id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 9530 Crash in garbage collection while drawing volume histogram after opening session chimerax-bug-report@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-12.6.5-x86_64-i386-64bit ChimeraX Version: 1.7.dev202307312254 (2023-07-31 22:54:15 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. Fatal Python error: Segmentation fault Thread 0x000070001517b000 (most recent call first): File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 579 in _handle_results File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x0000700014178000 (most recent call first): File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 531 in _handle_tasks File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x0000700013175000 (most recent call first): File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/selectors.py"", line 415 in select File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/connection.py"", line 930 in wait File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 502 in _wait_for_updates File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 522 in _handle_workers File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x0000700012172000 (most recent call first): File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000070001116f000 (most recent call first): File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000070001016c000 (most recent call first): File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000070000f169000 (most recent call first): File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000070000e166000 (most recent call first): File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000070000d163000 (most recent call first): File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000070000c160000 (most recent call first): File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000070000b15d000 (most recent call first): File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Current thread 0x0000000115176600 (most recent call first): Garbage-collecting File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/map/histogram.py"", line 47 in show_data File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/map/volume_viewer.py"", line 2754 in update_histogram File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/map/volume_viewer.py"", line 2729 in update_cb File ""/Applications/ChimeraX_Daily.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_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 893 in init File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1044 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.pdb_lib._load_libs, chimerax.map._map, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, chimerax.surface._surface, 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, psutil._psutil_osx, psutil._psutil_posix, lxml._elementpath, lxml.etree, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw, chimerax.atom_search.ast, chimerax.chem_group._chem_group, chimerax.coulombic._esp, chimerax.mlp._mlp (total: 66) {""app_name"":""ChimeraX"",""timestamp"":""2023-08-05 12:23:06.00 -0500"",""app_version"":""1.7.0"",""slice_uuid"":""194a3167-3db5-3029-8d22-1d742b826bb9"",""build_version"":""1.7.0.0"",""platform"":1,""bundleID"":""edu.ucsf.cgl.ChimeraX"",""share_with_app_devs"":0,""is_first_party"":0,""bug_type"":""309"",""os_version"":""macOS 12.6.5 (21G531)"",""incident_id"":""B93A63B7-3577-4219-8D43-DF4B81CB6E94"",""name"":""ChimeraX""} { ""uptime"" : 59000, ""procLaunch"" : ""2023-08-02 15:25:54.8323 -0500"", ""procRole"" : ""Foreground"", ""version"" : 2, ""userID"" : 501, ""deployVersion"" : 210, ""modelCode"" : ""MacBookPro16,2"", ""procStartAbsTime"" : 16925643071233, ""coalitionID"" : 1770, ""osVersion"" : { ""train"" : ""macOS 12.6.5"", ""build"" : ""21G531"", ""releaseType"" : ""User"" }, ""captureTime"" : ""2023-08-05 12:22:49.5992 -0500"", ""incident"" : ""B93A63B7-3577-4219-8D43-DF4B81CB6E94"", ""bug_type"" : ""309"", ""pid"" : 10757, ""procExitAbsTime"" : 59955252084609, ""cpuType"" : ""X86-64"", ""procName"" : ""ChimeraX"", ""procPath"" : ""\/Applications\/ChimeraX_Daily.app\/Contents\/MacOS\/ChimeraX"", ""bundleInfo"" : {""CFBundleShortVersionString"":""1.7.0"",""CFBundleVersion"":""1.7.0.0"",""CFBundleIdentifier"":""edu.ucsf.cgl.ChimeraX""}, ""storeInfo"" : {""deviceIdentifierForVendor"":""81823763-F42D-5626-9784-1E9E9F2AE57B"",""thirdParty"":true}, ""parentProc"" : ""launchd"", ""parentPid"" : 1, ""coalitionName"" : ""edu.ucsf.cgl.ChimeraX"", ""crashReporterKey"" : ""90E39C74-BFE4-E0B0-E0AF-7936AEE17B24"", ""wakeTime"" : 139, ""bridgeVersion"" : {""build"":""20P4252"",""train"":""7.4""}, ""sleepWakeUUID"" : ""C1B6D81F-02E2-4977-85EA-BABA2F607D37"", ""sip"" : ""enabled"", ""vmRegionInfo"" : ""0xa9 is not in any region. Bytes before following region: 140737486434135\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n VM_ALLOCATE 7fffffe2b000-7fffffe2c000 [ 4K] r-x\/r-x SM=ALI "", ""isCorpse"" : 1, ""exception"" : {""codes"":""0x0000000000000001, 0x00000000000000a9"",""rawCodes"":[1,169],""type"":""EXC_BAD_ACCESS"",""signal"":""SIGSEGV"",""subtype"":""KERN_INVALID_ADDRESS at 0x00000000000000a9""}, ""ktriageinfo"" : ""VM - Compressor failed a blocking pager_get\nVM - Compressor failed a blocking pager_get\nVM - Compressor failed a blocking pager_get\nVM - Compressor failed a blocking pager_get\nVM - Compressor failed a blocking pager_get\n"", ""vmregioninfo"" : ""0xa9 is not in any region. Bytes before following region: 140737486434135\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n VM_ALLOCATE 7fffffe2b000-7fffffe2c000 [ 4K] r-x\/r-x SM=ALI "", ""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"" : [{""triggered"":true,""id"":252772,""instructionState"":{""instructionStream"":{""bytes"":[255,255,255,255,72,137,216,72,139,0,72,255,194,72,57,195,117,245,72,141,61,197,18,22,0,72,141,181,112,255,255,255,49,192,232,191,131,254,255,72,139,5,104,231,22,0,72,139,0,72,59,69,216,117,13,72,131,196,112,91,65,92,65,94,65,95,93,195,232,205,174,14,0,102,46,15,31,132,0,0,0,0,0,15,31,0,85,72,137,229,83,80,72,139,71,8,246,128,169,0,0,0,64,117,9,49,192,72,131,196,8,91,93,195,72,137,251,72,139,128,72,1,0,0,72,133,192,117,18,72,139,67,248,168,2,116,224,72,131,192,252,72,137,67,248,235,214,72,137,223,255,208,133,192,117,229,235,203,15,31,132,0,0,0,0,0,85,72,137,229,65,86,83,72,139,71,8,246,128,169,0,0,0,64,117,7,49,192,91,65,94,93],""offset"":96}},""name"":""CrBrowserMain"",""threadState"":{""r13"":{""value"":140701886701057},""rax"":{""value"":0},""rflags"":{""value"":582},""cpu"":{""value"":0},""r14"":{""value"":11},""rsi"":{""value"":11},""r8"":{""value"":2},""cr2"":{""value"":4435709952},""rdx"":{""value"":0},""r10"":{""value"":4648822272},""r9"":{""value"":14757395258967641293},""r15"":{""value"":22},""rbx"":{""value"":4648822272},""trap"":{""value"":133},""err"":{""value"":33554760},""r11"":{""value"":582},""rip"":{""value"":140703562063870,""matchesCrashFrame"":1},""rbp"":{""value"":140159950377936},""rsp"":{""value"":140159950377896},""r12"":{""value"":259},""rcx"":{""value"":140159950377896},""flavor"":""x86_THREAD_STATE"",""rdi"":{""value"":259}},""frames"":[{""imageOffset"":32766,""imageIndex"":0},{""imageOffset"":279256,""imageIndex"":1},{""imageOffset"":2590164,""imageIndex"":2},{""imageOffset"":15869,""imageIndex"":3},{""imageOffset"":0,""imageIndex"":4},{""imageOffset"":848640,""imageIndex"":2},{""imageOffset"":2574472,""imageIndex"":2},{""imageOffset"":2580738,""imageIndex"":2},{""imageOffset"":2580887,""imageIndex"":2},{""imageOffset"":1292198,""imageIndex"":2},{""imageOffset"":1223445,""imageIndex"":2},{""imageOffset"":684907,""imageIndex"":2},{""imageOffset"":86612,""imageIndex"":5},{""imageOffset"":25077,""imageIndex"":5},{""imageOffset"":1939847,""imageIndex"":6},{""imageOffset"":1095620,""imageIndex"":2},{""imageOffset"":680881,""imageIndex"":2},{""imageOffset"":1917927,""imageIndex"":2},{""imageOffset"":1942736,""imageIndex"":2},{""imageOffset"":1257368,""imageIndex"":7},{""imageOffset"":1257114,""imageIndex"":7},{""imageOffset"":1261029,""imageIndex"":7},{""imageOffset"":1260890,""imageIndex"":7},{""imageOffset"":777575,""imageIndex"":8},{""imageOffset"":863063,""imageIndex"":8},{""imageOffset"":146281,""imageIndex"":7},{""imageOffset"":746701,""imageIndex"":8},{""imageOffset"":145898,""imageIndex"":7},{""imageOffset"":51847,""imageIndex"":9},{""imageOffset"":55875,""imageIndex"":9},{""imageOffset"":1282534,""imageIndex"":6},{""imageOffset"":449594,""imageIndex"":8},{""imageOffset"":2061601,""imageIndex"":8},{""imageOffset"":99493,""imageIndex"":10},{""imageOffset"":524635,""imageIndex"":11},{""imageOffset"":524483,""imageIndex"":11},{""imageOffset"":523935,""imageIndex"":11},{""imageOffset"":518232,""imageIndex"":11},{""imageOffset"":515612,""imageIndex"":11},{""imageOffset"":189926,""imageIndex"":12},{""imageOffset"":188947,""imageIndex"":12},{""imageOffset"":188645,""imageIndex"":12},{""imageOffset"":257901,""imageIndex"":13},{""imageOffset"":251434,""imageIndex"":13},{""imageOffset"":195801,""imageIndex"":13},{""imageOffset"":102572,""imageIndex"":10},{""imageOffset"":488230,""imageIndex"":8},{""imageOffset"":451125,""imageIndex"":8},{""imageOffset"":2252186,""imageIndex"":6},{""imageOffset"":1095658,""imageIndex"":2},{""imageOffset"":680881,""imageIndex"":2},{""imageOffset"":1917927,""imageIndex"":2},{""imageOffset"":1852538,""imageIndex"":2},{""imageOffset"":1830115,""imageIndex"":2},{""imageOffset"":1098052,""imageIndex"":2},{""imageOffset"":1917679,""imageIndex"":2},{""imageOffset"":1942736,""imageIndex"":2},{""imageOffset"":2561789,""imageIndex"":2},{""imageOffset"":2560449,""imageIndex"":2},{""imageOffset"":2564475,""imageIndex"":2},{""imageOffset"":2564426,""imageIndex"":2},{""imageOffset"":15770,""imageIndex"":14},{""imageOffset"":21806,""imageIndex"":15}]},{""id"":252915,""name"":""ThreadPoolServiceThread"",""frames"":[{""imageOffset"":43194,""imageIndex"":0},{""imageOffset"":66455847,""imageIndex"":16},{""imageOffset"":65919580,""imageIndex"":16},{""imageOffset"":65624472,""imageIndex"":16},{""imageOffset"":66059960,""imageIndex"":16},{""imageOffset"":65958573,""imageIndex"":16},{""imageOffset"":66060362,""imageIndex"":16},{""imageOffset"":66222344,""imageIndex"":16},{""imageOffset"":25825,""imageIndex"":17},{""imageOffset"":8043,""imageIndex"":17}]},{""id"":252918,""name"":""Chrome_IOThread"",""frames"":[{""imageOffset"":43194,""imageIndex"":0},{""imageOffset"":66455847,""imageIndex"":16},{""imageOffset"":65919580,""imageIndex"":16},{""imageOffset"":65624472,""imageIndex"":16},{""imageOffset"":66059960,""imageIndex"":16},{""imageOffset"":48386978,""imageIndex"":16},{""imageOffset"":66060362,""imageIndex"":16},{""imageOffset"":66222344,""imageIndex"":16},{""imageOffset"":25825,""imageIndex"":17},{""imageOffset"":8043,""imageIndex"":17}]},{""id"":252919,""name"":""NetworkConfigWatcher"",""frames"":[{""imageOffset"":6506,""imageIndex"":0},{""imageOffset"":7384,""imageIndex"":0},{""imageOffset"":66252326,""imageIndex"":16},{""imageOffset"":66251759,""imageIndex"":16},{""imageOffset"":65421769,""imageIndex"":16},{""imageOffset"":65919580,""imageIndex"":16},{""imageOffset"":65624472,""imageIndex"":16},{""imageOffset"":66059960,""imageIndex"":16},{""imageOffset"":66060362,""imageIndex"":16},{""imageOffset"":66222344,""imageIndex"":16},{""imageOffset"":25825,""imageIndex"":17},{""imageOffset"":8043,""imageIndex"":17}]},{""id"":252926,""name"":""CompositorTileWorker1"",""frames"":[{""imageOffset"":17370,""imageIndex"":0},{""imageOffset"":66219291,""imageIndex"":16},{""imageOffset"":100616493,""imageIndex"":16},{""imageOffset"":66222344,""imageIndex"":16},{""imageOffset"":25825,""imageIndex"":17},{""imageOffset"":8043,""imageIndex"":17}]},{""id"":252927,""name"":""Chrome_InProcGpuThread"",""frames"":[{""imageOffset"":6506,""imageIndex"":0},{""imageOffset"":7384,""imageIndex"":0},{""imageOffset"":66252326,""imageIndex"":16},{""imageOffset"":66251759,""imageIndex"":16},{""imageOffset"":65421769,""imageIndex"":16},{""imageOffset"":65919580,""imageIndex"":16},{""imageOffset"":65624472,""imageIndex"":16},{""imageOffset"":66059960,""imageIndex"":16},{""imageOffset"":66060362,""imageIndex"":16},{""imageOffset"":66222344,""imageIndex"":16},{""imageOffset"":25825,""imageIndex"":17},{""imageOffset"":8043,""imageIndex"":17}]},{""id"":252928,""name"":""Chrome_ChildIOThread"",""frames"":[{""imageOffset"":43194,""imageIndex"":0},{""imageOffset"":66455847,""imageIndex"":16},{""imageOffset"":65919580,""imageIndex"":16},{""imageOffset"":65624472,""imageIndex"":16},{""imageOffset"":66059960,""imageIndex"":16},{""imageOffset"":66060362,""imageIndex"":16},{""imageOffset"":66222344,""imageIndex"":16},{""imageOffset"":25825,""imageIndex"":17},{""imageOffset"":8043,""imageIndex"":17}]},{""id"":252929,""name"":""NetworkConfigWatcher"",""frames"":[{""imageOffset"":6506,""imageIndex"":0},{""imageOffset"":7384,""imageIndex"":0},{""imageOffset"":66252326,""imageIndex"":16},{""imageOffset"":66251759,""imageIndex"":16},{""imageOffset"":65421769,""imageIndex"":16},{""imageOffset"":65919580,""imageIndex"":16},{""imageOffset"":65624472,""imageIndex"":16},{""imageOffset"":66059960,""imageIndex"":16},{""imageOffset"":66060362,""imageIndex"":16},{""imageOffset"":66222344,""imageIndex"":16},{""imageOffset"":25825,""imageIndex"":17},{""imageOffset"":8043,""imageIndex"":17}]},{""id"":252930,""name"":""VizCompositorThread"",""frames"":[{""imageOffset"":6506,""imageIndex"":0},{""imageOffset"":7384,""imageIndex"":0},{""imageOffset"":66252326,""imageIndex"":16},{""imageOffset"":65421672,""imageIndex"":16},{""imageOffset"":65919580,""imageIndex"":16},{""imageOffset"":65624472,""imageIndex"":16},{""imageOffset"":66059960,""imageIndex"":16},{""imageOffset"":66060362,""imageIndex"":16},{""imageOffset"":66222344,""imageIndex"":16},{""imageOffset"":25825,""imageIndex"":17},{""imageOffset"":8043,""imageIndex"":17}]},{""id"":252942,""name"":""NetworkService"",""frames"":[{""imageOffset"":43194,""imageIndex"":0},{""imageOffset"":66455847,""imageIndex"":16},{""imageOffset"":65919580,""imageIndex"":16},{""imageOffset"":65624472,""imageIndex"":16},{""imageOffset"":66059960,""imageIndex"":16},{""imageOffset"":66060362,""imageIndex"":16},{""imageOffset"":66222344,""imageIndex"":16},{""imageOffset"":25825,""imageIndex"":17},{""imageOffset"":8043,""imageIndex"":17}]},{""id"":252943,""name"":""NetworkConfigWatcher"",""frames"":[{""imageOffset"":6506,""imageIndex"":0},{""imageOffset"":7384,""imageIndex"":0},{""imageOffset"":66252326,""imageIndex"":16},{""imageOffset"":66251759,""imageIndex"":16},{""imageOffset"":65421769,""imageIndex"":16},{""imageOffset"":65919580,""imageIndex"":16},{""imageOffset"":65624472,""imageIndex"":16},{""imageOffset"":66059960,""imageIndex"":16},{""imageOffset"":66060362,""imageIndex"":16},{""imageOffset"":66222344,""imageIndex"":16},{""imageOffset"":25825,""imageIndex"":17},{""imageOffset"":8043,""imageIndex"":17}]},{""id"":252945,""name"":""ThreadPoolSingleThreadForegroundBlocking0"",""frames"":[{""imageOffset"":6506,""imageIndex"":0},{""imageOffset"":7384,""imageIndex"":0},{""imageOffset"":66252326,""imageIndex"":16},{""imageOffset"":66009023,""imageIndex"":16},{""imageOffset"":66011756,""imageIndex"":16},{""imageOffset"":66010829,""imageIndex"":16},{""imageOffset"":66222344,""imageIndex"":16},{""imageOffset"":25825,""imageIndex"":17},{""imageOffset"":8043,""imageIndex"":17}]},{""id"":252975,""name"":""NetworkConfigWatcher"",""frames"":[{""imageOffset"":6506,""imageIndex"":0},{""imageOffset"":7384,""imageIndex"":0},{""imageOffset"":66252326,""imageIndex"":16},{""imageOffset"":66251759,""imageIndex"":16},{""imageOffset"":65421769,""imageIndex"":16},{""imageOffset"":65919580,""imageIndex"":16},{""imageOffset"":65624472,""imageIndex"":16},{""imageOffset"":66059960,""imageIndex"":16},{""imageOffset"":66060362,""imageIndex"":16},{""imageOffset"":66222344,""imageIndex"":16},{""imageOffset"":25825,""imageIndex"":17},{""imageOffset"":8043,""imageIndex"":17}]},{""id"":252984,""frames"":[{""imageOffset"":17370,""imageIndex"":0},{""imageOffset"":2482802,""imageIndex"":2},{""imageOffset"":13491,""symbol"":""_queue_SimpleQueue_get_impl"",""symbolLocation"":211,""imageIndex"":18},{""imageOffset"":12660,""symbol"":""_queue_SimpleQueue_get"",""symbolLocation"":196,""imageIndex"":18},{""imageOffset"":1099109,""imageIndex"":2},{""imageOffset"":1917679,""imageIndex"":2},{""imageOffset"":1942736,""imageIndex"":2},{""imageOffset"":1930570,""imageIndex"":2},{""imageOffset"":1942736,""imageIndex"":2},{""imageOffset"":698390,""imageIndex"":2},{""imageOffset"":3025702,""imageIndex"":2},{""imageOffset"":2481828,""imageIndex"":2},{""imageOffset"":25825,""imageIndex"":17},{""imageOffset"":8043,""imageIndex"":17}]},{""id"":252985,""frames"":[{""imageOffset"":17370,""imageIndex"":0},{""imageOffset"":2482802,""imageIndex"":2},{""imageOffset"":13491,""symbol"":""_queue_SimpleQueue_get_impl"",""symbolLocation"":211,""imageIndex"":18},{""imageOffset"":12660,""symbol"":""_queue_SimpleQueue_get"",""symbolLocation"":196,""imageIndex"":18},{""imageOffset"":1099109,""imageIndex"":2},{""imageOffset"":1917679,""imageIndex"":2},{""imageOffset"":1942736,""imageIndex"":2},{""imageOffset"":1930570,""imageIndex"":2},{""imageOffset"":1942736,""imageIndex"":2},{""imageOffset"":698390,""imageIndex"":2},{""imageOffset"":3025702,""imageIndex"":2},{""imageOffset"":2481828,""imageIndex"":2},{""imageOffset"":25825,""imageIndex"":17},{""imageOffset"":8043,""imageIndex"":17}]},{""id"":252986,""frames"":[{""imageOffset"":17370,""imageIndex"":0},{""imageOffset"":2482802,""imageIndex"":2},{""imageOffset"":13491,""symbol"":""_queue_SimpleQueue_get_impl"",""symbolLocation"":211,""imageIndex"":18},{""imageOffset"":12660,""symbol"":""_queue_SimpleQueue_get"",""symbolLocation"":196,""imageIndex"":18},{""imageOffset"":1099109,""imageIndex"":2},{""imageOffset"":1917679,""imageIndex"":2},{""imageOffset"":1942736,""imageIndex"":2},{""imageOffset"":1930570,""imageIndex"":2},{""imageOffset"":1942736,""imageIndex"":2},{""imageOffset"":698390,""imageIndex"":2},{""imageOffset"":3025702,""imageIndex"":2},{""imageOffset"":2481828,""imageIndex"":2},{""imageOffset"":25825,""imageIndex"":17},{""imageOffset"":8043,""imageIndex"":17}]},{""id"":252987,""frames"":[{""imageOffset"":17370,""imageIndex"":0},{""imageOffset"":2482802,""imageIndex"":2},{""imageOffset"":13491,""symbol"":""_queue_SimpleQueue_get_impl"",""symbolLocation"":211,""imageIndex"":18},{""imageOffset"":12660,""symbol"":""_queue_SimpleQueue_get"",""symbolLocation"":196,""imageIndex"":18},{""imageOffset"":1099109,""imageIndex"":2},{""imageOffset"":1917679,""imageIndex"":2},{""imageOffset"":1942736,""imageIndex"":2},{""imageOffset"":1930570,""imageIndex"":2},{""imageOffset"":1942736,""imageIndex"":2},{""imageOffset"":698390,""imageIndex"":2},{""imageOffset"":3025702,""imageIndex"":2},{""imageOffset"":2481828,""imageIndex"":2},{""imageOffset"":25825,""imageIndex"":17},{""imageOffset"":8043,""imageIndex"":17}]},{""id"":252988,""frames"":[{""imageOffset"":17370,""imageIndex"":0},{""imageOffset"":2482802,""imageIndex"":2},{""imageOffset"":13491,""symbol"":""_queue_SimpleQueue_get_impl"",""symbolLocation"":211,""imageIndex"":18},{""imageOffset"":12660,""symbol"":""_queue_SimpleQueue_get"",""symbolLocation"":196,""imageIndex"":18},{""imageOffset"":1099109,""imageIndex"":2},{""imageOffset"":1917679,""imageIndex"":2},{""imageOffset"":1942736,""imageIndex"":2},{""imageOffset"":1930570,""imageIndex"":2},{""imageOffset"":1942736,""imageIndex"":2},{""imageOffset"":698390,""imageIndex"":2},{""imageOffset"":3025702,""imageIndex"":2},{""imageOffset"":2481828,""imageIndex"":2},{""imageOffset"":25825,""imageIndex"":17},{""imageOffset"":8043,""imageIndex"":17}]},{""id"":252989,""frames"":[{""imageOffset"":17370,""imageIndex"":0},{""imageOffset"":2482802,""imageIndex"":2},{""imageOffset"":13491,""symbol"":""_queue_SimpleQueue_get_impl"",""symbolLocation"":211,""imageIndex"":18},{""imageOffset"":12660,""symbol"":""_queue_SimpleQueue_get"",""symbolLocation"":196,""imageIndex"":18},{""imageOffset"":1099109,""imageIndex"":2},{""imageOffset"":1917679,""imageIndex"":2},{""imageOffset"":1942736,""imageIndex"":2},{""imageOffset"":1930570,""imageIndex"":2},{""imageOffset"":1942736,""imageIndex"":2},{""imageOffset"":698390,""imageIndex"":2},{""imageOffset"":3025702,""imageIndex"":2},{""imageOffset"":2481828,""imageIndex"":2},{""imageOffset"":25825,""imageIndex"":17},{""imageOffset"":8043,""imageIndex"":17}]},{""id"":252990,""frames"":[{""imageOffset"":17370,""imageIndex"":0},{""imageOffset"":2482802,""imageIndex"":2},{""imageOffset"":13491,""symbol"":""_queue_SimpleQueue_get_impl"",""symbolLocation"":211,""imageIndex"":18},{""imageOffset"":12660,""symbol"":""_queue_SimpleQueue_get"",""symbolLocation"":196,""imageIndex"":18},{""imageOffset"":1099109,""imageIndex"":2},{""imageOffset"":1917679,""imageIndex"":2},{""imageOffset"":1942736,""imageIndex"":2},{""imageOffset"":1930570,""imageIndex"":2},{""imageOffset"":1942736,""imageIndex"":2},{""imageOffset"":698390,""imageIndex"":2},{""imageOffset"":3025702,""imageIndex"":2},{""imageOffset"":2481828,""imageIndex"":2},{""imageOffset"":25825,""imageIndex"":17},{""imageOffset"":8043,""imageIndex"":17}]},{""id"":252991,""frames"":[{""imageOffset"":17370,""imageIndex"":0},{""imageOffset"":2482802,""imageIndex"":2},{""imageOffset"":13491,""symbol"":""_queue_SimpleQueue_get_impl"",""symbolLocation"":211,""imageIndex"":18},{""imageOffset"":12660,""symbol"":""_queue_SimpleQueue_get"",""symbolLocation"":196,""imageIndex"":18},{""imageOffset"":1099109,""imageIndex"":2},{""imageOffset"":1917679,""imageIndex"":2},{""imageOffset"":1942736,""imageIndex"":2},{""imageOffset"":1930570,""imageIndex"":2},{""imageOffset"":1942736,""imageIndex"":2},{""imageOffset"":698390,""imageIndex"":2},{""imageOffset"":3025702,""imageIndex"":2},{""imageOffset"":2481828,""imageIndex"":2},{""imageOffset"":25825,""imageIndex"":17},{""imageOffset"":8043,""imageIndex"":17}]},{""id"":252992,""frames"":[{""imageOffset"":32922,""imageIndex"":0},{""imageOffset"":753176,""imageIndex"":2},{""imageOffset"":1917679,""imageIndex"":2},{""imageOffset"":1942736,""imageIndex"":2},{""imageOffset"":698143,""imageIndex"":2},{""imageOffset"":1930570,""imageIndex"":2},{""imageOffset"":1942736,""imageIndex"":2},{""imageOffset"":698390,""imageIndex"":2},{""imageOffset"":3025702,""imageIndex"":2},{""imageOffset"":2481828,""imageIndex"":2},{""imageOffset"":25825,""imageIndex"":17},{""imageOffset"":8043,""imageIndex"":17}]},{""id"":252993,""frames"":[{""imageOffset"":17370,""imageIndex"":0},{""imageOffset"":2482802,""imageIndex"":2},{""imageOffset"":13491,""symbol"":""_queue_SimpleQueue_get_impl"",""symbolLocation"":211,""imageIndex"":18},{""imageOffset"":12660,""symbol"":""_queue_SimpleQueue_get"",""symbolLocation"":196,""imageIndex"":18},{""imageOffset"":1099109,""imageIndex"":2},{""imageOffset"":872623,""imageIndex"":2},{""imageOffset"":1910669,""imageIndex"":2},{""imageOffset"":1942736,""imageIndex"":2},{""imageOffset"":1930570,""imageIndex"":2},{""imageOffset"":1942736,""imageIndex"":2},{""imageOffset"":698390,""imageIndex"":2},{""imageOffset"":3025702,""imageIndex"":2},{""imageOffset"":2481828,""imageIndex"":2},{""imageOffset"":25825,""imageIndex"":17},{""imageOffset"":8043,""imageIndex"":17}]},{""id"":252994,""frames"":[{""imageOffset"":17370,""imageIndex"":0},{""imageOffset"":2482802,""imageIndex"":2},{""imageOffset"":13491,""symbol"":""_queue_SimpleQueue_get_impl"",""symbolLocation"":211,""imageIndex"":18},{""imageOffset"":12660,""symbol"":""_queue_SimpleQueue_get"",""symbolLocation"":196,""imageIndex"":18},{""imageOffset"":1099109,""imageIndex"":2},{""imageOffset"":1917679,""imageIndex"":2},{""imageOffset"":1942736,""imageIndex"":2},{""imageOffset"":1930570,""imageIndex"":2},{""imageOffset"":1942736,""imageIndex"":2},{""imageOffset"":698390,""imageIndex"":2},{""imageOffset"":3025702,""imageIndex"":2},{""imageOffset"":2481828,""imageIndex"":2},{""imageOffset"":25825,""imageIndex"":17},{""imageOffset"":8043,""imageIndex"":17}]},{""id"":253042,""frames"":[{""imageOffset"":17370,""imageIndex"":0},{""imageOffset"":3466879,""imageIndex"":19},{""imageOffset"":25825,""imageIndex"":17},{""imageOffset"":8043,""imageIndex"":17}]},{""id"":253043,""frames"":[{""imageOffset"":17370,""imageIndex"":0},{""imageOffset"":3466879,""imageIndex"":19},{""imageOffset"":25825,""imageIndex"":17},{""imageOffset"":8043,""imageIndex"":17}]},{""id"":253044,""frames"":[{""imageOffset"":17370,""imageIndex"":0},{""imageOffset"":3466879,""imageIndex"":19},{""imageOffset"":25825,""imageIndex"":17},{""imageOffset"":8043,""imageIndex"":17}]},{""id"":253065,""name"":""com.apple.NSEventThread"",""frames"":[{""imageOffset"":6506,""imageIndex"":0},{""imageOffset"":7384,""imageIndex"":0},{""imageOffset"":525133,""imageIndex"":11},{""imageOffset"":518616,""imageIndex"":11},{""imageOffset"":515612,""imageIndex"":11},{""imageOffset"":1755534,""imageIndex"":13},{""imageOffset"":25825,""imageIndex"":17},{""imageOffset"":8043,""imageIndex"":17}]},{""id"":253134,""name"":""MemoryInfra"",""frames"":[{""imageOffset"":6506,""imageIndex"":0},{""imageOffset"":7384,""imageIndex"":0},{""imageOffset"":66252326,""imageIndex"":16},{""imageOffset"":66251759,""imageIndex"":16},{""imageOffset"":65421769,""imageIndex"":16},{""imageOffset"":65919580,""imageIndex"":16},{""imageOffset"":65624472,""imageIndex"":16},{""imageOffset"":66059960,""imageIndex"":16},{""imageOffset"":66060362,""imageIndex"":16},{""imageOffset"":66222344,""imageIndex"":16},{""imageOffset"":25825,""imageIndex"":17},{""imageOffset"":8043,""imageIndex"":17}]},{""id"":253135,""name"":""ThreadPoolSingleThreadSharedBackgroundBlocking1"",""frames"":[{""imageOffset"":6506,""imageIndex"":0},{""imageOffset"":7384,""imageIndex"":0},{""imageOffset"":66252326,""imageIndex"":16},{""imageOffset"":66009023,""imageIndex"":16},{""imageOffset"":66011034,""imageIndex"":16},{""imageOffset"":66010637,""imageIndex"":16},{""imageOffset"":66222344,""imageIndex"":16},{""imageOffset"":25825,""imageIndex"":17},{""imageOffset"":8043,""imageIndex"":17}]},{""id"":397163,""name"":""ThreadPoolBackgroundWorker"",""frames"":[{""imageOffset"":6506,""imageIndex"":0},{""imageOffset"":7384,""imageIndex"":0},{""imageOffset"":66252326,""imageIndex"":16},{""imageOffset"":66009023,""imageIndex"":16},{""imageOffset"":66011756,""imageIndex"":16},{""imageOffset"":66010589,""imageIndex"":16},{""imageOffset"":66222344,""imageIndex"":16},{""imageOffset"":25825,""imageIndex"":17},{""imageOffset"":8043,""imageIndex"":17}]},{""id"":821572,""name"":""ThreadPoolForegroundWorker"",""frames"":[{""imageOffset"":6506,""imageIndex"":0},{""imageOffset"":7384,""imageIndex"":0},{""imageOffset"":66252326,""imageIndex"":16},{""imageOffset"":66009023,""imageIndex"":16},{""imageOffset"":66011756,""imageIndex"":16},{""imageOffset"":66010733,""imageIndex"":16},{""imageOffset"":66222344,""imageIndex"":16},{""imageOffset"":25825,""imageIndex"":17},{""imageOffset"":8043,""imageIndex"":17}]},{""id"":871751,""name"":""QFileInfoGatherer"",""frames"":[{""imageOffset"":17370,""imageIndex"":0},{""imageOffset"":2107627,""imageIndex"":8},{""imageOffset"":2107486,""imageIndex"":8},{""imageOffset"":4529677,""imageIndex"":20},{""imageOffset"":2066019,""imageIndex"":8},{""imageOffset"":25825,""imageIndex"":17},{""imageOffset"":8043,""imageIndex"":17}]},{""id"":872748,""name"":""ThreadPoolForegroundWorker"",""frames"":[{""imageOffset"":6506,""imageIndex"":0},{""imageOffset"":7384,""imageIndex"":0},{""imageOffset"":66252326,""imageIndex"":16},{""imageOffset"":66009023,""imageIndex"":16},{""imageOffset"":66011756,""imageIndex"":16},{""imageOffset"":66010733,""imageIndex"":16},{""imageOffset"":66222344,""imageIndex"":16},{""imageOffset"":25825,""imageIndex"":17},{""imageOffset"":8043,""imageIndex"":17}]},{""id"":872749,""name"":""ThreadPoolForegroundWorker"",""frames"":[{""imageOffset"":6506,""imageIndex"":0},{""imageOffset"":7384,""imageIndex"":0},{""imageOffset"":66252326,""imageIndex"":16},{""imageOffset"":66009023,""imageIndex"":16},{""imageOffset"":66011034,""imageIndex"":16},{""imageOffset"":66010733,""imageIndex"":16},{""imageOffset"":66222344,""imageIndex"":16},{""imageOffset"":25825,""imageIndex"":17},{""imageOffset"":8043,""imageIndex"":17}]},{""id"":872785,""name"":""ThreadPoolBackgroundWorker"",""frames"":[{""imageOffset"":6506,""imageIndex"":0},{""imageOffset"":7384,""imageIndex"":0},{""imageOffset"":66252326,""imageIndex"":16},{""imageOffset"":66009023,""imageIndex"":16},{""imageOffset"":66011034,""imageIndex"":16},{""imageOffset"":66010589,""imageIndex"":16},{""imageOffset"":66222344,""imageIndex"":16},{""imageOffset"":25825,""imageIndex"":17},{""imageOffset"":8043,""imageIndex"":17}]},{""id"":873069,""frames"":[{""imageOffset"":8008,""imageIndex"":17}]}], ""usedImages"" : [ { ""source"" : ""P"", ""arch"" : ""x86_64"", ""base"" : 140703562031104, ""size"" : 229376, ""uuid"" : ""576ecf56-10c7-35bf-a391-e35d4bd74309"", ""path"" : ""\/usr\/lib\/system\/libsystem_kernel.dylib"", ""name"" : ""libsystem_kernel.dylib"" }, { ""source"" : ""P"", ""arch"" : ""x86_64"", ""base"" : 140703561015296, ""size"" : 561152, ""uuid"" : ""e42e9d7a-03b4-340b-b61e-dcd45fd4acc0"", ""path"" : ""\/usr\/lib\/system\/libsystem_c.dylib"", ""name"" : ""libsystem_c.dylib"" }, { ""source"" : ""P"", ""arch"" : ""x86_64"", ""base"" : 4477501440, ""CFBundleShortVersionString"" : ""3.11.2, (c) 2001-2023 Python Software Foundation."", ""CFBundleIdentifier"" : ""org.python.python"", ""size"" : 4079616, ""uuid"" : ""24670b23-d78a-3eaa-bca8-22faf877f190"", ""path"" : ""\/Applications\/ChimeraX_Daily.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/Python"", ""name"" : ""Python"", ""CFBundleVersion"" : ""3.11.2"" }, { ""source"" : ""P"", ""arch"" : ""x86_64"", ""base"" : 140703562358784, ""size"" : 40960, ""uuid"" : ""a8a33774-6d44-35e9-ad2a-bad9e4d5192a"", ""path"" : ""\/usr\/lib\/system\/libsystem_platform.dylib"", ""name"" : ""libsystem_platform.dylib"" }, { ""size"" : 0, ""source"" : ""A"", ""base"" : 0, ""uuid"" : ""00000000-0000-0000-0000-000000000000"" }, { ""source"" : ""P"", ""arch"" : ""x86_64"", ""base"" : 4602535936, ""size"" : 98304, ""uuid"" : ""17a32d1b-857d-3264-9bf6-9192cca7beb2"", ""path"" : ""\/Applications\/ChimeraX_Daily.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/sip.cpython-311-darwin.so"", ""name"" : ""sip.cpython-311-darwin.so"" }, { ""source"" : ""P"", ""arch"" : ""x86_64"", ""base"" : 4772749312, ""size"" : 2801664, ""uuid"" : ""babd94e3-ec19-3110-ab5b-11c39432d8c5"", ""path"" : ""\/Applications\/ChimeraX_Daily.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/QtWidgets.abi3.so"", ""name"" : ""QtWidgets.abi3.so"" }, { ""source"" : ""P"", ""arch"" : ""x86_64"", ""base"" : 4725661696, ""size"" : 1589248, ""uuid"" : ""2be8100b-aa99-3117-95ff-0200ddc4032f"", ""path"" : ""\/Applications\/ChimeraX_Daily.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/QtCore.abi3.so"", ""name"" : ""QtCore.abi3.so"" }, { ""source"" : ""P"", ""arch"" : ""x86_64"", ""base"" : 4718125056, ""size"" : 5259264, ""uuid"" : ""35b47b1c-6952-3d39-a5e7-711f3ca228f2"", ""path"" : ""\/Applications\/ChimeraX_Daily.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/Qt6\/lib\/QtCore.framework\/Versions\/A\/QtCore"", ""name"" : ""QtCore"" }, { ""source"" : ""P"", ""arch"" : ""x86_64"", ""base"" : 4779106304, ""size"" : 4964352, ""uuid"" : ""f36760e5-d1e7-3a93-ae8c-1c3e55e3fc35"", ""path"" : ""\/Applications\/ChimeraX_Daily.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/Qt6\/lib\/QtWidgets.framework\/Versions\/A\/QtWidgets"", ""name"" : ""QtWidgets"" }, { ""source"" : ""P"", ""arch"" : ""x86_64"", ""base"" : 4797648896, ""size"" : 655360, ""uuid"" : ""4bf756eb-ff87-3f7f-8c98-b1eda6463b81"", ""path"" : ""\/Applications\/ChimeraX_Daily.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/Qt6\/plugins\/platforms\/libqcocoa.dylib"", ""name"" : ""libqcocoa.dylib"" }, { ""source"" : ""P"", ""arch"" : ""x86_64h"", ""base"" : 140703562575872, ""CFBundleShortVersionString"" : ""6.9"", ""CFBundleIdentifier"" : ""com.apple.CoreFoundation"", ""size"" : 5255168, ""uuid"" : ""ce1edd4b-def1-3c89-a96b-46f62682ba77"", ""path"" : ""\/System\/Library\/Frameworks\/CoreFoundation.framework\/Versions\/A\/CoreFoundation"", ""name"" : ""CoreFoundation"", ""CFBundleVersion"" : ""1866"" }, { ""source"" : ""P"", ""arch"" : ""x86_64"", ""base"" : 140703710420992, ""CFBundleShortVersionString"" : ""2.1.1"", ""CFBundleIdentifier"" : ""com.apple.HIToolbox"", ""size"" : 3096576, ""uuid"" : ""06fdecd6-9f69-397b-b1e2-a8226c0ba7ed"", ""path"" : ""\/System\/Library\/Frameworks\/Carbon.framework\/Versions\/A\/Frameworks\/HIToolbox.framework\/Versions\/A\/HIToolbox"", ""name"" : ""HIToolbox"" }, { ""source"" : ""P"", ""arch"" : ""x86_64"", ""base"" : 140703607111680, ""CFBundleShortVersionString"" : ""6.9"", ""CFBundleIdentifier"" : ""com.apple.AppKit"", ""size"" : 15269888, ""uuid"" : ""f02d178c-7914-3fc4-b9f4-9881945b3165"", ""path"" : ""\/System\/Library\/Frameworks\/AppKit.framework\/Versions\/C\/AppKit"", ""name"" : ""AppKit"", ""CFBundleVersion"" : ""2113.60.148"" }, { ""source"" : ""P"", ""arch"" : ""x86_64"", ""base"" : 4462080000, ""CFBundleShortVersionString"" : ""1.7.0"", ""CFBundleIdentifier"" : ""edu.ucsf.cgl.ChimeraX"", ""size"" : 16384, ""uuid"" : ""194a3167-3db5-3029-8d22-1d742b826bb9"", ""path"" : ""\/Applications\/ChimeraX_Daily.app\/Contents\/MacOS\/ChimeraX"", ""name"" : ""ChimeraX"", ""CFBundleVersion"" : ""1.7.0.0"" }, { ""source"" : ""P"", ""arch"" : ""x86_64"", ""base"" : 4648296448, ""size"" : 442368, ""uuid"" : ""6376ba16-20f7-3c31-a5c5-a10648ae7b56"", ""path"" : ""\/usr\/lib\/dyld"", ""name"" : ""dyld"" }, { ""source"" : ""P"", ""arch"" : ""x86_64"", ""base"" : 5117353984, ""size"" : 165052416, ""uuid"" : ""4aa1de3e-464c-340c-ab61-bcd39bfc7658"", ""path"" : ""\/Applications\/ChimeraX_Daily.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/Qt6\/lib\/QtWebEngineCore.framework\/Versions\/A\/QtWebEngineCore"", ""name"" : ""QtWebEngineCore"" }, { ""source"" : ""P"", ""arch"" : ""x86_64"", ""base"" : 140703562260480, ""size"" : 49152, ""uuid"" : ""1239689d-21c9-36ce-96ba-be0ef8ee02e4"", ""path"" : ""\/usr\/lib\/system\/libsystem_pthread.dylib"", ""name"" : ""libsystem_pthread.dylib"" }, { ""source"" : ""P"", ""arch"" : ""x86_64"", ""base"" : 4840493056, ""size"" : 16384, ""uuid"" : ""e81a2322-9755-3b07-b226-bdaa988e1f3b"", ""path"" : ""\/Applications\/ChimeraX_Daily.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/lib-dynload\/_queue.cpython-311-darwin.so"", ""name"" : ""_queue.cpython-311-darwin.so"" }, { ""source"" : ""P"", ""arch"" : ""x86_64"", ""base"" : 4649050112, ""size"" : 64094208, ""uuid"" : ""9d768904-ac4b-327d-8126-cec11a08b966"", ""path"" : ""\/Applications\/ChimeraX_Daily.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/numpy\/.dylibs\/libopenblas64_.0.dylib"", ""name"" : ""libopenblas64_.0.dylib"" }, { ""source"" : ""P"", ""arch"" : ""x86_64"", ""base"" : 4759781376, ""size"" : 6979584, ""uuid"" : ""49d915f7-1c6d-3bbd-b96f-064260e7d998"", ""path"" : ""\/Applications\/ChimeraX_Daily.