Opened 9 months ago

Last modified 9 months ago

#17008 closed defect

ChimeraX bug report submission — at Initial Version

Reported by: chimerax-bug-report@… Owned by:
Priority: normal Milestone:
Component: Window Toolkit Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        macOS-15.3.1-arm64-arm-64bit
ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC)
Description
Last time you used ChimeraX it crashed.
This is a known crash that we are unable to fix. Here is information that may help you avoid this crash. The Qt window toolkit crashed due to a display configuration change, typically when waking from sleep or when an external display is disconnected or connected. This has only been seen on Mac computers. We hope a newer version of Qt will fix it. We update ChimeraX daily builds whenever a new Qt is released. You can check here https://www.cgl.ucsf.edu/chimerax/docs/troubleshoot.html#macdisplay to see if it has been fixed in a newer ChimeraX.
Fatal Python error: Segmentation fault

Thread 0x000000037dea3000 (most recent call first):
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 579 in _handle_results
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000000037ce97000 (most recent call first):
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 531 in _handle_tasks
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000000037be8b000 (most recent call first):
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/selectors.py", line 415 in select
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/connection.py", line 930 in wait
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 502 in _wait_for_updates
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 522 in _handle_workers
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000000037ae7f000 (most recent call first):
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x0000000379e73000 (most recent call first):
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x0000000378e67000 (most recent call first):
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x0000000377e5b000 (most recent call first):
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x0000000376e4f000 (most recent call first):
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x0000000375e43000 (most recent call first):
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x0000000374e37000 (most recent call first):
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x0000000373e2b000 (most recent call first):
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x0000000372e1f000 (most recent call first):
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x0000000371e13000 (most recent call first):
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x0000000370e07000 (most recent call first):
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000000036fdfb000 (most recent call first):
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000000036edef000 (most recent call first):
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000000036dde3000 (most recent call first):
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Current thread 0x00000001f2e48840 (most recent call first):
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 330 in event_loop
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1054 in init
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1217 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.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, charset_normalizer.md, requests.packages.charset_normalizer.md, requests.packages.chardet.md, PIL._imaging, kiwisolver._cext, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.pdb_lib._load_libs, chimerax.surface._surface, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, psutil._psutil_osx, psutil._psutil_posix, PIL._imagingmath, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.graphics._graphics, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, lxml._elementpath, lxml.etree (total: 60)


{"app_name":"ChimeraX","timestamp":"2025-03-03 15:55:50.00 -0600","app_version":"1.9.0","slice_uuid":"17982d98-65bc-3327-8526-577ec996453c","build_version":"1.9.0.0","platform":1,"bundleID":"edu.ucsf.cgl.ChimeraX","share_with_app_devs":0,"is_first_party":0,"bug_type":"309","os_version":"macOS 15.3.1 (24D70)","roots_installed":0,"name":"ChimeraX","incident_id":"37A10F69-EF68-4D38-BD8B-CD17713AA7B1"}
{
  "uptime" : 570000,
  "procRole" : "Foreground",
  "version" : 2,
  "userID" : 501,
  "deployVersion" : 210,
  "modelCode" : "Mac15,11",
  "coalitionID" : 44071,
  "osVersion" : {
    "train" : "macOS 15.3.1",
    "build" : "24D70",
    "releaseType" : "User"
  },
  "captureTime" : "2025-03-03 15:55:12.6718 -0600",
  "codeSigningMonitor" : 1,
  "incident" : "37A10F69-EF68-4D38-BD8B-CD17713AA7B1",
  "pid" : 23581,
  "translated" : false,
  "cpuType" : "ARM-64",
  "roots_installed" : 0,
  "bug_type" : "309",
  "procLaunch" : "2025-02-19 08:43:59.5648 -0600",
  "procStartAbsTime" : 4126564105854,
  "procExitAbsTime" : 13896021718937,
  "procName" : "ChimeraX",
  "procPath" : "\/Applications\/ChimeraX-1.9.app\/Contents\/MacOS\/ChimeraX",
  "bundleInfo" : {"CFBundleShortVersionString":"1.9.0","CFBundleVersion":"1.9.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
  "storeInfo" : {"deviceIdentifierForVendor":"0262D037-4938-5479-B386-8DE54511F617","thirdParty":true},
  "parentProc" : "launchd",
  "parentPid" : 1,
  "coalitionName" : "edu.ucsf.cgl.ChimeraX",
  "crashReporterKey" : "8DFA439A-F707-2332-B1DA-1DCB1CE3E141",
  "codeSigningID" : "edu.ucsf.cgl.ChimeraX",
  "codeSigningTeamID" : "LWV8X224YF",
  "codeSigningFlags" : 570491649,
  "codeSigningValidationCategory" : 6,
  "codeSigningTrustLevel" : 4294967295,
  "instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRcuD\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkWfg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
  "bootSessionUUID" : "A66B6B96-FA37-42E3-BB64-365127B94F3E",
  "wakeTime" : 14339,
  "sleepWakeUUID" : "A3A8E7E9-B9A8-4CC1-93E4-0569F51D349A",
  "sip" : "enabled",
  "vmRegionInfo" : "0x2e4a0466b708 is not in any region.  Bytes after previous region: 50414399960841  Bytes before following region: 54657679968504\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      commpage (reserved)        1000000000-7000000000   [384.0G] ---\/--- SM=NUL  reserved VM address space (unallocated)\n--->  GAP OF 0x5f9000000000 BYTES\n      MALLOC_NANO              600000000000-600020000000 [512.0M] rw-\/rwx SM=PRV  ",
  "exception" : {"codes":"0x0000000000000001, 0x0000ae4a0466b708","rawCodes":[1,191632924653320],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000ae4a0466b708 -> 0x00002e4a0466b708 (possible pointer authentication failure)"},
  "termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":23581},
  "ktriageinfo" : "VM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\n",
  "vmregioninfo" : "0x2e4a0466b708 is not in any region.  Bytes after previous region: 50414399960841  Bytes before following region: 54657679968504\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      commpage (reserved)        1000000000-7000000000   [384.0G] ---\/--- SM=NUL  reserved VM address space (unallocated)\n--->  GAP OF 0x5f9000000000 BYTES\n      MALLOC_NANO              600000000000-600020000000 [512.0M] rw-\/rwx SM=PRV  ",
  "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" : [{"threadState":{"x":[{"value":0},{"value":0},{"value":1},{"value":6099239192},{"value":108},{"value":115},{"value":0},{"value":1027},{"value":16837012982547051304},{"value":16837012974735457128},{"value":14757395258967641293},{"value":4294967286},{"value":6099239122},{"value":0},{"value":54},{"value":4294967280},{"value":328},{"value":8510808768},{"value":0},{"value":11},{"value":259},{"value":8370030880,"symbolLocation":224,"symbol":"_main_thread"},{"value":0},{"value":1},{"value":4390995504,"symbolLocation":0,"symbol":"faulthandler_handlers"},{"value":8333021184,"symbolLocation":0,"symbol":"OBJC_IVAR_$_NSTableView._rowSizeStyle"},{"value":8333021184,"symbolLocation":0,"symbol":"OBJC_IVAR_$_NSTableView._rowSizeStyle"},{"value":4},{"value":1}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6598524784},"cpsr":{"value":1073745920},"fp":{"value":6099239264},"sp":{"value":6099239232},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6598293280,"matchesCrashFrame":1},"far":{"value":0}},"id":4311918,"triggered":true,"name":"CrBrowserMain","queue":"com.apple.main-thread","frames":[{"imageOffset":38688,"symbol":"__pthread_kill","symbolLocation":8,"imageIndex":159},{"imageOffset":28528,"symbol":"pthread_kill","symbolLocation":288,"imageIndex":160},{"imageOffset":269336,"symbol":"raise","symbolLocation":32,"imageIndex":161},{"imageOffset":2417160,"symbol":"faulthandler_fatal_error","symbolLocation":392,"imageIndex":1},{"imageOffset":15844,"symbol":"_sigtramp","symbolLocation":56,"imageIndex":162},{"imageOffset":349344,"imageIndex":69},{"imageOffset":349160,"imageIndex":69},{"imageOffset":386264,"symbol":"_NSViewHierarchyDidChangeBackingProperties","symbolLocation":244,"imageIndex":163},{"imageOffset":11754200,"symbol":"-[NSWindow _postWindowDidChangeBackingPropertiesAndDisplayWindowForPreviousBackingScaleFactor:previousColorSpace:]","symbolLocation":192,"imageIndex":163},{"imageOffset":2081172,"symbol":"__67-[NSWindow _updateSettingsSendingScreenChangeNotificationToScreen:]_block_invoke","symbolLocation":440,"imageIndex":163},{"imageOffset":513240,"symbol":"NSPerformVisuallyAtomicChange","symbolLocation":108,"imageIndex":163},{"imageOffset":2080720,"symbol":"-[NSWindow _updateSettingsSendingScreenChangeNotificationToScreen:]","symbolLocation":96,"imageIndex":163},{"imageOffset":518736,"symbol":"-[NSWindow _setFrameCommon:display:fromServer:]","symbolLocation":2060,"imageIndex":163},{"imageOffset":11724000,"symbol":"-[NSWindow(NSScreenLayout) _setFrame:fromAdjustmentToScreen:anchorIfNeeded:animate:]","symbolLocation":628,"imageIndex":163},{"imageOffset":3247496,"symbol":"-[NSWindow _adjustWindowToScreen]","symbolLocation":1192,"imageIndex":163},{"imageOffset":3376636,"symbol":"-[NSWindow 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    "path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/mmcif\/mmcif.cpython-311-darwin.so",
    "name" : "mmcif.cpython-311-darwin.so"
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    "path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/mmcif\/_mmcif.cpython-311-darwin.so",
    "name" : "_mmcif.cpython-311-darwin.so"
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  {
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    "uuid" : "d7bd530c-3353-37a6-b81f-ee3179d65811",
    "path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/lz4\/_version.cpython-311-darwin.so",
    "name" : "_version.cpython-311-darwin.so"
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  {
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    "uuid" : "87eed069-25fc-30f6-aa30-1e54859d92e2",
    "path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/lz4\/frame\/_frame.cpython-311-darwin.so",
    "name" : "_frame.cpython-311-darwin.so"
  },
  {
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    "size" : 131072,
    "uuid" : "c1a3c2d3-b21b-3231-839d-fcbc83ca2028",
    "path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/core\/_serialize.cpython-311-darwin.so",
    "name" : "_serialize.cpython-311-darwin.so"
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  {
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    "size" : 131072,
    "uuid" : "650aead6-ce16-39bb-9ba1-4bf9986b96d6",
    "path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/msgpack\/_cmsgpack.cpython-311-darwin.so",
    "name" : "_cmsgpack.cpython-311-darwin.so"
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  {
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    "size" : 3817472,
    "uuid" : "579ef19c-6e85-36be-a566-c980f789fbc0",
    "path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/lxml\/etree.cpython-311-darwin.so",
    "name" : "etree.cpython-311-darwin.so"
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  {
    "source" : "P",
    "arch" : "arm64",
    "base" : 14100480000,
    "size" : 131072,
    "uuid" : "c8b24269-c8a2-3244-b044-b85c3449800d",
    "path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/lxml\/_elementpath.cpython-311-darwin.so",
    "name" : "_elementpath.cpython-311-darwin.so"
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    "base" : 6598254592,
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    "name" : "libsystem_kernel.dylib"
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    "size" : 53248,
    "uuid" : "642faf7a-874e-37e6-8aba-2b0cc09a3025",
    "path" : "\/usr\/lib\/system\/libsystem_pthread.dylib",
    "name" : "libsystem_pthread.dylib"
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    "path" : "\/usr\/lib\/system\/libsystem_c.dylib",
    "name" : "libsystem_c.dylib"
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    "path" : "\/usr\/lib\/system\/libsystem_platform.dylib",
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    "name" : "SkyLight"
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    "size" : 290816,
    "uuid" : "5576e4fd-aad2-3608-8c8f-4eec421236f9",
    "path" : "\/usr\/lib\/system\/libdispatch.dylib",
    "name" : "libdispatch.dylib"
  },
  {
    "source" : "P",
    "arch" : "arm64e",
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    "CFBundleShortVersionString" : "6.9",
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    "path" : "\/System\/Library\/Frameworks\/Carbon.framework\/Versions\/A\/Frameworks\/HIToolbox.framework\/Versions\/A\/HIToolbox",
    "name" : "HIToolbox"
  },
  {
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    "uuid" : "398a133c-9bcb-317f-a064-a40d3cea3c0f",
    "path" : "\/usr\/lib\/dyld",
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  "vmSummary" : "ReadOnly portion of Libraries: Total=1.9G resident=0K(0%) swapped_out_or_unallocated=1.9G(100%)\nWritable regions: Total=10.4G written=5831K(0%) resident=5831K(0%) swapped_out=0K(0%) unallocated=10.4G(100%)\n\n                                VIRTUAL   REGION \nREGION TYPE                        SIZE    COUNT (non-coalesced) \n===========                     =======  ======= \nAccelerate framework               384K        3 \nActivity Tracing                   256K        1 \nCG backing stores                 5536K        1 \nCG image                          2608K      136 \nColorSync                          736K       38 \nCoreAnimation                     6624K      304 \nCoreGraphics                        64K        4 \nCoreImage                          128K        4 \nCoreServices                       624K        2 \nCoreUI image data                 6016K       58 \nFoundation                          48K        2 \nKernel Alloc Once                 1456K        5 \nMALLOC                             9.3G      252 \nMALLOC guard page                  288K       18 \nMach message                        64K        2 \nOpenGL GLSL                        384K        4 \nSTACK GUARD                       57.0M       63 \nStack                            469.1M       63 \nVM_ALLOCATE                      300.4M      286 \nVM_ALLOCATE (reserved)           320.0M        3         reserved VM address space (unallocated)\n__AUTH                            5288K      672 \n__AUTH_CONST                      70.9M      920 \n__CTF                               824        1 \n__DATA                            33.5M     1069 \n__DATA_CONST                      34.3M     1086 \n__DATA_DIRTY                      2763K      342 \n__FONT_DATA                        2352        1 \n__GLSLBUILTINS                    5174K        1 \n__INFO_FILTER                         8        1 \n__LINKEDIT                       638.4M      160 \n__OBJC_RW                         2374K        1 \n__TEXT                             1.3G     1106 \n__TPRO_CONST                       272K        2 \ndyld private memory                 32K        2 \nmapped file                      368.8M       86 \nowned unmapped memory             84.9M        1 \npage table in kernel              5831K        1 \nshared memory                     3760K       29 \n===========                     =======  ======= \nTOTAL                             12.9G     6730 \nTOTAL, minus reserved VM space    12.6G     6730 \n",
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}
===== Log before crash start =====
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
You can double click a model's Name or ID in the model panel to edit those
fields  
UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "/Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/Final
> maps/Consensus/J1031_consensus_mask.mrc"

Opened J1031_consensus_mask.mrc as #1, grid size 540,540,540, pixel 0.818,
shown at level 1, step 4, values float32  

> volume #1 level 0.99

> volume #1 step 1

> volume #1 level 0.5232

> close #1

> open "/Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/Final
> maps/Consensus/J1031_mask.mrc"

Opened J1031_mask.mrc as #1, grid size 540,540,540, pixel 0.818, shown at
level 1, step 4, values float32  

> volume #1 step 1

> volume #1 level 0.99

> open "/Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/Final
> maps/Head/J1109_head_mask.mrc"

Opened J1109_head_mask.mrc as #2, grid size 540,540,540, pixel 0.818, shown at
level 0.453, step 4, values float32  

> volume #2 level 0.99

> volume #1 style mesh

> open "/Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/Final
> maps and masks/Body/J1033_body_mask.mrc"

Opened J1033_body_mask.mrc as #3, grid size 540,540,540, pixel 0.818, shown at
level 0.336, step 4, values float32  

> volume #3 step 1

> volume #3 level 0.99

> open "/Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/Final
> maps and masks/Body/055_body_full.mrc"

Opened 055_body_full.mrc as #4, grid size 540,540,540, pixel 0.818, shown at
level 0.000554, step 4, values float32  

> volume #4 step 1

> volume #4 level 0.003461

> volume #4 level 0.002842

> volume #4 level 0.004079

> open "/Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/Final
> maps and masks/Head/204_head_full.mrc"

Opened 204_head_full.mrc as #5, grid size 540,540,540, pixel 0.818, shown at
level 0.000481, step 4, values float32  

> volume #5 step 1

> volume #5 level 0.003727

> volume #5 level 0.002867

> volume #5 level 0.002515

> open "/Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/Final
> maps and masks/Head/204_head_denoised.mrc"

Opened 204_head_denoised.mrc as #6, grid size 540,540,540, pixel 0.818, shown
at level 0.000111, step 4, values float32  

> volume #6 step 1

> volume #6 level 0.002205

> volume #6 level 0.002166

> volume #6 level 0.002008

> volume #6 level 0.001534

> volume #6 level 0.00185

> volume #6 level 0.002047

> open "/Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/Final
> maps and masks/Body/055_body_angdist.bild"

Opened BILD data containing 11692 objects  

> close #4

> close #7

> open "/Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/Final
> maps and masks/Consensus/206_consensus_full.mrc"

Opened 206_consensus_full.mrc as #4, grid size 540,540,540, pixel 0.818, shown
at level 0.000217, step 4, values float32  

> volume #4 step 1

> volume #4 level 0.001665

> volume #4 level 0.002226

> open "/Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/Final
> maps and masks/Consensus/206_consensus_angdist.bild"

Opened BILD data containing 12282 objects  

> volume #4 color silver

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> close #2-3

> show #!6 models

> hide #!6 models

> close #5-6

> show #!1 models

> color #1 white models

> color #1 #fffb00ff models

> color #1 white models

> hide #7 models

> color #7 darkgrey

> show #7 models

> color #4 #929292ff models

> color #4 #5e5e5eff models

> color #4 #929292ff models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> open "/Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/Final
> maps and masks/Substrate/198_substrate_denoised.mrc"

Opened 198_substrate_denoised.mrc as #2, grid size 540,540,540, pixel 0.818,
shown at level 0.000277, step 4, values float32  

> volume #2 step 1

> volume #2 level 0.001181

> close #2

> close #4

> close #1

> close

> open "/Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/Final
> maps and masks/Head/204_head_full.mrc"

Opened 204_head_full.mrc as #1, grid size 540,540,540, pixel 0.818, shown at
level 0.000481, step 4, values float32  

> open "/Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/Final
> maps and masks/Head/219_head_locres.mrc"

Opened 219_head_locres.mrc as #2, grid size 540,540,540, pixel 0.818, shown at
level 50, step 4, values float32  

> hide #!2 models

> volume #1 step 1

> volume #1 level 0.001925

> ui tool show "Surface Color"

> color sample #1.1 map #2 palette #0000ff:#00ffff:#00ff00:#ffff00:#ff0000

Map values for surface "surface": minimum 3.737, mean 5.01, maximum 9.384  

> volume #1 level 0.004271

> volume #1 level 0.002472

> color sample #1.1 map #2 palette
> 3.7,#0000ff:4.2,#00ffff:4.7,#00ff00:5.2,#ffff00:5.9,#ff0000

Map values for surface "surface": minimum 3.738, mean 4.875, maximum 9.013  

> color sample #1.1 map #2 palette
> 3.7,#0000ff:4.7,#00ffff:5.7,#00ff00:6.7,#ffff00:7.7,#ff0000

Map values for surface "surface": minimum 3.738, mean 4.875, maximum 9.013  

> volume #1 level 0.002003

> volume #1 level 0.003645

> volume #1 level 0.004623

> close #2

> close #1

> open "/Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/Final
> maps and masks/Consensus/206_consensus_full.mrc"

Opened 206_consensus_full.mrc as #1, grid size 540,540,540, pixel 0.818, shown
at level 0.000217, step 4, values float32  

> open "/Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/Final
> maps and masks/Consensus/223_consensus_locres.mrc"

Opened 223_consensus_locres.mrc as #2, grid size 540,540,540, pixel 0.818,
shown at level 50, step 4, values float32  

> volume #1 step 1

> volume #1 level 0.002032

> color sample #1.1 map #2 palette #0000ff:#00ffff:#00ff00:#ffff00:#ff0000

Map values for surface "surface": minimum 2.794, mean 3.254, maximum 8.111  

> volume #1 level 0.002123

> color sample #1.1 map #2 palette
> 2.8,#0000ff:3.8,#00ffff:4.8,#00ff00:5.8,#ffff00:6.8,#ff0000

Map values for surface "surface": minimum 2.794, mean 3.229, maximum 8.069  

> volume #1 level 0.00353

> volume #1 level 0.002531

> volume #1 level 0.002123

> close #1

> close #2

> open "/Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/Final
> maps and masks/Body/055_body_full.mrc"

Opened 055_body_full.mrc as #1, grid size 540,540,540, pixel 0.818, shown at
level 0.000554, step 4, values float32  

> open "/Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/Final
> maps and masks/Body/220_body_locres.mrc"

Opened 220_body_locres.mrc as #2, grid size 540,540,540, pixel 0.818, shown at
level 50, step 4, values float32  

> volume #1 step 1

> volume #1 level 0.004098

> color sample #1.1 map #1 palette #0000ff:#00ffff:#00ff00:#ffff00:#ff0000

Map values for surface "surface": minimum 0.004098, mean 0.004098, maximum
0.004099  

> color sample #1.1 map #1 palette #0000ff:#00ffff:#00ff00:#ffff00:#ff0000

Map values for surface "surface": minimum 0.004098, mean 0.004098, maximum
0.004099  

> color sample #1.1 map #1 palette
> 2.7,#0000ff:3.7,#00ffff:4.7,#00ff00:5.7,#ffff00:6.7,#ff0000

Map values for surface "surface": minimum 0.004098, mean 0.004098, maximum
0.004099  

