users/ruchigautamsharma/Desktop/25HepE525K/cryosparc_P30_J280_class_02_00027_volume.mrc Opened cryosparc_P30_J280_class_02_00027_volume.mrc as #5, grid size 180,180,180, pixel 1.38, shown at level 0.119, step 1, values float32 > volume flip #5 Opened cryosparc_P30_J280_class_02_00027_volume.mrc z flip as #8, grid size 180,180,180, pixel 1.38, shown at step 1, values float32 > close #5 > select add #8 2 models selected > hide #!3 models > hide #!2 models > hide #!6 models > hide #!7 models > view matrix models #8,1,0,0,2.8324,0,1,0,-4.8659,0,0,1,8.6713 > ui mousemode right ""rotate selected models"" > view matrix models > #8,-0.96696,-0.17515,-0.18521,304.59,-0.10484,0.93554,-0.33731,57.912,0.23235,-0.30675,-0.92299,250.36 > ui mousemode right ""translate selected models"" > view matrix models > #8,-0.96696,-0.17515,-0.18521,302.83,-0.10484,0.93554,-0.33731,66.738,0.23235,-0.30675,-0.92299,248.15 > surface dust #8 size 13.8 > fitmap #8 inMap #4 Fit map cryosparc_P30_J280_class_02_00027_volume.mrc z flip in map cryosparc_P30_J279_map.mrc using 58302 points correlation = 0.9609, correlation about mean = 0.7291, overlap = 874.3 steps = 144, shift = 5.03, angle = 14.4 degrees Position of cryosparc_P30_J280_class_02_00027_volume.mrc z flip (#8) relative to cryosparc_P30_J279_map.mrc (#4) coordinates: Matrix rotation and translation -0.99999916 0.00002492 -0.00129399 249.16805302 -0.00002528 -0.99999996 0.00027762 248.99198953 -0.00129399 0.00027765 0.99999912 1.50291671 Axis 0.00064340 -0.00013133 -0.99999978 Axis point 124.58607228 124.49433268 0.00000000 Rotation angle (degrees) 179.99856201 Shift along axis -1.37530370 > show #!7 models > show #!6 models > hide #!6 models > hide #!7 models > select subtract #8 Nothing selected > hide #!4 models > volume #8 level 0.07811 > surface dust #8 size 13.8 > save /Users/ruchigautamsharma/Desktop/image7.png supersample 3 > movie record > turn y 2 180 > wait 180 > movie encode /Users/ruchigautamsharma/Desktop/movie5.mp4 Movie saved to /Users/ruchigautamsharma/Desktop/movie5.mp4 > show #!4 models > show #!3 models > show #!2 models > hide #!8 models > open > /Users/ruchigautamsharma/Desktop/25HepE525K/cryosparc_P30_J280_class_04_00027_volume.mrc Opened cryosparc_P30_J280_class_04_00027_volume.mrc as #5, grid size 180,180,180, pixel 1.38, shown at level 0.122, step 1, values float32 > volume flip #5 Opened cryosparc_P30_J280_class_04_00027_volume.mrc z flip as #9, grid size 180,180,180, pixel 1.38, shown at step 1, values float32 > close #5 > select add #9 2 models selected > hide #!2 models > hide #!3 models > hide #!4 models > show #!4 models > ui mousemode right ""rotate selected models"" > view matrix models > #9,-0.94987,-0.3125,-0.0095436,296.08,-0.29326,0.90112,-0.31935,89.841,0.1084,-0.30054,-0.94759,261.2 > ui mousemode right ""translate selected models"" > view matrix models > #9,-0.94987,-0.3125,-0.0095436,296.29,-0.29326,0.90112,-0.31935,94.465,0.1084,-0.30054,-0.94759,265.66 > surface dust #9 size 13.8 > fitmap #9 inMap #4 Fit map cryosparc_P30_J280_class_04_00027_volume.mrc z flip in map cryosparc_P30_J279_map.mrc using 58281 points correlation = 0.9434, correlation about mean = 0.6496, overlap = 833.5 steps = 116, shift = 5.59, angle = 6.08 degrees Position of cryosparc_P30_J280_class_04_00027_volume.mrc z flip (#9) relative to cryosparc_P30_J279_map.mrc (#4) coordinates: Matrix rotation and translation -0.99999961 -0.00086803 -0.00014872 249.12096554 0.00086814 -0.99999934 -0.00074800 249.01468160 -0.00014807 -0.00074812 0.99999971 1.52412702 Axis -0.00007408 -0.00037371 0.99999993 Axis point 124.50649781 124.56168997 0.00000000 Rotation angle (degrees) 179.95026257 Shift along axis 1.41261188 > hide #!4 models > select subtract #9 Nothing selected > volume #9 level 0.07975 > show #!4 models > hide #!4 models > volume #9 level 0.08919 > save /Users/ruchigautamsharma/Desktop/image7.png supersample 3 > movie record > turn y 2 180 > wait 180 > movie encode /Users/ruchigautamsharma/Desktop/movie5.mp4 Movie saved to /Users/ruchigautamsharma/Desktop/movie5.mp4 > show #!4 models > show #!3 models > show #!2 models > open > /Users/ruchigautamsharma/Desktop/25HepE525K/cryosparc_P30_J280_class_05_00027_volume.mrc Opened cryosparc_P30_J280_class_05_00027_volume.mrc as #5, grid size 180,180,180, pixel 1.38, shown at level 0.125, step 1, values float32 > volume flip #5 Opened cryosparc_P30_J280_class_05_00027_volume.mrc z flip as #10, grid size 180,180,180, pixel 1.38, shown at step 1, values float32 > close #5 > color #10 #4ab7ffff models > color #10 #fbd6ffff models > color #10 #ffb5b1ff models > color #10 #f7b45cff models > color #10 #30bdf7ff models > hide #!9 models > hide #!2 models > hide #!3 models > volume #10 level 0.09708 > select add #10 2 models selected > view matrix models #10,1,0,0,3.1115,0,1,0,-2.0096,0,0,1,8.118 > ui mousemode right ""rotate selected models"" > view matrix models > #10,-0.79927,-0.55558,-0.2291,334.52,-0.51624,0.8299,-0.21156,112.19,0.30768,-0.050826,-0.95013,212.13 > ui mousemode right ""translate selected models"" > view matrix models > #10,-0.79927,-0.55558,-0.2291,333.19,-0.51624,0.8299,-0.21156,115.1,0.30768,-0.050826,-0.95013,210.7 > surface dust #10 size 13.8 > fitmap #10 inMap #4 Fit map cryosparc_P30_J280_class_05_00027_volume.mrc z flip in map cryosparc_P30_J279_map.mrc using 84424 points correlation = 0.9741, correlation about mean = 0.8468, overlap = 1111 steps = 276, shift = 5.07, angle = 25.6 degrees Position of cryosparc_P30_J280_class_05_00027_volume.mrc z flip (#10) relative to cryosparc_P30_J279_map.mrc (#4) coordinates: Matrix rotation and translation -0.99999922 0.00035517 0.00119687 248.79666503 -0.00035522 -0.99999994 -0.00003695 249.05630070 0.00119686 -0.00003738 0.99999928 1.23988110 Axis -0.00059829 0.00001925 -0.99999982 Axis point 124.42007755 124.50606948 0.00000000 Rotation angle (degrees) 179.97964879 Shift along axis -1.38393827 > hide #!4 models > save /Users/ruchigautamsharma/Desktop/image7.png supersample 3 > movie record > turn y 2 180 > wait 180 > movie encode /Users/ruchigautamsharma/Desktop/movie5.mp4 Movie saved to /Users/ruchigautamsharma/Desktop/movie5.mp4 > show #!4 models > show #!2 models > show #!3 models > select subtract #10 Nothing selected > hide #!10 models > open > /Users/ruchigautamsharma/Desktop/25HepE525K/cryosparc_P30_J280_class_08_00027_volume.mrc Opened cryosparc_P30_J280_class_08_00027_volume.mrc as #5, grid size 180,180,180, pixel 1.38, shown at level 0.121, step 1, values float32 > volume flip #5 Opened cryosparc_P30_J280_class_08_00027_volume.mrc