id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
17991	Crash on Mac waking from sleep	chimerax-bug-report@…	Tom Goddard	"{{{
The following bug report has been submitted:
Platform:        macOS-15.3.2-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 0x0000000367a6b000 (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 0x0000000366a5f000 (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 0x0000000365a53000 (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 0x0000000364a47000 (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 0x0000000363a3b000 (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 0x0000000362a2f000 (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 0x0000000361a23000 (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 0x0000000360a17000 (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 0x000000035fa0b000 (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 0x000000035e9ff000 (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 0x000000035d9f3000 (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 0x000000035c9e7000 (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 0x000000035b9db000 (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 0x000000035a9cf000 (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 0x00000003599c3000 (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 0x00000003589b7000 (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 0x00000003579ab000 (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 0x000000035699f000 (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 0x0000000355993000 (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 0x0000000354987000 (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 0x000000035397b000 (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 0x000000035296f000 (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 0x0000000351963000 (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 0x0000000201220840 (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.pdb_lib._load_libs, 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.surface._surface, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, psutil._psutil_osx, psutil._psutil_posix, PIL._imagingmath, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw, imagecodecs._shared, imagecodecs._imcd, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets (total: 59)


{""app_name"":""ChimeraX"",""timestamp"":""2025-06-16 11:23:12.00 +0200"",""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 15.3.2 (24D81)"",""roots_installed"":0,""name"":""ChimeraX"",""incident_id"":""748DB26A-5515-4C5A-AACD-4A1A91EB68B5""}
{
  ""uptime"" : 7200000,
  ""procRole"" : ""Foreground"",
  ""version"" : 2,
  ""userID"" : 501,
  ""deployVersion"" : 210,
  ""modelCode"" : ""Mac13,2"",
  ""coalitionID"" : 1407321,
  ""osVersion"" : {
    ""train"" : ""macOS 15.3.2"",
    ""build"" : ""24D81"",
    ""releaseType"" : ""User""
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  ""captureTime"" : ""2025-06-16 11:23:04.5441 +0200"",
  ""codeSigningMonitor"" : 1,
  ""incident"" : ""748DB26A-5515-4C5A-AACD-4A1A91EB68B5"",
  ""pid"" : 56449,
  ""translated"" : false,
  ""cpuType"" : ""ARM-64"",
  ""roots_installed"" : 0,
  ""bug_type"" : ""309"",
  ""procLaunch"" : ""2025-06-04 09:00:08.1700 +0200"",
  ""procStartAbsTime"" : 149275144493727,
  ""procExitAbsTime"" : 174364185049320,
  ""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"":""F5F53219-9BE6-5E1E-B198-B93A19242616"",""thirdParty"":true},
  ""parentProc"" : ""launchd"",
  ""parentPid"" : 1,
  ""coalitionName"" : ""edu.ucsf.cgl.ChimeraX"",
  ""crashReporterKey"" : ""88AFF950-A49B-5485-38D1-6898FBC7C39E"",
  ""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"" : ""3E62848E-AF7C-44E3-8B06-9A018F573DF4"",
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===== Log before crash start =====
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
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/arne/Downloads/cryosparc_P46_J1908_002_volume_map_sharp.mrc

Opened cryosparc_P46_J1908_002_volume_map_sharp.mrc as #1, grid size
128,128,128, pixel 2.72, shown at level 0.129, step 1, values float32  

> open /Users/arne/Downloads/cryosparc_P46_J1909_002_volume_map_sharp.mrc

Opened cryosparc_P46_J1909_002_volume_map_sharp.mrc as #2, grid size
128,128,128, pixel 2.72, shown at level 0.121, step 1, values float32  

> hide #!2 models

> volume #1 level 0.1403

> volume #2 level 0.3308

> open /Users/arne/Downloads/cryosparc_P46_J1911_003_volume_map.mrc

Opened cryosparc_P46_J1911_003_volume_map.mrc as #3, grid size 128,128,128,
pixel 2.72, shown at level 0.142, step 1, values float32  

> volume #3 level 0.1331

> open /Users/arne/Downloads/cryosparc_P46_J1903_004_volume_map(1).mrc

Opened cryosparc_P46_J1903_004_volume_map(1).mrc as #4, grid size 128,128,128,
pixel 2.72, shown at level 0.145, step 1, values float32  

> volume #4 level 0.3

> volume #4 level 0.05037

> volume #4 level 0.1476

> volume #4 level 0.4156

> open /Users/arne/Documents/Projects/2025-ABCA2/Maps-
> and_Models/ABCA2_closed_ADP_poststate.pdb

Chain information for ABCA2_closed_ADP_poststate.pdb #5  
---  
Chain | Description  
A | No description available  
  

> open /Users/arne/Documents/Projects/2025-ABCA2/Maps-
> and_Models/ABCA2_open_prestate.pdb

Chain information for ABCA2_open_prestate.pdb #6  
---  
Chain | Description  
A | No description available  
  

> hide #!4 models

> show #!4 models

> hide #!6 models

> select add #5

14885 atoms, 15255 bonds, 6 pseudobonds, 1888 residues, 2 models selected  

> ui mousemode right zoom

> ui mousemode right ""translate selected models""

> view matrix models #5,1,0,0,-1.4415,0,1,0,4.3892,0,0,1,6.5551

> ui mousemode right ""rotate selected models""

> view matrix models
> #5,0.99887,0.032522,-0.034633,-1.8656,-0.023148,0.96975,0.24301,-20.935,0.041488,-0.24194,0.9694,44.877

> ui mousemode right ""translate selected models""

> view matrix models
> #5,0.99887,0.032522,-0.034633,1.0407,-0.023148,0.96975,0.24301,-23.685,0.041488,-0.24194,0.9694,27.348

> view matrix models
> #5,0.99887,0.032522,-0.034633,1.4008,-0.023148,0.96975,0.24301,-24.361,0.041488,-0.24194,0.9694,27.193

> fitmap #5 inMap #4

Fit molecule ABCA2_closed_ADP_poststate.pdb (#5) to map
cryosparc_P46_J1903_004_volume_map(1).mrc (#4) using 14885 atoms  
average map value = 0.2049, steps = 248  
shifted from previous position = 6.6  
rotated from previous position = 43.9 degrees  
atoms outside contour = 13202, contour level = 0.41559  
  