> color sample #1.1 map #2 palette #0000ff:#00ffff:#00ff00:#ffff00:#ff0000

Map values for surface "surface": minimum 2.818, mean 3.087, maximum 6.363  

> color sample #1.1 map #2 palette
> 2.8,#0000ff:3.3,#00ffff:3.8,#00ff00:4.3,#ffff00:4.8,#ff0000

Map values for surface "surface": minimum 2.818, mean 3.087, maximum 6.363  

> open "/Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/3D
> classes/Body/045/run_it035_class001.mrc"

Opened run_it035_class001.mrc as #3, grid size 540,540,540, pixel 0.818, shown
at level 1.24e-06, step 4, values float32  

> volume #3 level 0.001541

> volume #3 step 1

> volume #3 level 0.003412

> open "/Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/3D
> classes/Body/045/run_it035_class002.mrc"

Opened run_it035_class002.mrc as #4, grid size 540,540,540, pixel 0.818, shown
at level 1.4e-06, step 4, values float32  

> open "/Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/3D
> classes/Body/045/run_it035_class003.mrc"

Opened run_it035_class003.mrc as #5, grid size 540,540,540, pixel 0.818, shown
at level 7.73e-07, step 4, values float32  

> open "/Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/3D
> classes/Body/045/run_it035_class004.mrc"

Opened run_it035_class004.mrc as #6, grid size 540,540,540, pixel 0.818, shown
at level 9.89e-07, step 4, values float32  

> open "/Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/3D
> classes/Body/045/run_it035_class005.mrc"

Opened run_it035_class005.mrc as #7, grid size 540,540,540, pixel 0.818, shown
at level 3.7e-07, step 4, values float32  

> open "/Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/3D
> classes/Body/045/run_it035_class006.mrc"

Opened run_it035_class006.mrc as #8, grid size 540,540,540, pixel 0.818, shown
at level 1.67e-06, step 4, values float32  

> close #8

> close #7

> close #6

> close #3-5

> open "/Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/3D
> classes/Head/Round 2/085/run_it025_class001.mrc"

Opened run_it025_class001.mrc as #3, grid size 540,540,540, pixel 0.818, shown
at level 1.38e-07, step 4, values float32  

> open "/Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/3D
> classes/Head/Round 2/085/run_it025_class002.mrc"

Opened run_it025_class002.mrc as #4, grid size 540,540,540, pixel 0.818, shown
at level 6e-07, step 4, values float32  

> open "/Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/3D
> classes/Head/Round 2/085/run_it025_class003.mrc"

Opened run_it025_class003.mrc as #5, grid size 540,540,540, pixel 0.818, shown
at level 8.07e-08, step 4, values float32  

> open "/Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/3D
> classes/Head/Round 2/085/run_it025_class004.mrc"

Opened run_it025_class004.mrc as #6, grid size 540,540,540, pixel 0.818, shown
at level 3.08e-06, step 4, values float32  

> open "/Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/3D
> classes/Head/Round 2/085/run_it025_class005.mrc"

Opened run_it025_class005.mrc as #7, grid size 540,540,540, pixel 0.818, shown
at level 9.72e-07, step 4, values float32  

> open "/Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/3D
> classes/Head/Round 2/085/run_it025_class006.mrc"

Opened run_it025_class006.mrc as #8, grid size 540,540,540, pixel 0.818, shown
at level 3.31e-07, step 4, values float32  

> volume #3-8 step 1 level 0.005

> volume #3-8 step 1 level 0.05

> volume #3-8 step 1 level 0.0035

> hide #!8 models

> hide #!7 models

> hide #!6 models

> show #!6 models

> hide #!6 models

> show #!7 models

> show #!8 models

> volume #3-8 step 1 level 0.0015

> volume #3-8 step 1 level 0.002

> hide #!5 models

> hide #!4 models

> hide #!8 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> open "/Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/Final
> maps and masks/Substrate/237_substrate_sharpened.mrc"

Opened 237_substrate_sharpened.mrc as #9, grid size 540,540,540, pixel 0.818,
shown at level 0.000281, step 4, values float32  

> close #3-8

> volume #9 step 1

> volume #9 level 0.00115

> volume #9 level 0.001509

> volume #9 level 0.001764

> volume #9 level 0.002123

> volume #9 level 0.002078

> volume #9 level 0.001554

> volume #9 level 0.001764

> volume #9 level 0.002063

> volume #9 level 0.001869

> open /Users/mulline1/Desktop/Tmp/237_substrated_sharpened_masked.mrc

Opened 237_substrated_sharpened_masked.mrc as #3, grid size 540,540,540, pixel
0.818, shown at level 8.06e-06, step 4, values float32  

> volume #3 step 1

> volume #3 level 0.00185

> volume #3 level 0.00212

> volume #3 level 0.00209

> volume #3 level 0.001985

> show #!1 models

> volume #3 level 0.003977

> volume #3 level 0.00182

> volume #3 level 0.002779

> volume #3 level 0.00206

> volume #3 level 0.00188

> show #!2 models

> hide #!3 models

> hide #!2 models

> show #!1 models

> show #!9 models

> hide #!9 models

> show #!3 models

> show #!9 models

> hide #!9 models

> hide #!1 models

> close #1-3,9

> open "/Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/Final
> maps and masks/Consensus/J1169_consensus_sharpened.mrc"

Opened J1169_consensus_sharpened.mrc as #1, grid size 540,540,540, pixel
0.818, shown at level 0.000199, step 4, values float32  

> open "/Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/Final
> maps and masks/Body/J1068_body_sharpened.mrc"

Opened J1068_body_sharpened.mrc as #2, grid size 540,540,540, pixel 0.818,
shown at level 3.71e-05, step 4, values float32  

> open "/Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/Final
> maps and masks/Substrate/237_substrate_sharpened.mrc"

Opened 237_substrate_sharpened.mrc as #3, grid size 540,540,540, pixel 0.818,
shown at level 0.000281, step 4, values float32  

> volume #1 step 1

> volume #1 level 0.0317

> volume #2 step 1

> volume #2 level 0.0399

> volume #3 step 1

> volume #3 level 0.001015

> ui tool show "Fit in Map"

> fitmap #2 inMap #1

Fit map J1068_body_sharpened.mrc in map J1169_consensus_sharpened.mrc using
124728 points  
correlation = 0.9234, correlation about mean = 0.8157, overlap = 2.336e+04  
steps = 68, shift = 0.382, angle = 1.19 degrees  
  
Position of J1068_body_sharpened.mrc (#2) relative to
J1169_consensus_sharpened.mrc (#1) coordinates:  
Matrix rotation and translation  
0.99978443 0.02004485 -0.00541229 -2.73172076  
-0.02003564 0.99979773 0.00175138 4.26412471  
0.00544630 -0.00164257 0.99998382 -0.90382288  
Axis -0.08146033 -0.26062417 -0.96199753  
Axis point 211.17601142 138.63002073 0.00000000  
Rotation angle (degrees) 1.19366680  
Shift along axis -0.01933169  
  

> fitmap #3 inMap #1

Fit map 237_substrate_sharpened.mrc in map J1169_consensus_sharpened.mrc using
753317 points  
correlation = 0.4412, correlation about mean = 0.1902, overlap = 148  
steps = 84, shift = 4.55, angle = 4.03 degrees  
  
Position of 237_substrate_sharpened.mrc (#3) relative to
J1169_consensus_sharpened.mrc (#1) coordinates:  
Matrix rotation and translation  
0.99984441 0.01628946 0.00676834 -6.17845683  
-0.01671235 0.99754500 0.06800488 -13.60262380  
-0.00564396 -0.06810741 0.99766203 14.94284766  
Axis -0.96804793 0.08827788 -0.23471307  
Axis point 0.00000000 216.59655581 209.49587111  
Rotation angle (degrees) 4.03135928  
Shift along axis 1.27294990  
  

> volume #3 level 0.001467

> volume #1 level 0.07813

> volume #3 level 0.001737

> volume #3 style mesh

> open /Users/mulline1/Downloads/SCF(FBH1)-fork-full-model.pdb

Summary of feedback from opening /Users/mulline1/Downloads/SCF(FBH1)-fork-
full-model.pdb  
---  
warnings | Duplicate atom serial number found: 11  
Duplicate atom serial number found: 12  
Duplicate atom serial number found: 13  
Duplicate atom serial number found: 14  
Duplicate atom serial number found: 15  
5767 messages similar to the above omitted  
  
Chain information for SCF(FBH1)-fork-full-model.pdb #4  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
U | No description available  
V | No description available  
X | No description available  
Y | No description available  
  

> hide atoms

> show cartoons

> select add #4

17030 atoms, 17621 bonds, 8 pseudobonds, 1912 residues, 3 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #4,0.83512,-0.52001,-0.17935,128.47,-0.52161,-0.64512,-0.55835,405.08,0.17464,0.55984,-0.80999,163.95

> ui mousemode right "translate selected models"

> view matrix models
> #4,0.83512,-0.52001,-0.17935,166.71,-0.52161,-0.64512,-0.55835,525.57,0.17464,0.55984,-0.80999,224.47

> ui mousemode right translate

> ui mousemode right "translate selected models"

> view matrix models
> #4,0.83512,-0.52001,-0.17935,191.24,-0.52161,-0.64512,-0.55835,518.78,0.17464,0.55984,-0.80999,228.37

> ui mousemode right "rotate selected models"

> view matrix models
> #4,0.91254,-0.28213,-0.2961,162.08,-0.40475,-0.72696,-0.55472,509.92,-0.058747,0.62605,-0.77757,253.83

> view matrix models
> #4,0.91495,-0.29647,-0.2738,160.33,-0.39639,-0.78754,-0.47187,504.56,-0.075733,0.54027,-0.83808,277.94

> ui mousemode right "translate selected models"

> view matrix models
> #4,0.91495,-0.29647,-0.2738,158.66,-0.39639,-0.78754,-0.47187,497.63,-0.075733,0.54027,-0.83808,270.51

> fitmap #4 inMap #1

Fit molecule SCF(FBH1)-fork-full-model.pdb (#4) to map
J1169_consensus_sharpened.mrc (#1) using 17030 atoms  
average map value = 0.3039, steps = 256  
shifted from previous position = 2.06  
rotated from previous position = 19.8 degrees  
atoms outside contour = 7803, contour level = 0.07813  
  
Position of SCF(FBH1)-fork-full-model.pdb (#4) relative to
J1169_consensus_sharpened.mrc (#1) coordinates:  
Matrix rotation and translation  
0.99603941 -0.08809262 -0.01204898 68.08931873  
-0.08173721 -0.85387465 -0.51402054 462.40034064  
0.03499309 0.51296957 -0.85769325 260.64617100  
Axis 0.99893348 -0.04575692 0.00618179  
Axis point 0.00000000 196.70221723 194.46094939  
Rotation angle (degrees) 149.06647099  
Shift along axis 48.46994193  
  

> ui mousemode right translate

> select clear

> hide #!4 models

> hide #!3 models

> hide #!2 models

> show #!4 models

> show #!2 models

> hide #!1 models

> show #!1 models

> volume #3 level 0.00154

> volume #3 level 0.001765

> volume #1 level 0.04849

> volume #1 level 0.02544

> volume #1 level 0.1144

> volume #1 level 0.03861

> volume #3 level 0.001202

> surface dust #1 size 8.18

> surface dust #2 size 8.18

> hide #!4 models

> show #!4 models

> hide #!1 models

> hide #!4 models

> show #!1 models

> show #!2 models

> hide #!1 models

> show #!3 models

> hide #!2 models

> show #!2 models

> hide #!3 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!1 models

> volume #3 level 0.001512

> volume #3 level 0.002047

> open "/Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/Final
> maps and masks/Head/Revised/J1187_head_sharpened.mrc"

Opened J1187_head_sharpened.mrc as #5, grid size 540,540,540, pixel 0.818,
shown at level 0.000148, step 4, values float32  

> volume #5 step 1

> volume #5 level 0.06663

> fitmap #5 inMap #1

Fit map J1187_head_sharpened.mrc in map J1169_consensus_sharpened.mrc using
150205 points  
correlation = 0.47, correlation about mean = 0.1047, overlap = 6891  
steps = 80, shift = 1.61, angle = 1.79 degrees  
  
Position of J1187_head_sharpened.mrc (#5) relative to
J1169_consensus_sharpened.mrc (#1) coordinates:  
Matrix rotation and translation  
0.99951322 0.02623089 -0.01688992 -2.79303153  
-0.02620120 0.99965474 0.00197655 4.79852728  
0.01693593 -0.00153305 0.99985540 -1.93261563  
Axis -0.05615814 -0.54125656 -0.83898010  
Axis point 164.75721743 111.28954436 0.00000000  
Rotation angle (degrees) 1.79064236  
Shift along axis -0.81895687  
  

> hide #!3 models

> hide #!1 models

> show #!2 models

> volume #5 level 0.06663

> volume #5 color #ffd479

> volume #3 color #ff9300

> show #!4 models

> hide #!2 models

> hide #!5 models

Drag select of 9 residues  

> select up

1389 atoms, 1555 bonds, 68 residues, 1 model selected  

> select up

17030 atoms, 17621 bonds, 1912 residues, 1 model selected  

> select down

1389 atoms, 1555 bonds, 68 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel orange

> select clear

Drag select of 3 residues  

> select up

930 atoms, 1046 bonds, 45 residues, 1 model selected  

> color sel orange

Drag select of 1 residues  

> select up

321 atoms, 357 bonds, 16 residues, 1 model selected  

> color sel orange

> select clear

Drag select of 13 residues  

> select up

292 atoms, 298 bonds, 36 residues, 1 model selected  

> select up

4714 atoms, 4810 bonds, 591 residues, 1 model selected  

> select up

4741 atoms, 4836 bonds, 595 residues, 1 model selected  

> select up

6405 atoms, 6542 bonds, 802 residues, 1 model selected  

> select up

6458 atoms, 6594 bonds, 806 residues, 1 model selected  

> select up

17030 atoms, 17621 bonds, 1912 residues, 1 model selected  

> select down

6458 atoms, 6594 bonds, 806 residues, 1 model selected  

> select up

17030 atoms, 17621 bonds, 1912 residues, 1 model selected  

> select down

6458 atoms, 6594 bonds, 806 residues, 1 model selected  

> color sel cornflower blue

> color sel blue

> color sel cornflower blue

Drag select of 9 residues  

> select up

386 atoms, 391 bonds, 45 residues, 1 model selected  

> select up

4490 atoms, 4560 bonds, 552 residues, 1 model selected  

> select up

4535 atoms, 4604 bonds, 558 residues, 1 model selected  

> select up

5655 atoms, 5746 bonds, 693 residues, 1 model selected  

> select up

5674 atoms, 5764 bonds, 696 residues, 1 model selected  

> select up

5991 atoms, 6089 bonds, 733 residues, 1 model selected  

> color sel lime

> select clear

Drag select of 2 residues  

> select up

1207 atoms, 1228 bonds, 153 residues, 1 model selected  

> color sel magenta

Drag select of 4 residues  

> select up

731 atoms, 752 bonds, 88 residues, 1 model selected  

> color sel purple

> select clear

> volume #5 style mesh

> volume #5 style surface

> volume #5 level 0.05218

> volume #5 level 0.06663

> volume #5 style mesh

> volume #5 level 0.08108

> volume #5 level 0.2617

> volume #5 level 0.03412

> volume #5 style surface

> volume #3 level 0.001509

> volume #1 level 0.04881

> hide #!4 models

> volume #5 level 0.01245

> surface dust #5 size 8.18

> open "/Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/Final
> maps and masks/Consensus/223_consensus_locres.mrc"

Opened 223_consensus_locres.mrc as #6, grid size 540,540,540, pixel 0.818,
shown at level 50, step 4, values float32  

> ui tool show "Surface Color"

> color sample #1.1 map #6 palette #0000ff:#00ffff:#00ff00:#ffff00:#ff0000

Map values for surface "surface": minimum 2.794, mean 3.196, maximum 8.098  

> color sample #1.1 map #6 palette
> 2.8,#0000ff:3.8,#00ffff:4.8,#00ff00:5.8,#ffff00:6.8,#ff0000

Map values for surface "surface": minimum 2.794, mean 3.196, maximum 8.098  

> color sample #1.1 map #6 palette
> 2.8,#0000ff:3.3,#00ffff:3.8,#00ff00:4.3,#ffff00:4.8,#ff0000

Map values for surface "surface": minimum 2.794, mean 3.196, maximum 8.098  

> color sample #1.1 map #6 palette
> 2.8,#0000ff:3.3,#00ffff:3.8,#00ff00:4.3,#ffff00:6.8,#ff0000

Map values for surface "surface": minimum 2.794, mean 3.196, maximum 8.098  

> color sample #1.1 map #6 palette
> 2.8,#0000ff:3.1,#00ffff:3.4,#00ff00:3.7,#ffff00:6.8,#ff0000

Map values for surface "surface": minimum 2.794, mean 3.196, maximum 8.098  

> color sample #1.1 map #6 palette
> 2.8,#0000ff:3.3,#00ffff:3.8,#00ff00:4.3,#ffff00:6.8,#ff0000

Map values for surface "surface": minimum 2.794, mean 3.196, maximum 8.098  

> color sample #1.1 map #6 palette
> 2.8,#ff0000:3.3,#ffff00:3.8,#00ff00:4.3,#00ffff:6.8,#0000ff

Map values for surface "surface": minimum 2.794, mean 3.196, maximum 8.098  

> color sample #1.1 map #6 palette
> 2.8,#0000ff:3.3,#00ffff:3.8,#00ff00:4.3,#ffff00:6.8,#ff0000

Map values for surface "surface": minimum 2.794, mean 3.196, maximum 8.098  

> color single #1.1

> color sample #1.1 map #6 palette
> 2.8,#0000ff:3.3,#00ffff:3.8,#00ff00:4.3,#ffff00:6.8,#ff0000

Map values for surface "surface": minimum 2.794, mean 3.196, maximum 8.098  

> color single #1.1

> color sample #1.1 map #6 palette
> 2.8,#0000ff:3.3,#00ffff:3.8,#00ff00:4.3,#ffff00:6.8,#ff0000

Map values for surface "surface": minimum 2.794, mean 3.196, maximum 8.098  

> color single #1.1

> close #1-6

> open "/Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/Final
> maps and masks/Consensus/J1169_consensus_sharpened.mrc"

Opened J1169_consensus_sharpened.mrc as #1, grid size 540,540,540, pixel
0.818, shown at level 0.000199, step 4, values float32  

> open "/Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/Final
> maps and masks/Consensus/J1031_consensus_mask.mrc"

Opened J1031_consensus_mask.mrc as #2, grid size 540,540,540, pixel 0.818,
shown at level 1, step 4, values float32  

> volume #2 step 1

> volume #2 level 0.99

> volume #1 step 1

> volume #1 level 0.041

> volume multiply #1-2

Opened volume product as #3, grid size 540,540,540, pixel 0.818, shown at step
1, values float32  

> volume #3 level 0.05077

> hide #!3 models

> open "/Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/Final
> maps and masks/Body/J1068_body_sharpened.mrc"

Opened J1068_body_sharpened.mrc as #4, grid size 540,540,540, pixel 0.818,
shown at level 3.71e-05, step 4, values float32  

> open "/Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/Final
> maps and masks/Body/J1033_body_mask.mrc"

Opened J1033_body_mask.mrc as #5, grid size 540,540,540, pixel 0.818, shown at
level 0.336, step 4, values float32  

> volume #5 step 1

> volume #4 step 1

> volume multiply #4-5

Opened volume product as #6, grid size 540,540,540, pixel 0.818, shown at step
1, values float32  

> volume #6 level 0.07179

> volume #4 level 0.05983

> hide #!6 models

> open "/Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/Final
> maps and masks/Head/Revised/J1187_head_sharpened.mrc"

Opened J1187_head_sharpened.mrc as #7, grid size 540,540,540, pixel 0.818,
shown at level 0.000148, step 4, values float32  

> open "/Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/Final
> maps and masks/Head/J1032_head_mask.mrc"

Opened J1032_head_mask.mrc as #8, grid size 540,540,540, pixel 0.818, shown at
level 0.997, step 4, values float32  

> volume multiply #7-8

Opened volume product as #9, grid size 540,540,540, pixel 0.818, shown at step
1, values float32  

> volume #9 level 0.04106

> volume #9 level 0.01502

> open
> "/Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/Preliminary
> maps and masks/J1073_head_mask.mrc"

Opened J1073_head_mask.mrc as #10, grid size 540,540,540, pixel 0.818, shown
at level 5e-05, step 4, values float32  

> hide #!9 models

> hide #!10 models

> volume multiply #7,10

Opened volume product as #11, grid size 540,540,540, pixel 0.818, shown at
step 1, values float32  

> volume #11 level 0.0299

> volume #11 level 0.02246

> show #!9 models

> hide #!9 models

> show #!6 models

> show #!3 models

> show #!6 models

> show #!9 models

> hide #!9 models

> show #!9 models

> hide #!9 models

> save "/Users/mulline1/Dropbox/FBH1/cryoEM_revised/Final maps and
> masks/Consensus/J1169_consensus_sharpened_masked.mrc" models #3

> hide #!3 models

> volume #6 level 0.05584

> volume #11 level 0.05593

> save "/Users/mulline1/Dropbox/FBH1/cryoEM_revised/Final maps and
> masks/Body/J1068_body_sharpened_masked.mrc" models #6

> save "/Users/mulline1/Dropbox/FBH1/cryoEM_revised/Final maps and
> masks/Head/Revised/J1187_head_sharpened_masked.mrc" models #11

> close #1-11

> open "/Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/Final
> maps and masks/Consensus/J1169_consensus_sharpened_masked.mrc"

Opened J1169_consensus_sharpened_masked.mrc as #1, grid size 540,540,540,
pixel 0.818, shown at level 2.26e-05, step 4, values float32  

> open "/Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/Final
> maps and masks/Head/Revised/J1187_head_sharpened_masked.mrc"

Opened J1187_head_sharpened_masked.mrc as #2, grid size 540,540,540, pixel
0.818, shown at level 0.000148, step 4, values float32  

> open "/Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/Final
> maps and masks/Body/J1068_body_sharpened_masked.mrc"