z flip as #11, grid size 180,180,180, pixel 1.38, shown at step 1, values float32 > close #5 > volume #11 level 0.08441 > hide #!3 models > hide #!2 models > select add #11 2 models selected > view matrix models #11,1,0,0,1.1155,0,1,0,-3.8677,0,0,1,5.8448 > ui mousemode right ""rotate selected models"" > view matrix models > #11,0.99209,-0.0053981,-0.12542,17.552,0.081093,0.7902,0.60746,-62.634,0.095827,-0.61282,0.78439,87.413 > view matrix models > #11,0.99729,-0.013338,-0.072294,11.493,0.039229,0.92824,0.36991,-44.599,0.062172,-0.37174,0.92625,48.066 > view matrix models > #11,0.96616,0.092495,-0.24077,23.583,0.23126,0.10267,0.96746,-47.711,0.1142,-0.99041,0.077802,210.68 > view matrix models > #11,-0.87555,-0.41067,0.25448,270.56,-0.45727,0.87442,-0.16216,91.081,-0.15593,-0.25834,-0.95338,285.91 > ui mousemode right ""translate selected models"" > view matrix models > #11,-0.87555,-0.41067,0.25448,270.16,-0.45727,0.87442,-0.16216,97.04,-0.15593,-0.25834,-0.95338,295.44 > surface dust #11 size 13.8 > fitmap #11 inMap #4 Fit map cryosparc_P30_J280_class_08_00027_volume.mrc z flip in map cryosparc_P30_J279_map.mrc using 102298 points correlation = 0.8925, correlation about mean = 0.5767, overlap = 958.6 steps = 172, shift = 10.7, angle = 16.9 degrees Position of cryosparc_P30_J280_class_08_00027_volume.mrc z flip (#11) relative to cryosparc_P30_J279_map.mrc (#4) coordinates: Matrix rotation and translation -0.99999904 -0.00116328 0.00074464 249.06176278 0.00116310 -0.99999929 -0.00024302 248.90777913 0.00074493 -0.00024215 0.99999969 1.24883054 Axis 0.00037212 -0.00012116 0.99999992 Axis point 124.45826735 124.52639149 0.00000000 Rotation angle (degrees) 179.93335425 Shift along axis 1.31135186 > volume #11 level 0.05725 > volume #11 level 0.06342 > volume #11 level 0.07083 > select subtract #11 Nothing selected > hide #!4 models > save /Users/ruchigautamsharma/Desktop/image7.png supersample 3 > movie record > turn y 2 180 > wait 180 > movie encode /Users/ruchigautamsharma/Desktop/movie5.mp4 Movie saved to /Users/ruchigautamsharma/Desktop/movie5.mp4 > show #!4 models > show #!3 models > show #!2 models > show #!6 models > show #!7 models > show #!8 models > show #!9 models > show #!10 models > hide #!11 models > hide #!10 models > hide #!9 models > hide #!8 models > hide #!7 models > hide #!6 models > hide #!2 models > hide #!3 models > open /Users/ruchigautamsharma/Desktop/25HepE525K/8qyq.pdb 8qyq.pdb title: Beta-cardiac myosin S1 fragment In the pre-powerstroke state complexed to mavacamten [more info...] Chain information for 8qyq.pdb #5 --- Chain | Description | UniProt A B | myosin-7 | MYH7_BOVIN 1-807 C | myosin light chain 3 | MYL3_BOVIN 1-199 D | myosin light chain 3 | MYL3_BOVIN 1-199 Non-standard residues in 8qyq.pdb #5 --- ADP — adenosine-5'-diphosphate BEF — beryllium trifluoride ion FMT — formic acid GOL — glycerol (glycerin; propane-1,2,3-triol) MG — magnesium ion XB2 — 6-[[(1~{S})-1-phenylethyl]amino]-3-propan-2-yl-1~{H}-pyrimidine-2,4-dione > select #5/B 6497 atoms, 6383 bonds, 8 pseudobonds, 1018 residues, 3 models selected > hide sel cartoons > hide sel atoms > select #5/D 602 atoms, 605 bonds, 3 pseudobonds, 86 residues, 2 models selected > hide sel cartoons > select add #5 14943 atoms, 14737 bonds, 20 pseudobonds, 2292 residues, 3 models selected > ui mousemode right ""rotate selected models"" > view matrix models > #5,0.99553,0.05401,0.077471,-2.8146,-0.030633,0.96065,-0.27608,6.0307,-0.089333,0.27247,0.95801,-6.3562 > view matrix models > #5,0.99476,0.059463,0.083204,-3.0609,-0.032039,0.95383,-0.29862,6.6171,-0.097119,0.29439,0.95074,-6.797 > view matrix models > #5,0.84862,0.26572,-0.45743,1.348,0.52607,-0.33296,0.78255,20.637,0.05564,-0.90473,-0.42234,49.406 > view matrix models > #5,-0.20948,0.94179,-0.26296,-32.356,0.63406,0.33555,0.69669,9.3355,0.74437,-0.020792,-0.66744,44.88 > view matrix models > #5,-0.26135,0.93427,-0.24258,-33.342,0.74088,0.35525,0.57,12.994,0.61871,-0.030752,-0.78502,45.702 > view matrix models > #5,-0.27941,0.93151,-0.23283,-33.736,0.77438,0.36199,0.51894,14.36,0.56769,-0.035305,-0.82249,45.838 > view matrix models > #5,-0.37124,0.91598,-0.15218,-36.338,0.9014,0.39485,0.17771,22.376,0.22287,-0.071201,-0.97224,44.77 > view matrix models > #5,-0.41927,0.90453,-0.077722,-38.282,0.90689,0.41333,-0.08192,27.324,-0.041974,-0.10483,-0.9936,42.18 > view matrix models > #5,-0.44992,0.89092,0.061874,-41.255,0.77059,0.4223,-0.47733,33.225,-0.4514,-0.16708,-0.87654,35.351 > view matrix models > #5,-0.31556,0.89055,0.32762,-44.738,0.035597,0.35613,-0.93376,33.51,-0.94824,-0.28299,-0.14408,15.954 > view matrix models > #5,-0.16915,0.90579,0.3885,-44.23,-0.41809,0.29101,-0.86053,27.006,-0.89252,-0.30799,0.32948,7.6715 > view matrix models > #5,-0.31793,0.89036,0.32585,-44.732,0.044144,0.35721,-0.93298,33.592,-0.94709,-0.28224,-0.15287,16.132 > view matrix models > #5,-0.16449,0.90636,0.38916,-44.19,-0.4306,0.28897,-0.85503,26.761,-0.88742,-0.30822,0.34275,7.4794 > view matrix models > #5,0.9568,-0.19924,0.21174,-0.56848,0.28104,0.4472,-0.84914,33.288,0.074496,0.87196,0.48387,-7.475 > view matrix models > #5,0.93545,-0.26582,0.23296,0.14939,0.35203,0.64149,-0.68159,26.655,0.031741,0.71961,0.69366,-9.0199 > view matrix models > #5,0.91741,-0.3204,0.23603,1.0211,0.39769,0.75969,-0.51451,21.332,-0.014464,0.56588,0.82436,-8.9778 > view matrix models > #5,0.95721,-0.19796,0.21112,-0.57814,0.27948,0.44284,-0.85193,33.417,0.075155,0.87447,0.47922,-7.4258 > view matrix models > #5,0.97238,-0.14881,0.17983,-0.79935,0.21341,0.25467,-0.94319,38.437,0.094555,0.95551,0.27939,-4.8593 > view matrix models > #5,0.98941,-0.090123,0.11382,-0.49676,0.10944,-0.052142,-0.99262,44.656,0.095393,0.99456,-0.041726,0.82277 > view matrix models > #5,-0.35779,-0.60534,0.71102,-20.504,0.19127,-0.79279,-0.57871,53.561,0.914,-0.07106,0.39943,26.714 > view matrix models > #5,-0.60867,0.67803,0.41206,-45.977,-0.79266,-0.54248,-0.27823,28.041,0.034888,-0.49597,0.86764,13.998 > ui mousemode right ""translate selected models"" > view matrix models > #5,-0.60867,0.67803,0.41206,-23.555,-0.79266,-0.54248,-0.27823,128.79,0.034888,-0.49597,0.86764,182.06 > view matrix models > #5,-0.60867,0.67803,0.41206,37.381,-0.79266,-0.54248,-0.27823,174.2,0.034888,-0.49597,0.86764,205.17 > view matrix models > #5,-0.60867,0.67803,0.41206,99.031,-0.79266,-0.54248,-0.27823,162.54,0.034888,-0.49597,0.86764,155.36 > view matrix models > #5,-0.60867,0.67803,0.41206,98.801,-0.79266,-0.54248,-0.27823,159.71,0.034888,-0.49597,0.86764,149.89 > view matrix models > #5,-0.60867,0.67803,0.41206,105.09,-0.79266,-0.54248,-0.27823,156.53,0.034888,-0.49597,0.86764,147.11 > ui mousemode right ""rotate selected models"" > view matrix models > #5,-0.23298,0.92288,0.30662,107.22,-0.95501,-0.15762,-0.25124,145.28,-0.18353,-0.35136,0.91808,139.83 > view matrix models > #5,-0.098877,0.94921,0.29871,108.71,-0.97369,-0.030362,-0.22583,141.73,-0.20529,-0.31318,0.92724,138.51 > ui mousemode right ""translate selected models"" > view matrix models > #5,-0.098877,0.94921,0.29871,108.51,-0.97369,-0.030362,-0.22583,147.51,-0.20529,-0.31318,0.92724,141.89 > fitmap #5 inMap #4 Fit molecule 8qyq.pdb (#5) to map cryosparc_P30_J279_map.mrc (#4) using 14943 atoms average map value = 0.04173, steps = 400 shifted from previous position = 15.1 rotated from previous position = 20 degrees atoms outside contour = 9505, contour level = 0.04236 Position of 8qyq.pdb (#5) relative to cryosparc_P30_J279_map.mrc (#4) coordinates: Matrix rotation and translation -0.58239663 0.81290458 -0.00055383 102.85355786 0.70719581 0.50699846 0.49277443 96.93889710 0.40085939 0.28659850 -0.87015691 105.31002093 Axis -0.44484143 -0.86608184 -0.22807532 Axis point 21.76765973 0.00000000 42.22852380 Rotation angle (degrees) 166.60041068 Shift along axis -153.72915848 > ui mousemode right ""rotate selected models"" > view matrix models > #5,-0.37977,0.92425,0.039174,104.73,-0.87919,-0.37378,0.29547,144.57,0.28774,0.077772,0.95455,140.89 > view matrix models > #5,0.32827,-0.92374,-0.19734,159.88,0.44949,0.33651,-0.82748,170.74,0.83078,0.18294,0.52568,155.01 > ui mousemode right ""translate selected models"" > view matrix models > #5,0.32827,-0.92374,-0.19734,161.33,0.44949,0.33651,-0.82748,156.99,0.83078,0.18294,0.52568,143.67 > ui mousemode right ""rotate selected models"" > view matrix models > #5,0.52982,-0.80788,-0.25811,162.9,0.69083,0.58764,-0.42123,146.68,0.49198,0.044868,0.86945,134.89 > ui mousemode right ""translate selected models"" > view matrix models > #5,0.52982,-0.80788,-0.25811,162.52,0.69083,0.58764,-0.42123,163.45,0.49198,0.044868,0.86945,142.3 > ui mousemode right ""rotate selected models"" > view matrix models > #5,-0.72386,-0.68979,0.014695,136.61,0.19093,-0.22074,-0.95646,184.86,0.66301,-0.68954,0.29149,172.48 > view matrix models > #5,0.50281,-0.86437,-0.0066101,158.26,0.47814,0.28449,-0.83093,175.36,0.72011,0.41464,0.55634,143.83 > ui mousemode right ""translate selected models"" > view matrix models > #5,0.50281,-0.86437,-0.0066101,160.27,0.47814,0.28449,-0.83093,157.85,0.72011,0.41464,0.55634,140.82 > view matrix models > #5,0.50281,-0.86437,-0.0066101,169.69,0.47814,0.28449,-0.83093,74.983,0.72011,0.41464,0.55634,59.074 > view matrix models > #5,0.50281,-0.86437,-0.0066101,164.23,0.47814,0.28449,-0.83093,100.24,0.72011,0.41464,0.55634,83.15 > ui mousemode right ""rotate selected models"" > view matrix models > #5,0.35446,-0.92893,-0.10696,165.58,0.84213,0.36685,-0.39528,94.756,0.40642,0.050033,0.91231,79.421 > ui mousemode right ""translate selected models"" > view matrix models > #5,0.35446,-0.92893,-0.10696,172.36,0.84213,0.36685,-0.39528,136.98,0.40642,0.050033,0.91231,91.143 > ui mousemode right ""rotate selected models"" > view matrix models > #5,-0.56298,-0.74543,0.35692,145.92,0.33568,-0.60087,-0.72544,157.6,0.75523,-0.2886,0.58851,110.05 > ui mousemode right ""translate selected models"" > view matrix models > #5,-0.56298,-0.74543,0.35692,130.04,0.33568,-0.60087,-0.72544,145.96,0.75523,-0.2886,0.58851,88.151 > ui mousemode right ""rotate selected models"" > view matrix models > #5,-0.082785,-0.99082,0.10686,147.28,0.60357,-0.13517,-0.78577,140.83,0.793,-0.00055352,0.60922,81.985 > ui mousemode right ""translate selected models"" > view matrix models > #5,-0.082785,-0.99082,0.10686,146.82,0.60357,-0.13517,-0.78577,138.38,0.793,-0.00055352,0.60922,93.162 > ui mousemode right ""rotate selected models"" > view matrix models > #5,-0.3921,-0.86583,0.3108,135.56,0.71686,-0.49931,-0.48661,141.85,0.57651,0.032004,0.81646,85.171 > ui mousemode right ""translate selected models"" > view matrix models > #5,-0.3921,-0.86583,0.3108,138.82,0.71686,-0.49931,-0.48661,142.44,0.57651,0.032004,0.81646,82.838 > fitmap #5 inMap #4 Fit molecule 8qyq.pdb (#5) to map cryosparc_P30_J279_map.mrc (#4) using 14943 atoms average map value = 0.07346, steps = 220 shifted from previous position = 13.1 rotated from previous position = 20.7 degrees atoms outside contour = 3995, contour level = 0.04236 Position of 8qyq.pdb (#5) relative to cryosparc_P30_J279_map.mrc (#4) coordinates: Matrix rotation and translation -0.48628488 -0.87349851 -0.02296421 131.98115481 -0.50944434 0.26206455 0.81962712 104.75313384 -0.70992497 0.41027126 -0.57243691 157.52284441 Axis -0.46589276 0.78183820 0.41433437 Axis point 115.26114932 0.00000000 25.56332067 Rotation angle (degrees) 153.93923432 Shift along axis 85.67806483 > select ::name=""XB2"" 40 atoms, 42 bonds, 2 residues, 1 model selected > show sel atoms > style sel ball Changed 40 atom styles > rainbow sel > select add #5 14943 atoms, 14737 bonds, 20 pseudobonds, 2292 residues, 3 models selected > select subtract #5 Nothing selected > hide #!5 models > select ::name=""XB2"" 40 atoms, 42 bonds, 2 residues, 1 model selected > show #!5 models > select #5/A 6584 atoms, 6484 bonds, 9 pseudobonds, 1016 residues, 3 models selected > hide sel cartoons > hide sel atoms > select #5/C 1260 atoms, 1265 bonds, 172 residues, 1 model selected > hide sel cartoons > hide sel atoms > select ::name=""XB2"" 40 atoms, 42 bonds, 2 residues, 1 model selected > hide sel atoms > select ::name=""XB2"" 40 atoms, 42 bonds, 2 residues, 1 model selected > select #5/A 6584 atoms, 6484 bonds, 9 pseudobonds, 1016 residues, 3 models selected > select ::name=""XB2"" 40 atoms, 42 bonds, 2 residues, 1 model selected > style sel ball Changed 40 atom styles > show sel cartoons > select #5/A 6584 atoms, 6484 bonds, 9 pseudobonds, 1016 residues, 3 models selected > show sel cartoons > select ::name=""XB2"" 40 atoms, 42 bonds, 2 residues, 1 model selected > style sel ball Changed 40 atom styles > select add #5 14943 atoms, 14737 bonds, 20 pseudobonds, 2292 residues, 3 models selected > select ::name=""XB2"" 40 atoms, 42 bonds, 2 residues, 1 model selected > style sel ball Changed 40 atom styles > select add #5 14943 atoms, 14737 bonds, 20 pseudobonds, 2292 residues, 3 models selected > show sel atoms > show sel cartoons > hide sel atoms > select ::name=""XB2"" 40 atoms, 42 bonds, 2 residues, 1 model selected > style sel ball Changed 40 atom styles > select ::name=""ADP"" 108 atoms, 116 bonds, 4 residues, 2 