Position of ABCA2_closed_ADP_poststate.pdb (#5) relative to
cryosparc_P46_J1903_004_volume_map(1).mrc (#4) coordinates:  
Matrix rotation and translation  
0.70532098 0.68785618 0.17139486 -95.00816708  
-0.70817717 0.67288304 0.21380720 149.91980726  
0.03173991 -0.27218063 0.96172256 37.16106367  
Axis -0.32731116 0.09405713 -0.94022373  
Axis point 124.21053383 186.45273976 0.00000000  
Rotation angle (degrees) 47.93576868  
Shift along axis 10.25854662  
  

> ui mousemode right ""rotate selected models""

> view matrix models
> #5,-0.87428,-0.46167,-0.14995,426.45,0.48307,-0.79718,-0.36213,272.13,0.047645,-0.38904,0.91999,60.24

> view matrix models
> #5,-0.86722,-0.44644,-0.2205,432.64,0.49098,-0.84041,-0.22945,259.23,-0.082871,-0.30724,0.94802,65.375

> view matrix models
> #5,-0.95134,-0.30221,-0.060246,400.09,0.30815,-0.93292,-0.18629,301.23,9.2413e-05,-0.19579,0.98065,27.023

> show #!6 models

> hide #!5 models

> select add #6

28174 atoms, 28895 bonds, 11 pseudobonds, 3552 residues, 4 models selected  

> select subtract #5

13289 atoms, 13640 bonds, 5 pseudobonds, 1664 residues, 2 models selected  

> view matrix models
> #6,0.99857,0.023089,-0.04832,3.1613,-0.024443,0.99932,-0.027629,8.3615,0.047649,0.02877,0.99845,-13.131

> view matrix models
> #6,0.99652,0.028117,-0.078512,6.9793,-0.025712,0.99917,0.031485,0.11466,0.079332,-0.029356,0.99642,-8.2247

> ui mousemode right ""translate selected models""

> view matrix models
> #6,0.99652,0.028117,-0.078512,8.153,-0.025712,0.99917,0.031485,0.2573,0.079332,-0.029356,0.99642,-22.857

> fitmap #6 inMap #4

Fit molecule ABCA2_open_prestate.pdb (#6) to map
cryosparc_P46_J1903_004_volume_map(1).mrc (#4) using 13289 atoms  
average map value = 0.1989, steps = 188  
shifted from previous position = 6  
rotated from previous position = 12.4 degrees  
atoms outside contour = 11925, contour level = 0.41559  
  
Position of ABCA2_open_prestate.pdb (#6) relative to
cryosparc_P46_J1903_004_volume_map(1).mrc (#4) coordinates:  
Matrix rotation and translation  
0.98161937 -0.18423687 -0.04980143 38.85784205  
0.18622597 0.98174245 0.03875111 -36.78401828  
0.04175280 -0.04731316 0.99800710 -10.31652139  
Axis -0.22000466 -0.23403852 0.94700788  
Axis point 227.04665785 176.66587317 0.00000000  
Rotation angle (degrees) 11.27957136  
Shift along axis -9.70985602  
  

> ui mousemode right ""rotate selected models""

> view matrix models
> #6,0.9815,-0.18591,-0.04577,38.592,0.18692,0.9822,0.018724,-34.107,0.041474,-0.026933,0.99878,-13.938

> view matrix models
> #6,-0.98016,-0.14057,-0.13974,387.06,0.15124,-0.98609,-0.068877,328.49,-0.12811,-0.088644,0.98779,28.062

> view matrix models
> #6,-0.97375,-0.012907,-0.22725,376.22,0.028572,-0.99742,-0.06578,351.47,-0.22581,-0.070546,0.97161,44.303

> view matrix models
> #6,-0.97154,-0.015962,-0.23634,377.68,0.021574,-0.99954,-0.021179,346.65,-0.2359,-0.025675,0.97144,38.254

> view matrix models
> #6,-0.95857,0.26436,-0.10608,307.73,-0.26487,-0.96424,-0.009562,388.89,-0.10481,0.01893,0.99431,4.2631

> fitmap #6 inMap #4

Fit molecule ABCA2_open_prestate.pdb (#6) to map
cryosparc_P46_J1903_004_volume_map(1).mrc (#4) using 13289 atoms  
average map value = 0.2084, steps = 156  
shifted from previous position = 1.2  
rotated from previous position = 21.4 degrees  
atoms outside contour = 11833, contour level = 0.41559  
  
Position of ABCA2_open_prestate.pdb (#6) relative to
cryosparc_P46_J1903_004_volume_map(1).mrc (#4) coordinates:  
Matrix rotation and translation  
-0.84760685 0.51184035 0.13993594 209.18232450  
-0.50977925 -0.85867346 0.05296230 402.86590300  
0.14726752 -0.02644523 0.98874310 -31.35609494  
Axis -0.07749138 -0.00715467 -0.99696735  
Axis point 161.51505433 172.49718692 0.00000000  
Rotation angle (degrees) 149.17860200  
Shift along axis 12.16880420  
  

> flip #4

Unknown command: flip #4  

> vollume flip #4

Unknown command: vollume flip #4  

> volume flip #4

Opened cryosparc_P46_J1903_004_volume_map(1).mrc z flip as #7, grid size
128,128,128, pixel 2.72, shown at step 1, values float32  

> select add #7

13289 atoms, 13640 bonds, 5 pseudobonds, 1664 residues, 4 models selected  

> select subtract #6

2 models selected  

> view matrix models
> #7,-0.93482,-0.35505,0.0071622,396.42,-0.35477,0.93282,-0.063121,84.176,0.01573,-0.061548,-0.99798,352.97

> view matrix models
> #7,-0.9321,-0.36202,-0.011536,400.37,-0.3622,0.93165,0.028993,69.757,0.00025105,0.031203,-0.99951,340.01

> view matrix models
> #7,-0.97216,-0.23423,0.0067131,382.25,-0.23375,0.97137,0.042493,38.252,-0.016474,0.039741,-0.99907,341.38

> view matrix models
> #7,-0.86909,-0.48957,-0.07078,421.53,-0.49207,0.84101,0.22487,74.077,-0.050565,0.23026,-0.97181,309.9

> view matrix models
> #7,-0.87454,-0.48364,-0.03557,415.38,-0.48495,0.87232,0.062261,95.554,0.00091711,0.071699,-0.99743,332.58

> view matrix models
> #7,-0.93525,-0.35268,0.030342,392.08,-0.34908,0.93312,0.086241,57.332,-0.058728,0.070065,-0.99581,342.97

