id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 17008 Crash on Mac waking from sleep chimerax-bug-report@… Tom Goddard "{{{ 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"" : 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""deploymentId"" : 400000001 } ] } } ===== 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 [deleted to fit within ticket limits] > 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 > 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 #!8 models > hide #!8 models > show #!9 models > hide #!9 models > show #!10 models > hide #!10 models > show #!11 models > hide #!11 models > show #!12 models > hide #!12 models > show #!13 models > hide #!13 models > show #!14 models > hide #!14 models > show #!15 models > hide #!15 models > show #!16 models > hide #!16 models > show #!17 models > hide #!17 models > show #!18 models > hide #!18 models > show #!19 models > hide #!19 models > show #!20 models > hide #!20 models > show #!21 models > hide #!21 models > show #!22 models > hide #!22 models > show #!23 models > hide #!23 models > show #!24 models > hide #!24 models > show #!25 models > hide #!25 models > show #!26 models > hide #!26 models > show #!27 models > hide #!27 models > show #!28 models > hide #!28 models > show #!29 models > hide #!29 models > show #!30 models > hide #!30 models > show #!31 models > hide #!31 models > show #!30 models > show #!31 models > hide #!31 models > hide #!30 models > show #!32 models > hide #!32 models > show #!33 models > hide #!33 models > show #!34 models > hide #!34 models > show #!35 models > hide #!35 models > show #!35 models > hide #!35 models > show #!36 models > hide #!36 models > show #!37 models > hide #!37 models > show #!38 models > show #!36 models > hide #!36 models > hide #!38 models > show #!39 models > show #!38 models > hide #!38 models > 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 > show #!5 models > hide #!5 models > show #!8 models > hide #!8 models > hide #!35 models > show #!36 models > 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 > show #!10 models > hide #!10 models > show #!10 models > hide #!10 models > show #!10 models > hide #!10 models > 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 }}} " defect assigned normal Window Toolkit all ChimeraX