![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 2 years ago
Closed 2 years ago
#9530 closed defect (can't reproduce)
Crash in garbage collection while drawing volume histogram after opening session
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Core | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
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
Change History (2)
comment:1 by , 2 years ago
| Component: | Unassigned → Core |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash in garbage collection while drawing volume histogram after opening session |
comment:2 by , 2 years ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | assigned → closed |
Note:
See TracTickets
for help on using tickets.
Probably a reference count bug. Log had several hundred commands doing a variety of things. No telling where the bad ref count arose. But probably garbage collection runs frequently (every second?) and a session was just opened. I think we see crashes right after session opening quite often. So probably something in the session restore process is involved. Also see multiprocessing module doing things and that might be involved.