> fitmap #6 inMap #7

Fit molecule ABCA2_open_prestate.pdb (#6) to map
cryosparc_P46_J1903_004_volume_map(1).mrc z flip (#7) using 13289 atoms  
average map value = 0.2067, steps = 416  
shifted from previous position = 5.77  
rotated from previous position = 15.5 degrees  
atoms outside contour = 11699, contour level = 0.41559  
  
Position of ABCA2_open_prestate.pdb (#6) relative to
cryosparc_P46_J1903_004_volume_map(1).mrc z flip (#7) coordinates:  
Matrix rotation and translation  
0.99964445 0.01444877 -0.02241011 0.06810605  
0.01495583 -0.99963212 0.02262635 340.79641731  
-0.02207494 -0.02295346 -0.99949279 366.51656038  
Axis -0.99991110 -0.00735276 0.01112368  
Axis point 0.00000000 172.48672506 181.31631893  
Rotation angle (degrees) 178.69400541  
Shift along axis 1.50311845  
  

> show #!5 models

> select add #5

14885 atoms, 15255 bonds, 6 pseudobonds, 1888 residues, 4 models selected  

> select subtract #7

14885 atoms, 15255 bonds, 6 pseudobonds, 1888 residues, 2 models selected  

> hide #!6 models

> view matrix models
> #5,0.97437,0.16339,-0.1546,-6.6658,-0.16401,0.98642,0.0088265,29.288,0.15394,0.016756,0.98794,-37.523

> view matrix models
> #5,-0.95614,-0.22946,0.18204,354.04,0.13745,-0.90033,-0.41293,358.12,0.25865,-0.3698,0.89238,23.553

> view matrix models
> #5,-0.98846,-0.11829,0.094634,353.21,0.065937,-0.89839,-0.43423,373.47,0.13638,-0.42298,0.89582,53.774

> view matrix models
> #5,-0.99313,-0.11604,0.014816,365.02,0.11102,-0.97483,-0.19332,344.26,0.036877,-0.19035,0.98102,19.534

> view matrix models
> #5,-0.82672,-0.55512,-0.091537,425.68,0.56054,-0.79874,-0.21863,238.27,0.048251,-0.23206,0.97151,25.997

> show #!6 models

> hide #!5 models

> select subtract #5

Nothing selected  

> select add #6

13289 atoms, 13640 bonds, 5 pseudobonds, 1664 residues, 2 models selected  

> view matrix models
> #6,0.96583,-0.25894,0.011568,49.828,0.25584,0.94524,-0.20265,-5.0342,0.04154,0.19869,0.97918,-51.996

> view matrix models
> #6,0.96734,-0.25028,-0.040062,55.47,0.24891,0.96785,-0.036228,-31.686,0.047841,0.025073,0.99854,-25.556

> fitmap #6 inMap #7

Fit molecule ABCA2_open_prestate.pdb (#6) to map
cryosparc_P46_J1903_004_volume_map(1).mrc z flip (#7) using 13289 atoms  
average map value = 0.2547, steps = 84  
shifted from previous position = 4.38  
rotated from previous position = 7.63 degrees  
atoms outside contour = 10832, contour level = 0.41559  
  
Position of ABCA2_open_prestate.pdb (#6) relative to
cryosparc_P46_J1903_004_volume_map(1).mrc z flip (#7) coordinates:  
Matrix rotation and translation  
-0.98266833 -0.14715924 0.11272582 350.65766323  
-0.13799476 0.98675898 0.08523004 11.29328582  
-0.12377560 0.06819728 -0.98996401 366.36190003  
Axis -0.07178001 0.99667248 0.03862129  
Axis point 186.67695075 0.00000000 172.48893790  
Rotation angle (degrees) 173.18606280  
Shift along axis 0.23486555  
  

> open /Users/arne/Documents/Projects/2025-ABCA2/Maps-
> and_Models/ABCA2_alpha_fold.pdb

ABCA2_alpha_fold.pdb title:  
Alphafold monomer V2.0 prediction for atp-binding cassette sub-family A member
2 (Q9BZC7) [more info...]  
  
Chain information for ABCA2_alpha_fold.pdb #8  
---  
Chain | Description | UniProt  
A | atp-binding cassette sub-family A member 2 | ABCA2_HUMAN 1-2435  
  

> mmaker #8 to #6

Computing secondary structure  
Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker ABCA2_open_prestate.pdb, chain A (#6) with ABCA2_alpha_fold.pdb,
chain A (#8), sequence alignment score = 6850.5  
RMSD between 543 pruned atom pairs is 1.099 angstroms; (across all 1641 pairs:
10.641)  
  

> open /Users/arne/Documents/Projects/2025-ABCA2/Maps-
> and_Models/ABCA2_prestate_AFassembly_KP.pdb

Chain information for ABCA2_prestate_AFassembly_KP.pdb #9  
---  
Chain | Description  
A | No description available  
  

> mmaker #9 to #6

Computing secondary structure  
Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker ABCA2_open_prestate.pdb, chain A (#6) with
ABCA2_prestate_AFassembly_KP.pdb, chain A (#9), sequence alignment score =
7580.6  
RMSD between 1565 pruned atom pairs is 0.357 angstroms; (across all 1615
pairs: 3.615)  
  

> select subtract #6

Nothing selected  

> hide #!6 models

> hide #8 models

> volume #7 level 0.3788

> volume #7 level 0.2133

> volume #7 style image

> volume #7 style mesh

> volume #7 change image level -0.0176,0 level 0.1449,0.8 level 1.095,1

> volume #7 level 0.2212

> volume #7 style surface

> open /Users/arne/Downloads/cryosparc_P46_J1903_004_volume_map(1).mrc

Opened cryosparc_P46_J1903_004_volume_map(1).mrc as #10, grid size
128,128,128, pixel 2.72, shown at level 0.145, step 1, values float32  

> hide #!10 models

> close #10

> open /Users/arne/Downloads/cryosparc_P46_J1903_004_volume_map_sharp.mrc

Opened cryosparc_P46_J1903_004_volume_map_sharp.mrc as #10, grid size
128,128,128, pixel 2.72, shown at level 0.151, step 1, values float32  

> volume flip #10

Opened cryosparc_P46_J1903_004_volume_map_sharp.mrc z flip as #11, grid size
128,128,128, pixel 2.72, shown at step 1, values float32  
Must specify one map, got 0  