models selected > style sel & #!5 ball Changed 54 atom styles > rainbow sel & #!5 > select add #5 14997 atoms, 14795 bonds, 20 pseudobonds, 2294 residues, 4 models selected > select add #3 33777 atoms, 33932 bonds, 39 pseudobonds, 4620 residues, 6 models selected > select subtract #3 14943 atoms, 14737 bonds, 20 pseudobonds, 2292 residues, 3 models selected > select ::name=""ADP"" 108 atoms, 116 bonds, 4 residues, 2 models selected > select add #5 14997 atoms, 14795 bonds, 20 pseudobonds, 2294 residues, 4 models selected > select subtract #5 54 atoms, 58 bonds, 2 residues, 1 model selected > select ::name=""ADP"" 108 atoms, 116 bonds, 4 residues, 2 models selected > style sel & #!5 ball Changed 54 atom styles > rainbow sel & #!5 > select #5/A 6584 atoms, 6484 bonds, 9 pseudobonds, 1016 residues, 3 models selected > select ::name=""XB2"" 40 atoms, 42 bonds, 2 residues, 1 model selected > color sel byhetero > show #!3 models > show #!2 models > hide #!5 models > select add #5 14943 atoms, 14737 bonds, 20 pseudobonds, 2292 residues, 3 models selected > select subtract #5 Nothing selected > hide #!3 models > fitmap #2 inMap #4 Fit molecule 8g4l.pdb (#2) to map cryosparc_P30_J279_map.mrc (#4) using 99840 atoms average map value = 0.03324, steps = 212 shifted from previous position = 0.00596 rotated from previous position = 0.00292 degrees atoms outside contour = 78983, contour level = 0.04236 Position of 8g4l.pdb (#2) relative to cryosparc_P30_J279_map.mrc (#4) coordinates: Matrix rotation and translation -0.89771304 0.39493434 0.19528995 171.43072531 -0.43439308 -0.71937790 -0.54203144 713.12426462 -0.07357955 -0.57142130 0.81735167 187.01292814 Axis -0.03369168 0.30822422 -0.95071694 Axis point 167.15376056 366.03172418 0.00000000 Rotation angle (degrees) 154.14093715 Shift along axis 36.23002059 > hide #!2 models > show #!3 models > fitmap #3 inMap #4 Fit molecule 8act.pdb (#3) to map cryosparc_P30_J279_map.mrc (#4) using 18834 atoms average map value = 0.06921, steps = 64 shifted from previous position = 0.0125 rotated from previous position = 0.00171 degrees atoms outside contour = 5339, contour level = 0.04236 Position of 8act.pdb (#3) relative to cryosparc_P30_J279_map.mrc (#4) coordinates: Matrix rotation and translation 0.99529777 -0.04988324 0.08303014 -93.89145014 -0.05712784 -0.99454304 0.08729576 330.45021647 0.07822245 -0.09162861 -0.99271620 332.90769160 Axis -0.99882138 0.02683827 -0.04044199 Axis point 0.00000000 171.52297541 160.98536353 Rotation angle (degrees) 174.86125937 Shift along axis 89.18605104 > show #!2 models > show #!5 models > hide #!4 models > hide #!3 models > show #!4 models > hide #!2 models > fitmap #5 inMap #4 Fit molecule 8qyq.pdb (#5) to map cryosparc_P30_J279_map.mrc (#4) using 14943 atoms average map value = 0.07346, steps = 28 shifted from previous position = 0.026 rotated from previous position = 0.0648 degrees atoms outside contour = 4000, contour level = 0.04236 Position of 8qyq.pdb (#5) relative to cryosparc_P30_J279_map.mrc (#4) coordinates: Matrix rotation and translation -0.48597381 -0.87364307 -0.02402555 131.99331828 -0.50982761 0.26105496 0.81971099 104.73346858 -0.70986284 0.41060696 -0.57227324 157.51977670 Axis -0.46618686 0.78153309 0.41457912 Axis point 115.27505316 0.00000000 25.56334997 Rotation angle (degrees) 153.97413268 Shift along axis 85.62353087 > show #!3 models > show #!2 models > hide #!5 models > hide #!2 models > select add #3 18834 atoms, 19195 bonds, 19 pseudobonds, 2328 residues, 3 models selected > view matrix models > #3,0.95172,-0.29911,0.069057,-20.803,0.28197,0.94071,0.18854,-169,-0.12136,-0.15997,0.97963,-13.019 > fitmap #3 inMap #4 Fit molecule 8act.pdb (#3) to map cryosparc_P30_J279_map.mrc (#4) using 18834 atoms average map value = 0.06921, steps = 76 shifted from previous position = 3.09 rotated from previous position = 0.00809 degrees atoms outside contour = 5343, contour level = 0.04236 Position of 8act.pdb (#3) relative to cryosparc_P30_J279_map.mrc (#4) coordinates: Matrix rotation and translation 0.99529429 -0.04999011 0.08300768 -93.86164081 -0.05722488 -0.99454601 0.08719835 330.49357732 0.07819590 -0.09153812 -0.99272664 332.89632413 Axis -0.99882051 0.02688932 -0.04042956 Axis point 0.00000000 171.53441271 160.98537615 Rotation angle (degrees) 174.86666587 Shift along axis 89.17882775 > select subtract #3 Nothing selected > show #!2 models > select add #2 99840 atoms, 100312 bonds, 5 pseudobonds, 6146 residues, 3 models selected > hide #!3 models > view matrix models > #2,-0.97957,0.18401,0.081197,326.1,0.20088,0.91487,0.35022,-426.82,-0.0098435,0.35937,-0.93314,214.54,#1,1,0,0,0,0,1,0,0,0,0,1,0 > fitmap #2 inMap #4 Fit molecule 8g4l.pdb (#2) to map cryosparc_P30_J279_map.mrc (#4) using 99840 atoms average map value = 0.03324, steps = 224 shifted from previous position = 2.05 rotated from previous position = 0.0135 degrees atoms outside contour = 78989, contour level = 0.04236 Position of 8g4l.pdb (#2) relative to cryosparc_P30_J279_map.mrc (#4) coordinates: Matrix rotation and translation -0.89780391 0.39481948 0.19510437 171.55908545 -0.43419345 -0.71946808 -0.54207170 713.11615692 -0.07364910 -0.57138713 0.81736929 187.01348437 Axis -0.03361936 0.30821036 -0.95072399 Axis point 167.18733995 366.02013285 0.00000000 Rotation angle (degrees) 154.15167345 Shift along axis 36.22387450 > show #!3 models > select subtract #2 Nothing selected > volume #4 level 0.03302 > hide #!3 models > hide #!2 models > show #!5 models > select add #5 14943 atoms, 14737 bonds, 20 pseudobonds, 2292 residues, 3 models selected > select ::name=""XB2"" 40 atoms, 42 bonds, 2 residues, 1 model selected > color sel byhetero > select ::name=""XB2"" 40 atoms, 42 bonds, 2 residues, 1 model selected > show sel atoms > hide #!5 models > show #!5 models > select add #5 14943 atoms, 14737 bonds, 20 pseudobonds, 2292 residues, 3 models selected > hide sel cartoons > ui mousemode right translate > volume #4 level 0.04236 > volume #4 level 0.08254 > show sel cartoons > hide sel cartoons > show sel cartoons > fitmap #5 inMap #4 Fit molecule 8qyq.pdb (#5) to map cryosparc_P30_J279_map.mrc (#4) using 14943 atoms average map value = 0.07346, steps = 28 shifted from previous position = 0.0249 rotated from previous position = 0.0574 degrees atoms outside contour = 9432, contour level = 0.082538 Position of 8qyq.pdb (#5) relative to cryosparc_P30_J279_map.mrc (#4) coordinates: Matrix rotation and translation -0.48625976 -0.87350889 -0.02310098 131.98359794 -0.50952602 0.26196441 0.81960836 104.75385886 -0.70988356 0.41031312 -0.57245827 157.52305140 Axis -0.46592829 0.78181077 0.41434616 Axis point 115.26244630 0.00000000 25.56654333 Rotation angle (degrees) 153.94551965 Shift along axis 85.67187553 > volume #4 level 0.06852 > ui mousemode right ""rotate selected models"" > view matrix models > #5,-0.68456,-0.70867,0.17078,136.17,0.45982,-0.60159,-0.65319,142.81,0.56564,-0.36862,0.73768,90.628 > view matrix models > #5,-0.67257,-0.72389,0.15376,136.39,0.47921,-0.58434,-0.6549,142.55,0.56392,-0.36678,0.7399,90.602 > fitmap #5 inMap #4 Fit molecule 8qyq.pdb (#5) to map cryosparc_P30_J279_map.mrc (#4) using 14943 atoms average map value = 0.07346, steps = 84 shifted from previous position = 0.173 rotated from previous position = 4.64 degrees atoms outside contour = 7674, contour level = 0.068522 Position of 8qyq.pdb (#5) relative to cryosparc_P30_J279_map.mrc (#4) coordinates: Matrix rotation and translation -0.48604532 -0.87361366 -0.02364530 131.98433118 -0.50971212 0.26139904 0.81967316 104.73161110 -0.70989682 0.41045061 -0.57234325 157.51876880 Axis -0.46610167 0.78163575 0.41448135 Axis point 115.26785562 0.00000000 25.56530335 Rotation angle (degrees) 153.96091166 Shift along axis 85.63244638 > ui mousemode right translate > volume #4 level 0.05824 > hide sel cartoons > show #!3 models > show #!2 models > volume #4 level 0.03582 > select subtract #5 Nothing selected > select add #5 14943 atoms, 14737 bonds, 20 pseudobonds, 2292 residues, 3 models selected > save /Users/ruchigautamsharma/Desktop/25HepE525K/25HepE525KwithMava_3.cxs > volume #4 level 0.04703 > volume #4 level 0.03302 > show #!6 models > show #!7 models > show #!8 models > show #!9 models > show #!10 models > show #!11 models > hide #!11 models > hide #!10 models > hide #!9 models > hide #!8 models > hide #!7 models > hide #!6 models > save > /Users/ruchigautamsharma/Desktop/25HepE525K/25HepE525KwithMava_20240903.cxs > includeMaps true ——— End of log from Tue Sep 3 19:15:56 2024 ——— opened ChimeraX session > volume #4 level 0.04423 > select > #2/B:12-16,20-28,99-111,136-142,154-166,184-199,216-222,224-231,271-274,284-291,295-301,311-315,326-337,343-360,378-388,393-400,417-447,473-503,518-525,530-538,545-555,593-597,604-611,615-619,647-664,686-696,698-707,715-722,727-729,738-748,753-755,767-824,828-832,837-965,968-995,998-1165,1168-1171 11706 atoms, 11732 bonds, 715 residues, 1 model selected > hide #!4 models > show #!4 models > hide #!3 models > hide #!2 models > volume #4 level 0.06198 > volume #4 level 0.05357 > volume #4 level 0.04703 > show #!3 models > show #!2 models > hide #!3 models > select add #2 99840 atoms, 100312 bonds, 5 pseudobonds, 6146 residues, 3 models selected > select subtract #2 Nothing selected > hide #!2 models > show #!2 models > show #!3 models > show #!10 models > transparency #4.1#10.1 0 > hide #!4 models > transparency #10.1 50 > ui mousemode right select > hide #!10 models Drag select of 18 residues Drag select of 24 residues > style sel ball Changed 309 atom styles > show sel atoms > coulombic sel Using Amber 20 recommended default charges and atom types for standard residues Assigning partial charges to residue M3L (net charge +1) with am1-bcc method Running ANTECHAMBER command: /Applications/ChimeraX-1.7.1.app/Contents/bin/amber20/bin/antechamber -ek qm_theory='AM1', -i /var/folders/1r/q7x50qrs79s_c_5jlk649y5m0000gn/T/tmpytfstoqe/ante.in.mol2 -fi mol2 -o /var/folders/1r/q7x50qrs79s_c_5jlk649y5m0000gn/T/tmpytfstoqe/ante.out.mol2 -fo mol2 -c bcc -nc 1 -j 5 -s 2 -dr n (M3L) `` (M3L) `Welcome to antechamber 20.0: molecular input file processor.` (M3L) `` (M3L) `Info: Finished reading file (/var/folders/1r/q7x50qrs79s_c_5jlk649y5m0000gn/T/tmpytfstoqe/ante.in.mol2); atoms read (43), bonds read (42).` (M3L) `Info: Determining atomic numbers from atomic symbols which are case sensitive.` (M3L) `Running: /Applications/ChimeraX-1.7.1.app/Contents/bin/amber20/bin/bondtype -j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac` (M3L) `` (M3L) `` (M3L) `Running: /Applications/ChimeraX-1.7.1.app/Contents/bin/amber20/bin/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff` (M3L) `Info: Total number of electrons: 134; net charge: 1` (M3L) `` (M3L) `Running: /Applications/ChimeraX-1.7.1.app/Contents/bin/amber20/bin/sqm -O -i sqm.in -o sqm.out` (M3L) `` (M3L) `Running: /Applications/ChimeraX-1.7.1.app/Contents/bin/amber20/bin/am1bcc -i ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p /Applications/ChimeraX-1.7.1.app/Contents/bin/amber20/dat/antechamber/BCCPARM.DAT -s 2 -j 1` (M3L) `` (M3L) `Running: /Applications/ChimeraX-1.7.1.app/Contents/bin/amber20/bin/atomtype -f ac -p bcc -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC` (M3L) `` Charges for residue M3L determined Using Amber 20 recommended default charges and atom types for standard residues Coulombic values for 8g4l.pdb_A SES surface #2.2: minimum, -21.91, mean -0.65, maximum 19.75 Coulombic values for 8g4l.pdb_B SES surface #2.3: minimum, -23.19, mean -0.75, maximum 24.96 Coulombic values for 8act.pdb_A SES surface #3.3: minimum, -23.72, mean -1.16, maximum 15.27 Coulombic values for 8act.pdb_B SES surface #3.4: minimum, -25.84, mean -0.34, maximum 15.00 To also show corresponding color key, enter the above coulombic command and add key true > ui mousemode right translate Drag select of 8g4l.pdb_B SES surface, 200 of 1516366 triangles, 8act.pdb_A SES surface, 14 of 807322 triangles, 1 atoms, 12 residues > select add #3 18867 atoms, 19195 bonds, 19 pseudobonds, 2331 residues, 7 models selected > select add #2 118674 atoms, 119507 bonds, 24 pseudobonds, 8474 residues, 10 models selected > select subtract #3 99840 atoms, 100312 bonds, 5 pseudobonds, 6146 residues, 7 models selected > select subtract #2 2 models selected > save /Users/ruchigautamsharma/Desktop/image1.png supersample 3 > show #!10 models > hide #!3 models > hide #!2 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!10 models > show #!10 models > hide #!10 models > show #!10 models > hide #!10 models > ui mousemode right select > ui mousemode right translate > ui mousemode right select > show #!10 models > hide #!10 models Drag select of 42 residues > select add #3 18834 atoms, 19195 bonds, 19 pseudobonds, 2328 residues, 5 models selected > select subtract #3 2 models selected Drag select of 25 residues > style sel ball Changed 204 atom styles > show sel atoms > coulombic sel Coulombic values for 8act.pdb_A SES surface #3.3: minimum, -23.72, mean -1.16, maximum 15.27 Coulombic values for 8act.pdb_B SES surface #3.4: minimum, -25.84, mean -0.34, maximum 15.00 To also