Opened J1068_body_sharpened_masked.mrc as #3, grid size 540,540,540, pixel
0.818, shown at level 3.71e-05, step 4, values float32  

> open "/Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/Final
> maps and masks/Substrate/237_substrate_sharpened_masked.mrc"

Opened 237_substrate_sharpened_masked.mrc as #4, grid size 540,540,540, pixel
0.818, shown at level 8.06e-06, step 4, values float32  

> volume #1 step 1

> volume #2 step 1

> volume #3 step 1

> volume #4 step 1

> volume #4 level 5.17e-05

> volume #4 level 6.624e-05

> volume #4 level 9.534e-05

> volume #4 level 0.0001099

> volume #4 level 0.0001244

> volume #4 level 0.0001535

> volume #4 level 0.0001826

> volume #4 level 0.0001972

> volume #4 level 0.0002553

> volume #4 level 0.0002844

> volume #4 level 0.0003135

> volume #4 level 0.0003281

> volume #4 level 0.0003426

> volume #4 level 0.0003572

> volume #4 level 0.0003717

> volume #4 level 0.0003863

> volume #4 level 0.0004153

> volume #4 level 0.0004299

> volume #4 level 0.0004444

> volume #4 level 0.000459

> volume #4 level 0.0004735

> volume #4 level 0.0004881

> volume #4 level 0.0005026

> volume #4 level 0.0005172

> volume #4 level 0.0005317

> volume #4 level 0.0005463

> close #4

> open "/Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/Final
> maps and masks/Substrate/Revised/262_substrate_sharpened_masked.mrc"

Opened 262_substrate_sharpened_masked.mrc as #4, grid size 540,540,540, pixel
0.818, shown at level 1.48e-05, step 4, values float32  

> volume #4 step 1

> volume #4 level 0.0007471

> volume #4 level 0.001241

> volume #1 level 0.02042

> volume #2 level 0.06516

> volume #3 level 0.0465

> volume #1 level 0.07142

> volume #2 level 0.04349

> volume #3 level 0.06973

> volume #4 level 0.001686

> ui tool show "Fit in Map"

> fitmap #2 inMap #1

Fit map J1187_head_sharpened_masked.mrc in map
J1169_consensus_sharpened_masked.mrc using 56800 points  
correlation = 0.5222, correlation about mean = 0.2802, overlap = 3254  
steps = 216, shift = 2.19, angle = 1.41 degrees  
  
Position of J1187_head_sharpened_masked.mrc (#2) relative to
J1169_consensus_sharpened_masked.mrc (#1) coordinates:  
Matrix rotation and translation  
0.99969566 0.02370801 -0.00682039 -3.57433463  
-0.02370882 0.99971891 -0.00003754 4.43490885  
0.00681758 0.00019924 0.99997674 -0.19053019  
Axis 0.00479895 -0.27640972 -0.96102791  
Axis point 172.88925083 152.76969778 0.00000000  
Rotation angle (degrees) 1.41362159  
Shift along axis -1.05990014  
  

> fitmap #3 inMap #1

Fit map J1068_body_sharpened_masked.mrc in map
J1169_consensus_sharpened_masked.mrc using 102847 points  
correlation = 0.9368, correlation about mean = 0.816, overlap = 2.303e+04  
steps = 68, shift = 0.361, angle = 1.21 degrees  
  
Position of J1068_body_sharpened_masked.mrc (#3) relative to
J1169_consensus_sharpened_masked.mrc (#1) coordinates:  
Matrix rotation and translation  
0.99977978 0.02020549 -0.00566905 -2.71069053  
-0.02019621 0.99979461 0.00169013 4.30859413  
0.00570203 -0.00157527 0.99998250 -0.96829419  
Axis -0.07756628 -0.27010829 -0.95970047  
Axis point 211.62361753 136.55577568 0.00000000  
Rotation angle (degrees) 1.20611482  
Shift along axis -0.02425643  
  

> fitmap #4 inMap #1

Fit map 262_substrate_sharpened_masked.mrc in map
J1169_consensus_sharpened_masked.mrc using 263331 points  
correlation = 0.455, correlation about mean = 0.1361, overlap = 80.48  
steps = 108, shift = 3.44, angle = 7.29 degrees  
  
Position of 262_substrate_sharpened_masked.mrc (#4) relative to
J1169_consensus_sharpened_masked.mrc (#1) coordinates:  
Matrix rotation and translation  
0.99896011 0.01308895 0.04367363 -14.11352907  
-0.01817121 0.99283745 0.11808305 -24.51926830  
-0.04181523 -0.11875386 0.99204285 36.09570098  
Axis -0.93343294 0.33693280 -0.12320405  
Axis point 0.00000000 289.25896045 226.51819375  
Rotation angle (degrees) 7.28837631  
Shift along axis 0.46555048  
  

> volume #4 color #ff9300

> volume #3 color #ffd479

> volume #2 color #ffd479

> volume #4 color #ffd479

> volume #4 style mesh

> volume #4 style surface

> transparency #4.1 50

> volume copy #4

Opened 262_substrate_sharpened_masked.mrc copy as #5, grid size 540,540,540,
pixel 0.818, shown at step 1, values float32  

> ui mousemode right "map eraser"

> volume erase #5 center 213.96,203.15,200.62 radius 42.335

> volume erase #5 center 210.56,205.11,217.9 radius 42.335

> volume erase #5 center 205.41,245.35,235.44 radius 27.24

> volume erase #5 center 236.82,246.12,244.23 radius 22.523

> volume erase #5 center 240.14,220.11,243.41 radius 22.523

> volume erase #5 center 261.83,234.17,236.36 radius 22.523

> volume erase #5 center 223.52,236.05,190.19 radius 22.307

> volume erase #5 center 228.71,237.61,237.79 radius 22.307

> volume erase #5 center 228.99,247.93,242.84 radius 22.307

> volume erase #5 center 227.76,213.75,238.14 radius 22.307

> ui mousemode right translate

> close #5

> volume #4 style mesh

> open "/Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/Final
> maps and masks/Head/Revised/260_head_locres.mrc"

Opened 260_head_locres.mrc as #5, grid size 540,540,540, pixel 0.818, shown at
level 50, step 4, values float32  

> ui tool show "Surface Color"

> color sample #2.1 map #5 palette #0000ff:#00ffff:#00ff00:#ffff00:#ff0000

Map values for surface "surface": minimum 3.589, mean 3.997, maximum 7.3  

> color sample #2.1 map #5 palette
> 3.6,#0000ff:4.1,#00ffff:4.6,#00ff00:5.1,#ffff00:7.3,#ff0000

Map values for surface "surface": minimum 3.589, mean 3.997, maximum 7.3  

> volume #1 level 0.0657

> volume #2 level 0.02528

> volume #2 level 0.08598

> volume #2 level 0.02528

> color single #2.1

> color sample #2.1 map #5 palette
> 3.6,#0000ff:4.1,#00ffff:4.6,#00ff00:5.1,#ffff00:7.3,#ff0000

Map values for surface "surface": minimum 3.589, mean 4.018, maximum 7.701  

> color single #2.1

> close #5

> open "/Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/Final
> maps and masks/Consensus/223_consensus_locres.mrc"

Opened 223_consensus_locres.mrc as #5, grid size 540,540,540, pixel 0.818,
shown at level 50, step 4, values float32  

> ui tool show "Surface Color"

> color sample #1.1 map #5 palette #0000ff:#00ffff:#00ff00:#ffff00:#ff0000

Map values for surface "surface": minimum 2.794, mean 3.155, maximum 8.077  

> color sample #1.1 map #5 palette
> 2.8,#0000ff:3.3,#00ffff:3.8,#00ff00:4.3,#ffff00:8.1,#ff0000

Map values for surface "surface": minimum 2.794, mean 3.155, maximum 8.077  

> color single #1.1

> color sample #1.1 map #5 palette
> 2.8,#0000ff:3.3,#00ffff:3.8,#00ff00:4.3,#ffff00:8.1,#ff0000

Map values for surface "surface": minimum 2.794, mean 3.155, maximum 8.077  

> lighting full

> lighting soft

> set bgColor white

> graphics silhouettes true

> graphics silhouettes false

> graphics silhouettes true

> lighting shadows true intensity 0.5

> lighting shadows false

> lighting shadows true

> lighting shadows false

> lighting shadows true

> lighting shadows false

> lighting shadows true

> lighting shadows false

> lighting shadows true

> lighting soft

> lighting simple

> lighting shadows true

> lighting shadows false

> lighting soft

> lighting full

> lighting shadows false

> lighting soft

> lighting simple

> graphics silhouettes false

> set bgColor black

> set bgColor white

> lighting soft

> graphics silhouettes true

> lighting flat

> graphics silhouettes false

> graphics silhouettes true

> lighting soft

> lighting flat

> lighting soft

> lighting shadows true intensity 0.5

> lighting soft

> graphics silhouettes false

> color sample #1.1 map #5 palette
> 2.8,#0000ff:3.3,#00ffff:3.8,#00ff00:4.3,#ffff00:8.1,#ff0000

Map values for surface "surface": minimum 2.794, mean 3.155, maximum 8.077  

> graphics silhouettes true

> graphics silhouettes false

> graphics silhouettes true

> graphics silhouettes false

> graphics silhouettes true

> graphics silhouettes false

> graphics silhouettes true

> graphics silhouettes false

> graphics silhouettes true

> graphics silhouettes false

> graphics silhouettes true

> graphics silhouettes false

> set bgColor gray

> lighting simple

> set bgColor black

> lighting shadows true

> lighting shadows false

> lighting shadows true

> lighting shadows false

> lighting soft

> lighting simple

> lighting full

> lighting flat

> lighting simple

> set bgColor white

> color single #1.1

> volume #1 color #919191

> volume #1 color #797979

> volume #1 color #919191

> lighting soft

> graphics silhouettes false

> lighting simple

> lighting full

> lighting shadows false

> color sample #1.1 map #5 palette
> 2.8,#0000ff:3.3,#00ffff:3.8,#00ff00:4.3,#ffff00:8.1,#ff0000

Map values for surface "surface": minimum 2.794, mean 3.155, maximum 8.077  

> lighting soft

> graphics silhouettes true

> graphics silhouettes false

> graphics silhouettes true

> graphics silhouettes false

> graphics silhouettes true

> graphics silhouettes false

> graphics silhouettes true

> graphics silhouettes false

> graphics silhouettes true

> view

> view name side

> select ~sel & ##selected

Nothing selected  

> select ~sel & ##selected

Nothing selected  

> select ~sel & ##selected

Nothing selected  

> view side

> turn y 90

> view side

> turn y -90

> view side

> view name side

> turn y -90

> view side

> turn y -110

> view side

> turn y -130

> view side

> turn y -145

> view side

> turn y -180

> view side

> turn y 90

> view side

> turn y 110

> view side

> turn y 145

> view side

> turn x 90

> view side

> turn x -90

> view side

> turn x -180

> view side

> turn y 180

> view side

> turn y -90

> view side

> turn y -90

> view side

> turn y 180

> view side

> turn y -90

> view side

> turn y -90

> view side

> turn y -90

> view side

> turn y 180

> view side

> turn y -90

> view side

> turn y 90

> view side

> turn y 180

> view side

> turn y 180

> view side

> turn y -90

> view side

> turn y -90

> view side

> turn y -90

> view side

> turn y -90

> view side

> turn y -90

> view side

> turn y -90

> view side

> turn y -90

> view side

> turn y -90

> view side

> turn y -90

> view side

> turn y -90

> view side

> turn y -180

> view side

> turn y -90

> view side

> turn y -90

> view side

> turn y -90

> view side

> color single #1.1

> color sample #1.1 map #5 palette
> 2.8,#0000ff:3.3,#00ffff:3.8,#00ff00:4.3,#ffff00:8.1,#ff0000

Map values for surface "surface": minimum 2.794, mean 3.155, maximum 8.077  

> view side

> turn y -90

> turn x -90

> view side

> turn y -90

> turn x 90

> view side

> turn x 90

> view side

> turn y -45

> turn x 45

> view side

> turn y -75

> turn x 75

> view side

> turn y -60

> turn x 60

> view side

> turn y -180

> view side

> turn y -190

> view side

> turn y -90

> view side

> turn y -90

> view side

> turn y -110

> view side

> turn y -130

> view side

> turn y -110

> view side

> turn y -90

> view side

> turn y -180

> view side

> turn y -180

> view side

> turn y -180

> view side

> turn y -180

> view side

> turn y -180

> view side

> turn y -180

> view side

> turn y -190

> view side

> turn y -90

> view side

> turn y -90

> view side

> turn y -90

> view side

> turn y -90

> view side

> turn y -90

> view side

> turn y -90

> view side

> turn y -90

> view side

> turn y -90

> view side

> turn y -90

> view side

> turn y -90

> view side

> turn y -90

> view side

> turn y -90

> view side

> turn y -90

> view side

> turn y -90

> view side

> turn y -90

> view side

> turn y -90

> view side

> lighting simple

> lighting soft

> lighting full

> lighting flat

> turn y -90

> view side

> lighting simple

> lighting soft

> lighting full

> lighting shadows false

> lighting shadows true

> lighting shadows false

> lighting shadows true

> lighting full

> lighting simple

> lighting shadows true

> lighting shadows false

> lighting soft

> lighting full

> lighting flat

> lighting simple

> lighting soft

> view side

> turn y -90

> view side

> turn y -90

> view side

> turn y -180

> view side

> turn y -180

> view side

> turn y -90

> view side

> close #1

> close #2

> close #3

> close #4

> close #5

> open "/Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/Final
> maps and masks/Consensus/J1169_consensus_sharpened_masked.mrc"

Opened J1169_consensus_sharpened_masked.mrc as #1, grid size 540,540,540,
pixel 0.818, shown at level 2.26e-05, step 4, values float32  

> open "/Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/Final
> maps and masks/Head/Revised/J1187_head_sharpened_masked.mrc"

Opened J1187_head_sharpened_masked.mrc as #2, grid size 540,540,540, pixel
0.818, shown at level 0.000148, step 4, values float32  

> open "/Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/Final
> maps and masks/Body/J1068_body_sharpened_masked.mrc"

Opened J1068_body_sharpened_masked.mrc as #3, grid size 540,540,540, pixel
0.818, shown at level 3.71e-05, step 4, values float32  

> open "/Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/Final
> maps and masks/Substrate/237_substrate_sharpened_masked.mrc"

Opened 237_substrate_sharpened_masked.mrc as #4, grid size 540,540,540, pixel
0.818, shown at level 8.06e-06, step 4, values float32  

> open "/Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/Final
> maps and masks/Consensus/223_consensus_locres.mrc"

Opened 223_consensus_locres.mrc as #5, grid size 540,540,540, pixel 0.818,
shown at level 50, step 4, values float32  

> open "/Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/Final
> maps and masks/Head/Revised/260_head_locres.mrc"

Opened 260_head_locres.mrc as #6, grid size 540,540,540, pixel 0.818, shown at
level 50, step 4, values float32  

> open "/Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/Final
> maps and masks/Body/220_body_locres.mrc"

Opened 220_body_locres.mrc as #7, grid size 540,540,540, pixel 0.818, shown at
level 50, step 4, values float32  

> close #4

> close #5

> close #6

> close #7

> open "/Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/Final
> maps and masks/Substrate/Revised/262_substrate_sharpened_masked.mrc"

Opened 262_substrate_sharpened_masked.mrc as #4, grid size 540,540,540, pixel
0.818, shown at level 1.48e-05, step 4, values float32  

> open "/Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/Final
> maps and masks/Consensus/223_consensus_locres.mrc"

Opened 223_consensus_locres.mrc as #5, grid size 540,540,540, pixel 0.818,
shown at level 50, step 4, values float32  

> open "/Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/Final
> maps and masks/Head/Revised/260_head_locres.mrc"

Opened 260_head_locres.mrc as #6, grid size 540,540,540, pixel 0.818, shown at
level 50, step 4, values float32  

> open "/Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/Final
> maps and masks/Body/220_body_locres.mrc"

Opened 220_body_locres.mrc as #7, grid size 540,540,540, pixel 0.818, shown at
level 50, step 4, values float32  

> volume #1 step 1

> volume #1 level 0.02068

> volume #2 step 1

> volume #2 level 0.02575

> volume #3 step 1

> volume #3 level 0.02748

> volume #4 step 1

> volume #4 level 0.0009821

> volume #4 level 0.001305

> volume #4 level 0.001401

> volume #4 level 0.001595

> volume #4 level 0.0017

> volume #5 step 1

> volume #6 step 1

> volume #7 step 1

> volume #1 level 0.06544

> volume #2 level 0.05136

> volume #3 level 0.07061

> color sample #2.1 map #6 palette #0000ff:#00ffff:#00ff00:#ffff00:#ff0000

Map values for surface "surface": minimum 3.588, mean 3.975, maximum 7.243  

> color sample #2.1 map #6 palette
> 3.6,#0000ff:4.1,#00ffff:4.6,#00ff00:5.1,#ffff00:7.2,#ff0000

Map values for surface "surface": minimum 3.588, mean 3.975, maximum 7.243  

> view side

> turn y -90

> view side

> turn y -90

> ui tool show "Hide Dust"

> surface dust #2 size 4.91

> surface undust #2

> surface dust #2 size 52.99

> surface undust #2

> surface dust #2 size 3.49

> surface undust #2

> surface dust #2 size 1.93

> surface dust #2 size 1.9

> surface dust #2 size 2.16

> surface undust #2

> surface dust #2 size 2.16

> surface dust #2 size 2.09

> surface dust #2 size 2.31

> surface undust #2

> surface dust #2 size 2.31

> surface dust #2 size 2.35

> surface dust #2 size 2.55

> surface undust #2

> surface dust #2 size 2.55

> volume #2 level 0.08111

> volume #2 level 0.06995

> view side

> surface undust #2

> surface dust #2 size 2.55

> turn y -90

> view side

> volume #2 level 0.0402

> surface undust #2

> surface dust #2 size 2.55

> volume #2 level 0.06995

> surface undust #2

> volume #2 level 0.05136

> surface dust #2 size 2.55

> surface dust #2 size 2.47

> surface dust #2 size 2.64

> surface undust #2

> surface dust #2 size 2.64

> view side

> turn y -90

> volume #2 level 0.08111

> surface undust #2

> surface dust #2 size 2.64

> view side

> volume #4 color #ff0018

> view side

> turn y -90

> view side

> turn y -90

> view side

> color sample #1.1 map #5 palette #0000ff:#00ffff:#00ff00:#ffff00:#ff0000

Map values for surface "surface": minimum 2.794, mean 3.155, maximum 8.077  

> color sample #1.1 map #5 palette
> 2.8,#0000ff:3.3,#00ffff:3.8,#00ff00:4.3,#ffff00:8,#ff0000

Map values for surface "surface": minimum 2.794, mean 3.155, maximum 8.077  

> surface dust #1 size 4.91

> surface undust #1

> surface dust #1 size 1.89

> view side

> color sample #3.1 map #7 palette #0000ff:#00ffff:#00ff00:#ffff00:#ff0000

Map values for surface "surface": minimum 2.818, mean 3.082, maximum 4.439  

> color sample #3.1 map #7 palette
> 2.8,#0000ff:3.3,#00ffff:3.8,#00ff00:4.3,#ffff00:4.4,#ff0000

Map values for surface "surface": minimum 2.818, mean 3.082, maximum 4.439  

> surface dust #3 size 4.91

> color sample #3.1 map #7 palette
> 2.8,#0000ff:3.3,#00ffff:3.8,#00ff00:4.3,#ffff00:8,#ff0000

Map values for surface "surface": minimum 2.818, mean 3.082, maximum 4.439  

> color sample #2.1 map #6 palette
> 2.8,#0000ff:3.3,#00ffff:3.8,#00ff00:4.3,#ffff00:8,#ff0000

Map values for surface "surface": minimum 3.588, mean 3.957, maximum 7.165  

> view side

> open "/Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/Final
> maps and masks/Consensus/206_consensus_angdist.bild"

Opened BILD data containing 12282 objects  

> hide #8 models

> hide #!1 models

> open "/Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/Final
> maps and masks/Head/Revised/067_head_angdist.bild"

Opened BILD data containing 12270 objects  

> open "/Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/Final
> maps and masks/Body/055_body_angdist.bild"

Opened BILD data containing 11692 objects  

> hide #9 models

> open "/Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/Final
> maps and masks/Substrate/232_substrate_angdist.bild"

Opened BILD data containing 766 objects  

> hide #10 models

> view side

> show #10 models

> show #9 models

> show #8 models

> view name side_ang

> view side_ang

> hide #11 models

> hide #10 models

> hide #9 models

> show #9 models

> hide #8 models

> turn y -90

> view side_ang

> turn y -180

> view side_ang

> hide #9 models

> show #10 models

> show #9 models

> hide #10 models

> show #10 models

> hide #9 models

> show #9 models

> hide #10 models

> show #8 models

> hide #9 models

> show #10 models

> hide #8 models

> show #11 models

> hide #10 models

> turn y -90

> view side_ang

> turn y -90

> view side_ang

> turn y -180

> view side_ang

> view side

> hide #11 models

> show #!1 models

> hide #!1 models

> show #!2 models

> turn y -180

> view side

> hide #!2 models

> show #!3 models

> hide #!3 models

> show #!4 models

> turn y -180

> view side

> turn y -90

> hide #!4 models

> show #!1 models

> show #!2 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> hide #!2 models

> show #!3 models

> show #!1 models

> hide #!3 models

> show #!3 models

> hide #!1 models

> show #!1 models

> hide #!3 models

> hide #!1 models

> show #!3 models

> hide #!3 models

> show #!1 models

> view side

> lighting simple

> lighting soft

> lighting full

> lighting flat

> show #11 models

> hide #11 models

> lighting full

> lighting soft

> save /Users/mulline1/Dropbox/FBH1/cryoEM_revised/Figures/Locres.cxs

> turn y -90

> volume #4 level 0.0015

> volume #4 level 0.0013

> volume #4 level 0.0015

> view side

> volume #4 level 0.0017

> volume #4 level 0.0016

> turn y -90

> volume #4 level 0.0017

> view side

> key rainbow :2.8 :3.3 :3.8 :4.3 :8.0 showTool true

> ui mousemode right "color key"