> fitmap #10 inMap #7

Fit map cryosparc_P46_J1903_004_volume_map_sharp.mrc in map
cryosparc_P46_J1903_004_volume_map(1).mrc z flip using 20902 points  
correlation = 0.7441, correlation about mean = 0.339, overlap = 2067  
steps = 144, shift = 1.07, angle = 6.01 degrees  
  
Position of cryosparc_P46_J1903_004_volume_map_sharp.mrc (#10) relative to
cryosparc_P46_J1903_004_volume_map(1).mrc z flip (#7) coordinates:  
Matrix rotation and translation  
-0.95545175 -0.29479192 -0.01448036 394.44809914  
-0.29477908 0.95556053 -0.00306128 59.68053446  
0.01473930 0.00134360 -0.99989047 342.62981534  
Axis 0.14906628 -0.98882711 0.00043430  
Axis point 200.44253666 0.00000000 172.80157717  
Rotation angle (degrees) 179.15342930  
Shift along axis -0.06601758  
  

> volume #11 level 0.3806

> volume #11 level 0.4006

> volume #11 level 0.3506

> open ""/Users/arne/Documents/OLD_discs/Arne diss/maps/nph-deoxy-001.ccp4""

Opened nph-deoxy-001.ccp4 as #12, grid size 394,309,251, pixel 1.05,1.05,1.05,
shown at level 0.0386, step 2, values float32  

> hide #!9 models

> hide #!11 models

> view #12 clip false

> volume #12 level 0.006378

> open ""/Users/arne/Documents/OLD_discs/Arne diss/maps/nph-oxy-001.ccp4""

Opened nph-oxy-001.ccp4 as #13, grid size 362,346,241, pixel 1.05,1.05,1.05,
shown at level 0.0342, step 2, values float32  

> volume #13 level 0.0126

> fitmap #13 inMap #12

Fit map nph-oxy-001.ccp4 in map nph-deoxy-001.ccp4 using 204354 points  
correlation = 0.6589, correlation about mean = 0.2246, overlap = 87.51  
steps = 112, shift = 13.8, angle = 0.0256 degrees  
  
Position of nph-oxy-001.ccp4 (#13) relative to nph-deoxy-001.ccp4 (#12)
coordinates:  
Matrix rotation and translation  
0.99999990 0.00044460 -0.00001127 -7.35544284  
-0.00044460 0.99999990 0.00004036 4.20598279  
0.00001129 -0.00004035 1.00000000 10.84344314  
Axis -0.09036917 -0.02526644 -0.99558778  
Axis point 8874.29706947 18626.91246256 0.00000000  
Rotation angle (degrees) 0.02558634  
Shift along axis -10.23716442  
  

> open ""/Users/arne/Library/Containers/com.apple.mail/Data/Library/Mail
> Downloads/1BECC3D2-879F-405C-85CF-351AB05F3D0C/postprocess_masked_inward_C2.mrc""

Opened postprocess_masked_inward_C2.mrc as #14, grid size 140,140,140, pixel
1.12, shown at level 0.0516, step 1, values float32  

> view #14 clip false

> open ""/Users/arne/Library/Containers/com.apple.mail/Data/Library/Mail
> Downloads/A8443609-060F-4919-80D4-A005B86C1444/postprocess_masked_outward_C2.mrc""

Opened postprocess_masked_outward_C2.mrc as #15, grid size 140,140,140, pixel
1.12, shown at level 0.052, step 1, values float32  

> hide #!14 models

> hide #!15 models

> show #!12 models

> view #12 clip false

> show #!13 models

> hide #!12 models

> hide #!13 models

> show #!12 models

> lighting soft

> graphics silhouettes true

> graphics silhouettes false

> ui tool show ""Side View""

> show #!13 models

> morph #12,13

Require at least 2 structures for morph  

> volume #!12-13 projectionMode rays

> volume #!12-13 projectionMode 3d

> volume #!12-13 projectionMode 2d-xyz

> ui mousemode right ""play coordinates""

> hide #!13 models

> hide #!12 models

> open /Users/arne/Documents/OLD_discs/arne-diss-vortrag/ueberkreuz-
> pfeil0011.tif

Opened multi-channel map ueberkreuz-pfeil0011.tif as #16, 3 channels, grid
size 640,480,1, pixel 1, shown at step 1, values uint8  

> close #16

> open /Users/arne/Downloads/hSorCS1-mono-mask-3p4A-cryosparc-P372-J354-map-
> sharp.mrc

Opened hSorCS1-mono-mask-3p4A-cryosparc-P372-J354-map-sharp.mrc as #16, grid
size 320,320,320, pixel 1.08, shown at level 0.0477, step 2, values float32  

> volume #16 level 0.08021

> volume #16 step 1

> volume #16 level 0.1344

> view #16 clip false

> surface dust #16 size 10.8

> volume #16 level 0.342

> open
> /Users/arne/Downloads/hSorCS1-dimer-4p5A-cryosparc_P372_J140_004_volume_map_sharp.mrc

Opened hSorCS1-dimer-4p5A-cryosparc_P372_J140_004_volume_map_sharp.mrc as #17,
grid size 320,320,320, pixel 1.08, shown at level 0.0424, step 2, values
float32  

> volume #17 step 1

> volume #17 level 0.1055

> hide #!16 models

> show #!16 models

> hide #!17 models

> volume #16 color #d6d6d6

> volume #16 color white

> show #!17 models

> hide #!16 models

> color #17 #76d6ffff models

> color #17 #73fdffff models

> color #17 #00fdffff models

> color #17 #0096ffff models

> color #17 #0433ffff models

> color #17 #0096ffff models

> color #17 #d4fb79ff models

> color #17 #fffc79ff models

> color #17 #fffb00ff models

> color #17 #ffd479ff models

> show #!16 models

> hide #!17 models

> hide #!16 models

> show #!14 models

> show #!15 models

> view #14-15 clip false

> select add #15

2 models selected  

> ui mousemode right ""translate selected models""

> view matrix models #15,1,0,0,-76.501,0,1,0,4.9008,0,0,1,3.4908

> select clear

> close #12-17

> open /Users/arne/Downloads/cryosparc_P46_J1929_006_volume_map_sharp.mrc

Opened cryosparc_P46_J1929_006_volume_map_sharp.mrc as #12, grid size
512,512,512, pixel 0.68, shown at level 0.0168, step 2, values float32  