show corresponding color key, enter the above coulombic command and add key true Drag select of 8act.pdb_B SES surface, 36 of 774284 triangles, 13 residues Drag select of 8act.pdb_B SES surface, 335 of 774284 triangles, 1 atoms, 32 residues, 1 bonds > style sel ball Changed 263 atom styles > show sel atoms > coulombic sel Coulombic values for 8act.pdb_A SES surface #3.3: minimum, -23.72, mean -1.16, maximum 15.27 Coulombic values for 8act.pdb_B SES surface #3.4: minimum, -25.84, mean -0.34, maximum 15.00 To also show corresponding color key, enter the above coulombic command and add key true Drag select of 20 atoms, 46 residues, 17 bonds Drag select of 8act.pdb_A SES surface, 1775 of 807322 triangles, 8act.pdb_B SES surface, 1980 of 774284 triangles, 44 atoms, 78 residues, 37 bonds Drag select of 8act.pdb_B SES surface, 1283 of 774284 triangles, 62 atoms, 33 residues, 49 bonds > coulombic sel Coulombic values for 8act.pdb_A SES surface #3.3: minimum, -23.72, mean -1.16, maximum 15.27 Coulombic values for 8act.pdb_B SES surface #3.4: minimum, -25.84, mean -0.34, maximum 15.00 To also show corresponding color key, enter the above coulombic command and add key true > show #!10 models > select add #3 18834 atoms, 19195 bonds, 19 pseudobonds, 2328 residues, 5 models selected > select subtract #3 2 models selected > hide #!3 models > show #!3 models > hide #!10 models > save /Users/ruchigautamsharma/Desktop/image2.png supersample 3 > hide #!3 models > show #!2 models > show #!10 models > hide #!5 models > ui mousemode right translate > hide #!10 models > ui mousemode right select Drag select of 40 atoms, 31 residues, 37 bonds, 1 pseudobonds > style sel ball Changed 477 atom styles > show sel atoms > coulombic sel Coulombic values for 8g4l.pdb_A SES surface #2.2: minimum, -21.91, mean -0.65, maximum 19.75 Coulombic values for 8g4l.pdb_B SES surface #2.3: minimum, -23.19, mean -0.75, maximum 24.96 To also show corresponding color key, enter the above coulombic command and add key true > ui mousemode right translate > show #!10 models > hide #!2 models > show #!3 models > show #!2 models > hide #!10 models > save /Users/ruchigautamsharma/Desktop/image3.png supersample 3 > save ""/Users/ruchigautamsharma/Desktop/25HepE525K/interaction > 25HepE525K.cxs"" includeMaps true ——— End of log from Wed Sep 25 04:14:14 2024 ——— opened ChimeraX session > select add #2 99840 atoms, 100312 bonds, 5 pseudobonds, 6146 residues, 3 models selected > select subtract #2 2 models selected > hide #!2 models > ui mousemode right select Drag select of 50 atoms, 26 residues, 42 bonds Drag select of 8act.pdb_A SES surface, 9674 of 807322 triangles, 8act.pdb_B SES surface, 2496 of 774284 triangles, 48 atoms, 91 residues, 38 bonds Drag select of 8act.pdb_A SES surface, 5160 of 807322 triangles, 8act.pdb_B SES surface, 2203 of 774284 triangles, 69 atoms, 95 residues, 57 bonds > coulombic sel Coulombic values for 8act.pdb_A SES surface #3.3: minimum, -23.72, mean -1.16, maximum 15.27 Coulombic values for 8act.pdb_B SES surface #3.4: minimum, -25.84, mean -0.34, maximum 15.00 To also show corresponding color key, enter the above coulombic command and add key true Drag select of 8act.pdb_A SES surface, 1211 of 807322 triangles, 8act.pdb_B SES surface, 784 of 774284 triangles, 4 atoms, 22 residues, 4 bonds > ui mousemode right translate > ui mousemode right select Drag select of 8act.pdb_A SES surface, 9181 of 807322 triangles, 8act.pdb_B SES surface, 7593 of 774284 triangles, 46 atoms, 34 residues, 39 bonds > select add #3 18834 atoms, 19195 bonds, 19 pseudobonds, 2328 residues, 5 models selected > select subtract #3 2 models selected Drag select of 8act.pdb_A SES surface, 45732 of 807322 triangles, 8act.pdb_B SES surface, 16784 of 774284 triangles, 242 atoms, 415 residues, 1 pseudobonds, 201 bonds > select add #3 18834 atoms, 19195 bonds, 19 pseudobonds, 2328 residues, 5 models selected > select subtract #3 2 models selected Drag select of 8act.pdb_A SES surface, 170 of 807322 triangles, 8act.pdb_B SES surface, 459 of 774284 triangles > ui mousemode right translate > ui mousemode right select Drag select of 8act.pdb_A SES surface, 40121 of 807322 triangles, 8act.pdb_B SES surface, 13087 of 774284 triangles, 153 atoms, 281 residues, 127 bonds > select add #3 18834 atoms, 19195 bonds, 19 pseudobonds, 2328 residues, 5 models selected > coulombic sel The following heavy (non-hydrogen) atoms are missing, which may result in inaccurate electrostatics: 8act.pdb #3/D SER 195 OXT 8act.pdb #3/C SER 195 OXT 8act.pdb #3/E GLU 163 OXT Using Amber 20 recommended default charges and atom types for standard residues Coulombic values for 8act.pdb_A SES surface #3.3: minimum, -23.72, mean -1.16, maximum 15.27 Coulombic values for 8act.pdb_B SES surface #3.4: minimum, -25.84, mean -0.34, maximum 15.00 Coulombic values for 8act.pdb_C SES surface #3.5: minimum, -22.56, mean -3.87, maximum 14.68 Coulombic values for 8act.pdb_D SES surface #3.6: minimum, -19.82, mean -3.44, maximum 15.48 Coulombic values for 8act.pdb_E SES surface #3.7: minimum, -20.97, mean -5.04, maximum 8.16 Coulombic values for 8act.pdb_F SES surface #3.8: minimum, -22.95, mean -4.14, maximum 7.43 To also show corresponding color key, enter the above coulombic command and add key true > ui mousemode right translate > show #!10 models > show #!4 models > hide #!10 models > select subtract #3 6 models selected > hide #!3 models > show #!10 models > hide #!4 models > show #!3 models > save > /Users/ruchigautamsharma/Desktop/25HepE525K/25HepE525KwithMava_Interaction.cxs ——— End of log from Thu Sep 26 13:06:28 2024 ——— opened ChimeraX session > show #!2 models > close #6 > close #7 > close #8 > close #9 > close #11 > save > /Users/ruchigautamsharma/Desktop/25HepE525K/25HepE525KwithMava_Interaction.cxs ——— End of log from Thu Sep 26 13:21:30 2024 ——— opened ChimeraX session > hide #!3 models > hide #!2 models > show #!2 models > hide #!2 models > volume #10 level 0.07481 > show #!3 models > show #!2 models > hide #!2 models > open > /Users/ruchigautamsharma/Desktop/25HepE525K/cryosparc_P30_J276_map_sharp.mrc Opened cryosparc_P30_J276_map_sharp.mrc as #6, grid size 300,300,300, pixel 0.83, shown at level 0.0289, step 2, values float32 > hide #!3 models > select add #6 2 models selected > ui mousemode right ""translate selected models"" > view matrix models #6,1,0,0,-13.259,0,1,0,-59.644,0,0,1,-60.922 > ui mousemode right ""rotate selected models"" > view matrix models > #6,0.97989,-0.19467,-0.043828,17.497,0.19799,0.97586,0.092126,-93.748,0.024836,-0.09895,0.99478,-51.92 > undo [Repeated 1 time(s)] > volumeflip #6 Unknown command: volumeflip #6 > volume flip #6 Opened cryosparc_P30_J276_map_sharp.mrc z flip as #7, grid size 300,300,300, pixel 0.83, shown at step 1, values float32 > select subtract #6 Nothing selected > select add #7 2 models selected > view matrix models > #7,0.96691,0.024547,-0.25392,32.662,0.2299,0.34752,0.90905,-65.44,0.11056,-0.93735,0.33038,177.52 > view matrix models > #7,-0.99755,-0.034454,-0.060947,267.99,-0.00070731,0.87544,-0.48332,74.136,0.070008,-0.48209,-0.87332,277.93 > ui mousemode right ""translate selected models"" > view matrix models > #7,-0.99755,-0.034454,-0.060947,269.51,-0.00070731,0.87544,-0.48332,81.793,0.070008,-0.48209,-0.87332,283.92 > fitmap #7 inMap #10 Fit map cryosparc_P30_J276_map_sharp.mrc z flip in map cryosparc_P30_J280_class_05_00027_volume.mrc z flip using 270132 points correlation = 0.765, correlation about mean = 0.4371, overlap = 1.18e+04 steps = 156, shift = 3.04, angle = 18.9 degrees Position of cryosparc_P30_J276_map_sharp.mrc z flip (#7) relative to cryosparc_P30_J280_class_05_00027_volume.mrc z flip (#10) coordinates: Matrix rotation and translation 0.99868521 -0.01194978 0.04985040 -4.14668671 0.01153380 0.99989629 0.00862389 -2.79643992 -0.04994828 -0.00803759 0.99871946 7.43685902 Axis -0.16040788 0.96080890 0.22608753 Axis point 148.17070643 0.00000000 88.18561170 Rotation angle (degrees) 2.97697945 Shift along axis -0.34030206 > ui mousemode right translate > hide #!10 models > volume #7 level 0.009114 > transparency sel 50 > show #!2 models > volume #7 level 0.00811 > volume #7 level 0.00611 > volume #7 level 0.00111 > surface dust #7 size 8.3 > fitmap #2 inMap #7 Fit molecule 8g4l.pdb (#2) to map cryosparc_P30_J276_map_sharp.mrc z flip (#7) using 99840 atoms average map value = 0.07007, steps = 304 shifted from previous position = 0.129 rotated from previous position = 0.285 degrees atoms outside contour = 75934, contour level = 0.00111 Position of 8g4l.pdb (#2) relative to cryosparc_P30_J276_map_sharp.mrc z flip (#7) coordinates: Matrix rotation and translation 0.90356614 -0.36251243 -0.22837025 69.94133890 0.42750669 0.72750591 0.53663133 -463.88516185 -0.02839482 -0.58251171 0.81232619 178.12186061 Axis -0.80838767 -0.14444773 0.57065245 Axis point 0.00000000 -62.59090162 802.47834953 Rotation angle (degrees) 43.80505846 Shift along axis 112.11311861 > show #!3 models > select subtract #7 Nothing selected > hide #!2 models > show #!2 models > hide #!3 models > hide #!2 models > show #!2 models > open > /Users/ruchigautamsharma/Desktop/25HepE525K/cryosparc_P30_J366_003_volume_map_sharp.mrc Opened cryosparc_P30_J366_003_volume_map_sharp.mrc as #8, grid size 300,300,300, pixel 0.83, shown at level 0.0628, step 2, values float32 > volume flip #8 Opened cryosparc_P30_J366_003_volume_map_sharp.mrc z flip as #9, grid size 300,300,300, pixel 0.83, shown at step 1, values float32 > close #8 > close #6 > select add #9 2 models selected > ui mousemode right ""translate selected models"" > ui mousemode right ""rotate selected models"" > view matrix models > #9,0.72491,0.12345,-0.6777,107.22,-0.31498,0.93434,-0.16672,71.607,0.61261,0.33432,0.71619,-88.209 > view matrix models > #9,-0.78393,-0.37061,0.49809,227.29,-0.46679,0.88081,-0.079276,87.942,-0.40935,-0.29465,-0.86349,320.77 > view matrix models > #9,-0.9341,-0.13426,0.33081,241.15,-0.20068,0.96381,-0.17551,53.522,-0.29528,-0.23033,-0.92723,305.45 > ui mousemode right ""translate selected models"" > view matrix models > #9,-0.9341,-0.13426,0.33081,237.7,-0.20068,0.96381,-0.17551,58.891,-0.29528,-0.23033,-0.92723,312.4 > select subtract #9 Nothing selected > hide #!9 models > hide #!7 models > show #!10 models > show #!9 models Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps, got 1 atomic models, 2 maps. > hide #!2 models > fitmap #10 inMap #9 Fit map cryosparc_P30_J280_class_05_00027_volume.mrc z flip in map cryosparc_P30_J366_003_volume_map_sharp.mrc z flip using 110989 points correlation = 0.8661, correlation about mean = 0.6378, overlap = 1281 steps = 248, shift = 14.1, angle = 17.3 degrees Position of cryosparc_P30_J280_class_05_00027_volume.mrc z flip (#10) relative to cryosparc_P30_J366_003_volume_map_sharp.mrc z flip (#9) coordinates: Matrix rotation and translation 0.99912867 0.03701040 0.01929050 -6.45856044 -0.03695133 0.99931125 -0.00340957 4.82258956 -0.01940341 0.00269379 0.99980811 2.58781556 Axis 0.07292398 0.46232197 -0.88370838 Axis point 133.82942588 176.61647977 0.00000000 Rotation angle (degrees) 2.39837754 Shift along axis -0.52826911 > show #!2 models > hide #!9 models > fitmap #2 inMap #10 Fit molecule 8g4l.pdb (#2) to map cryosparc_P30_J280_class_05_00027_volume.mrc z flip (#10) using 99840 atoms average map value = 0.0705, steps = 2000 shifted from previous position = 42.4 rotated from previous position = 17.7 degrees atoms outside contour = 75484, contour level = 0.074814 Position of 8g4l.pdb (#2) relative to cryosparc_P30_J280_class_05_00027_volume.mrc z flip (#10) coordinates: Matrix rotation and translation 0.89869523 -0.39132784 -0.19801364 76.37796838 0.43305938 0.72042893 0.54170263 -464.23480660 -0.06932856 -0.57257723 0.81691423 184.96627548 Axis -0.80046161 -0.09244309 0.59221237 Axis point 0.00000000 -34.72317143 823.48795667 Rotation angle (degrees) 44.10881728 Shift along axis 91.31698418 > show #!9 models > hide #!10 models > surface dust #9 size 8.3 > volume #9 level 0.04335 > transparency #2.2-3#9.1 50 > volume #9 level 0.04552 > show #!3 models > hide #!2 models > fitmap #3 inMap #9 Fit molecule 8act.pdb (#3) to map cryosparc_P30_J366_003_volume_map_sharp.mrc z flip (#9) using 18834 atoms average map value = 0.07945, steps = 224 shifted from previous position = 13.7 rotated from previous position = 17.3 degrees atoms outside contour = 5855, contour level = 0.045517 Position of 8act.pdb (#3) relative to cryosparc_P30_J366_003_volume_map_sharp.mrc z flip (#9) coordinates: Matrix rotation and translation -0.99082281 0.08342546 -0.10635013 340.09974533 0.09230379 0.99239110 -0.08148569 -89.94149170 0.09874294 -0.09055440 -0.99098422 327.06025206 Axis -0.04413312 -0.99809091 0.04320662 Axis point 163.69830978 0.00000000 170.46022157 Rotation angle (degrees) 174.10287196 Shift along axis 88.89128906 > hide #!3 models > show #!3 models > save /Users/ruchigautamsharma/Desktop/25HepE525K/25HepE525KwithMava_4.cxs ——— End of log from Fri Sep 27 17:28:16 2024 ——— opened ChimeraX session OpenGL version: 4.1 INTEL-22.5.11 OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 645 OpenGL