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/Qt6\/lib\/QtGui.framework\/Versions\/A\/QtGui"", ""name"" : ""QtGui"" } ], ""sharedCache"" : { ""base"" : 140703559004160, ""size"" : 19331678208, ""uuid"" : ""e0be2d6e-28ef-33ab-8499-8d9d42337be7"" }, ""vmSummary"" : ""ReadOnly portion of Libraries: Total=1.5G resident=0K(0%) swapped_out_or_unallocated=1.5G(100%)\nWritable regions: Total=6.2G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=6.2G(100%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 1536K 12 \nActivity Tracing 256K 1 \nCG backing stores 5280K 12 \nCG image 1112K 79 \nColorSync 232K 28 \nCoreAnimation 5176K 155 \nCoreGraphics 24K 5 \nCoreImage 28K 7 \nCoreServices 624K 2 \nCoreUI image data 5340K 55 \nFoundation 32K 2 \nKernel Alloc Once 8K 1 \nMALLOC 5.6G 2461 \nMALLOC guard page 32K 8 \nMALLOC_LARGE (reserved) 384K 1 reserved VM address space (unallocated)\nMach message 24K 4 \nOpenGL GLSL 384K 4 \nSTACK GUARD 144K 36 \nStack 339.3M 37 \nStack Guard 56.0M 1 \nVM_ALLOCATE 298.9M 268 \n__CTF 756 1 \n__DATA 47.0M 700 \n__DATA_CONST 32.9M 352 \n__DATA_DIRTY 1664K 220 \n__FONT_DATA 4K 1 \n__GLSLBUILTINS 5176K 1 \n__LINKEDIT 678.3M 165 \n__TEXT 820.1M 699 \n__UNICODE 592K 1 \ndyld private memory 1184K 3 \nmapped file 233.1M 61 \nshared memory 3524K 31 \n=========== ======= ======= \nTOTAL 8.1G 5414 \nTOTAL, minus reserved VM space 8.1G 5414 \n"", ""legacyInfo"" : { ""threadTriggered"" : { ""name"" : ""CrBrowserMain"" } }, ""trialInfo"" : { ""rollouts"" : [ { ""rolloutId"" : ""63582c5f8a53461413999550"", ""factorPackIds"" : { }, ""deploymentId"" : 240000002 }, { ""rolloutId"" : ""5fb4245a1bbfe8005e33a1e1"", ""factorPackIds"" : { }, ""deploymentId"" : 240000021 } ], ""experiments"" : [ { ""treatmentId"" : ""8ca8349c-e2bc-482c-9ca7-3907b48a5341"", ""experimentId"" : ""648b5a581b04c12d4127bbb6"", ""deploymentId"" : 400000002 } ] } } ===== Log before crash start ===== UCSF ChimeraX version: 1.7.dev202307312254 (2023-07-31) © 2016-2023 Regents of the University of California. All rights reserved. > open ""/Users/elizabethmcfadden/Library/CloudStorage/Box-Box/McLellan > Lab/Share/files-from-eliza/CCHFV M segment tetramer TULV fit.cxs"" Opened emd_11236.map as #4, grid size 108,108,108, pixel 4, shown at level 1.64, step 1, values float32 Log from Sun Feb 19 21:51:52 2023 > set bgColor white > cd Current working directory is: /Users/elizabethmcfadden > cd Desktop Current working directory is: /Users/elizabethmcfadden/Desktop UCSF ChimeraX version: 1.4 (2022-06-03) © 2016-2022 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /Users/elizabethmcfadden/Desktop/GP38Gnfull_refine_1-coot-0.pdb Chain information for GP38Gnfull_refine_1-coot-0.pdb #1 --- Chain | Description A C | No description available B | No description available D | No description available > open > /Users/elizabethmcfadden/Desktop/GP38Gn_AlphaFold_AlignedToPhaser11-coot-3.pdb Chain information for GP38Gn_AlphaFold_AlignedToPhaser11-coot-3.pdb #2 --- Chain | Description A | No description available B | No description available C | No description available D | No description available > open /Users/elizabethmcfadden/Desktop/GP38Gnfull_refine_1-coot-0.pdb Chain information for GP38Gnfull_refine_1-coot-0.pdb #3 --- Chain | Description A C | No description available B | No description available D | No description available > hide #!3 models > hide #!2 models > show #!2 models > select #3/C:254-510 1823 atoms, 1857 bonds, 4 pseudobonds, 227 residues, 2 models selected > select #3/C:254-510 1823 atoms, 1857 bonds, 4 pseudobonds, 227 residues, 2 models selected > select add #3 4256 atoms, 4330 bonds, 9 pseudobonds, 536 residues, 2 models selected > select subtract #3 Nothing selected > select /C:254-510 5469 atoms, 5567 bonds, 12 pseudobonds, 681 residues, 6 models selected > select /C:254-510 5469 atoms, 5567 bonds, 12 pseudobonds, 681 residues, 6 models selected > select /A:254-510 5575 atoms, 5678 bonds, 9 pseudobonds, 693 residues, 6 models selected > select /B:540-587 964 atoms, 972 bonds, 2 pseudobonds, 128 residues, 5 models selected > select /D:540-580 856 atoms, 864 bonds, 1 pseudobond, 116 residues, 4 models selected > color sel orange > select /D:540-580 856 atoms, 864 bonds, 1 pseudobond, 116 residues, 4 models selected > select /D:540-580 856 atoms, 864 bonds, 1 pseudobond, 116 residues, 4 models selected > select /D:540-580 856 atoms, 864 bonds, 1 pseudobond, 116 residues, 4 models selected > select /C:254-510 5469 atoms, 5567 bonds, 12 pseudobonds, 681 residues, 6 models selected > color sel blue > dssp > hide #!1 models > show #!1 models > hide #!1 models > select add #2 8074 atoms, 8211 bonds, 14 pseudobonds, 1009 residues, 6 models selected > select add #3 10507 atoms, 10684 bonds, 19 pseudobonds, 1318 residues, 6 models selected > select subtract #2 6079 atoms, 6187 bonds, 13 pseudobonds, 763 residues, 4 models selected > select subtract #3 1823 atoms, 1857 bonds, 4 pseudobonds, 227 residues, 2 models selected > select add #1 4256 atoms, 4330 bonds, 9 pseudobonds, 536 residues, 2 models selected > select subtract #1 Nothing selected > show #!1 models > hide #!1 models > hide #!2 models > show #!1 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > color #2 #00fdff transparency 0 > show #!2 models > hide #!2 models > show #!2 models > open /Users/elizabethmcfadden/Desktop/EM27_correctNumbering.pdb Chain information for EM27_correctNumbering.pdb #4 --- Chain | Description A | No description available B | No description available > ui mousemode right select Drag select of 24 residues > mmaker #4 to sele > matchmaker #4 to sele Invalid ""to"" argument: invalid atoms specifier > mmaker #4 to sel Specify a single 'to' model only > select add #2 4519 atoms, 4497 bonds, 6 pseudobonds, 567 residues, 3 models selected > select subtract #2 91 atoms, 12 residues, 1 model selected > mmaker #4 to sel Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker GP38Gnfull_refine_1-coot-0.pdb, chain C (#1) with EM27_correctNumbering.pdb, chain A (#4), sequence alignment score = 40.1 RMSD between 10 pruned atom pairs is 0.786 angstroms; (across all 10 pairs: 0.786) > mmaker #4 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker GP38Gnfull_refine_1-coot-0.pdb, chain A (#1) with EM27_correctNumbering.pdb, chain A (#4), sequence alignment score = 1039.7 RMSD between 224 pruned atom pairs is 0.564 angstroms; (across all 227 pairs: 0.803) > mmaker #4 to #1/A Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker GP38Gnfull_refine_1-coot-0.pdb, chain A (#1) with EM27_correctNumbering.pdb, chain A (#4), sequence alignment score = 1039.7 RMSD between 224 pruned atom pairs is 0.564 angstroms; (across all 227 pairs: 0.803) > mmaker #4 to #1/C Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker GP38Gnfull_refine_1-coot-0.pdb, chain C (#1) with EM27_correctNumbering.pdb, chain A (#4), sequence alignment score = 1037.9 RMSD between 224 pruned atom pairs is 0.683 angstroms; (across all 227 pairs: 0.895) > select clear > hide #!2 models > hide #4 models > show #4 models > dssp [Repeated 1 time(s)] > color #4 #90ee9055 > color #4 #90ee9093 > color #4 #90ee90d0 > color #4 #90ee90d1 > graphics silhouettes true > select clear > ui mousemode right zoom > dssp > ui tool show ""Side View"" > graphics silhouettes false > graphics silhouettes true > save /Users/elizabethmcfadden/Desktop/image34.png supersample 3 > save /Users/elizabethmcfadden/Desktop/image35.png supersample 3 > show #!3 models > hide #!1 models > select #3/A:254-510 1823 atoms, 1857 bonds, 4 pseudobonds, 227 residues, 2 models selected > select #3/C:254-510 1823 atoms, 1857 bonds, 4 pseudobonds, 227 residues, 2 models selected > select #3/A:254-510 1823 atoms, 1857 bonds, 4 pseudobonds, 227 residues, 2 models selected > delete sel > select #3/B:540-587 309 atoms, 311 bonds, 1 pseudobond, 41 residues, 2 models selected > delete sel > hide #4 models > hide #!3 models > show #!3 models > show #!1 models > dssp > close #1 > show #!2 models Populating font family aliases took 362 ms. Replace uses of missing font family "".AppleSystemUIFont"" with one that exists to avoid this cost. > save /Users/elizabethmcfadden/Desktop/EM27it2monomer.pdb models #3 relModel > #2 > open /Users/elizabethmcfadden/Desktop/EM27it2monomer.pdb Chain information for EM27it2monomer.pdb #1 --- Chain | Description C | No description available D | No description available > hide #!3 models > show #!3 models > hide #!2 models > show #!2 models > close > open 6zjm format mmcif fromDatabase pdb 6zjm title: Atomic model of Andes virus glycoprotein spike tetramer generated by fitting into a Tula virus reconstruction [more info...] Chain information for 6zjm #1 --- Chain | Description A B C D E F G H | Envelope polyprotein,Envelope polyprotein,Envelope polyprotein,Envelope polyprotein,Envelope polyprotein,Envelope polyprotein,Envelope polyprotein,Envelope polyprotein,Envelope polyprotein Non-standard residues in 6zjm #1 --- BMA — beta-D-mannopyranose (beta-D-mannose; D-mannose; mannose) MAN — alpha-D-mannopyranose (alpha-D-mannose; D-mannose; mannose) NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine; 2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose; 2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE) > hide atoms > show cartoons > open /Users/elizabethmcfadden/Library/CloudStorage/Box- > Box/ElizabethMcFadden/CCHFV/AlphaFold/CCHFV_Aug22_ElizaModel.pdb Chain information for CCHFV_Aug22_ElizaModel.pdb #2 --- Chain | Description A | No description available B | No description available C | No description available D | No description available > select add #2 11282 atoms, 11507 bonds, 1437 residues, 1 model selected > ui mousemode right ""rotate selected models"" > ui mousemode right ""translate selected models"" > view matrix models #2,1,0,0,115.68,0,1,0,-34.596,0,0,1,159.72 > ui mousemode right zoom > ui mousemode right ""rotate selected models"" > view matrix models > #2,0.30114,-0.49083,0.81756,112.65,0.19651,0.8709,0.45047,-32.321,-0.93311,0.025007,0.35872,152.05 > view matrix models > #2,-0.86543,-0.29409,-0.40563,102.17,-0.49151,0.65539,0.57348,-36.733,0.097192,0.69568,-0.71174,156.8 > view matrix models > #2,-0.89707,-0.43795,-0.058809,102.68,-0.36098,0.64954,0.66917,-35.647,-0.25486,0.62152,-0.74078,154.35 > view matrix models > #2,-0.77677,-0.19694,-0.5982,102.37,-0.55132,0.67177,0.49474,-37.303,0.30442,0.7141,-0.63039,158.38 > view matrix models > #2,-0.0085282,-0.83876,-0.54444,96.763,-0.99949,0.023868,-0.021114,-51.464,0.030704,0.54398,-0.83854,153.58 > select #2/B:520-842 2508 atoms, 2551 bonds, 323 residues, 1 model selected > select #2/D:1041-1684 5077 atoms, 5194 bonds, 644 residues, 1 model selected > select #2/C:843-1040 1535 atoms, 1561 bonds, 198 residues, 1 model selected > delete sel > ui mousemode right select Drag select of 218 residues > delete sel > select #2/A:248-519 2162 atoms, 2201 bonds, 272 residues, 1 model selected > color sel blue > select #2/B:520-842 1453 atoms, 1473 bonds, 1 pseudobond, 192 residues, 2 models selected > color sel orange > select #2/D:1041-1684 4335 atoms, 4434 bonds, 1 pseudobond, 557 residues, 2 models selected > color sel yellow > color sel goldenrod > select #2/B:520-842 1453 atoms, 1473 bonds, 1 pseudobond, 192 residues, 2 models selected > select #2/D:1041-1684 4335 atoms, 4434 bonds, 1 pseudobond, 557 residues, 2 models selected > color sel medium sea green > select #2/A:248-519 2162 atoms, 2201 bonds, 272 residues, 1 model selected > color sel dodger blue > color sel royal blue Drag select of 1020 residues, 2 pseudobonds > ui mousemode right ""translate selected models"" > view matrix models > #2,-0.0085282,-0.83876,-0.54444,137.63,-0.99949,0.023868,-0.021114,-14.862,0.030704,0.54398,-0.83854,184.41 > view matrix models > #2,-0.0085282,-0.83876,-0.54444,167.53,-0.99949,0.023868,-0.021114,63.017,0.030704,0.54398,-0.83854,194.07 > view matrix models > #2,-0.0085282,-0.83876,-0.54444,180.6,-0.99949,0.023868,-0.021114,78.583,0.030704,0.54398,-0.83854,207.82 > ui mousemode right ""rotate selected models"" > view matrix models > #2,0.71271,-0.41142,-0.56814,172.98,-0.09767,0.74385,-0.66117,53.529,0.69463,0.52671,0.48996,235.12 > view matrix models > #2,-0.060633,-0.98434,-0.16555,190.74,-0.80673,-0.049346,0.58886,92.21,-0.58781,0.16926,-0.7911,215.05 > view matrix models > #2,-0.83715,-0.54696,0.0032139,182.98,-0.3557,0.54887,0.75645,84.022,-0.41551,0.63212,-0.65404,208.43 > view matrix models > #2,0.16345,-0.9831,0.0824,195.99,-0.98414,-0.15665,0.083229,84.373,-0.068915,-0.094698,-0.99312,217.94 > view matrix models > #2,-0.23013,-0.55249,0.80112,199.78,-0.78164,-0.38546,-0.49037,78.684,0.57972,-0.73904,-0.34314,245.33 > view matrix models > #2,-0.39571,-0.72166,0.568,198.46,-0.7277,-0.1309,-0.67329,70.017,0.56024,-0.67976,-0.47335,241.56 > ui mousemode right ""translate selected models"" > view matrix models > #2,-0.39571,-0.72166,0.568,215.15,-0.7277,-0.1309,-0.67329,86.414,0.56024,-0.67976,-0.47335,222.39 > ui mousemode right ""rotate selected models"" > view matrix models > #2,-0.69968,0.27424,-0.65972,170.24,-0.22935,0.7883,0.57094,92.191,0.67664,0.55079,-0.48866,196.73 > ui mousemode right ""translate selected models"" > view matrix models > #2,-0.69968,0.27424,-0.65972,214.31,-0.22935,0.7883,0.57094,125.48,0.67664,0.55079,-0.48866,194 > view matrix models > #2,-0.69968,0.27424,-0.65972,216.97,-0.22935,0.7883,0.57094,214.37,0.67664,0.55079,-0.48866,175 > ui mousemode right ""rotate selected models"" > view matrix models > #2,-0.44709,-0.15111,-0.88163,222.2,-0.73522,0.62346,0.26598,210.77,0.50947,0.76711,-0.38984,171.97 > ui mousemode right ""translate selected models"" > view matrix models > #2,-0.44709,-0.15111,-0.88163,175.21,-0.73522,0.62346,0.26598,180.76,0.50947,0.76711,-0.38984,195.27 > view matrix models > #2,-0.44709,-0.15111,-0.88163,170.43,-0.73522,0.62346,0.26598,199.18,0.50947,0.76711,-0.38984,201.33 > hide #!2 models > show #!2 models > select add #2 7950 atoms, 8108 bonds, 2 pseudobonds, 1021 residues, 2 models selected > select subtract #2 Nothing selected > hide #!1 models > show #!1 models > select add #2 7950 atoms, 8108 bonds, 2 pseudobonds, 1021 residues, 2 models selected > view matrix models > #2,-0.44709,-0.15111,-0.88163,172.6,-0.73522,0.62346,0.26598,194.57,0.50947,0.76711,-0.38984,202.43 > ui mousemode right ""rotate selected models"" > view matrix models > #2,-0.067165,-0.13241,-0.98892,171.07,-0.8998,0.43628,0.0026977,193.05,0.43109,0.89001,-0.14844,204.29 > view matrix models > #2,0.091317,-0.42727,-0.8995,179.3,-0.97515,0.14473,-0.16775,195.7,0.20186,0.89247,-0.40343,198.82 > ui mousemode right ""translate selected models"" > view matrix models > #2,0.091317,-0.42727,-0.8995,190,-0.97515,0.14473,-0.16775,198.39,0.20186,0.89247,-0.40343,191.73 > view matrix models > #2,0.091317,-0.42727,-0.8995,191.1,-0.97515,0.14473,-0.16775,197.6,0.20186,0.89247,-0.40343,193.32 > view matrix models > #2,0.091317,-0.42727,-0.8995,189.29,-0.97515,0.14473,-0.16775,200.79,0.20186,0.89247,-0.40343,187.09 > ui mousemode right ""rotate selected models"" > view matrix models > #2,0.68009,-0.6946,0.23453,217.91,-0.72868,-0.67562,0.11209,223.82,0.0806,-0.24713,-0.96562,199.83 > view matrix models > #2,0.78079,-0.61492,0.11065,214.12,-0.60151,-0.7877,-0.13308,221.79,0.16899,0.03735,-0.98491,193.74 > flip #2 Unknown command: flip #2 > view matrix models > #2,0.10065,-0.71405,-0.69282,199.23,-0.87598,0.26657,-0.402,194.02,0.47173,0.64735,-0.59867,189.12 > view matrix models > #2,0.78984,-0.4888,0.37045,216.47,-0.61271,-0.60207,0.51196,230.2,-0.027207,-0.63134,-0.77503,211.21 > view matrix models > #2,0.90299,-0.40033,0.15603,210.81,-0.42754,-0.80122,0.41864,233.01,-0.042579,-0.44474,-0.89465,205 > view matrix models > #2,0.92504,-0.3376,0.17414,209.9,-0.37793,-0.86421,0.33214,232.79,0.038364,-0.37306,-0.92701,203.09 > select subtract #2 Nothing selected > hide #!2 models > open ""/Users/elizabethmcfadden/Library/CloudStorage/Box- > Box/ElizabethMcFadden/CCHFV/AlphaFold/CCHFV M segment AF pred.pse"" Unrecognized file suffix '.pse' > open ""/Users/elizabethmcfadden/Library/CloudStorage/Box- > Box/ElizabethMcFadden/CCHFV/AlphaFold/CCHFV M segment AF pred.pse"" Unrecognized file suffix '.pse' > show #!2 models > close #2 > open ""/Users/elizabethmcfadden/Library/CloudStorage/Box- > Box/ElizabethMcFadden/CCHFV/AlphaFold/AF M seg model initial.pdb"" Chain information for AF M seg model initial.pdb #2 --- Chain | Description A | No description available B | No description available C | No description available D | No description available > mmaker #2 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 6zjm, chain B (#1) with AF M seg model initial.pdb, chain D (#2), sequence alignment score = 286.9 RMSD between 52 pruned atom pairs is 1.304 angstroms; (across all 405 pairs: 19.945) > select add #2 11282 atoms, 11507 bonds, 1437 residues, 1 model selected > ui mousemode right ""translate selected models"" > view matrix models > #2,0.47686,0.60826,0.63452,187.32,0.84648,-0.12333,-0.51793,296.69,-0.23679,0.7841,-0.57369,131.42 > ui mousemode right ""rotate selected models"" > view matrix models > #2,0.07123,0.22145,0.97257,187.83,0.11033,-0.97081,0.21296,298.82,0.99134,0.092135,-0.093584,145.33 > view matrix models > #2,0.020492,0.78522,-0.61887,163.04,0.47508,0.53701,0.69708,318.67,0.8797,-0.3083,-0.36204,137.51 > ui mousemode right zoom > open ""/Users/elizabethmcfadden/Library/CloudStorage/Box- > Box/ElizabethMcFadden/CCHFV/AlphaFold/AF M seg model initial.pdb"" Chain information for AF M seg model initial.pdb #3 --- Chain | Description A | No description available B | No description available C | No description available D | No description available > select subtract #2 Nothing selected > mmaker #3 to #2 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker AF M seg model initial.pdb, chain D (#2) with AF M seg model initial.pdb, chain D (#3), sequence alignment score = 3423.3 RMSD between 644 pruned atom pairs is 0.000 angstroms; (across all 644 pairs: 0.000) > ui mousemode right ""rotate selected models"" > select add #3 11282 atoms, 11507 bonds, 1437 residues, 1 model selected > view matrix models > #3,-0.28734,-0.53932,-0.79156,150.09,0.39336,0.68706,-0.61091,296.19,0.87333,-0.48691,0.014719,142.98 > ui mousemode right ""translate selected models"" > view matrix models > #3,-0.28734,-0.53932,-0.79156,74.9,0.39336,0.68706,-0.61091,283.19,0.87333,-0.48691,0.014719,139.62 > view matrix models > #3,-0.28734,-0.53932,-0.79156,103.7,0.39336,0.68706,-0.61091,314.72,0.87333,-0.48691,0.014719,126.45 > view matrix models > #3,-0.28734,-0.53932,-0.79156,129.35,0.39336,0.68706,-0.61091,308.16,0.87333,-0.48691,0.014719,123.61 > view matrix models > #3,-0.28734,-0.53932,-0.79156,131.93,0.39336,0.68706,-0.61091,293.65,0.87333,-0.48691,0.014719,126.9 > ui mousemode right ""rotate selected models"" > view matrix models > #3,-0.15095,-0.7247,-0.67233,134,0.30497,0.6128,-0.72902,290.49,0.94032,-0.31508,0.12851,130.37 > view matrix models > #3,-0.053988,-0.61284,-0.78836,133.38,0.31013,0.74018,-0.59662,293.56,0.94916,-0.27671,0.1501,131.04 > view matrix models > #3,0.11395,-0.84014,-0.53026,137.86,0.35969,0.53241,-0.76626,289.81,0.92609,-0.10342,0.36285,135.54 > view matrix models > #3,0.010109,-0.90921,-0.41621,138.64,0.80592,0.25381,-0.53486,295.7,0.59194,-0.33003,0.73532,138.12 > view matrix models > #3,-0.1629,-0.62182,-0.76603,132.87,0.77204,0.40309,-0.49139,297.04,0.61434,-0.67146,0.41441,130.77 > view matrix models > #3,-0.23888,-0.44633,-0.86239,131.61,0.79381,0.42175,-0.43816,298.24,0.55928,-0.78925,0.25355,126.88 > view matrix models > #3,-0.32558,-0.38467,-0.86373,131.27,0.64578,0.57678,-0.50029,296.9,0.69063,-0.72066,0.060621,124.94 > ui mousemode right ""translate selected models"" > view matrix models > #3,-0.32558,-0.38467,-0.86373,134.7,0.64578,0.57678,-0.50029,299.8,0.69063,-0.72066,0.060621,140.25 > view matrix models > #3,-0.32558,-0.38467,-0.86373,136.23,0.64578,0.57678,-0.50029,292.67,0.69063,-0.72066,0.060621,146.39 > ui mousemode right ""rotate selected models"" > view matrix models > #3,-0.22363,-0.45994,-0.85933,136.66,0.724,0.51189,-0.46238,293.56,0.65255,-0.72556,0.21852,148.8 > open /Users/elizabethmcfadden/Downloads/emd_11236.map Opened emd_11236.map as #4, grid size 108,108,108, pixel 4, shown at level 3.17, step 1, values float32 > view matrix models > #3,-0.40512,-0.26166,0.87602,166.5,0.62429,-0.77918,0.055968,294.41,0.66794,0.56957,0.47901,160.84 > undo > ui mousemode right zoom > surface dust #4 size 40 > volume #4 level 1.643 > hide #!4 models > hide #!1 models > show #!4 models > hide #!4 models > show #!1 models > show #!4 models > vop flip #4 Opened emd_11236.map z flip as #5, grid size 108,108,108, pixel 4, shown at step 1, values float32 > hide #!5 models > hide #!1 models > ui mousemode right select Drag select of 572 residues > select clear Drag select of 602 residues > delete sel > show #!5 models > color #3 #dda0dd72 > color #3 #dda0dd73 > ui mousemode right zoom > color #5 #b2b2b29a models > color #5 #b2b2b299 models > graphics silhouettes false > select add #3 9086 atoms, 9270 bonds, 3 pseudobonds, 1162 residues, 2 models selected > ui mousemode right ""translate selected models"" > view matrix models > #3,-0.22363,-0.45994,-0.85933,172.94,0.724,0.51189,-0.46238,207.46,0.65255,-0.72556,0.21852,161.8 > ui mousemode right ""rotate selected models"" > view matrix models > #3,0.3421,-0.0060564,0.93964,175.9,0.6365,0.73712,-0.22698,208.33,-0.69126,0.67573,0.25602,165.89 > ui mousemode right ""translate selected models"" > view matrix models > #3,0.3421,-0.0060564,0.93964,175.43,0.6365,0.73712,-0.22698,178.42,-0.69126,0.67573,0.25602,180.9 > view matrix models > #3,0.3421,-0.0060564,0.93964,169.64,0.6365,0.73712,-0.22698,178.41,-0.69126,0.67573,0.25602,190.05 > view matrix models > #3,0.3421,-0.0060564,0.93964,184.75,0.6365,0.73712,-0.22698,196.55,-0.69126,0.67573,0.25602,196.4 > view matrix models > #3,0.3421,-0.0060564,0.93964,161.32,0.6365,0.73712,-0.22698,237.17,-0.69126,0.67573,0.25602,198.1 > ui mousemode right ""rotate selected models"" > view matrix models > #3,0.43326,-0.9007,-0.031923,158.74,0.15157,0.037902,0.98772,243.29,-0.88843,-0.43278,0.15294,199.43 > ui mousemode right ""translate selected models"" > view matrix models > #3,0.43326,-0.9007,-0.031923,165.9,0.15157,0.037902,0.98772,200.66,-0.88843,-0.43278,0.15294,200.63 > view matrix models > #3,0.43326,-0.9007,-0.031923,177.42,0.15157,0.037902,0.98772,185.59,-0.88843,-0.43278,0.15294,194.02 > view matrix models > #3,0.43326,-0.9007,-0.031923,191.81,0.15157,0.037902,0.98772,183.63,-0.88843,-0.43278,0.15294,197.45 > ui tool show ""Fit in Map"" > fitmap #3 inMap #4 Fit molecule AF M seg model initial.pdb (#3) to map emd_11236.map (#4) using 9086 atoms average map value = 1.916, steps = 84 shifted from previous position = 26.4 rotated from previous position = 18.5 degrees atoms outside contour = 3660, contour level = 1.6431 Position of AF M seg model initial.pdb (#3) relative to emd_11236.map (#4) coordinates: Matrix rotation and translation 0.36084992 -0.92764312 -0.09625775 203.34198068 0.45013327 0.08284089 0.88911046 166.87170247 -0.81680314 -0.36416426 0.44745616 214.67931818 Axis -0.62756756 0.36080749 0.68991080 Axis point 104.77130314 201.61490720 0.00000000 Rotation angle (degrees) 93.11995119 Shift along axis 80.70731005 > hide #!5 models > ui mousemode right select Drag select of 111 residues, 3 pseudobonds > delete sel Drag select of 79 residues, 5 pseudobonds > delete sel Drag select of 1 pseudobonds > delete sel > fitmap #3 inMap #4 Fit molecule AF M seg model initial.pdb (#3) to map emd_11236.map (#4) using 7578 atoms average map value = 1.991, steps = 68 shifted from previous position = 3.12 rotated from previous position = 4.39 degrees atoms outside contour = 2972, contour level = 1.6431 Position of AF M seg model initial.pdb (#3) relative to emd_11236.map (#4) coordinates: Matrix rotation and translation 0.36124293 -0.91754498 -0.16617681 203.05397038 0.49568484 0.03801008 0.86767030 163.75988984 -0.78981015 -0.39581109 0.46854402 214.65670452 Axis -0.63312541 0.31250014 0.70816374 Axis point 104.67727465 199.92457420 0.00000000 Rotation angle (degrees) 93.79009988 Shift along axis 74.62845463 > show #!5 models > select add #3 7578 atoms, 7722 bonds, 6 pseudobonds, 972 residues, 2 models selected > ui mousemode right ""translate selected models"" > view matrix models > #3,0.36124,-0.91754,-0.16618,200.57,0.49568,0.03801,0.86767,199.62,-0.78981,-0.39581,0.46854,222.69 > fitmap #3 inMap #4 Fit molecule AF M seg model initial.pdb (#3) to map emd_11236.map (#4) using 7578 atoms average map value = 1.991, steps = 104 shifted from previous position = 36.8 rotated from previous position = 0.0292 degrees atoms outside contour = 2972, contour level = 1.6431 Position of AF M seg model initial.pdb (#3) relative to emd_11236.map (#4) coordinates: Matrix rotation and translation 0.36147325 -0.91746007 -0.16614478 203.06189213 0.49527979 0.03796651 0.86790349 163.77335921 -0.78995887 -0.39601205 0.46812331 214.63244902 Axis -0.63334787 0.31259314 0.70792372 Axis point 104.69122698 199.91772792 0.00000000 Rotation angle (degrees) 93.79681679 Shift along axis 74.52901341 > ui mousemode right zoom > ui mousemode right ""rotate selected models"" > view matrix models > #3,0.56654,-0.79479,-0.21758,200.36,0.14878,-0.16105,0.97567,168.26,-0.81049,-0.58513,0.027009,216.62 > ui mousemode right ""translate selected models"" > view matrix models > #3,0.56654,-0.79479,-0.21758,185.78,0.14878,-0.16105,0.97567,192.42,-0.81049,-0.58513,0.027009,215.96 > ui mousemode right ""rotate selected models"" > view matrix models > #3,0.32845,-0.94375,0.038147,188.23,0.032007,0.051486,0.99816,193.75,-0.94398,-0.32663,0.047117,217.49 > ui mousemode right ""translate selected models"" > view matrix models > #3,0.32845,-0.94375,0.038147,201.68,0.032007,0.051486,0.99816,188.72,-0.94398,-0.32663,0.047117,215.39 > ui mousemode right ""rotate selected models"" > view matrix models > #3,0.49468,-0.82357,0.27753,198.48,0.080972,0.36163,0.9288,188.05,-0.86529,-0.43699,0.24558,213.71 > view matrix models > #3,0.14262,-0.95766,0.2501,203.46,0.077275,0.26269,0.96178,188.06,-0.98676,-0.11784,0.11147,215.57 > ui mousemode right ""translate selected models"" > view matrix models > #3,0.14262,-0.95766,0.2501,230.8,0.077275,0.26269,0.96178,181.14,-0.98676,-0.11784,0.11147,221.66 > fitmap #3 inMap #4 Fit molecule AF M seg model initial.pdb (#3) to map emd_11236.map (#4) using 7578 atoms average map value = 2.117, steps = 128 shifted from previous position = 16.6 rotated from previous position = 28.5 degrees atoms outside contour = 2838, contour level = 1.6431 Position of AF M seg model initial.pdb (#3) relative to emd_11236.map (#4) coordinates: Matrix rotation and translation 0.06182642 -0.99808666 -0.00070650 250.38182354 -0.30960574 -0.01985144 0.95065777 187.03044887 -0.94885287 -0.05855703 -0.31024070 226.81587135 Axis -0.65260175 0.61311227 0.44520141 Axis point 0.00000000 284.92452176 142.62253832 Rotation angle (degrees) 129.35570039 Shift along axis 52.24979266 > view matrix models > #3,0.061826,-0.99809,-0.0007065,252.13,-0.30961,-0.019851,0.95066,185.32,-0.94885,-0.058557,-0.31024,228.01 > ui mousemode right ""rotate selected models"" > view matrix models > #3,0.35847,-0.81577,0.4539,246.36,-0.70876,0.078634,0.70106,191.53,-0.60759,-0.57301,-0.54999,224.64 > ui mousemode right ""translate selected models"" > view matrix models > #3,0.35847,-0.81577,0.4539,226.23,-0.70876,0.078634,0.70106,196.54,-0.60759,-0.57301,-0.54999,210.89 > fitmap #3 inMap #4 Fit molecule AF M seg model initial.pdb (#3) to map emd_11236.map (#4) using 7578 atoms average map value = 1.723, steps = 84 shifted from previous position = 23.2 rotated from previous position = 15.5 degrees atoms outside contour = 3099, contour level = 1.6431 Position of AF M seg model initial.pdb (#3) relative to emd_11236.map (#4) coordinates: Matrix rotation and translation 0.17864953 -0.91878647 0.35201669 218.55785109 -0.80785039 0.06725917 0.58553731 179.45899738 -0.56166012 -0.38898278 -0.73022619 203.98725765 Axis -0.72701060 0.68162034 0.08276044 Axis point 0.00000000 246.58833754 63.40101698 Rotation angle (degrees) 137.91563434 Shift along axis -19.68889648 > view matrix models > #3,0.17865,-0.91879,0.35202,202.36,-0.80785,0.067259,0.58554,224.16,-0.56166,-0.38898,-0.73023,204.33 > fitmap #3 inMap #5 Fit molecule AF M seg model initial.pdb (#3) to map emd_11236.map z flip (#5) using 7578 atoms average map value = 2.023, steps = 252 shifted from previous position = 27.6 rotated from previous position = 59.9 degrees atoms outside contour = 2994, contour level = 1.6431 Position of AF M seg model initial.pdb (#3) relative to emd_11236.map z flip (#5) coordinates: Matrix rotation and translation 0.75460980 -0.15649053 0.63723995 187.40333445 -0.65614835 -0.17140880 0.73490703 194.83073178 -0.00577746 -0.97269200 -0.23202777 194.69232327 Axis -0.90261721 0.33989160 -0.26411338 Axis point 0.00000000 193.59830832 -27.90999850 Rotation angle (degrees) 108.93003920 Shift along axis -154.35299139 > ui mousemode right ""rotate selected models"" > view matrix models > #3,0.43718,-0.88408,0.16515,193.96,-0.45398,-0.05841,0.88909,191.45,-0.77639,-0.46367,-0.42689,205.42 > view matrix models > #3,0.49284,-0.81627,0.30134,192.67,-0.19127,0.23621,0.95269,187.43,-0.84883,-0.52717,-0.039715,205.1 > ui mousemode right ""translate selected models"" > view matrix models > #3,0.49284,-0.81627,0.30134,184.81,-0.19127,0.23621,0.95269,190.18,-0.84883,-0.52717,-0.039715,212.46 > fitmap #3 inMap #5 Fit molecule AF M seg model initial.pdb (#3) to map emd_11236.map z flip (#5) using 7578 atoms average map value = 2.025, steps = 180 shifted from previous position = 18.6 rotated from previous position = 30.3 degrees atoms outside contour = 3143, contour level = 1.6431 Position of AF M seg model initial.pdb (#3) relative to emd_11236.map z flip (#5) coordinates: Matrix rotation and translation 0.85667010 -0.44218458 0.26568609 171.52304663 -0.18387923 0.21945582 0.95813754 193.07805358 -0.48198002 -0.86966195 0.10669268 225.07733827 Axis -0.91774197 0.37540473 0.12969566 Axis point 0.00000000 270.33408911 -3.12625854 Rotation angle (degrees) 84.75531174 Shift along axis -55.73993137 > ui mousemode right ""rotate selected models"" > view matrix models > #3,0.83719,-0.50821,0.20209,172.06,0.037954,0.4226,0.90552,190.09,-0.5456,-0.75042,0.37309,224.91 > ui mousemode right ""translate selected models"" > view matrix models > #3,0.83719,-0.50821,0.20209,180.61,0.037954,0.4226,0.90552,190.38,-0.5456,-0.75042,0.37309,217.89 > hide #!5 models > show #!5 models > select add #2 16227 atoms, 16540 bonds, 10 pseudobonds, 2082 residues, 4 models selected > select subtract #3 8649 atoms, 8818 bonds, 4 pseudobonds, 1110 residues, 2 models selected > view matrix models > #2,0.020492,0.78522,-0.61887,155.66,0.47508,0.53701,0.69708,269.5,0.8797,-0.3083,-0.36204,153.25 > color #5 #b2b2b25c models [Repeated 1 time(s)] > view matrix models > #2,0.020492,0.78522,-0.61887,157,0.47508,0.53701,0.69708,233.89,0.8797,-0.3083,-0.36204,183.5 > view matrix models > #2,0.020492,0.78522,-0.61887,185.11,0.47508,0.53701,0.69708,222.87,0.8797,-0.3083,-0.36204,192.29 > ui mousemode right ""rotate selected models"" > view matrix models > #2,-0.27655,0.15079,-0.94909,187.13,0.84083,0.51617,-0.163,222.47,0.46532,-0.84311,-0.26954,194.2 > hide #!5 models > hide #!3 models > ui mousemode right select Drag select of 129 residues, 4 pseudobonds > delete sel > select add #2 7663 atoms, 7811 bonds, 2 pseudobonds, 981 residues, 2 models selected > select subtract #2 Nothing selected > show #!5 models > select add #2 7663 atoms, 7811 bonds, 2 pseudobonds, 981 residues, 2 models selected > show #!3 models > color #3 plum transparency 0 Drag select of 57 residues, 5 emd_11236.map z flip > select add #2 7879 atoms, 7811 bonds, 2 pseudobonds, 1008 residues, 5 models selected > select add #3 15241 atoms, 15533 bonds, 8 pseudobonds, 1953 residues, 6 models selected > select subtract #3 7663 atoms, 7811 bonds, 2 pseudobonds, 981 residues, 4 models selected > select add #5 7663 atoms, 7811 bonds, 2 pseudobonds, 981 residues, 5 models selected > select subtract #5 7663 atoms, 7811 bonds, 2 pseudobonds, 981 residues, 2 models selected > ui mousemode right ""translate selected models"" > view matrix models > #2,-0.27655,0.15079,-0.94909,244.22,0.84083,0.51617,-0.163,218.77,0.46532,-0.84311,-0.26954,209.22 > view matrix models > #2,-0.27655,0.15079,-0.94909,215.29,0.84083,0.51617,-0.163,232.43,0.46532,-0.84311,-0.26954,220.88 > ui mousemode right ""rotate selected models"" > view matrix models > #2,0.14673,0.14928,0.97785,206.9,-0.6217,0.78282,-0.026214,237.3,-0.76939,-0.60408,0.20767,223.7 > view matrix models > #2,0.041789,0.29347,0.95505,207.27,-0.3301,0.90627,-0.26404,236.92,-0.94302,-0.30423,0.13475,224.38 > ui mousemode right ""translate selected models"" > view matrix models > #2,0.041789,0.29347,0.95505,184.27,-0.3301,0.90627,-0.26404,233.45,-0.94302,-0.30423,0.13475,211.61 > view matrix models > #2,0.041789,0.29347,0.95505,182.95,-0.3301,0.90627,-0.26404,234.37,-0.94302,-0.30423,0.13475,213.96 > fitmap #2 inMap #5 Fit molecule AF M seg model initial.pdb (#2) to map emd_11236.map z flip (#5) using 7663 atoms average map value = 2.119, steps = 88 shifted from previous position = 30.4 rotated from previous position = 26.1 degrees atoms outside contour = 2624, contour level = 1.6431 Position of AF M seg model initial.pdb (#2) relative to emd_11236.map z flip (#5) coordinates: Matrix rotation and translation -0.18281158 0.62104949 0.76215317 190.35451193 -0.39077409 0.66544968 -0.63598139 209.44194322 -0.90215050 -0.41409448 0.12103813 213.73040806 Axis 0.11318806 0.84898785 -0.51614735 Axis point 206.33062313 0.00000000 83.67656769 Rotation angle (degrees) 101.42949161 Shift along axis 89.04313862 > view matrix models > #2,-0.18281,0.62105,0.76215,175.7,-0.39077,0.66545,-0.63598,225.01,-0.90215,-0.41409,0.12104,223.9 > ui mousemode right ""rotate selected models"" > view matrix models > #2,-0.11874,-0.50542,0.85466,176.04,-0.29446,0.83995,0.45582,220.66,-0.94826,-0.19754,-0.24856,225.2 > ui mousemode right ""translate selected models"" > view matrix models > #2,-0.11874,-0.50542,0.85466,187.74,-0.29446,0.83995,0.45582,244.21,-0.94826,-0.19754,-0.24856,233.75 > fitmap #2 inMap #5 Fit molecule AF M seg model initial.pdb (#2) to map emd_11236.map z flip (#5) using 7663 atoms average map value = 2.035, steps = 140 shifted from previous position = 11.2 rotated from previous position = 50.1 degrees atoms outside contour = 2923, contour level = 1.6431 Position of AF M seg model initial.pdb (#2) relative to emd_11236.map z flip (#5) coordinates: Matrix rotation and translation -0.23330942 -0.96024842 0.15326344 187.73898147 -0.37088922 0.23357372 0.89882396 249.32081285 -0.89889260 0.15286034 -0.41064076 234.48496433 Axis -0.52605248 0.74197894 0.41561527 Axis point 226.56307687 -0.00000000 -32.26442725 Rotation angle (degrees) 134.84475207 Shift along axis 183.68576516 > view matrix models > #2,-0.23331,-0.96025,0.15326,187.19,-0.37089,0.23357,0.89882,243.63,-0.89889,0.15286,-0.41064,233.7 > ui mousemode right ""rotate selected models"" > view matrix models > #2,-0.066203,-0.35724,0.93166,183.33,-0.51868,0.80997,0.27372,245.92,-0.8524,-0.46511,-0.23892,233.42 > view matrix models > #2,-0.11123,-0.12312,0.98614,183.12,-0.71808,0.69593,0.0058929,247.72,-0.68701,-0.70747,-0.16582,232.73 > ui mousemode right ""translate selected models"" > view matrix models > #2,-0.11123,-0.12312,0.98614,193.6,-0.71808,0.69593,0.0058929,247.46,-0.68701,-0.70747,-0.16582,235.33 > view matrix models > #2,-0.11123,-0.12312,0.98614,191.49,-0.71808,0.69593,0.0058929,248,-0.68701,-0.70747,-0.16582,235.08 > ui mousemode right ""rotate selected models"" > view matrix models > #2,-0.33619,-0.044863,0.94072,192.44,-0.57352,0.80205,-0.16671,247.97,-0.74703,-0.59557,-0.29537,235.67 > ui mousemode right ""translate selected models"" > view matrix models > #2,-0.33619,-0.044863,0.94072,191.02,-0.57352,0.80205,-0.16671,235.69,-0.74703,-0.59557,-0.29537,227.61 > view matrix models > #2,-0.33619,-0.044863,0.94072,197.5,-0.57352,0.80205,-0.16671,243.21,-0.74703,-0.59557,-0.29537,219.39 > ui mousemode right zoom > ui mousemode right ""rotate selected models"" > view matrix models > #2,0.037375,0.25376,0.96654,195.75,-0.73954,0.65753,-0.14403,243.88,-0.67208,-0.70941,0.21224,217.41 > fitmap #2 inMap #5 Fit molecule AF M seg model initial.pdb (#2) to map emd_11236.map z flip (#5) using 7663 atoms average map value = 2.09, steps = 64 shifted from previous position = 15 rotated from previous position = 11.9 degrees atoms outside contour = 2968, contour level = 1.6431 Position of AF M seg model initial.pdb (#2) relative to emd_11236.map z flip (#5) coordinates: Matrix rotation and translation -0.11766915 0.13355516 0.98403102 190.68164000 -0.78113367 0.59940733 -0.17476003 257.08417417 -0.61317550 -0.78922360 0.03379268 223.94674463 Axis -0.31666272 0.82311756 -0.47138328 Axis point 261.25212490 0.00000000 88.26116215 Rotation angle (degrees) 104.01846362 Shift along axis 45.66398165 > select add #3 15241 atoms, 15533 bonds, 8 pseudobonds, 1953 residues, 4 models selected > select subtract #2 7578 atoms, 7722 bonds, 6 pseudobonds, 972 residues, 2 models selected > view matrix models > #3,0.83697,-0.51937,0.17243,180.73,-0.28878,-0.15152,0.94533,195.14,-0.46485,-0.84101,-0.2768,219.16 > open /Users/elizabethmcfadden/Library/CloudStorage/Box- > Box/ElizabethMcFadden/CCHFV/AlphaFold/CCHFV_Aug22_ElizaModel.pdb Chain information for CCHFV_Aug22_ElizaModel.pdb #6 --- Chain | Description A | No description available B | No description available C | No description available D | No description available > select subtract #3 Nothing selected > hide #!2 models > hide #!3 models > color #6 #00f900 transparency 0 > ui mousemode right ""translate selected models"" > ui mousemode right zoom > ui mousemode right ""translate selected models"" > select add #6 11282 atoms, 11507 bonds, 1437 residues, 1 model selected > view matrix models #6,1,0,0,90.393,0,1,0,274.36,0,0,1,10.448 > view matrix models #6,1,0,0,128.07,0,1,0,216.52,0,0,1,229.05 > ui mousemode right zoom > hide #!5 models > ui mousemode right select Drag select of 275 residues > select clear Drag select of 365 residues > delete sel > show #!5 models > select add #6 8352 atoms, 8515 bonds, 2 pseudobonds, 1072 residues, 2 models selected > ui mousemode right ""translate selected models"" > view matrix models #6,1,0,0,154.64,0,1,0,200.05,0,0,1,201.58 > select subtract #6 Nothing selected > select add #6 8352 atoms, 8515 bonds, 2 pseudobonds, 1072 residues, 2 models selected > view matrix models #6,1,0,0,172.9,0,1,0,184.99,0,0,1,184.16 > ui mousemode right ""rotate selected models"" > view matrix models > #6,0.89841,0.21633,0.38219,174.89,-0.42446,0.65104,0.62926,203.48,-0.11269,-0.72756,0.67673,194.22 > ui mousemode right ""translate selected models"" > view matrix models > #6,0.89841,0.21633,0.38219,171.59,-0.42446,0.65104,0.62926,193.89,-0.11269,-0.72756,0.67673,215.78 > fitmap #6 inMap #5 Fit molecule CCHFV_Aug22_ElizaModel.pdb (#6) to map emd_11236.map z flip (#5) using 8352 atoms average map value = 2.11, steps = 112 shifted from previous position = 25.6 rotated from previous position = 22.8 degrees atoms outside contour = 3309, contour level = 1.6431 Position of CCHFV_Aug22_ElizaModel.pdb (#6) relative to emd_11236.map z flip (#5) coordinates: Matrix rotation and translation 0.96240685 0.23069858 0.14335700 184.32166451 -0.23538390 0.44504892 0.86401730 220.09002769 0.13552669 -0.86528009 0.48262086 213.90991403 Axis -0.96553607 0.00437197 -0.26023254 Axis point 0.00000000 238.61388014 -102.64636975 Rotation angle (degrees) 63.57421013 Shift along axis -232.67330891 > hide #!5 models > show #!5 models > ui mousemode right ""rotate selected models"" > view matrix models > #6,0.60483,0.78547,-0.13119,165.16,-0.77714,0.61814,0.11813,200.01,0.17388,0.030503,0.98429,203.16 > ui mousemode right ""translate selected models"" > view matrix models > #6,0.60483,0.78547,-0.13119,151.12,-0.77714,0.61814,0.11813,193.09,0.17388,0.030503,0.98429,215.69 > fitmap #6 inMap #5 Fit molecule CCHFV_Aug22_ElizaModel.pdb (#6) to map emd_11236.map z flip (#5) using 8352 atoms average map value = 2.356, steps = 116 shifted from previous position = 10.3 rotated from previous position = 46.5 degrees atoms outside contour = 2876, contour level = 1.6431 Position of CCHFV_Aug22_ElizaModel.pdb (#6) relative to emd_11236.map z flip (#5) coordinates: Matrix rotation and translation 0.03871167 0.74909756 -0.66132765 149.06555496 -0.96412247 0.20193891 0.17230363 202.79374955 0.26262001 0.63093068 0.73003919 207.77289065 Axis 0.22933815 -0.46202344 -0.85670202 Axis point 155.86535060 -71.69129562 0.00000000 Rotation angle (degrees) 90.83970622 Shift along axis -237.50850214 > hide #!5 models > show #!5 models > view matrix models > #6,0.038712,0.7491,-0.66133,145.88,-0.96412,0.20194,0.1723,199.87,0.26262,0.63093,0.73004,211.14 > fitmap #6 inMap #5 Fit molecule CCHFV_Aug22_ElizaModel.pdb (#6) to map emd_11236.map z flip (#5) using 8352 atoms average map value = 2.357, steps = 64 shifted from previous position = 5.46 rotated from previous position = 0.0612 degrees atoms outside contour = 2879, contour level = 1.6431 Position of CCHFV_Aug22_ElizaModel.pdb (#6) relative to emd_11236.map z flip (#5) coordinates: Matrix rotation and translation 0.03917027 0.74860077 -0.66186296 149.00186620 -0.96393222 0.20281165 0.17234303 202.77327115 0.26324965 0.63124031 0.72954459 207.73006428 Axis 0.22947189 -0.46260319 -0.85635328 Axis point 155.81017100 -71.86058458 0.00000000 Rotation angle (degrees) 90.81573288 Shift along axis -237.50214340 > hide #!5 models > select #6/D:1041-1684 4320 atoms, 4419 bonds, 555 residues, 1 model selected > select #6/C:843-1040 522 atoms, 530 bonds, 1 pseudobond, 66 residues, 2 models selected > color #6 #009051 transparency 0 > select #6/C:843-1040 522 atoms, 530 bonds, 1 pseudobond, 66 residues, 2 models selected > delete sel > show #!5 models > show #!4 models > hide #!5 models > color #4 #b2b2b29c models [Repeated 1 time(s)] > ui mousemode right zoom > select add #6 7830 atoms, 7985 bonds, 1 pseudobond, 1006 residues, 2 models selected > ui mousemode right ""rotate selected models"" > view matrix models > #6,0.45211,-0.8917,-0.021539,199.68,-0.82999,-0.42942,0.35597,221.04,-0.32667,-0.14306,-0.93425,192.26 > fitmap #6 inMap #4 Fit molecule CCHFV_Aug22_ElizaModel.pdb (#6) to map emd_11236.map (#4) using 7830 atoms average map value = 1.65, steps = 80 shifted from previous position = 15 rotated from previous position = 15.9 degrees atoms outside contour = 3500, contour level = 1.6431 Position of CCHFV_Aug22_ElizaModel.pdb (#6) relative to emd_11236.map (#4) coordinates: Matrix rotation and translation 0.31800553 -0.93968131 -0.12598234 213.17268104 -0.92872531 -0.33546687 0.15789643 212.93764965 -0.19063523 0.06679105 -0.97938613 188.66779487 Axis -0.81162413 0.57596870 0.09760287 Axis point 0.00000000 185.42599442 103.14895652 Rotation angle (degrees) 176.78256342 Shift along axis -31.95615305 > ui mousemode right ""translate selected models"" > ui mousemode right ""rotate selected models"" > view matrix models > #6,0.35154,-0.93161,0.092333,217.23,-0.77936,-0.23659,0.5802,219.09,-0.51867,-0.27592,-0.80923,198.96 > ui mousemode right ""translate selected models"" > view matrix models > #6,0.35154,-0.93161,0.092333,199.13,-0.77936,-0.23659,0.5802,206.9,-0.51867,-0.27592,-0.80923,190.61 > fitmap #6 inMap #4 Fit molecule CCHFV_Aug22_ElizaModel.pdb (#6) to map emd_11236.map (#4) using 7830 atoms average map value = 1.65, steps = 100 shifted from previous position = 24.1 rotated from previous position = 29.4 degrees atoms outside contour = 3498, contour level = 1.6431 Position of CCHFV_Aug22_ElizaModel.pdb (#6) relative to emd_11236.map (#4) coordinates: Matrix rotation and translation 0.31811184 -0.93971476 -0.12546335 213.14117612 -0.92883227 -0.33543416 0.15733581 212.89047270 -0.18993548 0.06648402 -0.97954296 188.70664455 Axis -0.81165784 0.57598551 0.09722270 Axis point 0.00000000 185.38135074 103.12760720 Rotation angle (degrees) 176.79166197 Shift along axis -32.02930970 > ui mousemode right ""rotate selected models"" > view matrix models > #6,-0.51548,-0.53649,-0.66818,191.58,-0.84676,0.43854,0.30113,198.15,0.13147,0.72101,-0.68034,180.24 > ui mousemode right ""translate selected models"" > view matrix models > #6,-0.51548,-0.53649,-0.66818,169.61,-0.84676,0.43854,0.30113,214.23,0.13147,0.72101,-0.68034,190.53 > fitmap #6 inMap #4 Fit molecule CCHFV_Aug22_ElizaModel.pdb (#6) to map emd_11236.map (#4) using 7830 atoms average map value = 2.479, steps = 84 shifted from previous position = 13.6 rotated from previous position = 10.9 degrees atoms outside contour = 2632, contour level = 1.6431 Position of CCHFV_Aug22_ElizaModel.pdb (#6) relative to emd_11236.map (#4) coordinates: Matrix rotation and translation -0.63412679 -0.48858253 -0.59930822 173.37299866 -0.74460858 0.59477890 0.30297878 201.88198569 0.20842573 0.63837700 -0.74096797 199.21250742 Axis 0.36804198 -0.88634937 -0.28094464 Axis point 108.04686650 0.00000000 99.75108130 Rotation angle (degrees) 152.89309897 Shift along axis -171.09711578 > ui mousemode right zoom > open /Users/elizabethmcfadden/Library/CloudStorage/Box- > Box/ElizabethMcFadden/CCHFV/AlphaFold/CCHFV_Aug22_ElizaModel.pdb Chain information for CCHFV_Aug22_ElizaModel.pdb #7 --- Chain | Description A | No description available B | No description available C | No description available D | No description available > close #5 > select subtract #6 Nothing selected > select add #7 11282 atoms, 11507 bonds, 1437 residues, 1 model selected > ui mousemode right ""translate selected models"" > view matrix models #7,1,0,0,16.56,0,1,0,220.82,0,0,1,69.226 > ui mousemode right select > ui mousemode right zoom > ui mousemode right select Drag select of 314 residues > delete sel > ui mousemode right zoom > select add #7 8759 atoms, 8934 bonds, 2 pseudobonds, 1123 residues, 2 models selected > ui mousemode right ""translate selected models"" > view matrix models #7,1,0,0,159.63,0,1,0,108.64,0,0,1,346.98 > ui mousemode right ""rotate selected models"" > view matrix models > #7,0.54127,-0.83183,-0.12278,170.55,-0.83422,-0.54955,0.045567,134.02,-0.10538,0.077764,-0.99139,309.13 > view matrix models > #7,0.76291,-0.61642,-0.1949,166.2,-0.64649,-0.72896,-0.22509,132.95,-0.0033204,0.29773,-0.95465,306.25 > ui mousemode right ""translate selected models"" > view matrix models > #7,0.76291,-0.61642,-0.1949,226.82,-0.64649,-0.72896,-0.22509,104.34,-0.0033204,0.29773,-0.95465,250.41 > view matrix models > #7,0.76291,-0.61642,-0.1949,287.09,-0.64649,-0.72896,-0.22509,171.06,-0.0033204,0.29773,-0.95465,222.36 > view matrix models > #7,0.76291,-0.61642,-0.1949,238.47,-0.64649,-0.72896,-0.22509,178.08,-0.0033204,0.29773,-0.95465,202.94 > fitmap #7 inMap #4 Fit molecule CCHFV_Aug22_ElizaModel.pdb (#7) to map emd_11236.map (#4) using 8759 atoms average map value = 2.241, steps = 168 shifted from previous position = 8.09 rotated from previous position = 23.1 degrees atoms outside contour = 3237, contour level = 1.6431 Position of CCHFV_Aug22_ElizaModel.pdb (#7) relative to emd_11236.map (#4) coordinates: Matrix rotation and translation 0.78611752 -0.54465327 -0.29218491 229.20531396 -0.60121165 -0.56415002 -0.56593222 174.06590672 0.14340072 0.62055422 -0.77094012 200.02801154 Axis 0.93779953 -0.34428711 -0.04470377 Axis point 0.00000000 89.84592996 148.12048949 Rotation angle (degrees) 140.75848340 Shift along axis 146.07798036 > ui mousemode right zoom > select subtract #7 Nothing selected > open /Users/elizabethmcfadden/Library/CloudStorage/Box- > Box/ElizabethMcFadden/CCHFV/AlphaFold/CCHFV_Aug22_ElizaModel.pdb Chain information for CCHFV_Aug22_ElizaModel.pdb #5 --- Chain | Description A | No description available B | No description available C | No description available D | No description available > open /Users/elizabethmcfadden/Library/CloudStorage/Box- > Box/ElizabethMcFadden/CCHFV/AlphaFold/CCHFV_Aug22_ElizaModel.pdb Chain information for CCHFV_Aug22_ElizaModel.pdb #8 --- Chain | Description A | No description available B | No description available C | No description available D | No description available > select add #8 11282 atoms, 11507 bonds, 1437 residues, 1 model selected > ui mousemode right ""translate selected models"" > view matrix models #8,1,0,0,343.04,0,1,0,221.47,0,0,1,317.04 > ui mousemode right zoom > hide #!4 models > ui mousemode right select Drag select of 327 residues > delete sel > select clear Drag select of 42 residues, 2 pseudobonds > select clear [Repeated 1 time(s)]Drag select of 39 residues, 2 pseudobonds > delete sel > ui mousemode right zoom > ui mousemode right select > select clear [Repeated 1 time(s)]Drag select of 312 residues > delete sel > show #!4 models > ui mousemode right ""translate selected models"" > select add #8 8341 atoms, 8503 bonds, 3 pseudobonds, 1071 residues, 2 models selected > view matrix models #8,1,0,0,326.4,0,1,0,270.93,0,0,1,350.56 > view matrix models #8,1,0,0,187.54,0,1,0,303.43,0,0,1,267.81 > view matrix models #8,1,0,0,209.45,0,1,0,209.15,0,0,1,252.09 > ui mousemode right ""rotate selected models"" > view matrix models > #8,-0.65889,0.27357,-0.70073,184.04,0.64093,0.69182,-0.33256,212.08,0.3938,-0.66824,-0.63117,237.61 > view matrix models > #8,-0.78791,0.52804,-0.31681,185.1,0.61352,0.71721,-0.33044,211.44,0.052736,-0.45473,-0.88907,226.62 > ui mousemode right ""translate selected models"" > view matrix models > #8,-0.78791,0.52804,-0.31681,242.86,0.61352,0.71721,-0.33044,209.47,0.052736,-0.45473,-0.88907,177 > fitmap #7 inMap #4 Fit molecule CCHFV_Aug22_ElizaModel.pdb (#7) to map emd_11236.map (#4) using 8759 atoms average map value = 2.241, steps = 96 shifted from previous position = 0.047 rotated from previous position = 0.167 degrees atoms outside contour = 3234, contour level = 1.6431 Position of CCHFV_Aug22_ElizaModel.pdb (#7) relative to emd_11236.map (#4) coordinates: Matrix rotation and translation 0.78483392 -0.54603992 -0.29304624 229.20699772 -0.60251979 -0.56176586 -0.56691181 174.06081172 0.14493311 0.62149779 -0.76989276 200.04425210 Axis 0.93737461 -0.34546231 -0.04454928 Axis point 0.00000000 89.88679752 148.26005981 Rotation angle (degrees) 140.66131243 Shift along axis 145.80954288 > fitmap #8 inMap #4 Fit molecule CCHFV_Aug22_ElizaModel.pdb (#8) to map emd_11236.map (#4) using 8341 atoms average map value = 1.532, steps = 120 shifted from previous position = 21.7 rotated from previous position = 29.8 degrees atoms outside contour = 3836, contour level = 1.6431 Position of CCHFV_Aug22_ElizaModel.pdb (#8) relative to emd_11236.map (#4) coordinates: Matrix rotation and translation -0.85784858 0.07085563 -0.50899437 240.54068673 0.29502444 0.87887647 -0.37488226 186.01699568 0.42078066 -0.47175799 -0.77484709 184.48505089 Axis -0.10077464 -0.96719518 0.23319081 Axis point 81.18158846 0.00000000 144.36166238 Rotation angle (degrees) 151.27178864 Shift along axis -161.13492339 > view matrix models > #8,-0.85785,0.070856,-0.50899,211.78,0.29502,0.87888,-0.37488,229.48,0.42078,-0.47176,-0.77485,198.13 > ui mousemode right ""rotate selected models"" > view matrix models > #8,-0.95416,0.088385,-0.28594,215.29,0.29882,0.33441,-0.8938,232.02,0.016624,-0.93827,-0.3455,215.57 > ui mousemode right ""translate selected models"" > view matrix models > #8,-0.95416,0.088385,-0.28594,232.89,0.29882,0.33441,-0.8938,207.12,0.016624,-0.93827,-0.3455,206.82 > fitmap #8 inMap #4 Fit molecule CCHFV_Aug22_ElizaModel.pdb (#8) to map emd_11236.map (#4) using 8341 atoms average map value = 1.271, steps = 116 shifted from previous position = 16.8 rotated from previous position = 21.2 degrees atoms outside contour = 4170, contour level = 1.6431 Position of CCHFV_Aug22_ElizaModel.pdb (#8) relative to emd_11236.map (#4) coordinates: Matrix rotation and translation -0.98063421 -0.04396766 -0.19084902 242.71299918 0.19048582 0.01234642 -0.98161229 216.42849120 0.04551550 -0.99895664 -0.00373210 200.14065861 Axis -0.05202690 -0.70900955 0.70327709 Axis point 100.51566667 0.00000000 221.69746271 Rotation angle (degrees) 170.40478406 Shift along axis -25.32313180 > view matrix models > #8,-0.98063,-0.043968,-0.19085,230.4,0.19049,0.012346,-0.98161,211.1,0.045515,-0.99896,-0.0037321,220.86 > fitmap #8 inMap #4 Fit molecule CCHFV_Aug22_ElizaModel.pdb (#8) to map emd_11236.map (#4) using 8341 atoms average map value = 1.972, steps = 124 shifted from previous position = 29.5 rotated from previous position = 38.4 degrees atoms outside contour = 3301, contour level = 1.6431 Position of CCHFV_Aug22_ElizaModel.pdb (#8) relative to emd_11236.map (#4) coordinates: Matrix rotation and translation -0.91608332 0.34416198 -0.20577619 239.79328581 0.36251326 0.49147577 -0.79185584 200.56693012 -0.17139266 -0.80000254 -0.57499604 230.32838942 Axis -0.20460530 -0.86354662 0.46089468 Axis point 94.49979171 0.00000000 169.93304901 Rotation angle (degrees) 178.85926176 Shift along axis -116.10474148 > view matrix models > #8,-0.91608,0.34416,-0.20578,249.64,0.36251,0.49148,-0.79186,225.51,-0.17139,-0.8,-0.575,227.23 > hide #!4 models > ui mousemode right ""rotate selected models"" > view matrix models > #8,0.03703,0.97509,-0.21868,238.31,0.90583,-0.12517,-0.40472,248.88,-0.42202,-0.1831,-0.88791,206.29 > view matrix models > #8,0.074638,0.53271,0.843,268.81,0.97457,0.14014,-0.17485,247.44,-0.21128,0.83461,-0.50871,191.02 > view matrix models > #8,0.44068,0.14729,0.8855,279.7,0.89453,-0.15442,-0.41948,249.23,0.074957,0.97696,-0.1998,194.66 > ui mousemode right ""translate selected models"" > view matrix models > #8,0.44068,0.14729,0.8855,273.36,0.89453,-0.15442,-0.41948,217.84,0.074957,0.97696,-0.1998,206.7 > fitmap #8 inMap #4 Fit molecule CCHFV_Aug22_ElizaModel.pdb (#8) to map emd_11236.map (#4) using 8341 atoms average map value = 2.31, steps = 84 shifted from