> open /Users/arne/Downloads/cryosparc_P46_J1929_006_volume_map.mrc

Opened cryosparc_P46_J1929_006_volume_map.mrc as #13, grid size 512,512,512,
pixel 0.68, shown at level 0.0174, step 2, values float32  

> hide #!13 models

> view #12 clip false

> volume #12 level 0.05944

> volume #12 step 1

> volume #12 level 0.05653

> show #!9 models

> hide #!9 models

> show #!9 models

> hide #!9 models

> volume flip #12

Opened cryosparc_P46_J1929_006_volume_map_sharp.mrc z flip as #14, grid size
512,512,512, pixel 0.68, shown at step 1, values float32  

> show #!9 models

> hide #!14 models

> show #!12 models

> fitmap #9 inMap #12

Fit molecule ABCA2_prestate_AFassembly_KP.pdb (#9) to map
cryosparc_P46_J1929_006_volume_map_sharp.mrc (#12) using 16648 atoms  
average map value = 0.02472, steps = 96  
shifted from previous position = 2.87  
rotated from previous position = 3.15 degrees  
atoms outside contour = 13992, contour level = 0.05653  
  
Position of ABCA2_prestate_AFassembly_KP.pdb (#9) relative to
cryosparc_P46_J1929_006_volume_map_sharp.mrc (#12) coordinates:  
Matrix rotation and translation  
0.98646146 0.03808505 -0.15950960 31.04677798  
-0.07038483 0.97684290 -0.20204932 41.91819520  
0.14812076 0.21054092 0.96629848 -77.69230014  
Axis 0.78445326 -0.58489419 -0.20623258  
Axis point 0.00000000 386.93710220 209.02872745  
Rotation angle (degrees) 15.24692849  
Shift along axis 15.85972039  
  

> show #!14 models

> hide #!12 models

> select add #14

2 models selected  

> ui mousemode right ""rotate selected models""

> view matrix models
> #14,0.91801,-0.383,0.10281,62.136,-0.39496,-0.85979,0.32368,332.21,-0.03558,-0.33775,-0.94056,407.69

> view matrix models
> #14,0.91338,-0.40633,0.025305,80.673,-0.40705,-0.91041,0.073916,387.23,-0.0069961,-0.077814,-0.99694,367.86

> view matrix models
> #14,0.91976,-0.38799,0.059281,70.39,-0.39147,-0.91772,0.067316,386.94,0.028286,-0.085121,-0.99597,362.8

> volume #12 level 0.06138

> volume #14 level 0.07011

> view matrix models
> #14,-0.89632,-0.34332,0.2806,341.56,-0.34321,0.93786,0.051171,59.522,-0.28073,-0.050439,-0.95846,404.27

> ui mousemode right ""translate selected models""

> view matrix models
> #14,-0.89632,-0.34332,0.2806,342.25,-0.34321,0.93786,0.051171,60.078,-0.28073,-0.050439,-0.95846,402.62

> fitmap #9 inMap #14

Fit molecule ABCA2_prestate_AFassembly_KP.pdb (#9) to map
cryosparc_P46_J1929_006_volume_map_sharp.mrc z flip (#14) using 16648 atoms  
average map value = 0.03908, steps = 256  
shifted from previous position = 6.65  
rotated from previous position = 16.5 degrees  
atoms outside contour = 13789, contour level = 0.070109  
  
Position of ABCA2_prestate_AFassembly_KP.pdb (#9) relative to
cryosparc_P46_J1929_006_volume_map_sharp.mrc z flip (#14) coordinates:  
Matrix rotation and translation  
-0.88745653 -0.41344763 0.20367116 363.79290529  
-0.43456682 0.89784123 -0.07094200 94.45154456  
-0.15353357 -0.15146668 -0.97646570 418.66014652  
Axis -0.21954660 0.97390132 -0.05758046  
Axis point 212.38707986 0.00000000 194.97491209  
Rotation angle (degrees) 169.43280316  
Shift along axis -11.98965502  
  

> fitmap #9 inMap #14

Fit molecule ABCA2_prestate_AFassembly_KP.pdb (#9) to map
cryosparc_P46_J1929_006_volume_map_sharp.mrc z flip (#14) using 16648 atoms  
average map value = 0.03908, steps = 44  
shifted from previous position = 0.0146  
rotated from previous position = 0.0277 degrees  
atoms outside contour = 13786, contour level = 0.070109  
  
Position of ABCA2_prestate_AFassembly_KP.pdb (#9) relative to
cryosparc_P46_J1929_006_volume_map_sharp.mrc z flip (#14) coordinates:  
Matrix rotation and translation  
-0.88723714 -0.41382345 0.20386365 363.78645416  
-0.43497542 0.89764429 -0.07093019 94.55313057  
-0.15364447 -0.15160758 -0.97642639 418.68429519  
Axis -0.21976471 0.97384992 -0.05761782  
Axis point 212.42683998 0.00000000 194.97574777  
Rotation angle (degrees) 169.42316003  
Shift along axis -11.99053959  
  

> fitmap #9 inMap #14

Fit molecule ABCA2_prestate_AFassembly_KP.pdb (#9) to map
cryosparc_P46_J1929_006_volume_map_sharp.mrc z flip (#14) using 16648 atoms  
average map value = 0.03908, steps = 40  
shifted from previous position = 0.00443  
rotated from previous position = 0.00786 degrees  
atoms outside contour = 13786, contour level = 0.070109  
  
Position of ABCA2_prestate_AFassembly_KP.pdb (#9) relative to
cryosparc_P46_J1929_006_volume_map_sharp.mrc z flip (#14) coordinates:  
Matrix rotation and translation  
-0.88728351 -0.41378065 0.20374870 363.80818838  
-0.43491004 0.89767798 -0.07090468 94.53142515  
-0.15356174 -0.15152491 -0.97645224 418.66364629  
Axis -0.21973254 0.97385890 -0.05758872  
Axis point 212.42109069 0.00000000 194.97226603  
Rotation angle (degrees) 169.42917447  
Shift along axis -11.99052842  
  

> select clear

> select ::name=""Y01""

245 atoms, 266 bonds, 7 residues, 2 models selected  

> select ::name=""CLR""