vendor: Intel Inc. Python: 3.11.2 Locale: UTF-8 Qt version: PyQt6 6.3.1, Qt 6.3.1 Qt runtime version: 6.3.2 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro15,4 Processor Name: Quad-Core Intel Core i7 Processor Speed: 1.7 GHz Number of Processors: 1 Total Number of Cores: 4 L2 Cache (per Core): 256 KB L3 Cache: 8 MB Hyper-Threading Technology: Enabled Memory: 16 GB System Firmware Version: 2022.140.5.0.0 (iBridge: 21.16.6074.0.0,0) OS Loader Version: 580.140.1~8 Software: System Software Overview: System Version: macOS 14.6 (23G80) Kernel Version: Darwin 23.6.0 Time since boot: 11 hours, 48 minutes Graphics/Displays: Intel Iris Plus Graphics 645: Chipset Model: Intel Iris Plus Graphics 645 Type: GPU Bus: Built-In VRAM (Dynamic, Max): 1536 MB Vendor: Intel Device ID: 0x3ea6 Revision ID: 0x0001 Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-In Retina LCD Resolution: 2560 x 1600 Retina Framebuffer Depth: 24-Bit Color (ARGB8888) Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal Installed Packages: alabaster: 0.7.16 appdirs: 1.4.4 appnope: 0.1.3 asttokens: 2.4.1 Babel: 2.14.0 backcall: 0.2.0 beautifulsoup4: 4.11.2 blockdiag: 3.0.0 blosc2: 2.0.0 build: 0.10.0 certifi: 2022.12.7 cftime: 1.6.3 charset-normalizer: 3.3.2 ChimeraX-AddCharge: 1.5.13 ChimeraX-AddH: 2.2.5 ChimeraX-AlignmentAlgorithms: 2.0.1 ChimeraX-AlignmentHdrs: 3.4.1 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.12.2 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.1.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.49.1 ChimeraX-AtomicLibrary: 12.1.5 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.3.2 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.1.2 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.10.5 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2.2 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.3.2 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.3.2 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.2.4 ChimeraX-ColorActions: 1.0.3 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.5 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.7.1 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.2 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2 ChimeraX-DistMonitor: 1.4 ChimeraX-DockPrep: 1.1.3 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ESMFold: 1.0 ChimeraX-FileHistory: 1.0.1 ChimeraX-FunctionKey: 1.0.1 ChimeraX-Geometry: 1.3 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.1.1 ChimeraX-Hbonds: 2.4 ChimeraX-Help: 1.2.2 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-Label: 1.1.8 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.1.6 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 ChimeraX-Map: 1.1.4 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0.1 ChimeraX-MapFilter: 2.0.1 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1.1 ChimeraX-Markers: 1.0.1 ChimeraX-Mask: 1.0.2 ChimeraX-MatchMaker: 2.1.2 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.6.1 ChimeraX-MedicalToolbar: 1.0.2 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.12.1 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.14 ChimeraX-ModelPanel: 1.4 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0.3 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.2 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.1 ChimeraX-NRRD: 1.1 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.13.1 ChimeraX-PDB: 2.7.3 ChimeraX-PDBBio: 1.0.1 ChimeraX-PDBLibrary: 1.0.4 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1 ChimeraX-PubChem: 2.1 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.1 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.2 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 4.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.2 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.11 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.2 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.12.4 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.1.2 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.2.2 ChimeraX-TapeMeasure: 1.0 ChimeraX-TaskManager: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1.2 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.33.3 ChimeraX-uniprot: 2.3 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.3.2 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-vrml: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.3 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.2.1 contourpy: 1.2.0 cxservices: 1.2.2 cycler: 0.12.1 Cython: 0.29.33 debugpy: 1.8.0 decorator: 5.1.1 docutils: 0.19 executing: 2.0.1 filelock: 3.9.0 fonttools: 4.47.2 funcparserlib: 2.0.0a0 glfw: 2.6.4 grako: 3.16.5 h5py: 3.10.0 html2text: 2020.1.16 idna: 3.6 ihm: 0.38 imagecodecs: 2023.9.18 imagesize: 1.4.1 ipykernel: 6.23.2 ipython: 8.14.0 ipython-genutils: 0.2.0 ipywidgets: 8.1.1 jedi: 0.18.2 Jinja2: 3.1.2 jupyter-client: 8.2.0 jupyter-core: 5.7.1 jupyterlab-widgets: 3.0.9 kiwisolver: 1.4.5 line-profiler: 4.0.2 lxml: 4.9.2 lz4: 4.3.2 MarkupSafe: 2.1.4 matplotlib: 3.7.2 matplotlib-inline: 0.1.6 msgpack: 1.0.4 nest-asyncio: 1.6.0 netCDF4: 1.6.2 networkx: 3.1 nibabel: 5.0.1 nptyping: 2.5.0 numexpr: 2.8.8 numpy: 1.25.1 openvr: 1.23.701 packaging: 21.3 ParmEd: 3.4.3 parso: 0.8.3 pep517: 0.13.0 pexpect: 4.9.0 pickleshare: 0.7.5 pillow: 10.2.0 pip: 23.0 pkginfo: 1.9.6 platformdirs: 4.1.0 prompt-toolkit: 3.0.43 psutil: 5.9.5 ptyprocess: 0.7.0 pure-eval: 0.2.2 py-cpuinfo: 9.0.0 pycollada: 0.7.2 pydicom: 2.3.0 Pygments: 2.16.1 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.2801 pyparsing: 3.0.9 pyproject-hooks: 1.0.0 PyQt6-commercial: 6.3.1 PyQt6-Qt6: 6.3.2 PyQt6-sip: 13.4.0 PyQt6-WebEngine-commercial: 6.3.1 PyQt6-WebEngine-Qt6: 6.3.2 python-dateutil: 2.8.2 pytz: 2023.3.post1 pyzmq: 25.1.2 qtconsole: 5.4.3 QtPy: 2.4.1 RandomWords: 0.4.0 requests: 2.31.0 scipy: 1.11.1 setuptools: 67.4.0 setuptools-scm: 7.0.5 sfftk-rw: 0.7.3 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.5 sphinx: 6.1.3 sphinx-autodoc-typehints: 1.22 sphinxcontrib-applehelp: 1.0.8 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.6 sphinxcontrib-htmlhelp: 2.0.5 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.7 sphinxcontrib-serializinghtml: 1.1.10 stack-data: 0.6.3 superqt: 0.5.0 tables: 3.8.0 tcia-utils: 1.5.1 tifffile: 2023.7.18 tinyarray: 1.2.4 tomli: 2.0.1 tornado: 6.4 traitlets: 5.9.0 typing-extensions: 4.9.0 tzdata: 2023.4 urllib3: 2.1.0 wcwidth: 0.2.13 webcolors: 1.12 wheel: 0.38.4 wheel-filename: 1.4.1 widgetsnbextension: 4.0.9 }}} " defect feedback normal Core Tom Goddard all ChimeraX