previous position = 16.9 rotated from previous position = 29.3 degrees atoms outside contour = 3085, contour level = 1.6431 Position of CCHFV_Aug22_ElizaModel.pdb (#8) relative to emd_11236.map (#4) coordinates: Matrix rotation and translation 0.72860024 0.39940597 0.55643194 255.31489031 0.66733485 -0.23094657 -0.70804508 210.54409571 -0.15429139 0.88720827 -0.43480527 218.49815452 Axis 0.90288165 0.40225526 0.15164242 Axis point 0.00000000 -6.79317749 111.26756087 Rotation angle (degrees) 117.94188870 Shift along axis 348.34518917 > view matrix models > #8,0.7286,0.39941,0.55643,263.02,0.66733,-0.23095,-0.70805,241.1,-0.15429,0.88721,-0.43481,195.67 > fitmap #8 inMap #4 Fit molecule CCHFV_Aug22_ElizaModel.pdb (#8) to map emd_11236.map (#4) using 8341 atoms average map value = 2.26, steps = 128 shifted from previous position = 26.3 rotated from previous position = 31.4 degrees atoms outside contour = 3085, contour level = 1.6431 Position of CCHFV_Aug22_ElizaModel.pdb (#8) relative to emd_11236.map (#4) coordinates: Matrix rotation and translation 0.61763786 0.51986080 0.59014250 258.69997343 0.76615011 -0.56716039 -0.30223015 229.26949059 0.17758785 0.63880654 -0.74859116 199.70294678 Axis 0.89062470 0.39045381 0.23309541 Axis point 0.00000000 39.59658091 79.82094071 Rotation angle (degrees) 148.10923545 Shift along axis 366.47357222 > view matrix models > #8,0.61764,0.51986,0.59014,275.21,0.76615,-0.56716,-0.30223,243.23,0.17759,0.63881,-0.74859,127.78 > ui mousemode right ""rotate selected models"" > view matrix models > #8,-0.53705,0.80947,-0.23734,248.77,0.40739,0.0025204,-0.91325,217.31,-0.73865,-0.58715,-0.33113,160.55 > view matrix models > #8,0.72873,0.57464,0.37247,270.19,0.57479,-0.2176,-0.78884,225.3,-0.37225,0.78895,-0.48887,127.39 > ui mousemode right ""translate selected models"" > view matrix models > #8,0.72873,0.57464,0.37247,205.53,0.57479,-0.2176,-0.78884,217.7,-0.37225,0.78895,-0.48887,185.77 > show #!4 models > view matrix models > #8,0.72873,0.57464,0.37247,236.58,0.57479,-0.2176,-0.78884,221.36,-0.37225,0.78895,-0.48887,164.6 > ui mousemode right ""rotate selected models"" > view matrix models > #8,0.73901,0.48622,0.46632,240.43,0.67011,-0.4592,-0.58317,231.13,-0.069414,0.74345,-0.66518,163.33 > ui mousemode right ""translate selected models"" > view matrix models > #8,0.73901,0.48622,0.46632,234.12,0.67011,-0.4592,-0.58317,225.43,-0.069414,0.74345,-0.66518,167.61 > fitmap #8 inMap #4 Fit molecule CCHFV_Aug22_ElizaModel.pdb (#8) to map emd_11236.map (#4) using 8341 atoms average map value = 1.614, steps = 92 shifted from previous position = 19.1 rotated from previous position = 17.6 degrees atoms outside contour = 3531, contour level = 1.6431 Position of CCHFV_Aug22_ElizaModel.pdb (#8) relative to emd_11236.map (#4) coordinates: Matrix rotation and translation 0.87844712 0.41662087 0.23400354 211.72793134 0.46976682 -0.66332926 -0.58250612 226.27562679 -0.08746281 0.62162795 -0.77841436 170.59558493 Axis 0.96528496 0.25770107 0.04260405 Axis point 0.00000000 56.02604821 109.04189125 Rotation angle (degrees) 141.41173684 Shift along axis 269.95732152 > view matrix models > #8,0.87845,0.41662,0.234,250.56,0.46977,-0.66333,-0.58251,248.95,-0.087463,0.62163,-0.77841,185.11 > ui mousemode right ""rotate selected models"" > view matrix models > #8,0.60133,0.12276,0.78952,266.91,0.68317,-0.59142,-0.42837,250.99,0.41435,0.79696,-0.4395,189.32 > ui mousemode right ""translate selected models"" > view matrix models > #8,0.60133,0.12276,0.78952,264.33,0.68317,-0.59142,-0.42837,228.2,0.41435,0.79696,-0.4395,200.78 > fitmap #8 inMap #4 Fit molecule CCHFV_Aug22_ElizaModel.pdb (#8) to map emd_11236.map (#4) using 8341 atoms average map value = 2.26, steps = 128 shifted from previous position = 5.32 rotated from previous position = 25.8 degrees atoms outside contour = 3082, contour level = 1.6431 Position of CCHFV_Aug22_ElizaModel.pdb (#8) relative to emd_11236.map (#4) coordinates: Matrix rotation and translation 0.61739545 0.51996039 0.59030840 258.70179550 0.76617403 -0.56757027 -0.30139890 229.28876560 0.17832601 0.63836130 -0.74879547 199.69509808 Axis 0.89057800 0.39042135 0.23332809 Axis point 0.00000000 39.65093843 79.76355736 Rotation angle (degrees) 148.15571590 Shift along axis 366.50783313 > select subtract #8 Nothing selected > select add #5 8769 atoms, 8945 bonds, 2 pseudobonds, 1125 residues, 2 models selected > view matrix models #5,1,0,0,172.59,0,1,0,376.54,0,0,1,121.91 > ui mousemode right ""rotate selected models"" > view matrix models > #5,0.9817,0.11268,-0.15351,167.77,-0.11059,0.99362,0.022133,376.66,0.15502,-0.0047521,0.9879,122.32 > view matrix models > #5,0.86608,0.18769,-0.46333,160.54,-0.10145,0.97355,0.20473,380.28,0.4895,-0.13031,0.86221,123.56 > view matrix models > #5,0.99562,0.093476,-0.0024776,170.83,-0.093459,0.99387,-0.059002,375.29,-0.0030529,0.058975,0.99825,120.79 > view matrix models > #5,0.99541,0.09464,-0.014513,170.6,-0.09528,0.99405,-0.052703,375.39,0.0094385,0.053844,0.9985,120.93 > view matrix models > #5,0.62866,0.30726,-0.71441,153.11,-0.020968,0.925,0.37938,384.52,0.7774,-0.22352,0.58796,121.43 > ui mousemode right ""translate selected models"" > view matrix models > #5,0.62866,0.30726,-0.71441,134.26,-0.020968,0.925,0.37938,385.88,0.7774,-0.22352,0.58796,176.82 > ui mousemode right ""rotate selected models"" > view matrix models > #5,0.092676,0.53755,-0.83813,126.01,0.23174,0.80699,0.5432,391.79,0.96835,-0.24457,-0.049781,166.63 > view matrix models > #5,-0.54152,0.25799,0.80012,157.76,0.66838,0.70941,0.22361,389.46,-0.50993,0.65587,-0.5566,136.15 > view matrix models > #5,-0.58937,-0.35932,0.72355,167.48,0.16062,0.82564,0.54085,391.16,-0.79173,0.43498,-0.4289,141.43 > view matrix models > #5,-0.6603,0.51671,0.54499,148.14,0.22517,0.82851,-0.51271,372.77,-0.71645,-0.21583,-0.66342,149.4 > view matrix models > #5,-0.73687,0.31378,0.5988,152.52,0.21999,0.94884,-0.2265,375.6,-0.63924,-0.035165,-0.7682,144.54 > ui mousemode right ""translate selected models"" > view matrix models > #5,-0.73687,0.31378,0.5988,188.91,0.21999,0.94884,-0.2265,284.55,-0.63924,-0.035165,-0.7682,291.99 > ui mousemode right ""rotate selected models"" > view matrix models > #5,-0.95001,0.029873,0.3108,188.26,0.065217,0.99244,0.10396,289.05,-0.30535,0.11903,-0.94477,287.24 > ui mousemode right ""translate selected models"" > view matrix models > #5,-0.95001,0.029873,0.3108,150.2,0.065217,0.99244,0.10396,235,-0.30535,0.11903,-0.94477,239.72 > view matrix models > #5,-0.95001,0.029873,0.3108,206.05,0.065217,0.99244,0.10396,248.63,-0.30535,0.11903,-0.94477,230.35 > fitmap #5 inMap #4 Fit molecule CCHFV_Aug22_ElizaModel.pdb (#5) to map emd_11236.map (#4) using 8769 atoms average map value = 2.246, steps = 216 shifted from previous position = 27.5 rotated from previous position = 51 degrees atoms outside contour = 3217, contour level = 1.6431 Position of CCHFV_Aug22_ElizaModel.pdb (#5) relative to emd_11236.map (#4) coordinates: Matrix rotation and translation -0.78379403 0.54746113 0.29317766 202.79324261 0.60309990 0.55842222 0.56959200 258.07313443 0.14811258 0.62325826 -0.76786179 199.93660811 Axis 0.32648389 0.88251741 0.33848381 Axis point 55.46813359 0.00000000 48.50124778 Rotation angle (degrees) 175.28564368 Shift along axis 361.63806678 > hide #!4 models > ui mousemode right zoom > select subtract #5 Nothing selected > show #!4 models > open ""/Users/elizabethmcfadden/Library/CloudStorage/Box- > Box/ElizabethMcFadden/CCHFV/AlphaFold/AF M seg model initial.pdb"" Chain information for AF M seg model initial.pdb #9 --- Chain | Description A | No description available B | No description available C | No description available D | No description available > mmaker #9 to #8 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker CCHFV_Aug22_ElizaModel.pdb, chain D (#8) with AF M seg model initial.pdb, chain D (#9), sequence alignment score = 3192.9 RMSD between 306 pruned atom pairs is 0.905 angstroms; (across all 556 pairs: 19.759) > hide #9 models > hide #!4 models > show #!4 models > ui mousemode right translate > ui mousemode right zoom > save /Users/elizabethmcfadden/Desktop/image36.png supersample 3 > save /Users/elizabethmcfadden/Desktop/image37.png supersample 3 > hide #!4 models > show #!4 models > save /Users/elizabethmcfadden/Desktop/image37.png supersample 3 > close #3 > close #2 > close #9 > save ""/Users/elizabethmcfadden/Desktop/CCHFV M segment tetramer TULV > fit.cxs"" includeMaps true > hide #!4 models > ui mousemode right select Drag select of 63 residues, 2 pseudobonds > delete sel Drag select of 75 residues, 2 pseudobonds > ~select Nothing selected > select clear Drag select of 17 residues, 1 pseudobonds > delete Missing or invalid ""atoms"" argument: empty atom specifier > delete sel > ui mousemode right zoom > ui mousemode right select > ui mousemode right rotate > ui mousemode right select Drag select of 27 residues, 1 pseudobonds > delete sel > ui mousemode right zoom > Color #5/A medium sea green Unknown command: Color #5/A medium sea green > color #5/A medium sea green > color #5/D medium sea green > color #6/D medium sea green > color #7/D medium sea green > color #8/D medium sea green > color #8/A dodger blue > color #7/A dodger blue > color #6/A dodger blue > color #5/A dodger blue > color #5/B orange > color #5/B oran6e Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword > color #6/B orange > color #7/B orange > color #8/B orange > color #5/C gray > color #6/C gray > color #7/C gray > color #8/C gray > show #!5-8 surfaces > hide #!5-8 surfaces > show #!5-8 atoms > style #!5-8 sphere Changed 32847 atom styles > hide #!5-8 atoms > show #!5-8 cartoons > show #!4 models > hide #!4 models > show #!1 models > color #1 #d4fb79 transparency 0 > show #!4 models > hide #!5 models > show #!5 models > hide #!1 models > hide #!4 models > show #!1 models > hide #!5 models > ui mousemode right translate > hide #!1 models > show #!5 models > show #!1 models > hide #!5 models > ui mousemode right translate > ui mousemode right zoom > show #!5 models > hide #!1 models > save ""/Users/elizabethmcfadden/Desktop/CCHFV M segment tetramer TULV > fit.cxs"" includeMaps true ——— End of log from Sun Feb 19 21:51:52 2023 ——— opened ChimeraX session > color #5/A cornflower blue > color #6/A cornflower blue > lighting soft > lighting flat > graphics silhouettes false > graphics silhouettes true > graphics silhouettes false > lighting simple > lighting soft > show #!4 models > graphics silhouettes true > graphics silhouettes false > ui tool show ""Side View"" > ui mousemode right zoom > lighting soft > lighting simple > lighting soft > lighting flat > lighting shadows true intensity 0.5 > graphics silhouettes false > lighting soft > color #7/A cornflower blue > color #8/A cornflower blue > color #5/A cornflower blue > color #5/B dark orange > color #6/B dark orange > color #7/B dark orange > color #8/B dark orange > hide #!7 models > hide #!8 models > show #!8 models > hide #!6 models > hide #!5 models > graphics silhouettes true > graphics silhouettes false > lighting simple > lighting soft > lighting shadows true intensity 0.5 > lighting shadows false > lighting shadows true > lighting simple > save /Users/elizabethmcfadden/Desktop/image35.png supersample 3 > show #!5 models > show #!6 models > show #!7 models > save /Users/elizabethmcfadden/Desktop/image36.png supersample 3 > hide #!8 models > hide #!7 models > hide #!6 models > show #!1 models > hide #!5 models > hide #!4 models > color #1/A/C/E/G > color #1/A/C/E/G dark blue > color #1/A/C/E/G blue > color #1 #102f9dff > color #1 #125a9dff > color #1 #225a9dff > color #1/A/C/E/G #225A9D > color #1/B /D /F /H dark green > color #1/B /D /F /H sea green > color #1 #bade86ff > color #1/B /D /F /H yellow green > color #1/A/C/E/G goldenrod > color #1/B /D /F /H dark sea green > color #1/A/C/E/G pale goldenrod > color #1/A/C/E/G goldenrod > color #1/A/C/E/G gold > show #!4 models > color #1/A: 22-176,205-218, 361-374 blue > hide #!4 models > color #1/A:205-218, 361-374 white > color #1/A: 22-176 /C: 22-176 /E: 22-176 /G: 22-176 > color #1/A: 22-176 /C: 22-176 /E: 22-176 /G: 22-176 slateblue > color #1/A: 22-176 /C: 22-176 /E: 22-176 /G: 22-176 dark slate blue > show #!4 models > color #1/A: 22-176 /C: 22-176 /E: 22-176 /G: 22-176 slateblue > color #1/A: 22-176 /C: 22-176 /E: 22-176 /G: 22-176 blue > color #1/A: 22-176 /C: 22-176 /E: 22-176 /G: 22-176 royal blue > color #1/A: 22-176 /C: 22-176 /E: 22-176 /G: 22-176 cornflower blue > show #!5 models > hide #!4 models > show #!4 models > hide #!1 models > show #!1 models > hide #!4 models > show #!4 models > color #4 #b2b2b276 models > color #4 #b2b2b26b models > hide #!4 models > hide #!1 models > show #!1 models > hide #!5 models > show #!4 models > color #4 #b2b2b24d models > color #1/A: 22-176 /C: 22-176 /E: 22-176 /G: 22-176 blue > color #1/A: 22-176 /C: 22-176 /E: 22-176 /G: 22-176 cornflower blue > color #1/A/C/E/G dark orange > color #1/A: 22-176 /C: 22-176 /E: 22-176 /G: 22-176 cornflower blue > color #1/B /D /F /H medium sea green > hide #!4 models > show #!4 models > hide #!4 models > color #1/A: 918-985 /C: 918-985 /E: 918-985 /G: 918-985 red > color #1/A: 986-1200 /C: 986-1200 /E: 986-1200 /G: 986-1200 gray > show #!4 models > hide #!4 models > hide #!1 models > show #!5 models > color #5/B: 659-685 gray > color #5/B: 585-658 red > color #6/B: 659-685 gray > color #7/B: 659-685 gray > color #8/B: 659-685 gray > color #6/B: 585-658 red > color #7/B: 585-658 red > color #8/B: 585-658 red > show #!6 models > show #!7 models > show #!8 models > show #!4 models > show #!1 models > hide #!4 models > hide #!5 models > hide #!6 models > hide #!7 models > hide #!8 models > show #!4 models > save /Users/elizabethmcfadden/Desktop/image37.png supersample 3 > hide #!1 models > show #!5 models > show #!6 models > show #!7 models > show #!8 models > save /Users/elizabethmcfadden/Desktop/image38.png supersample 3 > hide #!8 models > hide #!7 models > hide #!6 models > hide #!5 models > show #!1 models > save /Users/elizabethmcfadden/Desktop/image39.png supersample 3 > show #!5 models > show #!6 models > hide #!5 models > hide #!6 models > save /Users/elizabethmcfadden/Desktop/image40.png supersample 3 > hide #!4 models > show #!5 models > show #!6 models > show #!4 models > hide #!1 models > show #!7 models > show #!8 models > save /Users/elizabethmcfadden/Desktop/image41.png supersample 3 > hide #!4 models > show #!4 models > hide #!5 models > hide #!8 models > hide #!7 models > hide #!6 models > hide #!4 models > show #!1 models > save ""/Users/elizabethmcfadden/Desktop/CCHFV in TULV domain colors.cxs"" > includeMaps true > show #!4 models > hide #!1 models > hide #!4 models > show #!5 models > lighting soft > graphics silhouettes true > show #!4 models > hide #!4 models > color #5/B: 585-661 red > save /Users/elizabethmcfadden/Desktop/image42.png supersample 3 > ui mousemode right select Drag select of 9 residues > delete sel > select #5/B:842-855 8 atoms, 7 bonds, 1 residue, 1 model selected > select #5/B:830-842 49 atoms, 50 bonds, 7 residues, 1 model selected > delete sel Drag select of 11 residues > select #5/B:687 7 atoms, 7 bonds, 1 residue, 1 model selected > delete sel > select #5/B:686 10 atoms, 10 bonds, 1 residue, 1 model selected > delete sel > ui mousemode right zoom > select #5/C:991-1041 389 atoms, 396 bonds, 49 residues, 1 model selected > color sel light green > select add #5 8143 atoms, 8303 bonds, 1044 residues, 2 models selected > select subtract #5 4 models selected > select #5/C:991-1041 389 atoms, 396 bonds, 49 residues, 1 model selected > color sel yellow green > select add #5 8143 atoms, 8303 bonds, 1044 residues, 2 models selected > select add #6 15973 atoms, 16288 bonds, 1 pseudobond, 2050 residues, 7 models selected > select subtract #6 8143 atoms, 8303 bonds, 1044 residues, 8 models selected > select subtract #5 4 models selected > ui mousemode right select Drag select of 4 residues > delete sel > select clear > ui mousemode right zoom > save /Users/elizabethmcfadden/Desktop/image43.png supersample 3 > save /Users/elizabethmcfadden/Desktop/image44.png supersample 3 > save /Users/elizabethmcfadden/Desktop/image45.png supersample 3 > save /Users/elizabethmcfadden/Desktop/image46.png supersample 3 > show #!6 models > show #!7 models > show #!8 models > hide #!8 models > hide #!7 models > hide #!6 models > hide #!5 models > show #!1 models > select #1/A /B 6668 atoms, 6837 bonds, 3 pseudobonds, 871 residues, 2 models selected > select ~sel 53107 atoms, 54284 bonds, 15 pseudobonds, 6844 residues, 11 models selected > delete sel > save /Users/elizabethmcfadden/Desktop/image47.png supersample 3 > open 6F9C Summary of feedback from opening 6F9C fetched from pdb --- note | Fetching compressed mmCIF 6f9c from http://files.rcsb.org/download/6f9c.cif 6f9c title: Model of the Rift Valley fever virus glycoprotein hexamer type 1 [more info...] Chain information for 6f9c #2 --- Chain | Description | UniProt A C E G I K | Glycoprotein | A2T085_RVFV 154-469 B D F H J L | Glycoprotein | A2T072_RVFV 691-1118 > select #2/A/B 5508 atoms, 5617 bonds, 2 pseudobonds, 732 residues, 2 models selected > select ~sel 34208 atoms, 34922 bonds, 13 pseudobonds, 4531 residues, 6 models selected > select subtract #1 27540 atoms, 28085 bonds, 10 pseudobonds, 3660 residues, 4 models selected > delete sel > close #4 > mmaker #2 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 6zjm, chain B (#1) with 6f9c, chain B (#2), sequence alignment score = 135.4 RMSD between 26 pruned atom pairs is 1.453 angstroms; (across all 338 pairs: 26.774) > hide atoms > show cartoons > hide #!1 models > dssp > undo > color #2/B medium sea green > color #2/A dark orange > close #2 > open 6Y62 6y62 title: Crystal structure of the envelope glycoprotein complex of Maporal virus in a