112 atoms, 124 bonds, 4 residues, 1 model selected  

> color sel orange

> select clear

> volume #14 level 0.05071

> surface #9 resolution 5

1 Gaussian surfaces, threshold level 0.191  

> hide #14.1 models

> show #14.1 models

> hide #!14 models

> show #!14 models

> hide #9.2 models

> color #!9 byhetero

> volume #14 level 0.05556

> open /Users/arne/Documents/ChimeraX-commands/Color-ABCA2-with_alpha-fold.cxc

> close session

> cd /Users/arne/Documents/Projects/2025-ABCA2

Current working directory is: /Users/arne/Documents/Projects/2025-ABCA2  

> open /Users/arne/Documents/Projects/2025-ABCA2/Maps-
> and_Models/ABCA2_open_prestate.pdb

Chain information for ABCA2_open_prestate.pdb #1  
---  
Chain | Description  
A | No description available  
  

> open /Users/arne/Documents/Projects/2025-ABCA2/Maps-
> and_Models/ABCA2_closed_ADP_poststate.pdb

Chain information for ABCA2_closed_ADP_poststate.pdb #2  
---  
Chain | Description  
A | No description available  
  

> mmaker #1:811-836 to #2:811-836

Computing secondary structure  
Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker ABCA2_closed_ADP_poststate.pdb, chain A (#2) with
ABCA2_open_prestate.pdb, chain A (#1), sequence alignment score = 122.1  
RMSD between 24 pruned atom pairs is 0.816 angstroms; (across all 26 pairs:
1.131)  
  

> view matrix camera
> 0.4295,0.065969,0.90065,741.54,-0.8689,0.30192,0.39225,416.92,-0.24605,-0.95105,0.187,259.7

> open /Users/arne/Documents/Projects/2025-ABCA2/Maps-
> and_Models/ABCA2-morph.pdb

Chain information for ABCA2-morph.pdb #3  
---  
Chain | Description  
A | No description available  
  

> open /Users/arne/Documents/Projects/2025-ABCA2/Maps-
> and_Models/ABCA2-morph.dcd structureModel #3

Replaced existing frames of ABCA2-morph.pdb #3 with 61 new frames  

> open /Users/arne/Documents/Projects/2025-ABCA2/Maps-
> and_Models/ABCA2_prestate_AFassembly_KP.pdb

Chain information for ABCA2_prestate_AFassembly_KP.pdb #4  
---  
Chain | Description  
A | No description available  
  

> open /Users/arne/Documents/Projects/2025-ABCA2/Maps-
> and_Models/ABCA2_poststate_AFassembly.pdb

ABCA2_poststate_AFassembly.pdb title:  
Alphafold monomer V2.0 prediction for atp-binding cassette sub-family A member
2 (Q9BZC7) [more info...]  
  
Chain information for ABCA2_poststate_AFassembly.pdb #5  
---  
Chain | Description | UniProt  
A | atp-binding cassette sub-family A member 2 | ABCA2_HUMAN 1-2435  
B C | No description available |   
  
Non-standard residues in ABCA2_poststate_AFassembly.pdb #5  
---  
3PE — (3PE)  
ADP — (ADP)  
LMN — (LMN)  
MG — (MG)  
NAG — (NAG)  
Y01 — (Y01)  
  

> view matrix camera
> 0.10605,-0.14587,0.9836,918.88,-0.99229,0.048234,0.11413,258.3,-0.064087,-0.98812,-0.13962,57.431

> select :194-219

764 atoms, 784 bonds, 104 residues, 4 models selected  

> delete atoms sel

> delete bonds sel

> select #4:194-219,2364-2435,1330-1436,924-961,1222-1249

Nothing selected  

> delete atoms sel

> delete bonds sel

> color #4.2 #6495ed80

> color #4.3 #ff8c0080

> color #4.4 #daa52080

> color #4.5 #1e90ff80

> color #4.6 #00ced17f

> open /Users/arne/Documents/Projects/2025-ABCA2/Maps-and_Models/ABCA2-Pre-to-
> Post.pdb

ABCA2-Pre-to-Post.pdb title:  
Alphafold monomer V2.0 prediction for atp-binding cassette sub-family A member
2 (Q9BZC7) [more info...]  
  
Chain information for ABCA2-Pre-to-Post.pdb #6  
---  
Chain | Description | UniProt  
A | atp-binding cassette sub-family A member 2 | ABCA2_HUMAN 1-2435  
B C | No description available |   
  
Non-standard residues in ABCA2-Pre-to-Post.pdb #6  
---  
NAG — (NAG)  
  

> open /Users/arne/Documents/Projects/2025-ABCA2/Maps-and_Models/ABCA2-Pre-to-
> Post.dcd structureModel #6

Replaced existing frames of ABCA2-Pre-to-Post.pdb #6 with 101 new frames  

> mmaker #6 to #4

Computing secondary structure  
Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker ABCA2_prestate_AFassembly_KP.pdb, chain A (#4) with ABCA2-Pre-to-
Post.pdb, chain C (#6), sequence alignment score = 7531  
RMSD between 299 pruned atom pairs is 0.659 angstroms; (across all 333 pairs:
1.293)  
  

> dssp

Computing secondary structure  

> show #!6 surfaces

> select :1-695

28486 atoms, 29132 bonds, 16 pseudobonds, 3662 residues, 12 models selected  

> color sel dark turquoise

> select :696-1250

20003 atoms, 20432 bonds, 7 pseudobonds, 2599 residues, 11 models selected  

> color sel dodger blue

> select :1251-1775

15546 atoms, 15943 bonds, 5 pseudobonds, 2007 residues, 10 models selected  

> color sel coral

> select :1776-2270

20942 atoms, 21423 bonds, 4 pseudobonds, 2746 residues, 10 models selected  

> color sel goldenrod

> select clear

> select :1204-1312

1941 atoms, 1974 bonds, 3 pseudobonds, 247 residues, 6 models selected  

> color sel cornflower blue

> select :2269-2363

2331 atoms, 2373 bonds, 285 residues, 3 models selected  

> color sel dark orange

> select clear

> select ::name=""Y01""

350 atoms, 380 bonds, 10 residues, 3 models selected  

> color sel lime

> color sel & #!1 byhetero

> select clear

> graphics silhouettes true

> lighting full

executed Color-ABCA2-with_alpha-fold.cxc  

> close session

> open ""/Users/arne/Documents/OLD_discs/Arne diss/maps/nph-oxy-001.ccp4""
> format ccp4

Opened nph-oxy-001.ccp4 as #1, grid size 362,346,241, pixel 1.05,1.05,1.05,
shown at level 0.0342, step 2, values float32  