> key pos 0.738154,0.0952705 size 0,0

> key pos 0.72139,-0.037061 size 0.0132362,0.119166

Key is partially or completely offscreen  

> key pos 0.724228,0.0473076 size 0.0661502,0.621165

> key pos 0.426843,0.195826 size 0.353538,0.0277699

> key pos 0.608755,0.0507685

> view side

> key pos 0.613836,0.938746

> view side

> hide #!4 models

> show #!1 models

> show #!2 models

> hide #!2 models

> save /Users/mulline1/Dropbox/FBH1/cryoEM_revised/Figures/Locres.cxs

> hide #!1 models

> show #!2 models

> hide #!2 models

> show #!3 models

> hide #!3 models

> show #!3 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!2 models

> show #!4 models

> hide #!4 models

> show #!4 models

> show #!2 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> view side

> turn y -90

> view side

> turn y -90

> view side

> hide #!2 models

> show #!2 models

> hide #!2 models

> hide #!3 models

> show #!1 models

> view side

> turn y -90

> view side

> hide #!3 models

> hide #!2 models

> show #8 models

> view side_ang

> hide #12 models

> hide #8 models

> show #9 models

> hide #9 models

> show #8 models

> hide #8 models

> show #9 models

> hide #9 models

> show #10 models

> hide #10 models

> show #11 models

> view side_ang

> view side

> hide #11 models

> show #12 models

> show #!1 models

> key ticks true

> key ticks false

> key border false

> key border true

> key border false

> key border true

> key colorTreatment distinct

> key colorTreatment blended

> key colorTreatment distinct

> key colorTreatment blended

> key colorTreatment distinct

> key colorTreatment blended

> ui mousemode right translate

> hide #!1 models

> show #!2 models

> hide #!2 models

> show #!3 models

> hide #!3 models

> show #!4 models

> hide #!4 models

> show #!3 models

> hide #!3 models

> show #!2 models

> hide #!2 models

> show #!1 models

> hide #!1 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!3 models

> show #!1 models

> hide #!1 models

> hide #!3 models

> show #!4 models

> view side

> turn y -90

> view side

> hide #!4 models

> show #!3 models

> hide #!3 models

> show #!2 models

> turn y -90

> view side

> show #!3 models

> hide #!3 models

> show #!3 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 #!2 models

> show #!2 models

> hide #!2 models

> hide #!3 models

> show #!1 models

> show #!2 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 #!2 models

> show #!2 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

> view side

> turn y -90

> 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 #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> view side

> save /Users/mulline1/Dropbox/FBH1/cryoEM_revised/Figures/Locres.cxs

> view side

> show #!2 models

> hide #!3 models

> turn y -90

> view side

> turn y -90

> view side

> show #!1 models

> hide #!2 models

> view side

> show #!2 models

> hide #!4 models

> volume #2 level 0.04392

> surface dust #2 size 2.64

> surface dust #2 size 2.47

> surface dust #2 size 2.91

> view side

> turn y -90

> volume #2 level 0.02161

> surface dust #2 size 2.91

> view side

> turn y -90

> view side

> surface dust #2 size 2.91

> surface dust #2 size 3.06

> surface dust #2 size 3.38

> surface dust #2 size 3.73

> surface dust #2 size 3.06

> surface dust #2 size 3.01

> surface dust #2 size 3.85

> view side

> turn y -90

> view side

> volume #2 level 0.02905

> volume #2 level 0.006734

> volume #2 level 0.01417

> view side

> volume #2 level 0.015

> surface undust #2

> volume #2 level 0.018

> volume #2 level 0.02

> surface dust #2 size 3.85

> volume #2 level 0.019

> volume #2 level 0.022

> view side

> turn y -90

> volume #2 level 0.05919

> volume #2 level 0.022

> view side

> turn y -90

> view side

> save /Users/mulline1/Dropbox/FBH1/cryoEM_revised/Figures/Locres.cxs

> volume #4 color #ff2600

> hide #!1 models

> show #!2 models

> hide #!2 models

> show #!3 models

> hide #!3 models

> show #!4 models

> turn y -90

> hide #!4 models

> show #!3 models

> hide #!3 models

> show #!2 models

> hide #!2 models

> show #!1 models

> hide #!1 models

> show #!2 models

> show #!1 models

> hide #!2 models

> hide #!1 models

> show #!2 models

> hide #!2 models

> show #!3 models

> show #!2 models

> hide #!3 models

> hide #!2 models

> show #!3 models

> hide #!3 models

> show #!4 models

> view side

> hide #!4 models

> show #!3 models

> show #!2 models

> hide #!3 models

> show #!1 models

> hide #!2 models

> show #!2 models

> hide #!1 models

> turn y -90

> show #!1 models

> hide #!2 models

> show #!2 models

> hide #!1 models

> show #!3 models

> hide #!2 models

> show #!2 models

> hide #!3 models

> hide #!2 models

> show #!1 models

> show #!3 models

> hide #!1 models

> show #!1 models

> hide #!3 models

> show #!4 models

> hide #!1 models

> show #!3 models

> show #!2 models

> show #!1 models

> view side

> turn y -90

> view side

> turn y -90

> view side

> turn y -90

> view side

> hide #!4 models

> hide #!3 models

> hide #!2 models

> show #!2 models

> hide #!1 models

> show #!3 models

> volume #3 level 0.0467

> volume #3 level 0.0706

> view side

> show #!4 models

> view side

> hide #!4 models

> hide #!3 models

> hide #!2 models

> show #!1 models

> show #!2 models

> hide #!1 models

> view side

> hide #!2 models

> show #!1 models

> view side

> show #!2 models

> hide #!1 models

> view side

> show #!1 models

> show #!3 models

> show #!4 models

> turn y -90

> hide #!4 models

> hide #!2 models

> hide #!3 models

> turn y -90

> turn y 90

> turn y -110

> show #!4 models

> hide #!4 models

> turn y 110

> show #!2 models

> show #!3 models

> show #!4 models

> turn y -110

> turn y 110

> view side

> turn y -90

> view side

> hide #!4 models

> hide #!3 models

> hide #!2 models

> show #!2 models

> hide #!1 models

> hide #!2 models

> show #!3 models

> hide #!3 models

> show #!4 models

> show #!3 models

> show #!2 models

> show #!1 models

> hide #!4 models

> hide #!3 models

> hide #!2 models

> show #!4 models

> show #!2 models

> show #!3 models

> view side

> turn y -90

> view side

> turn y -90

> view side

> turn y -30

> hide #!4 models

> show #!4 models

> hide #!2 models

> hide #!3 models

> hide #!4 models

> show #!2 models

> hide #!1 models

> hide #!2 models

> show #!3 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!1 models

> hide #!3 models

> hide #!1 models

> show #!2 models

> hide #!2 models

> show #!3 models

> hide #!3 models

> show #!4 models

> hide #!4 models

> show #!1 models

> hide #!1 models

> show #!2 models

> show #!3 models

> hide #!2 models

> show #!1 models

> hide #!3 models

> show #!3 models

> hide #!1 models

> show #!4 models

> hide #!3 models

> hide #!4 models

> show #!3 models

> hide #!3 models

> show #!2 models

> hide #!2 models

> show #!1 models

> view side

> show #!2 models

> hide #!1 models

> turn y -15

> show #!3 models

> hide #!2 models

> hide #!3 models

> show #!1 models

> hide #!1 models

> show #!4 models

> turn y -5

> hide #!4 models

> show #!3 models

> hide #!3 models

> show #!2 models

> hide #!2 models

> show #!1 models

> view side

> show #!2 models

> show #!3 models

> show #!4 models

> turn y -25

> hide #!4 models

> hide #!3 models

> hide #!2 models

> hide #!1 models

> show #!2 models

> show #!3 models

> hide #!2 models

> hide #!3 models

> show #!4 models

> view side

> show #!1 models

> hide #!4 models

> hide #!1 models

> show #!2 models

> show #!3 models

> view side

> show #!1 models

> show #!4 models

> turn y -90

> hide #!2 models

> hide #!3 models

> hide #!4 models

> show #!2 models

> hide #!1 models

> hide #!2 models

> show #!3 models

> show #!4 models

> hide #!3 models

> view side

> show #!3 models

> show #!2 models

> show #!1 models

> turn y -25

> hide #!3 models

> hide #!2 models

> hide #!1 models

> show #!3 models

> hide #!4 models

> show #!2 models

> hide #!3 models

> hide #!2 models

> show #!3 models

> hide #!3 models

> show #!4 models

> view side

> show #!1 models

> show #!3 models

> show #!2 models

> turn y -15

> turn y -5

> hide #!3 models

> hide #!2 models

> hide #!1 models

> show #!3 models

> hide #!4 models

> show #!2 models

> hide #!3 models

> show #!1 models

> hide #!2 models

> show #!2 models

> hide #!1 models

> view side

> turn y -90

> view side

> close session

> open
> "/Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/Preliminary
> maps and masks/J845_prepreconsensus_full.mrc"

Opened J845_prepreconsensus_full.mrc as #1, grid size 100,100,100, pixel 3.27,
shown at level 0.261, step 1, values float32  

> open
> "/Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/Preliminary
> maps and masks/J918_preconsensus_full.mrc"

Opened J918_preconsensus_full.mrc as #2, grid size 540,540,540, pixel 0.818,
shown at level 0.00679, step 4, values float32  

> volume #2 step 1

> volume #2 level 0.1071

> open "/Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/Final
> maps and masks/Consensus/206_consensus_full.mrc"

Opened 206_consensus_full.mrc as #3, grid size 540,540,540, pixel 0.818, shown
at level 0.000217, step 4, values float32  

> volume #3 step 1

> volume #3 level 0.002226

> ui tool show "Fit in Map"

> fitmap #1 inMap #2

Fit map J845_prepreconsensus_full.mrc in map J918_preconsensus_full.mrc using
10000 points  
correlation = 0.3969, correlation about mean = 0.09316, overlap = 166.4  
steps = 700, shift = 62.5, angle = 19.7 degrees  
  
Position of J845_prepreconsensus_full.mrc (#1) relative to
J918_preconsensus_full.mrc (#2) coordinates:  
Matrix rotation and translation  
0.98942181 0.14301702 -0.02430273 40.70976741  
-0.12864653 0.94244668 0.30861681 0.10306915  
0.06704148 -0.30222574 0.95087594 39.79727002  
Axis -0.90530123 -0.13537700 -0.40261987  
Axis point 0.00000000 55.81056270 33.27536695  
Rotation angle (degrees) 19.71670733  
Shift along axis -52.89172722  
  

> select add #1

2 models selected  

> ui mousemode right "translate selected models"

> view matrix models
> #1,0.98942,0.14302,-0.024303,45.01,-0.12865,0.94245,0.30862,33.617,0.067041,-0.30223,0.95088,71.744

> ui mousemode right "rotate selected models"

> view matrix models
> #1,0.9852,0.16333,-0.052013,46.617,-0.16584,0.98497,-0.04828,88.765,0.043346,0.056191,0.99748,7.3339

> ui mousemode right "translate selected models"

> view matrix models
> #1,0.9852,0.16333,-0.052013,47.558,-0.16584,0.98497,-0.04828,96.957,0.043346,0.056191,0.99748,12.784

> fitmap #1 inMap #2

Fit map J845_prepreconsensus_full.mrc in map J918_preconsensus_full.mrc using
10000 points  
correlation = 0.8689, correlation about mean = 0.6293, overlap = 547.5  
steps = 144, shift = 7.21, angle = 11.2 degrees  
  
Position of J845_prepreconsensus_full.mrc (#1) relative to
J918_preconsensus_full.mrc (#2) coordinates:  
Matrix rotation and translation  
0.99993739 -0.00856537 0.00720019 57.59147711  
0.00844916 0.99983602 0.01601703 53.94647800  
-0.00733620 -0.01595519 0.99984579 33.23887074  
Axis -0.81925571 0.37248012 0.43598009  
Axis point 0.00000000 2462.61126627 -3635.79739833  
Rotation angle (degrees) 1.11808154  
Shift along axis -12.59666952  
  

> ui mousemode right translate

> select clear

> open "/Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/Final
> maps and masks/Head/Revised/067_head_full.mrc"

Opened 067_head_full.mrc as #4, grid size 540,540,540, pixel 0.818, shown at
level 0.000251, step 4, values float32  

> open "/Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/Final
> maps and masks/Body/055_body_full.mrc"

Opened 055_body_full.mrc as #5, grid size 540,540,540, pixel 0.818, shown at
level 0.000554, step 4, values float32  

> open "/Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/Final
> maps and masks/Substrate/232_substrate_full.mrc"

Opened 232_substrate_full.mrc as #6, grid size 540,540,540, pixel 0.818, shown
at level 0.000291, step 4, values float32  

> close #4-6

> hide #!1 models

> hide #!2 models

> show #!2 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> show #!1 models

> hide #!1 models

> open "/Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/3D
> classes/Head/058/run_it000_class001.mrc"

Opened run_it000_class001.mrc as #4, grid size 540,540,540, pixel 0.818, shown
at level 0.000143, step 4, values float32  

> open "/Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/3D
> classes/Head/058/run_it000_class002.mrc"

Opened run_it000_class002.mrc as #5, grid size 540,540,540, pixel 0.818, shown
at level 0.000143, step 4, values float32  

> open "/Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/3D
> classes/Head/058/run_it000_class003.mrc"

Opened run_it000_class003.mrc as #6, grid size 540,540,540, pixel 0.818, shown
at level 0.000143, step 4, values float32  

> open "/Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/3D
> classes/Head/058/run_it000_class004.mrc"

Opened run_it000_class004.mrc as #7, grid size 540,540,540, pixel 0.818, shown
at level 0.000143, step 4, values float32  

> open "/Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/3D
> classes/Head/058/run_it000_class005.mrc"

Opened run_it000_class005.mrc as #8, grid size 540,540,540, pixel 0.818, shown
at level 0.000143, step 4, values float32  

> open "/Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/3D
> classes/Head/058/run_it000_class006.mrc"

Opened run_it000_class006.mrc as #9, grid size 540,540,540, pixel 0.818, shown
at level 0.000143, step 4, values float32  

> open "/Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/Final
> maps and masks/Head/Revised/067_head_full.mrc"

Opened 067_head_full.mrc as #10, grid size 540,540,540, pixel 0.818, shown at
level 0.000251, step 4, values float32  

> volume #10 step 1

> volume #10 level 0.0009942

> volume #9 step 1

> volume #9 level 0.0002468

> volume #8 step 1

> volume #8 level 0.0002562

> volume #7 step 1

> volume #7 level 0.0002562

> volume #6 step 1

> volume #6 level 0.0002468

> volume #5 step 1

> volume #5 level 0.0003318

> volume #4 step 1

> volume #4 level 0.0004831

> hide #!2 models

> hide #!3 models

> hide #!10 models

> hide #!9 models

> hide #!8 models

> hide #!7 models

> hide #!6 models

> hide #!5 models

> close #4-10

> show #!1 models

> show #!2 models

> hide #!1 models

> volume #2 level 0.07096

> show #!3 models

> hide #!2 models

> volume #3 level 0.002039

> show #!2 models

> hide #!3 models

> show #!3 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!3 models

> show #!3 models

> hide #!2 models

> show #!1 models

> hide #!3 models

> hide #!1 models

> show #!2 models

> show #!3 models

> hide #!2 models

> hide #!3 models

> show #!1 models

> hide #!1 models

> open "/Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/3D
> classes/Head/058/run_it025_class001.mrc"

Opened run_it025_class001.mrc as #4, grid size 540,540,540, pixel 0.818, shown
at level 5.87e-07, step 4, values float32  

> open "/Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/3D
> classes/Head/058/run_it025_class002.mrc"

Opened run_it025_class002.mrc as #5, grid size 540,540,540, pixel 0.818, shown
at level 6.93e-08, step 4, values float32  

> open "/Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/3D
> classes/Head/058/run_it025_class003.mrc"

Opened run_it025_class003.mrc as #6, grid size 540,540,540, pixel 0.818, shown
at level 4.3e-07, step 4, values float32  

> open "/Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/3D
> classes/Head/058/run_it025_class004.mrc"

Opened run_it025_class004.mrc as #7, grid size 540,540,540, pixel 0.818, shown
at level 5.13e-07, step 4, values float32  

> open "/Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/3D
> classes/Head/058/run_it025_class005.mrc"

Opened run_it025_class005.mrc as #8, grid size 540,540,540, pixel 0.818, shown
at level 5.47e-07, step 4, values float32  

> open "/Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/3D
> classes/Head/058/run_it025_class006.mrc"

Opened run_it025_class006.mrc as #9, grid size 540,540,540, pixel 0.818, shown
at level 3.57e-07, step 4, values float32  

> show #!1 models

> hide #!4 models

> hide #!5 models

> hide #!6 models

> hide #!7 models

> hide #!8 models

> hide #!9 models

> open "/Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/Final
> maps and masks/Head/Revised/067_head_full.mrc"

Opened 067_head_full.mrc as #10, grid size 540,540,540, pixel 0.818, shown at
level 0.000251, step 4, values float32  

> volume #10 step 1

> volume #10 level 0.002525

> open "/Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/3D
> classes/Body/045/run_it035_class001.mrc"

Opened run_it035_class001.mrc as #11, grid size 540,540,540, pixel 0.818,
shown at level 1.24e-06, step 4, values float32  

> open "/Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/3D
> classes/Body/045/run_it035_class002.mrc"

Opened run_it035_class002.mrc as #12, grid size 540,540,540, pixel 0.818,
shown at level 1.4e-06, step 4, values float32  

> open "/Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/3D
> classes/Body/045/run_it035_class003.mrc"

Opened run_it035_class003.mrc as #13, grid size 540,540,540, pixel 0.818,
shown at level 7.73e-07, step 4, values float32  

> open "/Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/3D
> classes/Body/045/run_it035_class004.mrc"

Opened run_it035_class004.mrc as #14, grid size 540,540,540, pixel 0.818,
shown at level 9.89e-07, step 4, values float32  

> open "/Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/3D
> classes/Body/045/run_it035_class005.mrc"

Opened run_it035_class005.mrc as #15, grid size 540,540,540, pixel 0.818,
shown at level 3.7e-07, step 4, values float32  

> open "/Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/3D
> classes/Body/045/run_it035_class006.mrc"

Opened run_it035_class006.mrc as #16, grid size 540,540,540, pixel 0.818,
shown at level 1.67e-06, step 4, values float32  

> hide #!11 models

> hide #!12 models

> hide #!13 models

> hide #!14 models

> hide #!15 models

> hide #!16 models

> open "/Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/Final
> maps and masks/Body/055_body_full.mrc"

Opened 055_body_full.mrc as #17, grid size 540,540,540, pixel 0.818, shown at
level 0.000554, step 4, values float32  

> volume #17 step 1

> volume #17 level 0.002409

> open "/Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/3D
> classes/Substrate/Round 1/124/run_it025_class001.mrc"

Opened run_it025_class001.mrc as #18, grid size 540,540,540, pixel 0.818,
shown at level 1.21e-05, step 4, values float32  

> open "/Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/3D
> classes/Substrate/Round 1/124/run_it025_class002.mrc"

Opened run_it025_class002.mrc as #19, grid size 540,540,540, pixel 0.818,
shown at level 1.11e-05, step 4, values float32  

> open "/Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/3D
> classes/Substrate/Round 1/124/run_it025_class003.mrc"

Opened run_it025_class003.mrc as #20, grid size 540,540,540, pixel 0.818,
shown at level 2.68e-05, step 4, values float32  

> open "/Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/3D
> classes/Substrate/Round 1/124/run_it025_class004.mrc"

Opened run_it025_class004.mrc as #21, grid size 540,540,540, pixel 0.818,
shown at level 1.57e-05, step 4, values float32  

> open "/Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/3D
> classes/Substrate/Round 1/124/run_it025_class005.mrc"

Opened run_it025_class005.mrc as #22, grid size 540,540,540, pixel 0.818,
shown at level 1.87e-05, step 4, values float32  

> open "/Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/3D
> classes/Substrate/Round 1/124/run_it025_class006.mrc"

Opened run_it025_class006.mrc as #23, grid size 540,540,540, pixel 0.818,
shown at level 2.32e-05, step 4, values float32  

> open "/Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/3D
> classes/Substrate/Round 1/124/run_it025_class007.mrc"

Opened run_it025_class007.mrc as #24, grid size 540,540,540, pixel 0.818,
shown at level 1.39e-05, step 4, values float32  

> open "/Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/3D
> classes/Substrate/Round 1/124/run_it025_class008.mrc"

Opened run_it025_class008.mrc as #25, grid size 540,540,540, pixel 0.818,
shown at level 2.51e-05, step 4, values float32  

> open "/Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/3D
> classes/Substrate/Round 1/124/run_it025_class009.mrc"

Opened run_it025_class009.mrc as #26, grid size 540,540,540, pixel 0.818,
shown at level 2.3e-05, step 4, values float32  

> open "/Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/3D
> classes/Substrate/Round 1/124/run_it025_class010.mrc"

Opened run_it025_class010.mrc as #27, grid size 540,540,540, pixel 0.818,
shown at level 2.02e-05, step 4, values float32  

> open "/Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/3D
> classes/Substrate/Round 1/124/run_it025_class011.mrc"

Opened run_it025_class011.mrc as #28, grid size 540,540,540, pixel 0.818,
shown at level 1.7e-05, step 4, values float32  

> open "/Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/3D
> classes/Substrate/Round 1/124/run_it025_class012.mrc"

Opened run_it025_class012.mrc as #29, grid size 540,540,540, pixel 0.818,
shown at level 1.99e-05, step 4, values float32  

> open "/Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/3D
> classes/Substrate/Round 2/159/run_it025_class001.mrc"