prefusion conformation [more info...] Chain information for 6y62 #2 --- Chain | Description | UniProt A B | Envelope polyprotein,Envelope polyprotein | Q5MYC0_9VIRU 21-374 255-607 419-874 652-1107 Non-standard residues in 6y62 #2 --- BMA — beta-D-mannopyranose (beta-D-mannose; D-mannose; mannose) MAN — alpha-D-mannopyranose (alpha-D-mannose; D-mannose; mannose) NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine; 2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose; 2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE) > mmaker #2 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 6zjm, chain B (#1) with 6y62, chain B (#2), sequence alignment score = 3546.4 RMSD between 167 pruned atom pairs is 0.717 angstroms; (across all 408 pairs: 6.602) > hide #!2 atoms > color #2/B medium sea green > color #2/A dark orange > show #!1 models > mmaker #2/B to #1/B Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 6zjm, chain B (#1) with 6y62, chain B (#2), sequence alignment score = 3546.4 RMSD between 167 pruned atom pairs is 0.717 angstroms; (across all 408 pairs: 6.602) > mmaker #2/A to #1/A Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 6zjm, chain A (#1) with 6y62, chain A (#2), sequence alignment score = 3493.6 RMSD between 325 pruned atom pairs is 0.753 angstroms; (across all 352 pairs: 1.267) > close #2 > save /Users/elizabethmcfadden/Desktop/image48.png supersample 3 > save /Users/elizabethmcfadden/Desktop/image49.png supersample 3 > close > open 6vkf 6vkf title: CCHFV GP38 (IbAr10200) [more info...] Chain information for 6vkf #1 --- Chain | Description | UniProt A B | GP38 | A0A1V0G0G3_9VIRU 248-515 Non-standard residues in 6vkf #1 --- NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose 6vkf mmCIF Assemblies --- 1| software_defined_assembly 2| software_defined_assembly > delete #1/B > ui mousemode right select Drag select of 28 atoms, 29 bonds > delete sel > color #1 violet > color #1 #e4aeecff > color byattribute hetero No known/registered numeric attribute hetero > color byhetero > hide all > select ::name=""NAG"" 56 atoms, 58 bonds, 4 residues, 1 model selected > show sel > select add #1 1998 atoms, 2034 bonds, 1 pseudobond, 250 residues, 2 models selected > select subtract #1 Nothing selected > select clear > ui mousemode right zoom > ui mousemode right select > select clear > select /A:376 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel > select /A:425 7 atoms, 6 bonds, 1 residue, 1 model selected > select /A:426 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel > select add #1 1998 atoms, 2034 bonds, 1 pseudobond, 250 residues, 2 models selected > select subtract #1 Nothing selected > select clear > ui mousemode right zoom > lighting soft > open /Users/elizabethmcfadden/Desktop/Em27ref47coot1-coot-4.pdb Chain information for Em27ref47coot1-coot-4.pdb #2 --- Chain | Description A | No description available B | No description available C | No description available D | No description available > mmaker #2 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 6vkf, chain A (#1) with Em27ref47coot1-coot-4.pdb, chain A (#2), sequence alignment score = 1229.9 RMSD between 223 pruned atom pairs is 0.576 angstroms; (across all 240 pairs: 1.577) > hide #!1 models > show #!1 models > hide #!1 models > dssp > show #!1 models > hide #!2 models > save /Users/elizabethmcfadden/Desktop/image50.png supersample 3 > save /Users/elizabethmcfadden/Desktop/image51.png supersample 3 > close #2 > close > open /Users/elizabethmcfadden/Library/CloudStorage/Box- > Box/ElizabethMcFadden/CCHFV/GcEctoBase36125_46152_Phenix/RealSpaceRefine_2/GP38GnHGc36125_46152_Fit3_real_space_refined_001-coot-4_real_space_refined_002.pdb Chain information for GP38GnHGc36125_46152_Fit3_real_space_refined_001-coot-4_real_space_refined_002.pdb #1 --- Chain | Description A | No description available B | No description available D | No description available E | No description available F | No description available H | No description available L | No description available > hide atoms > show cartoons > coulombic Using Amber 20 recommended default charges and atom types for standard residues Coulombic values for GP38GnHGc36125_46152_Fit3_real_space_refined_001-coot-4_real_space_refined_002.pdb_A SES surface #1.2: minimum, -20.60, mean -0.39, maximum 15.52 Coulombic values for GP38GnHGc36125_46152_Fit3_real_space_refined_001-coot-4_real_space_refined_002.pdb_B SES surface #1.3: minimum, -16.76, mean -0.19, maximum 13.37 Coulombic values for GP38GnHGc36125_46152_Fit3_real_space_refined_001-coot-4_real_space_refined_002.pdb_D SES surface #1.4: minimum, -13.78, mean -1.56, maximum 9.23 Coulombic values for GP38GnHGc36125_46152_Fit3_real_space_refined_001-coot-4_real_space_refined_002.pdb_E SES surface #1.5: minimum, -9.83, mean 0.35, maximum 8.55 Coulombic values for GP38GnHGc36125_46152_Fit3_real_space_refined_001-coot-4_real_space_refined_002.pdb_F SES surface #1.6: minimum, -12.35, mean 0.67, maximum 15.14 Coulombic values for GP38GnHGc36125_46152_Fit3_real_space_refined_001-coot-4_real_space_refined_002.pdb_H SES surface #1.7: minimum, -7.64, mean 2.15, maximum 12.48 Coulombic values for GP38GnHGc36125_46152_Fit3_real_space_refined_001-coot-4_real_space_refined_002.pdb_L SES surface #1.8: minimum, -8.75, mean 0.71, maximum 12.41 To also show corresponding color key, enter the above coulombic command and add key true > delete #1/D > open /Users/elizabethmcfadden/Library/CloudStorage/Box- > Box/ElizabethMcFadden/CCHFV/GcEctoBase36125_46152_Phenix/RealSpaceRefine_2/GP38GnHGc36125_46152_Fit3_real_space_refined_001-coot-4_real_space_refined_002.pdb Chain information for GP38GnHGc36125_46152_Fit3_real_space_refined_001-coot-4_real_space_refined_002.pdb #2 --- Chain | Description A | No description available B | No description available D | No description available E | No description available F | No description available H | No description available L | No description available > delete #2/A/B > hide atoms > show cartoons > coulombic Using Amber 20 recommended default charges and atom types for standard residues Coulombic values for GP38GnHGc36125_46152_Fit3_real_space_refined_001-coot-4_real_space_refined_002.pdb_A SES surface #1.2: minimum, -20.60, mean -0.39, maximum 15.52 Coulombic values for GP38GnHGc36125_46152_Fit3_real_space_refined_001-coot-4_real_space_refined_002.pdb_B SES surface #1.3: minimum, -16.76, mean -0.19, maximum 13.37 Coulombic values for GP38GnHGc36125_46152_Fit3_real_space_refined_001-coot-4_real_space_refined_002.pdb_E SES surface #1.5: minimum, -9.83, mean 0.35, maximum 8.55 Coulombic values for GP38GnHGc36125_46152_Fit3_real_space_refined_001-coot-4_real_space_refined_002.pdb_F SES surface #1.6: minimum, -12.35, mean 0.67, maximum 15.14 Coulombic values for GP38GnHGc36125_46152_Fit3_real_space_refined_001-coot-4_real_space_refined_002.pdb_H SES surface #1.7: minimum, -7.64, mean 2.15, maximum 12.48 Coulombic values for GP38GnHGc36125_46152_Fit3_real_space_refined_001-coot-4_real_space_refined_002.pdb_L SES surface #1.8: minimum, -8.75, mean 0.71, maximum 12.41 Coulombic values for GP38GnHGc36125_46152_Fit3_real_space_refined_001-coot-4_real_space_refined_002.pdb_D SES surface #2.2: minimum, -13.78, mean -1.56, maximum 9.23 Coulombic values for GP38GnHGc36125_46152_Fit3_real_space_refined_001-coot-4_real_space_refined_002.pdb_E SES surface #2.3: minimum, -9.83, mean 0.35, maximum 8.55 Coulombic values for GP38GnHGc36125_46152_Fit3_real_space_refined_001-coot-4_real_space_refined_002.pdb_F SES surface #2.4: minimum, -12.35, mean 0.67, maximum 15.14 Coulombic values for GP38GnHGc36125_46152_Fit3_real_space_refined_001-coot-4_real_space_refined_002.pdb_H SES surface #2.5: minimum, -7.64, mean 2.15, maximum 12.48 Coulombic values for GP38GnHGc36125_46152_Fit3_real_space_refined_001-coot-4_real_space_refined_002.pdb_L SES surface #2.6: minimum, -8.75, mean 0.71, maximum 12.41 To also show corresponding color key, enter the above coulombic command and add key true > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!2 models > show #!2 models > hide #!1 models > show #!1 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!1 models > show #!1 models > hide #!2 models > show #!2 models > close #2 > open /Users/elizabethmcfadden/Library/CloudStorage/Box- > Box/ElizabethMcFadden/CCHFV/GcEctoBase36125_46152_Phenix/RealSpaceRefine_2/GP38GnHGc36125_46152_Fit3_real_space_refined_001-coot-4_real_space_refined_002.pdb Chain information for GP38GnHGc36125_46152_Fit3_real_space_refined_001-coot-4_real_space_refined_002.pdb #2 --- Chain | Description A | No description available B | No description available D | No description available E | No description available F | No description available H | No description available L | No description available > delete #2/B > hide atoms > show cartoons > coulombic Using Amber 20 recommended default charges and atom types for standard residues Coulombic values for GP38GnHGc36125_46152_Fit3_real_space_refined_001-coot-4_real_space_refined_002.pdb_A SES surface #1.2: minimum, -20.60, mean -0.39, maximum 15.52 Coulombic values for GP38GnHGc36125_46152_Fit3_real_space_refined_001-coot-4_real_space_refined_002.pdb_B SES surface #1.3: minimum, -16.76, mean -0.19, maximum 13.37 Coulombic values for GP38GnHGc36125_46152_Fit3_real_space_refined_001-coot-4_real_space_refined_002.pdb_E SES surface #1.5: minimum, -9.83, mean 0.35, maximum 8.55 Coulombic values for GP38GnHGc36125_46152_Fit3_real_space_refined_001-coot-4_real_space_refined_002.pdb_F SES surface #1.6: minimum, -12.35, mean 0.67, maximum 15.14 Coulombic values for GP38GnHGc36125_46152_Fit3_real_space_refined_001-coot-4_real_space_refined_002.pdb_H SES surface #1.7: minimum, -7.64, mean 2.15, maximum 12.48 Coulombic values for GP38GnHGc36125_46152_Fit3_real_space_refined_001-coot-4_real_space_refined_002.pdb_L SES surface #1.8: minimum, -8.75, mean 0.71, maximum 12.41 Coulombic values for GP38GnHGc36125_46152_Fit3_real_space_refined_001-coot-4_real_space_refined_002.pdb_A SES surface #2.2: minimum, -20.60, mean -0.39, maximum 15.51 Coulombic values for GP38GnHGc36125_46152_Fit3_real_space_refined_001-coot-4_real_space_refined_002.pdb_D SES surface #2.3: minimum, -13.78, mean -1.56, maximum 9.23 Coulombic values for GP38GnHGc36125_46152_Fit3_real_space_refined_001-coot-4_real_space_refined_002.pdb_E SES surface #2.4: minimum, -9.83, mean 0.35, maximum 8.55 Coulombic values for GP38GnHGc36125_46152_Fit3_real_space_refined_001-coot-4_real_space_refined_002.pdb_F SES surface #2.5: minimum, -12.35, mean 0.67, maximum 15.14 Coulombic values for GP38GnHGc36125_46152_Fit3_real_space_refined_001-coot-4_real_space_refined_002.pdb_H SES surface #2.6: minimum, -7.64, mean 2.15, maximum 12.48 Coulombic values for GP38GnHGc36125_46152_Fit3_real_space_refined_001-coot-4_real_space_refined_002.pdb_L SES surface #2.7: minimum, -8.75, mean 0.71, maximum 12.41 To also show corresponding color key, enter the above coulombic command and add key true > hide #!1 models > hide #!2 models > show #!1 models > delete #1/A > show #!2 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!1 models > show #!1 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!1 models > show #!1 models > hide #!2 models > select ::name=""BMA""::name=""LYS""::name=""NAG"" 727 atoms, 664 bonds, 77 residues, 2 models selected > delete #1/B:1554 > select #1/B:1584 14 atoms, 14 bonds, 1 residue, 1 model selected > show sel > coulombic Coulombic values for GP38GnHGc36125_46152_Fit3_real_space_refined_001-coot-4_real_space_refined_002.pdb_B SES surface #1.3: minimum, -16.76, mean -0.19, maximum 13.37 Coulombic values for GP38GnHGc36125_46152_Fit3_real_space_refined_001-coot-4_real_space_refined_002.pdb_E SES surface #1.5: minimum, -9.83, mean 0.35, maximum 8.55 Coulombic values for GP38GnHGc36125_46152_Fit3_real_space_refined_001-coot-4_real_space_refined_002.pdb_F SES surface #1.6: minimum, -12.35, mean 0.67, maximum 15.14 Coulombic values for GP38GnHGc36125_46152_Fit3_real_space_refined_001-coot-4_real_space_refined_002.pdb_H SES surface #1.7: minimum, -7.64, mean 2.15, maximum 12.48 Coulombic values for GP38GnHGc36125_46152_Fit3_real_space_refined_001-coot-4_real_space_refined_002.pdb_L SES surface #1.8: minimum, -8.75, mean 0.71, maximum 12.41 Coulombic values for GP38GnHGc36125_46152_Fit3_real_space_refined_001-coot-4_real_space_refined_002.pdb_A SES surface #2.2: minimum, -20.60, mean -0.39, maximum 15.51 Coulombic values for GP38GnHGc36125_46152_Fit3_real_space_refined_001-coot-4_real_space_refined_002.pdb_D SES surface #2.3: minimum, -13.78, mean -1.56, maximum 9.23 Coulombic values for GP38GnHGc36125_46152_Fit3_real_space_refined_001-coot-4_real_space_refined_002.pdb_E SES surface #2.4: minimum, -9.83, mean 0.35, maximum 8.55 Coulombic values for GP38GnHGc36125_46152_Fit3_real_space_refined_001-coot-4_real_space_refined_002.pdb_F SES surface #2.5: minimum, -12.35, mean 0.67, maximum 15.14 Coulombic values for GP38GnHGc36125_46152_Fit3_real_space_refined_001-coot-4_real_space_refined_002.pdb_H SES surface #2.6: minimum, -7.64, mean 2.15, maximum 12.48 Coulombic values for GP38GnHGc36125_46152_Fit3_real_space_refined_001-coot-4_real_space_refined_002.pdb_L SES surface #2.7: minimum, -8.75, mean 0.71, maximum 12.41 > show #!2 models > hide #!1 models > show #!1 models > select add #1 3863 atoms, 3951 bonds, 1 pseudobond, 502 residues, 2 models selected > select subtract #1 5 models selected > select #1/B:1584-1586 39 atoms, 41 bonds, 3 residues, 1 model selected > show sel > select add #1 3863 atoms, 3951 bonds, 1 pseudobond, 502 residues, 2 models selected > select add #2 11012 atoms, 11282 bonds, 8 pseudobonds, 1411 residues, 9 models selected > mlp sel Map values for surface ""GP38GnHGc36125_46152_Fit3_real_space_refined_001-coot-4_real_space_refined_002.pdb_A SES surface"": minimum -26.9, mean -4.564, maximum 22.07 Map values for surface ""GP38GnHGc36125_46152_Fit3_real_space_refined_001-coot-4_real_space_refined_002.pdb_D SES surface"": minimum -28.54, mean -4.29, maximum 23.51 Map values for surface ""GP38GnHGc36125_46152_Fit3_real_space_refined_001-coot-4_real_space_refined_002.pdb_E SES surface"": minimum -28.69, mean -4.377, maximum 23.22 Map values for surface ""GP38GnHGc36125_46152_Fit3_real_space_refined_001-coot-4_real_space_refined_002.pdb_F SES surface"": minimum -25.47, mean -5.319, maximum 22.92 Map values for surface ""GP38GnHGc36125_46152_Fit3_real_space_refined_001-coot-4_real_space_refined_002.pdb_H SES surface"": minimum -25.88, mean -5.847, maximum 22.53 Map values for surface ""GP38GnHGc36125_46152_Fit3_real_space_refined_001-coot-4_real_space_refined_002.pdb_L SES surface"": minimum -24.83, mean -5.613, maximum 22.01 Map values for surface ""GP38GnHGc36125_46152_Fit3_real_space_refined_001-coot-4_real_space_refined_002.pdb_B SES surface"": minimum -28.33, mean -5.339, maximum 21.98 Map values for surface ""GP38GnHGc36125_46152_Fit3_real_space_refined_001-coot-4_real_space_refined_002.pdb_E SES surface"": minimum -28.69, mean -4.377, maximum 23.22 Map values for surface ""GP38GnHGc36125_46152_Fit3_real_space_refined_001-coot-4_real_space_refined_002.pdb_F SES surface"": minimum -25.47, mean -5.319, maximum 22.92 Map values for surface ""GP38GnHGc36125_46152_Fit3_real_space_refined_001-coot-4_real_space_refined_002.pdb_H SES surface"": minimum -25.88, mean -5.847, maximum 22.53 Map values for surface ""GP38GnHGc36125_46152_Fit3_real_space_refined_001-coot-4_real_space_refined_002.pdb_L SES surface"": minimum -24.83, mean -5.613, maximum 22.01 To also show corresponding color key, enter the above mlp command and add key true > select subtract #2 3863 atoms, 3951 bonds, 1 pseudobond, 502 residues, 13 models selected > select subtract #1 5 models selected > hide #!1 models > hide #!2 models > show #!2 models > show #!1 models > hide #!2 models > show #!2 models > hide #!1 models > show #!1 models > hide #!2 models > show #!2 models > hide #!1 models > delete #2/D > delete #2/H/L > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!1 models > show #!1 models > hide #!2 models > show #!2 models > hide #!1 models > show #!1 models > open /Users/elizabethmcfadden/Library/CloudStorage/Box- > Box/ElizabethMcFadden/CCHFV/GcEctoBase36125_46152_Phenix/RealSpaceRefine_2/GP38GnHGc36125_46152_Fit3_real_space_refined_001-coot-4_real_space_refined_002.pdb Chain information for GP38GnHGc36125_46152_Fit3_real_space_refined_001-coot-4_real_space_refined_002.pdb #3 --- Chain | Description A | No description available B | No description available D | No description available E | No description available F | No description available H | No description available L | No description available > delete #3/H/L/A/B/E/F > mlp Map values for surface ""GP38GnHGc36125_46152_Fit3_real_space_refined_001-coot-4_real_space_refined_002.pdb_A SES surface"": minimum -26.9, mean -4.564, maximum 22.07 Map values for surface ""GP38GnHGc36125_46152_Fit3_real_space_refined_001-coot-4_real_space_refined_002.pdb_E SES surface"": minimum -28.69, mean -4.377, maximum 23.22 Map values for surface ""GP38GnHGc36125_46152_Fit3_real_space_refined_001-coot-4_real_space_refined_002.pdb_F SES surface"": minimum -25.47, mean -5.319, maximum 22.92 Map values for surface ""GP38GnHGc36125_46152_Fit3_real_space_refined_001-coot-4_real_space_refined_002.pdb_B SES surface"": minimum -28.33, mean -5.339, maximum 21.98 Map values for surface ""GP38GnHGc36125_46152_Fit3_real_space_refined_001-coot-4_real_space_refined_002.pdb_E SES surface"": minimum -28.69, mean -4.377, maximum 23.22 Map values for surface ""GP38GnHGc36125_46152_Fit3_real_space_refined_001-coot-4_real_space_refined_002.pdb_F SES surface"": minimum -25.47, mean -5.319, maximum 22.92 Map values for surface ""GP38GnHGc36125_46152_Fit3_real_space_refined_001-coot-4_real_space_refined_002.pdb_H SES surface"": minimum -25.88, mean -5.847, maximum 22.53 Map values for surface ""GP38GnHGc36125_46152_Fit3_real_space_refined_001-coot-4_real_space_refined_002.pdb_L SES surface"": minimum -24.83, mean -5.613, maximum 22.01 Map values for surface ""GP38GnHGc36125_46152_Fit3_real_space_refined_001-coot-4_real_space_refined_002.pdb_D SES surface"": minimum -28.54, mean -4.29, maximum 23.51 To also show corresponding color key, enter the above mlp command and add key true > hide atoms > show cartoons > delete #1/H/L/E/F > delete #2/H/L/E/F > hide #!3 models > show #!3 models > hide #!2 models > hide #!1 models > show #!2 models > hide #!2 models > show #!1 models > hide #!1 models > show #!1 models > hide #!3 models > show #!2 models > hide #!2 models > show #!3 models > hide #!3 models > show #!2 models > hide #!2 models > show #!2 models > hide #!1 models > show #!1 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > show #!3 models > hide #!3 models > show #!3 models > hide #!2 models > show #!2 models > hide #!1 models > show #!1 models > hide #!3 models > show #!3 models > hide #!1 models > hide #!3 models > show #!3 models > show #!1 models > hide #!1 models > hide #!2 models > show #!1 models > hide #!3 models > show #!3 models > show #!2 models > hide #!3 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!3 models > hide #!3 models > show #!2 models > hide #!2 models > show #!3 models > hide #!1 models > show #!2 models > hide #!2 models > show #!1 models > hide #!3 models > show #!2 models > hide #!2 models > show #!3 models > show #!2 models > hide #!3 models > hide #!1 models > show #!1 models > show #!3 models > hide #!1 models > hide #!3 models > show #!1 models > hide #!2 models > show #!2 models > hide #!1 models > show #!1 models > hide #!2 models > show #!2 models > hide #!1 models > show #!3 models > hide #!2 models > show #!2 models > hide #!2 models > show #!1 models > hide #!3 models > show #!3 models > show #!2 models > hide #!2 models > show #!2 models > select #1/B:1584-1586 39 atoms, 41 bonds, 3 residues, 1 model selected > hide #!1 models > show #!1 models > select #1/B:1584-1586 39 atoms, 41 bonds, 3 residues, 1 model selected > show sel > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > select add #1 447 atoms, 454 bonds, 56 residues, 1 model selected > select subtract #1 1 model selected > hide #!1 models > hide #!3 models > hide #!2 models > show #!2 models > show #!1 models > show #!3 models > coulombic Using Amber 20 recommended default charges and atom types for standard residues Coulombic values for GP38GnHGc36125_46152_Fit3_real_space_refined_001-coot-4_real_space_refined_002.pdb_B SES surface #1.3: minimum, -16.76, mean -0.19, maximum 13.37 Coulombic values for GP38GnHGc36125_46152_Fit3_real_space_refined_001-coot-4_real_space_refined_002.pdb_A SES surface #2.2: minimum, -20.60, mean -0.39, maximum 15.51 Coulombic values for GP38GnHGc36125_46152_Fit3_real_space_refined_001-coot-4_real_space_refined_002.pdb_D SES surface #3.2: minimum, -13.78, mean -1.56, maximum 9.23 To also show corresponding color key, enter the above coulombic command and add key true > mlp Map values for surface ""GP38GnHGc36125_46152_Fit3_real_space_refined_001-coot-4_real_space_refined_002.pdb_A SES surface"": minimum -26.9, mean -4.564, maximum 22.07 Map values for surface ""GP38GnHGc36125_46152_Fit3_real_space_refined_001-coot-4_real_space_refined_002.pdb_B SES surface"": minimum -28.33, mean -5.339, maximum 21.98 Map values for surface ""GP38GnHGc36125_46152_Fit3_real_space_refined_001-coot-4_real_space_refined_002.pdb_D SES surface"": minimum -28.54, mean -4.29, maximum 23.51 To also show corresponding color key, enter the above mlp command and add key true > coulombic Coulombic values for GP38GnHGc36125_46152_Fit3_real_space_refined_001-coot-4_real_space_refined_002.pdb_B SES surface #1.3: minimum, -16.76, mean -0.19, maximum 13.37 Coulombic values for GP38GnHGc36125_46152_Fit3_real_space_refined_001-coot-4_real_space_refined_002.pdb_A SES surface #2.2: minimum, -20.60, mean -0.39, maximum 15.51 Coulombic values for GP38GnHGc36125_46152_Fit3_real_space_refined_001-coot-4_real_space_refined_002.pdb_D SES surface #3.2: minimum, -13.78, mean -1.56, maximum 9.23 To also show corresponding color key, enter the above coulombic command and add key true > hide #!1 models > hide #!3 models > show #!1 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!1 models > show #!3 models > hide #!3 models > show #!1 models > hide #!2 models > show #!2 models > show #!3 models > hide #!2 models > hide #!1 models > show #!2 models > hide #!2 models > show #!1 models > show #!2 models > hide #!3 models > hide #!2 models > show #!3 models > hide #!1 models > show #!2 models > hide #!2 models > show #!1 models > hide #!3 models > show #!3 models > open > ""/Users/elizabethmcfadden/Documents/P1P8_Gc_36124_42437_refine_15-coot-0-LSQ > (1).pdb"" Chain information for P1P8_Gc_36124_42437_refine_15-coot-0-LSQ (1).pdb #4 --- Chain | Description A | No description available B | No description available G | No description available H | No description available L | No description available > hide #!4 models > close #4 > close > open /Users/elizabethmcfadden/Desktop/GP38GnHGc36125_46152_FixFusionLoops- > coot-5.pdb Chain information for GP38GnHGc36125_46152_FixFusionLoops-coot-5.pdb #1 --- Chain | Description A | No description available B | No description available D | No description available E | No description available F | No description available H | No description available L | No description available > open /Users/elizabethmcfadden/Desktop/GP38GnHGc36125_46152_FixFusionLoops- > coot-5.pdb Chain information for GP38GnHGc36125_46152_FixFusionLoops-coot-5.pdb #2 --- Chain | Description A | No description available B | No description available D | No description available E | No description available F | No description available H | No description available L | No description available > open /Users/elizabethmcfadden/Desktop/GP38GnHGc36125_46152_FixFusionLoops- > coot-5.pdb Chain information for GP38GnHGc36125_46152_FixFusionLoops-coot-5.pdb #3 --- Chain | Description A | No description available B | No description available D | No description available E | No description available F | No description available H | No description available L | No description available > delete #1/H/L/E/F/B/D > delete #2/H/L/E/F/A/D > delete #3/H/L/E/F/A/B > style stick Changed 4155 atom styles > mlp Map values for surface ""GP38GnHGc36125_46152_FixFusionLoops-coot-5.pdb_B SES surface"": minimum -28.03, mean -5.42, maximum 20.58 Map values for surface ""GP38GnHGc36125_46152_FixFusionLoops-coot-5.pdb_D SES surface"": minimum -28.06, mean -4.499, maximum 23.21 Map values for surface ""GP38GnHGc36125_46152_FixFusionLoops-coot-5.pdb_A SES surface"": minimum -26.49, mean -4.719, maximum 22.41 To also show corresponding color key, enter the above mlp command and add key true > open /Users/elizabethmcfadden/Desktop/GP38GnHGc36125_46152_FixFusionLoops- > coot-5.pdb Chain information for GP38GnHGc36125_46152_FixFusionLoops-coot-5.pdb #4 --- Chain | Description A | No description available B | No description available D | No description available E | No description available F | No description available H | No description available L | No description available > hide #!1 models > hide #!2 models > hide #!3 models > hide #!4 atoms > show #!4 cartoons > dssp > open /Users/elizabethmcfadden/Library/CloudStorage/Box- > Box/ElizabethMcFadden/CCHFV/GcEctoBase36125_46152_Phenix/cryosparc_P607_J142_map_sharp.mrc Opened cryosparc_P607_J142_map_sharp.mrc as #5, grid size 480,480,480, pixel 0.833, shown at level 0.000596, step 2, values float32 > surface dust #5 size 8.33 > volume #5 level 0.03432 > volume #5 level 0.05456 > volume #5 step 1 > volume #5 level 0.05826 > volume #5 level 0.085 > volume #5 level 0.08 > volume #5 level 0.07 > color #4/A cornflower blue > color #4/B dark orange > color #4/D medium sea green > color #4/L pink > hide #!5 models > show #!5 models > color #4/H #941751 > color #4/E goldenrod > color #4/F pale goldenrod > hide #!5 models > show #!5 models > hide #!5 models > show #!5 models > color zone #5 near #4 distance 5 > color zone #5 near #4 distance 4 > color zone #5 near #4 distance 3 > color zone #5 near #4 distance 4 > color zone #5 near #4 distance 5 > surface dust #5 size 8.33 > volume #5 level 0.06 > volume #5 level 0.08 > volume #5 level 0.07 > volume #5 level 0.08 > volume #5 level 0.07 > volume #5 level 0.06 > color zone #5 near #4 distance 4 > color zone #5 near #4 distance 3 > hide #!5 models > show #!5 models > hide #!5 models > show #!5 models > hide #!5 models > show #!5 models > hide #!5 models > show #!5 models > hide #!5 models > show #!5 models > hide #!5 models > show #!4 atoms > show #!5 models > style #!4 stick Changed 7571 atom styles > close #4 > open /Users/elizabethmcfadden/Desktop/GP38GnHGc36125_46152_FixFusionLoops- > coot-6.pdb Chain information for GP38GnHGc36125_46152_FixFusionLoops-coot-6.pdb #4 --- Chain | Description A | No description available B | No description available D | No description available E | No description available F | No description available H | No description available L | No description available > hide #!4 atoms > show #!4 cartoons > color #4/A cornflower blue > color #4/B dark orange > color #4/D medium sea green > color #4/H #941751 > color #4/L pink > color #4/E goldenrod > color #4/F pale goldenrod > color zone #5 near #4 distance 4 > color zone #5 near #4 distance 3 > color zone #5 near #4 distance 4 > color zone #5 near #4 distance 3 > color zone #5 near #4 distance 4 > volume splitbyzone #5 Opened cryosparc_P607_J142_map_sharp.mrc 0 as #6.1, grid size 480,480,480, pixel 0.833, shown at level 0.06, step 1, values float32 Opened cryosparc_P607_J142_map_sharp.mrc 1 as #6.2, grid size 480,480,480, pixel 0.833, shown at level 0.06, step 1, values float32 Opened cryosparc_P607_J142_map_sharp.mrc 2 as #6.3, grid size 480,480,480, pixel 0.833, shown at level 0.06, step 1, values float32 Opened cryosparc_P607_J142_map_sharp.mrc 3 as #6.4, grid size 480,480,480, pixel 0.833, shown at level 0.06, step 1, values float32 Opened cryosparc_P607_J142_map_sharp.mrc 4 as #6.5, grid size 480,480,480, pixel 0.833, shown at level 0.06, step 1, values float32 Opened cryosparc_P607_J142_map_sharp.mrc 5 as #6.6, grid size 480,480,480, pixel 0.833, shown at level 0.06, step 1, values float32 Opened cryosparc_P607_J142_map_sharp.mrc 6 as #6.7, grid size 480,480,480, pixel 0.833, shown at level 0.06, step 1, values float32 Opened cryosparc_P607_J142_map_sharp.mrc 7 as #6.8, grid size 480,480,480, pixel 0.833, shown at level 0.06, step 1, values float32 > hide #!6.1 models > surface dust #6.2 size 8.33 > surface dust #6.3 size 8.33 > surface dust #6.4 size 8.33 > surface dust #6.5 size 8.33 > surface dust #6.6 size 8.33 > surface dust #6.7 size 8.33 > surface dust #6.8 size 8.33 > lighting soft > graphics silhouettes false > graphics silhouettes true > lighting shadows true intensity 0.5 > lighting shadows false > lighting soft > ui tool show ""Side View"" > view orient > save /Users/elizabethmcfadden/Desktop/GP38GnGcfig.cxs includeMaps true > close #6.6-8 > close > open /Users/elizabethmcfadden/Desktop/GP38GnGcfig.cxs format session Opened cryosparc_P607_J142_map_sharp.mrc as #5, grid size 480,480,480, pixel 0.833, shown at level 0.06, step 1, values float32 Opened cryosparc_P607_J142_map_sharp.mrc 0 as #6.1, grid size 480,480,480, pixel 0.833, shown at level 0.06, step 1, values float32 Opened cryosparc_P607_J142_map_sharp.mrc 1 as #6.2, grid size 480,480,480, pixel 0.833, shown at level 0.06, step 1, values float32 Opened cryosparc_P607_J142_map_sharp.mrc 2 as #6.3, grid size 480,480,480, pixel 0.833, shown at level 0.06, step 1, values float32 Opened cryosparc_P607_J142_map_sharp.mrc 3 as #6.4, grid size 480,480,480, pixel 0.833, shown at level 0.06, step 1, values float32 Opened cryosparc_P607_J142_map_sharp.mrc 4 as #6.5, grid size 480,480,480, pixel 0.833, shown at level 0.06, step 1, values float32 Opened cryosparc_P607_J142_map_sharp.mrc 5 as #6.6, grid size 480,480,480, pixel 0.833, shown at level 0.06, step 1, values float32 Opened cryosparc_P607_J142_map_sharp.mrc 6 as #6.7, grid size 480,480,480, pixel 0.833, shown at level 0.06, step 1, values float32 Opened cryosparc_P607_J142_map_sharp.mrc 7 as #6.8, grid size 480,480,480, pixel 0.833, shown at level 0.06, step 1, values float32 opened ChimeraX session ===== Log before crash end ===== Log: > set bgColor white > cd Current working directory is: /Users/elizabethmcfadden > cd Desktop Current working directory is: /Users/elizabethmcfadden/Desktop UCSF ChimeraX version: 1.7.dev202307312254 (2023-07-31) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 INTEL-18.8.6 OpenGL renderer: Intel(R) Iris(TM) Plus Graphics OpenGL Engine 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: MacBookPro16,2 Processor Name: Quad-Core Intel Core i5 Processor Speed: 2 GHz Number of Processors: 1 Total Number of Cores: 4 L2 Cache (per Core): 512 KB L3 Cache: 6 MB Hyper-Threading Technology: Enabled Memory: 16 GB System Firmware Version: 1968.100.17.0.0 (iBridge: 20.16.4252.0.0,0) OS Loader Version: 540.120.3~22 Software: System Software Overview: System Version: macOS 12.6.5 (21G531) Kernel Version: Darwin 21.6.0 Time since boot: 3 days 1:39 Graphics/Displays: Intel Iris Plus Graphics: Chipset Model: Intel Iris Plus Graphics Type: GPU Bus: Built-In VRAM (Dynamic, Max): 1536 MB Vendor: Intel Device ID: 0x8a53 Revision ID: 0x0007 Metal Family: Supported, Metal GPUFamily macOS 2 Displays: Color LCD: Display Type: Built-In Retina LCD Resolution: 2560 x 1600 Retina Framebuffer Depth: 30-Bit Color (ARGB2101010) Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: No Connection Type: Internal Installed Packages: alabaster: 0.7.13 appdirs: 1.4.4 appnope: 0.1.3 asttokens: 2.2.1 Babel: 2.12.1 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: 1.6.2 charset-normalizer: 3.2.0 ChimeraX-AddCharge: 1.5.11 ChimeraX-AddH: 2.2.5 ChimeraX-AlignmentAlgorithms: 2.0.1 ChimeraX-AlignmentHdrs: 3.4 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.9.3 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.1.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.46.1 ChimeraX-AtomicLibrary: 10.0.8 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: 2.10.4 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: 1.0.2 ChimeraX-CheckWaters: 1.3.1 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.2.4 ChimeraX-ColorActions: 1.0.3 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.3 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.7.dev202307312254 ChimeraX-CoreFormats: 1.1 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: 1.1.2 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: 1.2.1 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 ChimeraX-Log: 1.1.5 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.8.2 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: 2.1.1 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.2 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.12 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.9 ChimeraX-ModelPanel: 1.4 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0 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: 1.10.2 ChimeraX-PDB: 2.7.2 ChimeraX-PDBBio: 1.0.1 ChimeraX-PDBLibrary: 1.0.2 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: 1.1.1 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: 3.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.1 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.9 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.1 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.12.1 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-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: 1.31.1 ChimeraX-uniprot: 2.3 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.2.2 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.1 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.1.3 contourpy: 1.1.0 cxservices: 1.2.2 cycler: 0.11.0 Cython: 0.29.33 debugpy: 1.6.7 decorator: 5.1.1 docutils: 0.19 executing: 1.2.0 filelock: 3.9.0 fonttools: 4.41.1 funcparserlib: 1.0.1 grako: 3.16.5 h5py: 3.9.0 html2text: 2020.1.16 idna: 3.4 ihm: 0.38 imagecodecs: 2023.7.10 imagesize: 1.4.1 ipykernel: 6.23.2 ipython: 8.14.0 ipython-genutils: 0.2.0 ipywidgets: 8.1.0 jedi: 0.18.2 Jinja2: 3.1.2 jupyter-client: 8.2.0 jupyter-core: 5.3.1 jupyterlab-widgets: 3.0.8 kiwisolver: 1.4.4 line-profiler: 4.0.2 lxml: 4.9.2 lz4: 4.3.2 MarkupSafe: 2.1.3 matplotlib: 3.7.2 matplotlib-inline: 0.1.6 msgpack: 1.0.4 nest-asyncio: 1.5.7 netCDF4: 1.6.2 networkx: 3.1 nibabel: 5.0.1 nptyping: 2.5.0 numexpr: 2.8.4 numpy: 1.25.1 openvr: 1.23.701 packaging: 21.3 ParmEd: 3.4.3 parso: 0.8.3 pep517: 0.13.0 pexpect: 4.8.0 pickleshare: 0.7.5 Pillow: 10.0.0 pip: 23.0 pkginfo: 1.9.6 platformdirs: 3.10.0 prompt-toolkit: 3.0.39 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: 2.14.0 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 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 pyzmq: 25.1.0 qtconsole: 5.4.3 QtPy: 2.3.1 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: 2.4.1 sphinx: 6.1.3 sphinx-autodoc-typehints: 1.22 sphinxcontrib-applehelp: 1.0.4 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.2 sphinxcontrib-htmlhelp: 2.0.1 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.3 sphinxcontrib-serializinghtml: 1.1.5 stack-data: 0.6.2 tables: 3.8.0 tcia-utils: 1.5.1 tifffile: 2023.7.18 tinyarray: 1.2.4 tomli: 2.0.1 tornado: 6.3.2 traitlets: 5.9.0 typing-extensions: 4.7.1 tzdata: 2023.3 urllib3: 2.0.4 wcwidth: 0.2.6 webcolors: 1.12 wheel: 0.38.4 wheel-filename: 1.4.1 widgetsnbextension: 4.0.8 }}} " defect closed normal Core can't reproduce all ChimeraX