> volume #1 level 0.01357

> volume #1 level 0.00539

> open /Users/arne/Downloads/cryosparc_P46_J1929_006_volume_map.mrc

Opened cryosparc_P46_J1929_006_volume_map.mrc as #2, grid size 512,512,512,
pixel 0.68, shown at level 0.0174, step 2, values float32  

> select add #2

2 models selected  

> view matrix models #2,1,0,0,3.0613,0,1,0,-7.3334,0,0,1,-172.57

> volume #2 level 0.04289

> volume #2 level 0.05407

> close session

> open /Users/arne/Downloads/cryosparc_P46_J2062_006_volume_map_sharp.mrc

Opened cryosparc_P46_J2062_006_volume_map_sharp.mrc as #1, grid size
512,512,512, pixel 0.68, shown at level 0.0479, step 2, values float32  

> volume #1 level 0.1411

> volume #1 step 1

> surface dust #1 size 6.8

> open /Users/arne/Documents/ChimeraX-commands/Color-ABCA2-with_alpha-fold.cxc

> close session

> cd /Users/arne/Documents/Projects/2025-ABCA2

Current working directory is: /Users/arne/Documents/Projects/2025-ABCA2  

> open /Users/arne/Documents/Projects/2025-ABCA2/Maps-
> and_Models/ABCA2_open_prestate.pdb

Chain information for ABCA2_open_prestate.pdb #1  
---  
Chain | Description  
A | No description available  
  

> open /Users/arne/Documents/Projects/2025-ABCA2/Maps-
> and_Models/ABCA2_closed_ADP_poststate.pdb

Chain information for ABCA2_closed_ADP_poststate.pdb #2  
---  
Chain | Description  
A | No description available  
  

> mmaker #1:811-836 to #2:811-836

Computing secondary structure  
Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker ABCA2_closed_ADP_poststate.pdb, chain A (#2) with
ABCA2_open_prestate.pdb, chain A (#1), sequence alignment score = 122.1  
RMSD between 24 pruned atom pairs is 0.816 angstroms; (across all 26 pairs:
1.131)  
  

> view matrix camera
> 0.4295,0.065969,0.90065,741.54,-0.8689,0.30192,0.39225,416.92,-0.24605,-0.95105,0.187,259.7

> open /Users/arne/Documents/Projects/2025-ABCA2/Maps-
> and_Models/ABCA2-morph.pdb

Chain information for ABCA2-morph.pdb #3  
---  
Chain | Description  
A | No description available  
  

> open /Users/arne/Documents/Projects/2025-ABCA2/Maps-
> and_Models/ABCA2-morph.dcd structureModel #3

Replaced existing frames of ABCA2-morph.pdb #3 with 61 new frames  

> open /Users/arne/Documents/Projects/2025-ABCA2/Maps-
> and_Models/ABCA2_prestate_AFassembly_KP.pdb

Chain information for ABCA2_prestate_AFassembly_KP.pdb #4  
---  
Chain | Description  
A | No description available  
  

> open /Users/arne/Documents/Projects/2025-ABCA2/Maps-
> and_Models/ABCA2_poststate_AFassembly.pdb

ABCA2_poststate_AFassembly.pdb title:  
Alphafold monomer V2.0 prediction for atp-binding cassette sub-family A member
2 (Q9BZC7) [more info...]  
  
Chain information for ABCA2_poststate_AFassembly.pdb #5  
---  
Chain | Description | UniProt  
A | atp-binding cassette sub-family A member 2 | ABCA2_HUMAN 1-2435  
B C | No description available |   
  
Non-standard residues in ABCA2_poststate_AFassembly.pdb #5  
---  
3PE — (3PE)  
ADP — (ADP)  
LMN — (LMN)  
MG — (MG)  
NAG — (NAG)  
Y01 — (Y01)  
  

> view matrix camera
> 0.10605,-0.14587,0.9836,918.88,-0.99229,0.048234,0.11413,258.3,-0.064087,-0.98812,-0.13962,57.431

> select :194-219

764 atoms, 784 bonds, 104 residues, 4 models selected  

> delete atoms sel

> delete bonds sel

> select #4:194-219,2364-2435,1330-1436,924-961,1222-1249

Nothing selected  

> delete atoms sel

> delete bonds sel

> color #4.2 #6495ed80

> color #4.3 #ff8c0080

> color #4.4 #daa52080

> color #4.5 #1e90ff80

> color #4.6 #00ced17f

> open /Users/arne/Documents/Projects/2025-ABCA2/Maps-and_Models/ABCA2-Pre-to-
> Post.pdb

ABCA2-Pre-to-Post.pdb title:  
Alphafold monomer V2.0 prediction for atp-binding cassette sub-family A member
2 (Q9BZC7) [more info...]  
  
Chain information for ABCA2-Pre-to-Post.pdb #6  
---  
Chain | Description | UniProt  
A | atp-binding cassette sub-family A member 2 | ABCA2_HUMAN 1-2435  
B C | No description available |   
  
Non-standard residues in ABCA2-Pre-to-Post.pdb #6  
---  
NAG — (NAG)  
  

> open /Users/arne/Documents/Projects/2025-ABCA2/Maps-and_Models/ABCA2-Pre-to-
> Post.dcd structureModel #6

Replaced existing frames of ABCA2-Pre-to-Post.pdb #6 with 101 new frames  

> mmaker #6 to #4

Computing secondary structure  
Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker ABCA2_prestate_AFassembly_KP.pdb, chain A (#4) with ABCA2-Pre-to-
Post.pdb, chain C (#6), sequence alignment score = 7531  
RMSD between 299 pruned atom pairs is 0.659 angstroms; (across all 333 pairs:
1.293)  
  

> dssp

Computing secondary structure  

> show #!6 surfaces

> select :1-695

28486 atoms, 29132 bonds, 16 pseudobonds, 3662 residues, 12 models selected  

> color sel dark turquoise

> select :696-1250

20003 atoms, 20432 bonds, 7 pseudobonds, 2599 residues, 11 models selected  

> color sel dodger blue

> select :1251-1775

15546 atoms, 15943 bonds, 5 pseudobonds, 2007 residues, 10 models selected  

> color sel coral

> select :1776-2270

20942 atoms, 21423 bonds, 4 pseudobonds, 2746 residues, 10 models selected  

> color sel goldenrod

> select clear

> select :1204-1312

1941 atoms, 1974 bonds, 3 pseudobonds, 247 residues, 6 models selected  

> color sel cornflower blue

> select :2269-2363

2331 atoms, 2373 bonds, 285 residues, 3 models selected  

> color sel dark orange

> select clear

> select ::name=""Y01""