Opened run_it025_class001.mrc as #30, grid size 540,540,540, pixel 0.818,
shown at level 2.03e-07, step 4, values float32  

> open "/Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/3D
> classes/Substrate/Round 2/159/run_it025_class002.mrc"

Opened run_it025_class002.mrc as #31, grid size 540,540,540, pixel 0.818,
shown at level 2.63e-07, step 4, values float32  

> open "/Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/3D
> classes/Substrate/Round 2/159/run_it025_class003.mrc"

Opened run_it025_class003.mrc as #32, grid size 540,540,540, pixel 0.818,
shown at level 6.38e-07, step 4, values float32  

> open "/Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/3D
> classes/Substrate/Round 2/159/run_it025_class004.mrc"

Opened run_it025_class004.mrc as #33, grid size 540,540,540, pixel 0.818,
shown at level 7.37e-07, step 4, values float32  

> hide #!18 models

> hide #!19 models

> hide #!20 models

> hide #!21 models

> hide #!22 models

> hide #!23 models

> hide #!24 models

> hide #!25 models

> hide #!26 models

> hide #!27 models

> hide #!28 models

> hide #!29 models

> hide #!30 models

> hide #!31 models

> hide #!32 models

> hide #!33 models

> open "/Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/Final
> maps and masks/Substrate/232_substrate_full.mrc"

Opened 232_substrate_full.mrc as #34, grid size 540,540,540, pixel 0.818,
shown at level 0.000291, step 4, values float32  

> volume #34 step 1

> volume #34 level 0.0009319

> fitmap #34 inMap #2

Fit map 232_substrate_full.mrc in map J918_preconsensus_full.mrc using 818244
points  
correlation = 0.7032, correlation about mean = 0.2384, overlap = 107.4  
steps = 88, shift = 4.78, angle = 3.41 degrees  
  
Position of 232_substrate_full.mrc (#34) relative to
J918_preconsensus_full.mrc (#2) coordinates:  
Matrix rotation and translation  
0.99994086 0.00092699 0.01083631 -4.32567070  
-0.00155919 0.99828742 0.05847901 -15.00632349  
-0.01076354 -0.05849245 0.99822982 13.69905736  
Axis -0.98315976 0.18154950 -0.02089670  
Axis point 0.00000000 226.56252672 267.10172357  
Rotation angle (degrees) 3.41039703  
Shift along axis 1.24216969  
  

> open "/Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/Final
> maps and masks/Consensus/J1031_consensus_mask.mrc"

Opened J1031_consensus_mask.mrc as #35, grid size 540,540,540, pixel 0.818,
shown at level 1, step 4, values float32  

> open "/Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/Final
> maps and masks/Head/J1032_head_mask.mrc"

Opened J1032_head_mask.mrc as #36, grid size 540,540,540, pixel 0.818, shown
at level 0.997, step 4, values float32  

> volume #35 step 1

> volume #36 step 1

> volume #35 level 0.99

> volume #36 level 0.99

> hide #!35 models

> hide #!36 models

> open "/Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/Final
> maps and masks/Body/J1033_body_mask.mrc"

Opened J1033_body_mask.mrc as #37, grid size 540,540,540, pixel 0.818, shown
at level 0.336, step 4, values float32  

> volume #37 step 1

> volume #37 level 0.99

> open "/Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/Final
> maps and masks/Substrate/J1034_substrate_mask.mrc"

Opened J1034_substrate_mask.mrc as #38, grid size 540,540,540, pixel 0.818,
shown at level 1, step 4, values float32  

> hide #!37 models

> volume #38 step 1

> volume #38 level 0.99

> open "/Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/Final
> maps and masks/Substrate/J1094_substrate_mask.mrc"

Opened J1094_substrate_mask.mrc as #39, grid size 540,540,540, pixel 0.818,
shown at level 1, step 4, values float32  

> hide #!38 models

> volume #39 step 1

> volume #39 level 0.99

> show #!38 models

> hide #!38 models

> hide #!39 models

> hide #!34 models

> hide #!10 models

> hide #!17 models

> select all

78 models selected  

> color all gray

> ui tool show "Color Actions"

> color sel dark gray

> color sel light gray

> color sel dark gray

> color sel dim gray

> color sel gray

> color sel dark gray

> color sel silver

> color sel light gray

> color sel gray

> color sel dark gray

> lighting simple

> lighting soft

> lighting full

> lighting simple

> color sel gray

> color sel dim gray

> color sel gray

> hide #!1 models

> show #!2 models

> graphics silhouettes false

> select clear

> show #!35 models

> show #!36 models

> show #!37 models

> show #!38 models

> show #!39 models

> color orange

> transparency #35-39 50

> hide #!36 models

> hide #!37 models

> hide #!38 models

> hide #!39 models

> transparency #35-39 70

> hide #!35 models

> show #!35 models

> hide #!35 models

> show #!35 models

> hide #!35 models

> hide #!2 models

> show #!2 models

> color all gray

> color gray

> color dim gray

> color gray

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!35 models

> show #!36 models

> show #!37 models

> show #!38 models

> show #!39 models

> color orange

> hide #!39 models

> hide #!38 models

> hide #!37 models

> hide #!36 models

> hide #!35 models

> show #!34 models

> hide #!34 models

> color #1-34 gray

> show #!34 models

> hide #!34 models

> show #!33 models

> hide #!33 models

> show #!2 models

> show #!35 models

> transparency #35-39 80

> transparency #35-39 70

> hide #!35 models

> show #!36 models

> hide #!36 models

> show #!37 models

> hide #!37 models

> show #!38 models

> hide #!38 models

> show #!39 models

> hide #!39 models

> hide #!2 models

> show #!3 models

> show #!36 models

> hide #!36 models

> show #!37 models

> save /Users/mulline1/Dropbox/FBH1/cryoEM_revised/Figures/Workflow.cxs

> view list

No named views.  

> hide #!37 models

> show #!39 models

> hide #!39 models

> show #!38 models

> hide #!38 models

> show #!37 models

> hide #!37 models

> show #!36 models

> hide #!36 models

> show #!35 models

> hide #!35 models

> hide #!3 models

> show #!1 models

> volume all level 1

> volume all level 0.99

> volume all step 1 level 0.99

> volume #1 level 0.2042

> volume #1 level 0.1125

> volume #1 level 0.1404

> volume #1 level 0.1205

> show #!2 models

> hide #!1 models

> hide #!2 models

> show #!2 models

> volume #2 level 0.07969

> volume #3 level 0.002132

> volume #3 level 0.002179

> volume #2 level 0.0728

> show #!4 models

> hide #!3 models

> volume #4 level 0.001121

> hide #!4 models

> show #!8 models

> volume #8 level 0.001456

> volume #8 level 0.0015

> volume #4-9 step 1 level 0.0015

> hide #!8 models

> show #!4 models

> hide #!4 models

> show #!5 models

> hide #!5 models

> show #!6 models

> hide #!6 models

> show #!7 models

> hide #!7 models

> show #!8 models

> hide #!8 models

> show #!9 models

> hide #!9 models

> show #!10 models

> volume #10 level 0.002452

> volume #10 level 0.002627

> volume #10 level 0.002364

> hide #!10 models

> show #!11 models

> hide #!11 models

> show #!1 models

> hide #!1 models

> show #!2 models

> hide #!2 models

> show #!3 models

> hide #!3 models

> show #!4 models

> hide #!4 models

> show #!8 models

> hide #!8 models

> show #!10 models

> hide #!10 models

> show #!11 models

> hide #!11 models

> show #!16 models

> volume #16 level 0.003266

> volume #16 level 0.002857

> volume #16 level 0.003215

> volume #11-16 step 1 level 0.003

> hide #!16 models

> show #!15 models

> hide #!15 models

> show #!14 models

> hide #!14 models

> show #!13 models

> hide #!13 models

> show #!12 models

> hide #!12 models

> show #!11 models

> hide #!11 models

> show #!16 models

> volume #11-16 step 1 level 0.0025

> volume #11-16 step 1 level 0.0027

> hide #!16 models

> show #!15 models

> hide #!15 models

> show #!14 models

> hide #!14 models

> show #!13 models

> hide #!13 models

> show #!12 models

> hide #!12 models

> show #!11 models

> show #!16 models

> hide #!11 models

> volume #11-16 step 1 level 0.003

> volume #11-16 step 1 level 0.0027

> volume #11-16 step 1 level 0.0028

> show #!3 models

> hide #!16 models

> show #!16 models

> hide #!3 models

> show #!17 models

> hide #!16 models

> volume #17 level 0.003578

> volume #17 level 0.002898

> show #!3 models

> hide #!17 models

> show #!17 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!17 models

> show #!17 models

> hide #!17 models

> show #!17 models

> hide #!3 models

> volume #17 level 0.003331

> show #!3 models

> hide #!17 models

> show #!17 models

> hide #!3 models

> show #!10 models

> hide #!10 models

> volume #17 level 0.003022

> show #!10 models

> hide #!10 models

> show #!10 models

> hide #!10 models

> hide #!17 models

> show #!17 models

> hide #!17 models

> show #!18 models

> volume #18 level 0.001598

> volume #18 level 0.001057

> volume #18 level 0.001566

> volume #18 level 0.0015

> volume #18-33 step 1 level 0.0015

> show #!30 models

> hide #!18 models

> show #!18 models

> hide #!30 models

> show #!30 models

> hide #!18 models

> show #!34 models

> hide #!30 models

> volume #34 level 0.001624

> volume #34 level 0.001805

> show #!30 models

> hide #!34 models

> show #!34 models

> hide #!34 models

> show #!34 models

> hide #!30 models

> hide #!34 models

> show #!30 models

> hide #!30 models

> show #!18 models

> show #!34 models

> hide #!18 models

> hide #!34 models

> hide #!39 models

> show #!1 models

> save /Users/mulline1/Dropbox/FBH1/cryoEM_revised/Figures/Workflow.cxs

> close session

> open /Users/mulline1/Dropbox/FBH1/cryoEM_revised/Figures/Locres.cxs format
> session

Opened J1169_consensus_sharpened_masked.mrc as #1, grid size 540,540,540,
pixel 0.818, shown at level 0.0654, step 1, values float32  
Opened J1187_head_sharpened_masked.mrc as #2, grid size 540,540,540, pixel
0.818, shown at level 0.022, step 1, values float32  
Opened J1068_body_sharpened_masked.mrc as #3, grid size 540,540,540, pixel
0.818, shown at level 0.0706, step 1, values float32  
Opened 262_substrate_sharpened_masked.mrc as #4, grid size 540,540,540, pixel
0.818, shown at level 0.0017, step 1, values float32  
Opened 223_consensus_locres.mrc as #5, grid size 540,540,540, pixel 0.818,
shown at level 50, step 1, values float32  
Opened 260_head_locres.mrc as #6, grid size 540,540,540, pixel 0.818, shown at
level 50, step 1, values float32  
Opened 220_body_locres.mrc as #7, grid size 540,540,540, pixel 0.818, shown at
level 50, step 1, values float32  
Map values for surface "surface": minimum 2.794, mean 3.155, maximum 8.077  
opened ChimeraX session  

> view matrix camera

Missing "camera" keyword's argument  

> view matrix

view matrix camera
-0.021492,0.035484,-0.99914,-403.95,0.70539,0.70875,0.0099977,247.22,0.70849,-0.70457,-0.040263,168.98  
view matrix models
#1,1,0,0,0,0,1,0,0,0,0,1,0,#1.1,1,0,0,0,0,1,0,0,0,0,1,0,#2,1,0,0,0,0,1,0,0,0,0,1,0,#2.1,1,0,0,0,0,1,0,0,0,0,1,0,#3,1,0,0,0,0,1,0,0,0,0,1,0,#3.1,1,0,0,0,0,1,0,0,0,0,1,0,#4,1,0,0,0,0,1,0,0,0,0,1,0,#4.1,1,0,0,0,0,1,0,0,0,0,1,0,#5,1,0,0,0,0,1,0,0,0,0,1,0,#5.1,1,0,0,0,0,1,0,0,0,0,1,0,#6,1,0,0,0,0,1,0,0,0,0,1,0,#6.1,1,0,0,0,0,1,0,0,0,0,1,0,#7,1,0,0,0,0,1,0,0,0,0,1,0,#7.1,1,0,0,0,0,1,0,0,0,0,1,0,#8,1,0,0,0,0,1,0,0,0,0,1,0,#9,1,0,0,0,0,1,0,0,0,0,1,0,#10,1,0,0,0,0,1,0,0,0,0,1,0,#11,1,0,0,0,0,1,0,0,0,0,1,0  
  

> view matrix camera
> -0.021492,0.035484,-0.99914,-403.95,0.70539,0.70875,0.0099977,247.22,0.70849,-0.70457,-0.040263,168.98

> close session

> open /Users/mulline1/Dropbox/FBH1/cryoEM_revised/Figures/Workflow.cxs format
> session

restore_snapshot for "Volume" returned None  

restore_snapshot for "VolumeSurface" returned None  

Opened J845_prepreconsensus_full.mrc as #1, grid size 100,100,100, pixel 3.27,
shown at level 0.12, step 1, values float32  
Opened J918_preconsensus_full.mrc as #2, grid size 540,540,540, pixel 0.818,
shown at level 0.0728, step 1, values float32  
Opened 206_consensus_full.mrc as #3, grid size 540,540,540, pixel 0.818, shown
at level 0.00218, step 1, values float32  
Opened run_it025_class001.mrc as #4, grid size 540,540,540, pixel 0.818, shown
at level 0.0015, step 1, values float32  
Opened run_it025_class002.mrc as #5, grid size 540,540,540, pixel 0.818, shown
at level 0.0015, step 1, values float32  
Opened run_it025_class003.mrc as #6, grid size 540,540,540, pixel 0.818, shown
at level 0.0015, step 1, values float32  
Opened run_it025_class004.mrc as #7, grid size 540,540,540, pixel 0.818, shown
at level 0.0015, step 1, values float32  
Opened run_it025_class005.mrc as #8, grid size 540,540,540, pixel 0.818, shown
at level 0.0015, step 1, values float32  
Opened run_it025_class006.mrc as #9, grid size 540,540,540, pixel 0.818, shown
at level 0.0015, step 1, values float32  
Opened 067_head_full.mrc as #10, grid size 540,540,540, pixel 0.818, shown at
level 0.00236, step 1, values float32  
Opened run_it035_class001.mrc as #11, grid size 540,540,540, pixel 0.818,
shown at level 0.0028, step 1, values float32  
Opened run_it035_class002.mrc as #12, grid size 540,540,540, pixel 0.818,
shown at level 0.0028, step 1, values float32  
Opened run_it035_class003.mrc as #13, grid size 540,540,540, pixel 0.818,
shown at level 0.0028, step 1, values float32  
Opened run_it035_class004.mrc as #14, grid size 540,540,540, pixel 0.818,
shown at level 0.0028, step 1, values float32  
Opened run_it035_class005.mrc as #15, grid size 540,540,540, pixel 0.818,
shown at level 0.0028, step 1, values float32  
Opened run_it035_class006.mrc as #16, grid size 540,540,540, pixel 0.818,
shown at level 0.0028, step 1, values float32  
Opened 055_body_full.mrc as #17, grid size 540,540,540, pixel 0.818, shown at
level 0.00302, step 1, values float32  
Opened run_it025_class001.mrc as #18, grid size 540,540,540, pixel 0.818,
shown at level 0.0015, step 1, values float32  
Opened run_it025_class002.mrc as #19, grid size 540,540,540, pixel 0.818,
shown at level 0.0015, step 1, values float32  
Opened run_it025_class003.mrc as #20, grid size 540,540,540, pixel 0.818,
shown at level 0.0015, step 1, values float32  
Opened run_it025_class004.mrc as #21, grid size 540,540,540, pixel 0.818,
shown at level 0.0015, step 1, values float32  
Opened run_it025_class005.mrc as #22, grid size 540,540,540, pixel 0.818,
shown at level 0.0015, step 1, values float32  
Opened run_it025_class006.mrc as #23, grid size 540,540,540, pixel 0.818,
shown at level 0.0015, step 1, values float32  
Opened run_it025_class007.mrc as #24, grid size 540,540,540, pixel 0.818,
shown at level 0.0015, step 1, values float32  
Opened run_it025_class008.mrc as #25, grid size 540,540,540, pixel 0.818,
shown at level 0.0015, step 1, values float32  
Opened run_it025_class009.mrc as #26, grid size 540,540,540, pixel 0.818,
shown at level 0.0015, step 1, values float32  
Opened run_it025_class010.mrc as #27, grid size 540,540,540, pixel 0.818,
shown at level 0.0015, step 1, values float32  
Opened run_it025_class011.mrc as #28, grid size 540,540,540, pixel 0.818,
shown at level 0.0015, step 1, values float32  
Opened run_it025_class012.mrc as #29, grid size 540,540,540, pixel 0.818,
shown at level 0.0015, step 1, values float32  
Opened run_it025_class001.mrc as #30, grid size 540,540,540, pixel 0.818,
shown at level 0.0015, step 1, values float32  
Opened run_it025_class002.mrc as #31, grid size 540,540,540, pixel 0.818,
shown at level 0.0015, step 1, values float32  
Opened run_it025_class003.mrc as #32, grid size 540,540,540, pixel 0.818,
shown at level 0.0015, step 1, values float32  
Opened run_it025_class004.mrc as #33, grid size 540,540,540, pixel 0.818,
shown at level 0.0015, step 1, values float32  
Opened 232_substrate_full.mrc as #34, grid size 540,540,540, pixel 0.818,
shown at level 0.0018, step 1, values float32  
Opened J1031_consensus_mask.mrc as #35, grid size 540,540,540, pixel 0.818,
shown at level 0.99, step 1, values float32  
Opened J1032_head_mask.mrc as #36, grid size 540,540,540, pixel 0.818, shown
at level 0.99, step 1, values float32  
Opened J1033_body_mask.mrc as #37, grid size 540,540,540, pixel 0.818, shown
at level 0.99, step 1, values float32  
Opened J1094_substrate_mask.mrc as #39, grid size 540,540,540, pixel 0.818,
shown at level 0.99, step 1, values float32  
opened ChimeraX session  

> hide #!1 models

> show #!2 models

> hide #!2 models

> view matrix camera
> -0.021492,0.035484,-0.99914,-403.95,0.70539,0.70875,0.0099977,247.22,0.70849,-0.70457,-0.040263,168.98

> show #!1 models

> hide #!1 models

> show #!2 models

> hide #!2 models

> show #!3 models

> hide #!3 models

> show #!35 models

> view name side

> show #!2 models

> hide #!2 models

> show #!3 models

> hide #!3 models

> show #!1 models

> hide #!1 models

> show #!2 models

> hide #!2 models

> show #!3 models

> hide #!3 models

> show #!4 models

> hide #!4 models

> hide #!35 models

> show #!36 models

> hide #!36 models

> show #!37 models

> hide #!37 models

> show #!39 models

> hide #!39 models

> show #!39 models

> hide #!39 models

> show #!39 models

> hide #!39 models

> show #!16 models

> hide #!16 models

> show #!16 models

> show #!15 models

> show #!17 models

> hide #!16 models

> hide #!15 models

> hide #!17 models

> show #!16 models

> hide #!16 models

> show #!15 models

> hide #!15 models

> show #!14 models

> hide #!14 models

> show #!3 models

> hide #!3 models

> show #!4 models

> hide #!4 models

> show #!5 models

> hide #!5 models

> show #!6 models

> hide #!6 models

> show #!7 models

> hide #!7 models

> show #!8 models

> hide #!8 models

> show #!35 models

> hide #!35 models

> show #!36 models

> hide #!36 models

> show #!37 models

> hide #!37 models

> show #!39 models

> hide #!39 models

> close #39

> open
> "/Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/Preliminary
> maps and masks/J1034_substrate_mask.mrc"

Opened J1034_substrate_mask.mrc as #38, grid size 540,540,540, pixel 0.818,
shown at level 1, step 4, values float32  

> open "/Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/Final
> maps and masks/Substrate/J1094_substrate_mask.mrc"

Opened J1094_substrate_mask.mrc as #39, grid size 540,540,540, pixel 0.818,
shown at level 1, step 4, values float32  

> color #38-39 orange

> hide #!38 models

> show #!38 models

> hide #!39 models

> show #!39 models

> volume #38 step 1

> volume #39 step 1

> volume #38 level 0.99

> volume #39 level 0.99

> transparency #38-39 70

> hide #!39 models

> hide #!38 models

> show #!37 models

> hide #!37 models

> show #!39 models

> hide #!39 models

> show #!2 models

> show #!35 models

> view side

> turn y -30

> hide #!35 models

> show #!34 models

> show #!39 models

> hide #!39 models

> hide #!34 models

> view side

> turn y -30

> show #!39 models

> hide #!39 models

> show #!38 models

> hide #!38 models

> show #!35 models

> view side

> view name side

> turn y -30

> hide #!35 models

> hide #!2 models

> show #!4 models

> hide #!4 models

> show #!5 models

> hide #!5 models

> show #!6 models

> hide #!6 models

> show #!7 models

> hide #!7 models

> show #!8 models

> hide #!8 models

> show #!9 models

> show #!8 models

> hide #!9 models

> view side

> hide #!8 models

> show #!9 models

> hide #!9 models

> show #!10 models

> turn y -25

> view side

> hide #!10 models

> show #!1 models

> save
> /Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/Figures/Workflow.cxs

> hide #!1 models

> show #!3 models

> show #!35 models

> hide #!35 models

> show #!36 models

> hide #!36 models

> show #!37 models

> show #!36 models

> hide #!36 models

> hide #!37 models

> show #!38 models

> hide #!38 models

> show #!39 models

> hide #!39 models

> close session

> open
> /Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/Figures/Locres.cxs

Opened J1169_consensus_sharpened_masked.mrc as #1, grid size 540,540,540,
pixel 0.818, shown at level 0.0654, step 1, values float32  
Opened J1187_head_sharpened_masked.mrc as #2, grid size 540,540,540, pixel
0.818, shown at level 0.022, step 1, values float32  
Opened J1068_body_sharpened_masked.mrc as #3, grid size 540,540,540, pixel
0.818, shown at level 0.0706, step 1, values float32  
Opened 262_substrate_sharpened_masked.mrc as #4, grid size 540,540,540, pixel
0.818, shown at level 0.0017, step 1, values float32  
Opened 223_consensus_locres.mrc as #5, grid size 540,540,540, pixel 0.818,
shown at level 50, step 1, values float32  
Opened 260_head_locres.mrc as #6, grid size 540,540,540, pixel 0.818, shown at
level 50, step 1, values float32  
Opened 220_body_locres.mrc as #7, grid size 540,540,540, pixel 0.818, shown at
level 50, step 1, values float32  
Map values for surface "surface": minimum 2.794, mean 3.155, maximum 8.077  
opened ChimeraX session  

> close session

> open
> /Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/Figures/Workflow.cxs

Opened J845_prepreconsensus_full.mrc as #1, grid size 100,100,100, pixel 3.27,
shown at level 0.12, step 1, values float32  
Opened J918_preconsensus_full.mrc as #2, grid size 540,540,540, pixel 0.818,
shown at level 0.0728, step 1, values float32  
Opened 206_consensus_full.mrc as #3, grid size 540,540,540, pixel 0.818, shown
at level 0.00218, step 1, values float32  
Opened run_it025_class001.mrc as #4, grid size 540,540,540, pixel 0.818, shown
at level 0.0015, step 1, values float32  
Opened run_it025_class002.mrc as #5, grid size 540,540,540, pixel 0.818, shown
at level 0.0015, step 1, values float32  
Opened run_it025_class003.mrc as #6, grid size 540,540,540, pixel 0.818, shown
at level 0.0015, step 1, values float32  
Opened run_it025_class004.mrc as #7, grid size 540,540,540, pixel 0.818, shown
at level 0.0015, step 1, values float32  
Opened run_it025_class005.mrc as #8, grid size 540,540,540, pixel 0.818, shown
at level 0.0015, step 1, values float32  
Opened run_it025_class006.mrc as #9, grid size 540,540,540, pixel 0.818, shown
at level 0.0015, step 1, values float32  
Opened 067_head_full.mrc as #10, grid size 540,540,540, pixel 0.818, shown at
level 0.00236, step 1, values float32  
Opened run_it035_class001.mrc as #11, grid size 540,540,540, pixel 0.818,
shown at level 0.0028, step 1, values float32  
Opened run_it035_class002.mrc as #12, grid size 540,540,540, pixel 0.818,
shown at level 0.0028, step 1, values float32  
Opened run_it035_class003.mrc as #13, grid size 540,540,540, pixel 0.818,
shown at level 0.0028, step 1, values float32  
Opened run_it035_class004.mrc as #14, grid size 540,540,540, pixel 0.818,
shown at level 0.0028, step 1, values float32  
Opened run_it035_class005.mrc as #15, grid size 540,540,540, pixel 0.818,
shown at level 0.0028, step 1, values float32  
Opened run_it035_class006.mrc as #16, grid size 540,540,540, pixel 0.818,
shown at level 0.0028, step 1, values float32  
Opened 055_body_full.mrc as #17, grid size 540,540,540, pixel 0.818, shown at
level 0.00302, step 1, values float32  
Opened run_it025_class001.mrc as #18, grid size 540,540,540, pixel 0.818,
shown at level 0.0015, step 1, values float32  
Opened run_it025_class002.mrc as #19, grid size 540,540,540, pixel 0.818,
shown at level 0.0015, step 1, values float32  
Opened run_it025_class003.mrc as #20, grid size 540,540,540, pixel 0.818,
shown at level 0.0015, step 1, values float32  
Opened run_it025_class004.mrc as #21, grid size 540,540,540, pixel 0.818,
shown at level 0.0015, step 1, values float32  
Opened run_it025_class005.mrc as #22, grid size 540,540,540, pixel 0.818,
shown at level 0.0015, step 1, values float32  
Opened run_it025_class006.mrc as #23, grid size 540,540,540, pixel 0.818,
shown at level 0.0015, step 1, values float32  
Opened run_it025_class007.mrc as #24, grid size 540,540,540, pixel 0.818,
shown at level 0.0015, step 1, values float32  
Opened run_it025_class008.mrc as #25, grid size 540,540,540, pixel 0.818,
shown at level 0.0015, step 1, values float32  
Opened run_it025_class009.mrc as #26, grid size 540,540,540, pixel 0.818,
shown at level 0.0015, step 1, values float32  
Opened run_it025_class010.mrc as #27, grid size 540,540,540, pixel 0.818,
shown at level 0.0015, step 1, values float32  
Opened run_it025_class011.mrc as #28, grid size 540,540,540, pixel 0.818,
shown at level 0.0015, step 1, values float32  
Opened run_it025_class012.mrc as #29, grid size 540,540,540, pixel 0.818,
shown at level 0.0015, step 1, values float32  
Opened run_it025_class001.mrc as #30, grid size 540,540,540, pixel 0.818,
shown at level 0.0015, step 1, values float32  
Opened run_it025_class002.mrc as #31, grid size 540,540,540, pixel 0.818,
shown at level 0.0015, step 1, values float32  
Opened run_it025_class003.mrc as #32, grid size 540,540,540, pixel 0.818,
shown at level 0.0015, step 1, values float32  
Opened run_it025_class004.mrc as #33, grid size 540,540,540, pixel 0.818,
shown at level 0.0015, step 1, values float32  
Opened 232_substrate_full.mrc as #34, grid size 540,540,540, pixel 0.818,
shown at level 0.0018, step 1, values float32  
Opened J1031_consensus_mask.mrc as #35, grid size 540,540,540, pixel 0.818,
shown at level 0.99, step 1, values float32  
Opened J1032_head_mask.mrc as #36, grid size 540,540,540, pixel 0.818, shown
at level 0.99, step 1, values float32  
Opened J1033_body_mask.mrc as #37, grid size 540,540,540, pixel 0.818, shown
at level 0.99, step 1, values float32  
Opened J1034_substrate_mask.mrc as #38, grid size 540,540,540, pixel 0.818,
shown at level 0.99, step 1, values float32  
Opened J1094_substrate_mask.mrc as #39, grid size 540,540,540, pixel 0.818,
shown at level 0.99, step 1, values float32  
opened ChimeraX session  

> close session

> open
> /Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/Figures/Locres.cxs

Opened J1169_consensus_sharpened_masked.mrc as #1, grid size 540,540,540,
pixel 0.818, shown at level 0.0654, step 1, values float32  
Opened J1187_head_sharpened_masked.mrc as #2, grid size 540,540,540, pixel
0.818, shown at level 0.022, step 1, values float32  
Opened J1068_body_sharpened_masked.mrc as #3, grid size 540,540,540, pixel
0.818, shown at level 0.0706, step 1, values float32  
Opened 262_substrate_sharpened_masked.mrc as #4, grid size 540,540,540, pixel
0.818, shown at level 0.0017, step 1, values float32  
Opened 223_consensus_locres.mrc as #5, grid size 540,540,540, pixel 0.818,
shown at level 50, step 1, values float32  
Opened 260_head_locres.mrc as #6, grid size 540,540,540, pixel 0.818, shown at
level 50, step 1, values float32  
Opened 220_body_locres.mrc as #7, grid size 540,540,540, pixel 0.818, shown at
level 50, step 1, values float32  
Map values for surface "surface": minimum 2.794, mean 3.155, maximum 8.077  
opened ChimeraX session  

> hide #!1 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!3 models

> hide #!3 models

> show #!4 models

> hide #!4 models

> show #!1 models

> show #!2 models

> hide #!1 models

> show #!1 models

> hide #!2 models

> hide #!1 models

> show #!2 models

> hide #!2 models

> show #!3 models

> hide #!3 models

> show #!5 models

> hide #!5 models

> show #!4 models

> hide #!4 models

> show #!1 models

> hide #!1 models

> show #!2 models

> turn y -25

> view side

> hide #!2 models

> show #!1 models

> show #!2 models

> show #!3 models

> show #!4 models

> turn y -25

> hide #!4 models

> hide #!3 models

> hide #!2 models

> view side

> close session

> open
> /Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/Figures/Locres.cxs

Opened J1169_consensus_sharpened_masked.mrc as #1, grid size 540,540,540,
pixel 0.818, shown at level 0.0654, step 1, values float32  
Opened J1187_head_sharpened_masked.mrc as #2, grid size 540,540,540, pixel
0.818, shown at level 0.022, step 1, values float32  
Opened J1068_body_sharpened_masked.mrc as #3, grid size 540,540,540, pixel
0.818, shown at level 0.0706, step 1, values float32  
Opened 262_substrate_sharpened_masked.mrc as #4, grid size 540,540,540, pixel
0.818, shown at level 0.0017, step 1, values float32  
Opened 223_consensus_locres.mrc as #5, grid size 540,540,540, pixel 0.818,
shown at level 50, step 1, values float32  
Opened 260_head_locres.mrc as #6, grid size 540,540,540, pixel 0.818, shown at
level 50, step 1, values float32  
Opened 220_body_locres.mrc as #7, grid size 540,540,540, pixel 0.818, shown at
level 50, step 1, values float32  
Map values for surface "surface": minimum 2.794, mean 3.155, maximum 8.077  
opened ChimeraX session  

> view side

> turn y -25

> turn y 25

> view list

Named views: side, side_ang  

> view side_ang

> hide #!1 models

> show #!7 models

> hide #!7 models

> show #8 models

> show #!1 models

> view side

> hide #8 models

> turn y -25

> hide #!1 models

> show #!2 models

> view side

> turn y -25

> hide #!2 models

> show #!3 models

> hide #!3 models

> show #!4 models

> ui tool show "Surface Color"

> hide #!4 models

> show #!2 models

> hide #!2 models

> show #!1 models

> color sample #1.1 map #5 palette
> 2.8,#0000ff:3.3,#00ffff:3.8,#00ff00:4.3,#ffff00:8,#ff0000

Map values for surface "surface": minimum 2.794, mean 3.155, maximum 8.077  

> color sample #1.1 map #5 palette
> 2.8,#0000ff:3.3,#00ffff:3.8,#00ff00:4.3,#ffff00:8,#ff0000

Map values for surface "surface": minimum 2.794, mean 3.155, maximum 8.077  

> color single #1.1

> color sample #1.1 map #5 palette #0000ff:#00ffff:#00ff00:#ffff00:#ff0000

Map values for surface "surface": minimum 2.794, mean 3.155, maximum 8.077  

> color sample #1.1 map #5 palette #0000ff:#00ffff:#00ff00:#ffff00:#ff0000

Map values for surface "surface": minimum 2.794, mean 3.155, maximum 8.077  

> color single #1.1

> color sample #1.1 map #5 palette #0000ff:#00ffff:#00ff00:#ffff00:#ff0000

Map values for surface "surface": minimum 2.794, mean 3.155, maximum 8.077  

> color single #1.1

> color sample #1.1 map #5 palette
> 2.794,#0fc6ce:4.115,#87e2e6:5.436,#ffffff:6.756,#ce8fae:8.077,#9e1f5e

Map values for surface "surface": minimum 2.794, mean 3.155, maximum 8.077  

> color sample #1.1 map #5 palette
> 2.794,#ff0000:4.115,#ff7f7f:5.436,#ffffff:6.756,#7f7fff:8.077,#0000ff

Map values for surface "surface": minimum 2.794, mean 3.155, maximum 8.077  

> key red:2.79 #ff7f7f:4.11 white:5.44 #7f7fff:6.76 blue:8.08 showTool true

> ui mousemode right "color key"

> key pos 0.590994,0.837032

> key pos 0.597209,0.811312

> key pos 0.628649,0.810502 size 0.328318,0.0418582

> ui mousemode right translate

> hide #12 models

> show #12 models

> hide #12 models

> show #12 models

> close session

> open
> /Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/Figures/Workflow.cxs
> format session

Opened J845_prepreconsensus_full.mrc as #1, grid size 100,100,100, pixel 3.27,
shown at level 0.12, step 1, values float32  
Opened J918_preconsensus_full.mrc as #2, grid size 540,540,540, pixel 0.818,
shown at level 0.0728, step 1, values float32  
Opened 206_consensus_full.mrc as #3, grid size 540,540,540, pixel 0.818, shown
at level 0.00218, step 1, values float32  
Opened run_it025_class001.mrc as #4, grid size 540,540,540, pixel 0.818, shown
at level 0.0015, step 1, values float32  
Opened run_it025_class002.mrc as #5, grid size 540,540,540, pixel 0.818, shown
at level 0.0015, step 1, values float32  
Opened run_it025_class003.mrc as #6, grid size 540,540,540, pixel 0.818, shown
at level 0.0015, step 1, values float32  
Opened run_it025_class004.mrc as #7, grid size 540,540,540, pixel 0.818, shown
at level 0.0015, step 1, values float32  
Opened run_it025_class005.mrc as #8, grid size 540,540,540, pixel 0.818, shown
at level 0.0015, step 1, values float32  
Opened run_it025_class006.mrc as #9, grid size 540,540,540, pixel 0.818, shown
at level 0.0015, step 1, values float32  
Opened 067_head_full.mrc as #10, grid size 540,540,540, pixel 0.818, shown at
level 0.00236, step 1, values float32  
Opened run_it035_class001.mrc as #11, grid size 540,540,540, pixel 0.818,
shown at level 0.0028, step 1, values float32  
Opened run_it035_class002.mrc as #12, grid size 540,540,540, pixel 0.818,
shown at level 0.0028, step 1, values float32  
Opened run_it035_class003.mrc as #13, grid size 540,540,540, pixel 0.818,
shown at level 0.0028, step 1, values float32  
Opened run_it035_class004.mrc as #14, grid size 540,540,540, pixel 0.818,
shown at level 0.0028, step 1, values float32  
Opened run_it035_class005.mrc as #15, grid size 540,540,540, pixel 0.818,
shown at level 0.0028, step 1, values float32  
Opened run_it035_class006.mrc as #16, grid size 540,540,540, pixel 0.818,
shown at level 0.0028, step 1, values float32  
Opened 055_body_full.mrc as #17, grid size 540,540,540, pixel 0.818, shown at
level 0.00302, step 1, values float32  
Opened run_it025_class001.mrc as #18, grid size 540,540,540, pixel 0.818,
shown at level 0.0015, step 1, values float32  
Opened run_it025_class002.mrc as #19, grid size 540,540,540, pixel 0.818,
shown at level 0.0015, step 1, values float32  
Opened run_it025_class003.mrc as #20, grid size 540,540,540, pixel 0.818,
shown at level 0.0015, step 1, values float32  
Opened run_it025_class004.mrc as #21, grid size 540,540,540, pixel 0.818,
shown at level 0.0015, step 1, values float32  
Opened run_it025_class005.mrc as #22, grid size 540,540,540, pixel 0.818,
shown at level 0.0015, step 1, values float32  
Opened run_it025_class006.mrc as #23, grid size 540,540,540, pixel 0.818,
shown at level 0.0015, step 1, values float32  
Opened run_it025_class007.mrc as #24, grid size 540,540,540, pixel 0.818,
shown at level 0.0015, step 1, values float32  
Opened run_it025_class008.mrc as #25, grid size 540,540,540, pixel 0.818,
shown at level 0.0015, step 1, values float32  
Opened run_it025_class009.mrc as #26, grid size 540,540,540, pixel 0.818,
shown at level 0.0015, step 1, values float32  
Opened run_it025_class010.mrc as #27, grid size 540,540,540, pixel 0.818,
shown at level 0.0015, step 1, values float32  
Opened run_it025_class011.mrc as #28, grid size 540,540,540, pixel 0.818,
shown at level 0.0015, step 1, values float32  
Opened run_it025_class012.mrc as #29, grid size 540,540,540, pixel 0.818,
shown at level 0.0015, step 1, values float32  
Opened run_it025_class001.mrc as #30, grid size 540,540,540, pixel 0.818,
shown at level 0.0015, step 1, values float32  
Opened run_it025_class002.mrc as #31, grid size 540,540,540, pixel 0.818,
shown at level 0.0015, step 1, values float32  
Opened run_it025_class003.mrc as #32, grid size 540,540,540, pixel 0.818,
shown at level 0.0015, step 1, values float32  
Opened run_it025_class004.mrc as #33, grid size 540,540,540, pixel 0.818,
shown at level 0.0015, step 1, values float32  
Opened 232_substrate_full.mrc as #34, grid size 540,540,540, pixel 0.818,
shown at level 0.0018, step 1, values float32  
Opened J1031_consensus_mask.mrc as #35, grid size 540,540,540, pixel 0.818,
shown at level 0.99, step 1, values float32  
Opened J1032_head_mask.mrc as #36, grid size 540,540,540, pixel 0.818, shown
at level 0.99, step 1, values float32  
Opened J1033_body_mask.mrc as #37, grid size 540,540,540, pixel 0.818, shown
at level 0.99, step 1, values float32  
Opened J1034_substrate_mask.mrc as #38, grid size 540,540,540, pixel 0.818,
shown at level 0.99, step 1, values float32  
Opened J1094_substrate_mask.mrc as #39, grid size 540,540,540, pixel 0.818,
shown at level 0.99, step 1, values float32  
opened ChimeraX session  

> show #!4 models

> hide #!1 models

> hide #!4 models

> show #!5 models

> hide #!5 models

> show #!6 models

> hide #!6 models

> show #!7 models

> hide #!7 models

> show #!1 models

> hide #!1 models

> show #!2 models

> show #!35 models

> hide #!35 models

> show #!36 models

> hide #!36 models

> show #!37 models

> hide #!37 models

> show #!38 models

> hide #!38 models

> save /Users/mulline1/Desktop/test.png width 1580 height 1210 supersample 3
> transparentBackground true

> show #!23 models

> hide #!2 models

> hide #!23 models

> show #!1 models

> hide #!1 models

> show #!2 models

> view matric

Expected an objects specifier or a view name or a keyword  

> view matrix

view matrix camera
-0.021492,0.035484,-0.99914,-537.67,0.70539,0.70875,0.0099977,243.74,0.70849,-0.70457,-0.040263,169.27  
view matrix models
#1,0.99994,-0.0085654,0.0072002,57.591,0.0084492,0.99984,0.016017,53.946,-0.0073362,-0.015955,0.99985,33.239,#1.1,1,0,0,0,0,1,0,0,0,0,1,0,#2,1,0,0,0,0,1,0,0,0,0,1,0,#2.1,1,0,0,0,0,1,0,0,0,0,1,0,#3,1,0,0,0,0,1,0,0,0,0,1,0,#3.1,1,0,0,0,0,1,0,0,0,0,1,0,#4,1,0,0,0,0,1,0,0,0,0,1,0,#4.1,1,0,0,0,0,1,0,0,0,0,1,0,#5,1,0,0,0,0,1,0,0,0,0,1,0,#5.1,1,0,0,0,0,1,0,0,0,0,1,0,#6,1,0,0,0,0,1,0,0,0,0,1,0,#6.1,1,0,0,0,0,1,0,0,0,0,1,0,#7,1,0,0,0,0,1,0,0,0,0,1,0,#7.1,1,0,0,0,0,1,0,0,0,0,1,0,#8,1,0,0,0,0,1,0,0,0,0,1,0,#8.1,1,0,0,0,0,1,0,0,0,0,1,0,#9,1,0,0,0,0,1,0,0,0,0,1,0,#9.1,1,0,0,0,0,1,0,0,0,0,1,0,#10,1,0,0,0,0,1,0,0,0,0,1,0,#10.1,1,0,0,0,0,1,0,0,0,0,1,0,#11,1,0,0,0,0,1,0,0,0,0,1,0,#11.1,1,0,0,0,0,1,0,0,0,0,1,0,#12,1,0,0,0,0,1,0,0,0,0,1,0,#12.1,1,0,0,0,0,1,0,0,0,0,1,0,#13,1,0,0,0,0,1,0,0,0,0,1,0,#13.1,1,0,0,0,0,1,0,0,0,0,1,0,#14,1,0,0,0,0,1,0,0,0,0,1,0,#14.1,1,0,0,0,0,1,0,0,0,0,1,0,#15,1,0,0,0,0,1,0,0,0,0,1,0,#15.1,1,0,0,0,0,1,0,0,0,0,1,0,#16,1,0,0,0,0,1,0,0,0,0,1,0,#16.1,1,0,0,0,0,1,0,0,0,0,1,0,#17,1,0,0,0,0,1,0,0,0,0,1,0,#17.1,1,0,0,0,0,1,0,0,0,0,1,0,#18,1,0,0,0,0,1,0,0,0,0,1,0,#18.1,1,0,0,0,0,1,0,0,0,0,1,0,#19,1,0,0,0,0,1,0,0,0,0,1,0,#19.1,1,0,0,0,0,1,0,0,0,0,1,0,#20,1,0,0,0,0,1,0,0,0,0,1,0,#20.1,1,0,0,0,0,1,0,0,0,0,1,0,#21,1,0,0,0,0,1,0,0,0,0,1,0,#21.1,1,0,0,0,0,1,0,0,0,0,1,0,#22,1,0,0,0,0,1,0,0,0,0,1,0,#22.1,1,0,0,0,0,1,0,0,0,0,1,0,#23,1,0,0,0,0,1,0,0,0,0,1,0,#23.1,1,0,0,0,0,1,0,0,0,0,1,0,#24,1,0,0,0,0,1,0,0,0,0,1,0,#24.1,1,0,0,0,0,1,0,0,0,0,1,0,#25,1,0,0,0,0,1,0,0,0,0,1,0,#25.1,1,0,0,0,0,1,0,0,0,0,1,0,#26,1,0,0,0,0,1,0,0,0,0,1,0,#26.1,1,0,0,0,0,1,0,0,0,0,1,0,#27,1,0,0,0,0,1,0,0,0,0,1,0,#27.1,1,0,0,0,0,1,0,0,0,0,1,0,#28,1,0,0,0,0,1,0,0,0,0,1,0,#28.1,1,0,0,0,0,1,0,0,0,0,1,0,#29,1,0,0,0,0,1,0,0,0,0,1,0,#29.1,1,0,0,0,0,1,0,0,0,0,1,0,#30,1,0,0,0,0,1,0,0,0,0,1,0,#30.1,1,0,0,0,0,1,0,0,0,0,1,0,#31,1,0,0,0,0,1,0,0,0,0,1,0,#31.1,1,0,0,0,0,1,0,0,0,0,1,0,#32,1,0,0,0,0,1,0,0,0,0,1,0,#32.1,1,0,0,0,0,1,0,0,0,0,1,0,#33,1,0,0,0,0,1,0,0,0,0,1,0,#33.1,1,0,0,0,0,1,0,0,0,0,1,0,#34,0.99994,0.00092699,0.010836,-4.3257,-0.0015592,0.99829,0.058479,-15.006,-0.010764,-0.058492,0.99823,13.699,#34.1,1,0,0,0,0,1,0,0,0,0,1,0,#35,1,0,0,0,0,1,0,0,0,0,1,0,#35.1,1,0,0,0,0,1,0,0,0,0,1,0,#36,1,0,0,0,0,1,0,0,0,0,1,0,#36.1,1,0,0,0,0,1,0,0,0,0,1,0,#37,1,0,0,0,0,1,0,0,0,0,1,0,#37.1,1,0,0,0,0,1,0,0,0,0,1,0,#38,1,0,0,0,0,1,0,0,0,0,1,0,#38.1,1,0,0,0,0,1,0,0,0,0,1,0,#39,1,0,0,0,0,1,0,0,0,0,1,0,#39.1,1,0,0,0,0,1,0,0,0,0,1,0  
  

> view side

> hide #!2 models

> show #!3 models

> lighting soft

> lighting simple

> lighting full

> lighting simple

> lighting shadows true

> lighting shadows false

> graphics silhouettes true

> graphics silhouettes false

> lighting soft

> lighting full

> graphics silhouettes true

> graphics silhouettes false

> graphics silhouettes true

> graphics silhouettes false

> ui tool show "Side View"

> close session

> open
> /Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/Figures/Workflow.cxs
> format session

Opened J845_prepreconsensus_full.mrc as #1, grid size 100,100,100, pixel 3.27,
shown at level 0.12, step 1, values float32  
Opened J918_preconsensus_full.mrc as #2, grid size 540,540,540, pixel 0.818,
shown at level 0.0728, step 1, values float32  
Opened 206_consensus_full.mrc as #3, grid size 540,540,540, pixel 0.818, shown
at level 0.00218, step 1, values float32  
Opened run_it025_class001.mrc as #4, grid size 540,540,540, pixel 0.818, shown
at level 0.0015, step 1, values float32  
Opened run_it025_class002.mrc as #5, grid size 540,540,540, pixel 0.818, shown
at level 0.0015, step 1, values float32  
Opened run_it025_class003.mrc as #6, grid size 540,540,540, pixel 0.818, shown
at level 0.0015, step 1, values float32  
Opened run_it025_class004.mrc as #7, grid size 540,540,540, pixel 0.818, shown
at level 0.0015, step 1, values float32  
Opened run_it025_class005.mrc as #8, grid size 540,540,540, pixel 0.818, shown
at level 0.0015, step 1, values float32  
Opened run_it025_class006.mrc as #9, grid size 540,540,540, pixel 0.818, shown
at level 0.0015, step 1, values float32  
Opened 067_head_full.mrc as #10, grid size 540,540,540, pixel 0.818, shown at
level 0.00236, step 1, values float32  
Opened run_it035_class001.mrc as #11, grid size 540,540,540, pixel 0.818,
shown at level 0.0028, step 1, values float32  
Opened run_it035_class002.mrc as #12, grid size 540,540,540, pixel 0.818,
shown at level 0.0028, step 1, values float32  
Opened run_it035_class003.mrc as #13, grid size 540,540,540, pixel 0.818,
shown at level 0.0028, step 1, values float32  
Opened run_it035_class004.mrc as #14, grid size 540,540,540, pixel 0.818,
shown at level 0.0028, step 1, values float32  
Opened run_it035_class005.mrc as #15, grid size 540,540,540, pixel 0.818,
shown at level 0.0028, step 1, values float32  
Opened run_it035_class006.mrc as #16, grid size 540,540,540, pixel 0.818,
shown at level 0.0028, step 1, values float32  
Opened 055_body_full.mrc as #17, grid size 540,540,540, pixel 0.818, shown at
level 0.00302, step 1, values float32  
Opened run_it025_class001.mrc as #18, grid size 540,540,540, pixel 0.818,
shown at level 0.0015, step 1, values float32  
Opened run_it025_class002.mrc as #19, grid size 540,540,540, pixel 0.818,
shown at level 0.0015, step 1, values float32  
Opened run_it025_class003.mrc as #20, grid size 540,540,540, pixel 0.818,
shown at level 0.0015, step 1, values float32  
Opened run_it025_class004.mrc as #21, grid size 540,540,540, pixel 0.818,
shown at level 0.0015, step 1, values float32  
Opened run_it025_class005.mrc as #22, grid size 540,540,540, pixel 0.818,
shown at level 0.0015, step 1, values float32  
Opened run_it025_class006.mrc as #23, grid size 540,540,540, pixel 0.818,
shown at level 0.0015, step 1, values float32  
Opened run_it025_class007.mrc as #24, grid size 540,540,540, pixel 0.818,
shown at level 0.0015, step 1, values float32  
Opened run_it025_class008.mrc as #25, grid size 540,540,540, pixel 0.818,
shown at level 0.0015, step 1, values float32  
Opened run_it025_class009.mrc as #26, grid size 540,540,540, pixel 0.818,
shown at level 0.0015, step 1, values float32  
Opened run_it025_class010.mrc as #27, grid size 540,540,540, pixel 0.818,
shown at level 0.0015, step 1, values float32  
Opened run_it025_class011.mrc as #28, grid size 540,540,540, pixel 0.818,
shown at level 0.0015, step 1, values float32  
Opened run_it025_class012.mrc as #29, grid size 540,540,540, pixel 0.818,
shown at level 0.0015, step 1, values float32  
Opened run_it025_class001.mrc as #30, grid size 540,540,540, pixel 0.818,
shown at level 0.0015, step 1, values float32  
Opened run_it025_class002.mrc as #31, grid size 540,540,540, pixel 0.818,
shown at level 0.0015, step 1, values float32  
Opened run_it025_class003.mrc as #32, grid size 540,540,540, pixel 0.818,
shown at level 0.0015, step 1, values float32  
Opened run_it025_class004.mrc as #33, grid size 540,540,540, pixel 0.818,
shown at level 0.0015, step 1, values float32  
Opened 232_substrate_full.mrc as #34, grid size 540,540,540, pixel 0.818,
shown at level 0.0018, step 1, values float32  
Opened J1031_consensus_mask.mrc as #35, grid size 540,540,540, pixel 0.818,
shown at level 0.99, step 1, values float32  
Opened J1032_head_mask.mrc as #36, grid size 540,540,540, pixel 0.818, shown
at level 0.99, step 1, values float32  
Opened J1033_body_mask.mrc as #37, grid size 540,540,540, pixel 0.818, shown
at level 0.99, step 1, values float32  
Opened J1034_substrate_mask.mrc as #38, grid size 540,540,540, pixel 0.818,
shown at level 0.99, step 1, values float32  
Opened J1094_substrate_mask.mrc as #39, grid size 540,540,540, pixel 0.818,
shown at level 0.99, step 1, values float32  
opened ChimeraX session  

> hide #!1 models

> show #!2 models

> hide #!2 models

> show #!3 models

> hide #!3 models

> show #!3 models

> lighting simple

> lighting full

> lighting simple

> hide #!3 models

> show #!4 models

> hide #!4 models

> show #!4 models

> show #!5 models

> show #!6 models

> show #!7 models

> show #!8 models

> hide #!8 models

> hide #!7 models

> hide #!6 models

> hide #!5 models

> hide #!4 models

> show #!8 models

> turn y -25

> show #!1 models

> view side

> hide #!8 models

> hide #!1 models

> show #!2 models

> show #!35 models

> hide #!35 models

> show #!36 models

> hide #!36 models

> show #!37 models

> hide #!37 models

> show #!38 models

> hide #!38 models

> show #!39 models

> show #!38 models

> show #!35 models

> turn y -25

> show #!34 models

> hide #!38 models

> hide #!39 models

> hide #!35 models

> show #!39 models

> hide #!39 models

> show #!38 models

> hide #!38 models

> show #!38 models

> hide #!38 models

> hide #!2 models

> show #!8 models

> view side

> turn y -25

> show #!5 models

> hide #!8 models

> hide #!34 models

> hide #!5 models

> show #!3 models

> close session

> open
> /Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/Figures/Locres.cxs
> format session

Opened J1169_consensus_sharpened_masked.mrc as #1, grid size 540,540,540,
pixel 0.818, shown at level 0.0654, step 1, values float32  
Opened J1187_head_sharpened_masked.mrc as #2, grid size 540,540,540, pixel
0.818, shown at level 0.022, step 1, values float32  
Opened J1068_body_sharpened_masked.mrc as #3, grid size 540,540,540, pixel
0.818, shown at level 0.0706, step 1, values float32  
Opened 262_substrate_sharpened_masked.mrc as #4, grid size 540,540,540, pixel
0.818, shown at level 0.0017, step 1, values float32  
Opened 223_consensus_locres.mrc as #5, grid size 540,540,540, pixel 0.818,
shown at level 50, step 1, values float32  
Opened 260_head_locres.mrc as #6, grid size 540,540,540, pixel 0.818, shown at
level 50, step 1, values float32  
Opened 220_body_locres.mrc as #7, grid size 540,540,540, pixel 0.818, shown at
level 50, step 1, values float32  
Map values for surface "surface": minimum 2.794, mean 3.155, maximum 8.077  
opened ChimeraX session  

> turn y -25

> view side

> show #!2 models

> hide #!1 models

> hide #!2 models

> show #!3 models

> hide #!3 models

> show #!4 models

> show #!3 models

> show #!2 models

> show #!1 models

> turn y -25

> hide #!3 models

> hide #!2 models

> hide #!1 models

> ui tool show "Side View"

> hide #!4 models

> show #!3 models

> hide #!3 models

> show #!2 models

> hide #!2 models

> show #!1 models

> hide #!1 models

> show #!4 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!4 models

> hide #!3 models

> show #!2 models

> hide #!2 models

> show #!1 models

> hide #!1 models

> show #!2 models

> hide #!2 models

> show #!3 models

> hide #!3 models

> show #!4 models

> hide #!4 models

> show #!1 models

> view side

> turn x 1

> view side

> turn z 1

> turn y -25

> hide #!1 models

> show #!2 models

> hide #!2 models

> show #!3 models

> hide #!3 models

> show #!4 models

> hide #!4 models

> show #!3 models

> hide #!3 models

> show #!2 models

> hide #!2 models

> show #!1 models

> show #!4 models

> hide #!1 models

> show #!1 models

> hide #!4 models

> view side

> turn y -25

> show #!2 models

> hide #!1 models

> show #!3 models

> hide #!3 models

> show #!4 models

> hide #!2 models

> show #!2 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!2 models

> hide #!3 models

> hide #!4 models

> show #!1 models

> show #!2 models

> hide #!1 models

> hide #!2 models

> show #!3 models

> hide #!3 models

> show #!4 models

> hide #!4 models

> show #!5 models

> hide #!5 models

> show #!6 models

> hide #!6 models

> show #!7 models

> hide #!7 models

> show #11 models

> hide #11 models

> show #10 models

> hide #10 models

> show #!4 models

> hide #!4 models

> show #!3 models

> hide #!3 models

> show #!2 models

> view side

> show #!4 models

> show #!3 models

> show #!1 models

> turn y -90

> hide #!3 models

> hide #!2 models

> hide #!1 models

> show #!3 models

> hide #!4 models

> hide #!3 models

> show #!2 models

> hide #!2 models

> show #!1 models

> turn x 45

> hide #!1 models

> show #!2 models

> hide #!2 models

> show #!3 models

> hide #!3 models

> show #!4 models

> hide #!4 models

> show #!1 models

> show #!2 models

> hide #!1 models

> hide #!2 models

> show #!3 models

> view side

> hide #!3 models

> show #!1 models

> hide #!1 models

> show #!2 models

> show #!1 models

> show #!3 models

> hide #!3 models

> hide #!2 models

> show #!2 models

> hide #!1 models

> show #!3 models

> hide #!2 models

> hide #!3 models

> show #!4 models

> show #!3 models

> show #!2 models

> show #!1 models

> turn y -90

> hide #!4 models

> hide #!3 models

> hide #!1 models

> view name front

> view side

> view front

> show #!1 models

> show #!3 models

> show #!4 models

> view side

> turn y -90

> view front

> hide #!3 models

> hide #!2 models

> hide #!4 models

> view side

> show #!2 models

> show #!3 models

> show #!4 models

> turn y -25

> turn y -5

> view side

> view front

> view side

> turn y -25

> hide #!3 models

> hide #!2 models

> hide #!4 models

> view side

> close session

> open
> /Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/Figures/Workflow.cxs
> format session

Opened J845_prepreconsensus_full.mrc as #1, grid size 100,100,100, pixel 3.27,
shown at level 0.12, step 1, values float32  
Opened J918_preconsensus_full.mrc as #2, grid size 540,540,540, pixel 0.818,
shown at level 0.0728, step 1, values float32  
Opened 206_consensus_full.mrc as #3, grid size 540,540,540, pixel 0.818, shown
at level 0.00218, step 1, values float32  
Opened run_it025_class001.mrc as #4, grid size 540,540,540, pixel 0.818, shown
at level 0.0015, step 1, values float32  
Opened run_it025_class002.mrc as #5, grid size 540,540,540, pixel 0.818, shown
at level 0.0015, step 1, values float32  
Opened run_it025_class003.mrc as #6, grid size 540,540,540, pixel 0.818, shown
at level 0.0015, step 1, values float32  
Opened run_it025_class004.mrc as #7, grid size 540,540,540, pixel 0.818, shown
at level 0.0015, step 1, values float32  
Opened run_it025_class005.mrc as #8, grid size 540,540,540, pixel 0.818, shown
at level 0.0015, step 1, values float32  
Opened run_it025_class006.mrc as #9, grid size 540,540,540, pixel 0.818, shown
at level 0.0015, step 1, values float32  
Opened 067_head_full.mrc as #10, grid size 540,540,540, pixel 0.818, shown at
level 0.00236, step 1, values float32  
Opened run_it035_class001.mrc as #11, grid size 540,540,540, pixel 0.818,
shown at level 0.0028, step 1, values float32  
Opened run_it035_class002.mrc as #12, grid size 540,540,540, pixel 0.818,
shown at level 0.0028, step 1, values float32  
Opened run_it035_class003.mrc as #13, grid size 540,540,540, pixel 0.818,
shown at level 0.0028, step 1, values float32  
Opened run_it035_class004.mrc as #14, grid size 540,540,540, pixel 0.818,
shown at level 0.0028, step 1, values float32  
Opened run_it035_class005.mrc as #15, grid size 540,540,540, pixel 0.818,
shown at level 0.0028, step 1, values float32  
Opened run_it035_class006.mrc as #16, grid size 540,540,540, pixel 0.818,
shown at level 0.0028, step 1, values float32  
Opened 055_body_full.mrc as #17, grid size 540,540,540, pixel 0.818, shown at
level 0.00302, step 1, values float32  
Opened run_it025_class001.mrc as #18, grid size 540,540,540, pixel 0.818,
shown at level 0.0015, step 1, values float32  
Opened run_it025_class002.mrc as #19, grid size 540,540,540, pixel 0.818,
shown at level 0.0015, step 1, values float32  
Opened run_it025_class003.mrc as #20, grid size 540,540,540, pixel 0.818,
shown at level 0.0015, step 1, values float32  
Opened run_it025_class004.mrc as #21, grid size 540,540,540, pixel 0.818,
shown at level 0.0015, step 1, values float32  
Opened run_it025_class005.mrc as #22, grid size 540,540,540, pixel 0.818,
shown at level 0.0015, step 1, values float32  
Opened run_it025_class006.mrc as #23, grid size 540,540,540, pixel 0.818,
shown at level 0.0015, step 1, values float32  
Opened run_it025_class007.mrc as #24, grid size 540,540,540, pixel 0.818,
shown at level 0.0015, step 1, values float32  
Opened run_it025_class008.mrc as #25, grid size 540,540,540, pixel 0.818,
shown at level 0.0015, step 1, values float32  
Opened run_it025_class009.mrc as #26, grid size 540,540,540, pixel 0.818,
shown at level 0.0015, step 1, values float32  
Opened run_it025_class010.mrc as #27, grid size 540,540,540, pixel 0.818,
shown at level 0.0015, step 1, values float32  
Opened run_it025_class011.mrc as #28, grid size 540,540,540, pixel 0.818,
shown at level 0.0015, step 1, values float32  
Opened run_it025_class012.mrc as #29, grid size 540,540,540, pixel 0.818,
shown at level 0.0015, step 1, values float32  
Opened run_it025_class001.mrc as #30, grid size 540,540,540, pixel 0.818,
shown at level 0.0015, step 1, values float32  
Opened run_it025_class002.mrc as #31, grid size 540,540,540, pixel 0.818,
shown at level 0.0015, step 1, values float32  
Opened run_it025_class003.mrc as #32, grid size 540,540,540, pixel 0.818,
shown at level 0.0015, step 1, values float32  
Opened run_it025_class004.mrc as #33, grid size 540,540,540, pixel 0.818,
shown at level 0.0015, step 1, values float32  
Opened 232_substrate_full.mrc as #34, grid size 540,540,540, pixel 0.818,
shown at level 0.0018, step 1, values float32  
Opened J1031_consensus_mask.mrc as #35, grid size 540,540,540, pixel 0.818,
shown at level 0.99, step 1, values float32  
Opened J1032_head_mask.mrc as #36, grid size 540,540,540, pixel 0.818, shown
at level 0.99, step 1, values float32  
Opened J1033_body_mask.mrc as #37, grid size 540,540,540, pixel 0.818, shown
at level 0.99, step 1, values float32  
Opened J1034_substrate_mask.mrc as #38, grid size 540,540,540, pixel 0.818,
shown at level 0.99, step 1, values float32  
Opened J1094_substrate_mask.mrc as #39, grid size 540,540,540, pixel 0.818,
shown at level 0.99, step 1, values float32  
opened ChimeraX session  

> hide #!1 models

> show #!2 models

> show #!1 models

> hide #!2 models

> hide #!1 models

> show #!2 models

> hide #!2 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!2 models

> hide #!2 models

> show #!3 models

> hide #!3 models

> show #!2 models

> hide #!2 models

> show #!1 models

> show #!35 models

> show #!34 models

> hide #!34 models

> hide #!35 models

> show #!2 models

> hide #!1 models

> show #!3 models

> hide #!2 models

> hide #!3 models

> show #!2 models

> hide #!2 models

> show #!1 models

> view side

> show #!35 models

> turn y -25

> view side

> turn y -30

> view side

> turn y -25

> hide #!35 models

> show #!34 models

> hide #!1 models

> show #!2 models

> hide #!34 models

> hide #!2 models

> show #!3 models

> hide #!3 models

> show #!4 models

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> show #!9 models

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> show #!8 models

> hide #!8 models

> show #!9 models

> hide #!9 models

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> hide #!35 models

> show #!35 models

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> show #!37 models

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> hide #!36 models

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> show #!38 models

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> show #!38 models

> hide #!38 models

> show #!38 models

> hide #!38 models

> show #!38 models

> hide #!38 models

> show #!38 models

> hide #!38 models

> view side

> show #!38 models

> hide #!39 models

> show #!39 models

> hide #!38 models

> show #!38 models

> hide #!39 models

> show #!39 models

> hide #!38 models

> hide #!39 models

> show #!37 models

> hide #!37 models

> show #!36 models

> hide #!36 models

> show #!35 models

> view side

> hide #!35 models

> show #!30 models

> hide #!30 models

> show #!30 models

> hide #!30 models

> show #!1 models

> hide #!1 models

> show #!2 models

> hide #!2 models

> show #!3 models

> hide #!3 models

> show #!4 models

> hide #!4 models

> show #!5 models

> show #!8 models

> hide #!5 models

> view side

> show #!35 models

> show #!30 models

> hide #!30 models

> hide #!8 models

> view side

> turn y -25

> show #!1 models

> hide #!1 models

> show #!2 models

> hide #!2 models

> show #!3 models

> show #!2 models

> show #!4 models

> hide #!2 models

> hide #!3 models

> hide #!4 models

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> show #!8 models

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> hide #!35 models

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> hide #!36 models

> show #!36 models

> show #!3 models

> hide #!36 models

> show #!37 models

> hide #!37 models

> show #!38 models

> hide #!38 models

> show #!39 models

> hide #!39 models

> show #!38 models

> show #!39 models

> hide #!38 models

> show #!18 models

> hide #!3 models

> show #!30 models

> hide #!30 models

> show #!30 models

> hide #!30 models

> show #!30 models

> view name oblique

> hide #!30 models

> show #!30 models

> hide #!30 models

> show #!30 models

> hide #!30 models

> show #!30 models

> show #!34 models

> hide #!18 models

> hide #!30 models

> view oblique

> hide #!34 models

> hide #!39 models

> show #!35 models

> show #!2 models

> hide #!2 models

> show #!3 models

> hide #!35 models

> show #!36 models

> show #!10 models

> hide #!10 models

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> hide #!10 models

> show #!10 models

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> show #!10 models

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> show #!10 models

> hide #!10 models

> show #!10 models

> hide #!10 models

> show #!37 models

> hide #!36 models

> hide #!37 models

> show #!38 models

> close session

> open
> /Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/Figures/Locres.cxs
> format session

Opened J1169_consensus_sharpened_masked.mrc as #1, grid size 540,540,540,
pixel 0.818, shown at level 0.0654, step 1, values float32  
Opened J1187_head_sharpened_masked.mrc as #2, grid size 540,540,540, pixel
0.818, shown at level 0.022, step 1, values float32  
Opened J1068_body_sharpened_masked.mrc as #3, grid size 540,540,540, pixel
0.818, shown at level 0.0706, step 1, values float32  
Opened 262_substrate_sharpened_masked.mrc as #4, grid size 540,540,540, pixel
0.818, shown at level 0.0017, step 1, values float32  
Opened 223_consensus_locres.mrc as #5, grid size 540,540,540, pixel 0.818,
shown at level 50, step 1, values float32  
Opened 260_head_locres.mrc as #6, grid size 540,540,540, pixel 0.818, shown at
level 50, step 1, values float32  
Opened 220_body_locres.mrc as #7, grid size 540,540,540, pixel 0.818, shown at
level 50, step 1, values float32  
Map values for surface "surface": minimum 2.794, mean 3.155, maximum 8.077  
opened ChimeraX session  

> show #!4 models

> show #!2 models

> show #!3 models

> turn y -25

> hide #!4 models

> hide #!3 models

> hide #!2 models

> hide #!1 models

> show #!2 models

> hide #!2 models

> show #!3 models

> hide #!3 models

> show #!4 models

> hide #!4 models

> show #!1 models

> graphics silhouettes false

> graphics silhouettes true

> graphics silhouettes false

> view side

> graphics silhouettes true

> turn y -25

> view name oblique

> view side_ang

> show #11 models

> show #10 models

> show #9 models

> show #8 models

> hide #12 models

> hide #!1 models

> turn y -25

> view name oblique_ang

> view list

Named views: oblique, oblique_ang, side, side_ang  

> hide #11 models

> hide #10 models

> hide #9 models

> hide #8 models

> show #!1 models

> view oblique

> show #!4 models

> hide #!4 models

> save /Users/mulline1/Dropbox/FBH1/cryoEM_revised/Figures/Locres.cxs

> close session

> open
> /Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/Figures/Workflow.cxs
> format session

Opened J845_prepreconsensus_full.mrc as #1, grid size 100,100,100, pixel 3.27,
shown at level 0.12, step 1, values float32  
Opened J918_preconsensus_full.mrc as #2, grid size 540,540,540, pixel 0.818,
shown at level 0.0728, step 1, values float32  
Opened 206_consensus_full.mrc as #3, grid size 540,540,540, pixel 0.818, shown
at level 0.00218, step 1, values float32  
Opened run_it025_class001.mrc as #4, grid size 540,540,540, pixel 0.818, shown
at level 0.0015, step 1, values float32  
Opened run_it025_class002.mrc as #5, grid size 540,540,540, pixel 0.818, shown
at level 0.0015, step 1, values float32  
Opened run_it025_class003.mrc as #6, grid size 540,540,540, pixel 0.818, shown
at level 0.0015, step 1, values float32  
Opened run_it025_class004.mrc as #7, grid size 540,540,540, pixel 0.818, shown
at level 0.0015, step 1, values float32  
Opened run_it025_class005.mrc as #8, grid size 540,540,540, pixel 0.818, shown
at level 0.0015, step 1, values float32  
Opened run_it025_class006.mrc as #9, grid size 540,540,540, pixel 0.818, shown
at level 0.0015, step 1, values float32  
Opened 067_head_full.mrc as #10, grid size 540,540,540, pixel 0.818, shown at
level 0.00236, step 1, values float32  
Opened run_it035_class001.mrc as #11, grid size 540,540,540, pixel 0.818,
shown at level 0.0028, step 1, values float32  
Opened run_it035_class002.mrc as #12, grid size 540,540,540, pixel 0.818,
shown at level 0.0028, step 1, values float32  
Opened run_it035_class003.mrc as #13, grid size 540,540,540, pixel 0.818,
shown at level 0.0028, step 1, values float32  
Opened run_it035_class004.mrc as #14, grid size 540,540,540, pixel 0.818,
shown at level 0.0028, step 1, values float32  
Opened run_it035_class005.mrc as #15, grid size 540,540,540, pixel 0.818,
shown at level 0.0028, step 1, values float32  
Opened run_it035_class006.mrc as #16, grid size 540,540,540, pixel 0.818,
shown at level 0.0028, step 1, values float32  
Opened 055_body_full.mrc as #17, grid size 540,540,540, pixel 0.818, shown at
level 0.00302, step 1, values float32  
Opened run_it025_class001.mrc as #18, grid size 540,540,540, pixel 0.818,
shown at level 0.0015, step 1, values float32  
Opened run_it025_class002.mrc as #19, grid size 540,540,540, pixel 0.818,
shown at level 0.0015, step 1, values float32  
Opened run_it025_class003.mrc as #20, grid size 540,540,540, pixel 0.818,
shown at level 0.0015, step 1, values float32  
Opened run_it025_class004.mrc as #21, grid size 540,540,540, pixel 0.818,
shown at level 0.0015, step 1, values float32  
Opened run_it025_class005.mrc as #22, grid size 540,540,540, pixel 0.818,
shown at level 0.0015, step 1, values float32  
Opened run_it025_class006.mrc as #23, grid size 540,540,540, pixel 0.818,
shown at level 0.0015, step 1, values float32  
Opened run_it025_class007.mrc as #24, grid size 540,540,540, pixel 0.818,
shown at level 0.0015, step 1, values float32  
Opened run_it025_class008.mrc as #25, grid size 540,540,540, pixel 0.818,
shown at level 0.0015, step 1, values float32  
Opened run_it025_class009.mrc as #26, grid size 540,540,540, pixel 0.818,
shown at level 0.0015, step 1, values float32  
Opened run_it025_class010.mrc as #27, grid size 540,540,540, pixel 0.818,
shown at level 0.0015, step 1, values float32  
Opened run_it025_class011.mrc as #28, grid size 540,540,540, pixel 0.818,
shown at level 0.0015, step 1, values float32  
Opened run_it025_class012.mrc as #29, grid size 540,540,540, pixel 0.818,
shown at level 0.0015, step 1, values float32  
Opened run_it025_class001.mrc as #30, grid size 540,540,540, pixel 0.818,
shown at level 0.0015, step 1, values float32  
Opened run_it025_class002.mrc as #31, grid size 540,540,540, pixel 0.818,
shown at level 0.0015, step 1, values float32  
Opened run_it025_class003.mrc as #32, grid size 540,540,540, pixel 0.818,
shown at level 0.0015, step 1, values float32  
Opened run_it025_class004.mrc as #33, grid size 540,540,540, pixel 0.818,
shown at level 0.0015, step 1, values float32  
Opened 232_substrate_full.mrc as #34, grid size 540,540,540, pixel 0.818,
shown at level 0.0018, step 1, values float32  
Opened J1031_consensus_mask.mrc as #35, grid size 540,540,540, pixel 0.818,
shown at level 0.99, step 1, values float32  
Opened J1032_head_mask.mrc as #36, grid size 540,540,540, pixel 0.818, shown
at level 0.99, step 1, values float32  
Opened J1033_body_mask.mrc as #37, grid size 540,540,540, pixel 0.818, shown
at level 0.99, step 1, values float32  
Opened J1034_substrate_mask.mrc as #38, grid size 540,540,540, pixel 0.818,
shown at level 0.99, step 1, values float32  
Opened J1094_substrate_mask.mrc as #39, grid size 540,540,540, pixel 0.818,
shown at level 0.99, step 1, values float32  
opened ChimeraX session  

> show #!35 models

> turn y -25

> view name oblique

> view list

Named views: oblique, side  

> hide #!35 models

> save /Users/mulline1/Dropbox/FBH1/cryoEM_revised/Figures/Workflow.cxs

> hide #!1 models

> show #!2 models

> hide #!2 models

> show #!3 models

> hide #!3 models

> show #!2 models

> hide #!2 models

> show #!4 models

> hide #!4 models

> show #!8 models

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> view oblique

> hide #!8 models

> show #!34 models

> hide #!34 models

> show #!33 models

> show #!32 models

> show #!31 models

> show #!30 models

> hide #!31 models

> hide #!32 models

> hide #!33 models

> view oblique

> hide #!30 models

> show #!29 models

> hide #!29 models

> show #!18 models

> show #!38 models

> hide #!38 models

> show #!39 models

> show #!38 models

> hide #!38 models

> show #!38 models

> hide #!39 models

> show #!39 models

> hide #!38 models

> show #!34 models

> hide #!18 models

> view oblique

> hide #!34 models

> hide #!39 models

> show #!35 models

> show #!2 models

> hide #!2 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!35 models

> show #!36 models

> hide #!36 models

> show #!37 models

> hide #!37 models

> show #!38 models

> hide #!38 models

> show #!39 models

> hide #!39 models

> show #!38 models

> hide #!38 models

> hide #!3 models

> close session

> open
> /Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/Figures/Locres.cxs

Opened J1169_consensus_sharpened_masked.mrc as #1, grid size 540,540,540,
pixel 0.818, shown at level 0.0654, step 1, values float32  
Opened J1187_head_sharpened_masked.mrc as #2, grid size 540,540,540, pixel
0.818, shown at level 0.022, step 1, values float32  
Opened J1068_body_sharpened_masked.mrc as #3, grid size 540,540,540, pixel
0.818, shown at level 0.0706, step 1, values float32  
Opened 262_substrate_sharpened_masked.mrc as #4, grid size 540,540,540, pixel
0.818, shown at level 0.0017, step 1, values float32  
Opened 223_consensus_locres.mrc as #5, grid size 540,540,540, pixel 0.818,
shown at level 50, step 1, values float32  
Opened 260_head_locres.mrc as #6, grid size 540,540,540, pixel 0.818, shown at
level 50, step 1, values float32  
Opened 220_body_locres.mrc as #7, grid size 540,540,540, pixel 0.818, shown at
level 50, step 1, values float32  
opened ChimeraX session  

> show #12 models

> hide #12 models

> show #!2 models

> hide #!1 models

> show #!1 models

> show #!3 models

> show #!4 models

> turn y -90

> view oblique

> hide #!1 models

> hide #!2 models

> hide #!3 models

> view oblique

> hide #!4 models

> show #!1 models

> hide #!1 models

> show #!2 models

> hide #!2 models

> show #!3 models

> hide #!3 models

> show #!2 models

> hide #!2 models

> show #!3 models

> show #!2 models

> show #!4 models

> hide #!4 models

> hide #!3 models

> close session

> open
> /Users/mulline1/Library/CloudStorage/Dropbox/FBH1/cryoEM_revised/Figures/Workflow.cxs

Opened J845_prepreconsensus_full.mrc as #1, grid size 100,100,100, pixel 3.27,
shown at level 0.12, step 1, values float32  
Opened J918_preconsensus_full.mrc as #2, grid size 540,540,540, pixel 0.818,
shown at level 0.0728, step 1, values float32  
Opened 206_consensus_full.mrc as #3, grid size 540,540,540, pixel 0.818, shown
at level 0.00218, step 1, values float32  
Opened run_it025_class001.mrc as #4, grid size 540,540,540, pixel 0.818, shown
at level 0.0015, step 1, values float32  
Opened run_it025_class002.mrc as #5, grid size 540,540,540, pixel 0.818, shown
at level 0.0015, step 1, values float32  
Opened run_it025_class003.mrc as #6, grid size 540,540,540, pixel 0.818, shown
at level 0.0015, step 1, values float32  
Opened run_it025_class004.mrc as #7, grid size 540,540,540, pixel 0.818, shown
at level 0.0015, step 1, values float32  
Opened run_it025_class005.mrc as #8, grid size 540,540,540, pixel 0.818, shown
at level 0.0015, step 1, values float32  
Opened run_it025_class006.mrc as #9, grid size 540,540,540, pixel 0.818, shown
at level 0.0015, step 1, values float32  
Opened 067_head_full.mrc as #10, grid size 540,540,540, pixel 0.818, shown at
level 0.00236, step 1, values float32  
Opened run_it035_class001.mrc as #11, grid size 540,540,540, pixel 0.818,
shown at level 0.0028, step 1, values float32  
Opened run_it035_class002.mrc as #12, grid size 540,540,540, pixel 0.818,
shown at level 0.0028, step 1, values float32  
Opened run_it035_class003.mrc as #13, grid size 540,540,540, pixel 0.818,
shown at level 0.0028, step 1, values float32  
Opened run_it035_class004.mrc as #14, grid size 540,540,540, pixel 0.818,
shown at level 0.0028, step 1, values float32  
Opened run_it035_class005.mrc as #15, grid size 540,540,540, pixel 0.818,
shown at level 0.0028, step 1, values float32  
Opened run_it035_class006.mrc as #16, grid size 540,540,540, pixel 0.818,
shown at level 0.0028, step 1, values float32  
Opened 055_body_full.mrc as #17, grid size 540,540,540, pixel 0.818, shown at
level 0.00302, step 1, values float32  
Opened run_it025_class001.mrc as #18, grid size 540,540,540, pixel 0.818,
shown at level 0.0015, step 1, values float32  
Opened run_it025_class002.mrc as #19, grid size 540,540,540, pixel 0.818,
shown at level 0.0015, step 1, values float32  
Opened run_it025_class003.mrc as #20, grid size 540,540,540, pixel 0.818,
shown at level 0.0015, step 1, values float32  
Opened run_it025_class004.mrc as #21, grid size 540,540,540, pixel 0.818,
shown at level 0.0015, step 1, values float32  
Opened run_it025_class005.mrc as #22, grid size 540,540,540, pixel 0.818,
shown at level 0.0015, step 1, values float32  
Opened run_it025_class006.mrc as #23, grid size 540,540,540, pixel 0.818,
shown at level 0.0015, step 1, values float32  
Opened run_it025_class007.mrc as #24, grid size 540,540,540, pixel 0.818,
shown at level 0.0015, step 1, values float32  
Opened run_it025_class008.mrc as #25, grid size 540,540,540, pixel 0.818,
shown at level 0.0015, step 1, values float32  
Opened run_it025_class009.mrc as #26, grid size 540,540,540, pixel 0.818,
shown at level 0.0015, step 1, values float32  
Opened run_it025_class010.mrc as #27, grid size 540,540,540, pixel 0.818,
shown at level 0.0015, step 1, values float32  
Opened run_it025_class011.mrc as #28, grid size 540,540,540, pixel 0.818,
shown at level 0.0015, step 1, values float32  
Opened run_it025_class012.mrc as #29, grid size 540,540,540, pixel 0.818,
shown at level 0.0015, step 1, values float32  
Opened run_it025_class001.mrc as #30, grid size 540,540,540, pixel 0.818,
shown at level 0.0015, step 1, values float32  
Opened run_it025_class002.mrc as #31, grid size 540,540,540, pixel 0.818,
shown at level 0.0015, step 1, values float32  
Opened run_it025_class003.mrc as #32, grid size 540,540,540, pixel 0.818,
shown at level 0.0015, step 1, values float32  
Opened run_it025_class004.mrc as #33, grid size 540,540,540, pixel 0.818,
shown at level 0.0015, step 1, values float32  
Opened 232_substrate_full.mrc as #34, grid size 540,540,540, pixel 0.818,
shown at level 0.0018, step 1, values float32  
Opened J1031_consensus_mask.mrc as #35, grid size 540,540,540, pixel 0.818,
shown at level 0.99, step 1, values float32  
Opened J1032_head_mask.mrc as #36, grid size 540,540,540, pixel 0.818, shown
at level 0.99, step 1, values float32  
Opened J1033_body_mask.mrc as #37, grid size 540,540,540, pixel 0.818, shown
at level 0.99, step 1, values float32  
Opened J1034_substrate_mask.mrc as #38, grid size 540,540,540, pixel 0.818,
shown at level 0.99, step 1, values float32  
Opened J1094_substrate_mask.mrc as #39, grid size 540,540,540, pixel 0.818,
shown at level 0.99, step 1, values float32  
opened ChimeraX session  

> hide #!1 models

> show #!34 models

> show #!30 models

> hide #!34 models

> show #!34 models

> hide #!30 models

> show #!1 models

> hide #!34 models

> view oblique

> hide #!1 models

> show #!2 models

> hide #!2 models

> show #!3 models

> hide #!3 models

> show #!2 models

> show #!35 models


===== Log before crash end =====

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
You can double click a model's Name or ID in the model panel to edit those
fields  
UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 4.1 Metal - 89.3
OpenGL renderer: Apple M3 Max
OpenGL vendor: Apple

Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: Mac15,11
      Model Number: MRW33LL/A
      Chip: Apple M3 Max
      Total Number of Cores: 14 (10 performance and 4 efficiency)
      Memory: 36 GB
      System Firmware Version: 11881.81.4
      OS Loader Version: 11881.81.4

Software:

    System Software Overview:

      System Version: macOS 15.3.1 (24D70)
      Kernel Version: Darwin 24.3.0
      Time since boot: 17 days, 8 hours, 54 minutes

Graphics/Displays:

    Apple M3 Max:

      Chipset Model: Apple M3 Max
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 30
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-in Liquid Retina XDR Display
          Resolution: 3456 x 2234 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal
        DELL UP2716D:
          Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition)
          UI Looks like: 2560 x 1440 @ 60.00Hz
          Mirror: Off
          Online: Yes
          Rotation: Supported


Installed Packages:
    alabaster: 1.0.0
    anyio: 4.7.0
    appdirs: 1.4.4
    appnope: 0.1.4
    asttokens: 3.0.0
    auditwheel: 6.1.0
    babel: 2.16.0
    beautifulsoup4: 4.12.3
    blockdiag: 3.0.0
    blosc2: 3.0.0
    build: 1.2.1
    certifi: 2023.11.17
    cftime: 1.6.4.post1
    charset-normalizer: 3.4.0
    ChimeraX-AddCharge: 1.5.18
    ChimeraX-AddH: 2.2.6
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.5
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.16.1
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.58.8
    ChimeraX-AtomicLibrary: 14.1.11
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 3.0.0
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.13.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.4.0
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.4
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.3
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.6
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.9
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.4
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2.6
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.3
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.4.1
    ChimeraX-Hbonds: 2.5
    ChimeraX-Help: 1.3
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.3
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-KVFinder: 1.2.1
    ChimeraX-Label: 1.1.14
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.3
    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: 2.1.6
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.7.2
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.14.2
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.18
    ChimeraX-ModelPanel: 1.5
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-MutationScores: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.2
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.2
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.14
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.6
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.4
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1.2
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.6.2
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.3.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.2
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.5.6
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.14
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.2.0
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-SimilarStructures: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.18.1
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.2.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.5
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.2.3
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.41
    ChimeraX-Umap: 1.0
    ChimeraX-uniprot: 2.3.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.4
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.4
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    contourpy: 1.3.1
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.0.10
    debugpy: 1.8.9
    decorator: 5.1.1
    docutils: 0.21.2
    executing: 2.1.0
    filelock: 3.15.4
    fonttools: 4.55.3
    funcparserlib: 2.0.0a0
    glfw: 2.8.0
    grako: 3.16.5
    h11: 0.14.0
    h5py: 3.12.1
    html2text: 2024.2.26
    httpcore: 1.0.7
    httpx: 0.28.1
    idna: 3.10
    ihm: 1.3
    imagecodecs: 2024.6.1
    imagesize: 1.4.1
    ipykernel: 6.29.5
    ipython: 8.26.0
    ipywidgets: 8.1.5
    jedi: 0.19.1
    Jinja2: 3.1.4
    jupyter_client: 8.6.2
    jupyter_core: 5.7.2
    jupyterlab_widgets: 3.0.13
    kiwisolver: 1.4.7
    line_profiler: 4.1.3
    lxml: 5.2.2
    lz4: 4.3.3
    MarkupSafe: 3.0.2
    matplotlib: 3.9.2
    matplotlib-inline: 0.1.7
    msgpack: 1.0.8
    ndindex: 1.9.2
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.10.2
    numpy: 1.26.4
    openvr: 1.26.701
    packaging: 23.2
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pexpect: 4.9.0
    pillow: 10.4.0
    pip: 24.2
    pkginfo: 1.11.1
    platformdirs: 4.3.6
    prompt_toolkit: 3.0.48
    psutil: 6.0.0
    ptyprocess: 0.7.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    pyelftools: 0.31
    Pygments: 2.18.0
    pynmrstar: 3.3.4
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.3401
    pyparsing: 3.2.0
    pyproject_hooks: 1.2.0
    PyQt6-commercial: 6.7.1
    PyQt6-Qt6: 6.7.3
    PyQt6-WebEngine-commercial: 6.7.0
    PyQt6-WebEngine-Qt6: 6.7.3
    PyQt6-WebEngineSubwheel-Qt6: 6.7.3
    PyQt6_sip: 13.8.0
    python-dateutil: 2.9.0.post0
    pytz: 2024.2
    pyzmq: 26.2.0
    qtconsole: 5.5.2
    QtPy: 2.4.2
    qtshim: 1.0
    RandomWords: 0.4.0
    requests: 2.32.3
    scipy: 1.14.0
    setuptools: 72.1.0
    sfftk-rw: 0.8.1
    six: 1.16.0
    sniffio: 1.3.1
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.6
    Sphinx: 8.0.2
    sphinx-autodoc-typehints: 2.2.3
    sphinxcontrib-applehelp: 2.0.0
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 2.0.0
    sphinxcontrib-htmlhelp: 2.1.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 2.0.0
    sphinxcontrib-serializinghtml: 2.0.0
    stack-data: 0.6.3
    superqt: 0.6.3
    tables: 3.10.1
    tcia_utils: 1.5.1
    tifffile: 2024.7.24
    tinyarray: 1.2.4
    tornado: 6.4.2
    traitlets: 5.14.3
    typing_extensions: 4.12.2
    tzdata: 2024.2
    urllib3: 2.2.3
    wcwidth: 0.2.13
    webcolors: 24.6.0
    wheel: 0.43.0
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.13

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