350 atoms, 380 bonds, 10 residues, 3 models selected  

> color sel lime

> color sel & #!1 byhetero

> select clear

> graphics silhouettes true

> lighting full

executed Color-ABCA2-with_alpha-fold.cxc  

> open /Users/arne/Downloads/cryosparc_P46_J2062_006_volume_map_sharp.mrc

Opened cryosparc_P46_J2062_006_volume_map_sharp.mrc as #7, grid size
512,512,512, pixel 0.68, shown at level 0.0479, step 2, values float32  

> hide #!2 models

> hide #!1 models

> hide #!3 models

> hide #!4 models

> hide #!5 models

> hide #!6 models

> show #!5 models

> volume #7 level 0.1085

> select add #5

16378 atoms, 16772 bonds, 8 pseudobonds, 2043 residues, 3 models selected  

> ui mousemode right ""rotate selected models""

> view matrix models
> #5,-0.93093,-0.31811,0.17938,355.9,-0.31834,0.94756,0.028277,58.887,-0.17896,-0.030778,-0.98337,360.93

> view matrix models
> #5,-0.94176,-0.25099,0.2238,338.78,-0.25874,0.96593,-0.0055124,51.041,-0.21479,-0.063097,-0.97462,371.25

> view matrix models
> #5,-0.92992,-0.24759,0.27193,328.28,-0.22519,0.96795,0.11123,25.829,-0.29075,0.042197,-0.95587,362.82

> view matrix models
> #5,-0.90465,-0.37281,0.20646,356.49,-0.34261,0.92435,0.1679,44.195,-0.25344,0.081152,-0.96394,350.98

> view matrix models
> #5,-0.90843,-0.37265,0.18944,359.9,-0.35371,0.92672,0.12679,52.416,-0.2228,0.048171,-0.97367,353.09

> ui mousemode right ""translate selected models""

> view matrix models
> #5,-0.90843,-0.37265,0.18944,393.85,-0.35371,0.92672,0.12679,134.98,-0.2228,0.048171,-0.97367,362.26

> ui mousemode right ""rotate selected models""

> view matrix models
> #5,-0.89223,-0.37594,0.2502,381.69,-0.30756,0.91155,0.2729,105.8,-0.33067,0.16654,-0.92894,352.74

> view matrix models
> #5,-0.2815,0.95103,0.12766,66.354,0.92321,0.3047,-0.23417,84.29,-0.2616,0.051942,-0.96378,366.61

> view matrix models
> #5,0.90604,-0.16789,-0.38847,142.89,-0.21613,-0.97277,-0.083683,476.75,-0.36384,0.15978,-0.91765,357.74

> view matrix models
> #5,0.9334,-0.17717,-0.31204,127.3,-0.15143,-0.98287,0.10508,436.52,-0.32531,-0.050833,-0.94424,392.19

> view matrix models
> #5,0.98435,0.10841,-0.13892,40.503,0.087234,-0.98478,-0.15035,437.93,-0.15311,0.13588,-0.97882,335.92

> hide #!5 models

> show #!4 models

> select subtract #5

Nothing selected  

> select add #4

16648 atoms, 17044 bonds, 6 pseudobonds, 2095 residues, 2 models selected  

> view matrix models
> #4,0.085715,0.16025,-0.98335,290.83,0.64351,0.74459,0.17744,-92.116,0.76062,-0.648,-0.039302,164.35

> view matrix models
> #4,-0.41088,0.91112,-0.032138,76.473,0.88771,0.39179,-0.24182,2.1193,-0.20774,-0.12789,-0.96979,388.11

> view matrix models
> #4,-0.98742,0.13959,0.074291,302.6,0.11925,0.9659,-0.22981,24.248,-0.10384,-0.21806,-0.9704,387.31

> view matrix models
> #4,-0.99047,-0.040556,0.13165,327.39,-0.067983,0.9751,-0.21108,51.546,-0.11981,-0.21802,-0.96856,389.74

> view matrix models
> #4,-0.97755,0.00077084,0.21068,304.23,-0.053211,0.96667,-0.25043,57.155,-0.20385,-0.25602,-0.94493,407.36

> view matrix models
> #4,-0.99745,0.035114,0.062122,325.97,0.021275,0.9773,-0.2108,35.761,-0.068113,-0.20894,-0.97555,380.32

> view matrix models
> #4,-0.99288,-0.014456,0.11823,325.14,-0.040599,0.97424,-0.22182,48.797,-0.11198,-0.22504,-0.96789,389.6

> view matrix models
> #4,-0.97913,-0.18116,0.092149,358.43,-0.19553,0.96336,-0.18361,71.07,-0.055508,-0.1978,-0.97867,376.58

> view matrix models
> #4,-0.97727,-0.17474,0.12,352.26,-0.18851,0.97532,-0.11496,56.17,-0.096951,-0.13497,-0.98609,373.14

> view matrix models
> #4,-0.98881,-0.12275,0.084762,350.36,-0.13154,0.98548,-0.10739,43.219,-0.070349,-0.11734,-0.9906,366.01

> ui mousemode right ""translate selected models""

> view matrix models
> #4,-0.98881,-0.12275,0.084762,384.62,-0.13154,0.98548,-0.10739,127.27,-0.070349,-0.11734,-0.9906,363.32

> view matrix models
> #4,-0.98881,-0.12275,0.084762,382.4,-0.13154,0.98548,-0.10739,119.6,-0.070349,-0.11734,-0.9906,400.86

> view matrix models
> #4,-0.98881,-0.12275,0.084762,381.99,-0.13154,0.98548,-0.10739,118.69,-0.070349,-0.11734,-0.9906,399.34

> volume flip #7

Opened cryosparc_P46_J2062_006_volume_map_sharp.mrc z flip as #8, grid size
512,512,512, pixel 0.68, shown at step 1, values float32  

> view matrix models
> #4,-0.98881,-0.12275,0.084762,353.66,-0.13154,0.98548,-0.10739,48.113,-0.070349,-0.11734,-0.9906,419.39

> view matrix models
> #4,-0.98881,-0.12275,0.084762,355.81,-0.13154,0.98548,-0.10739,53.463,-0.070349,-0.11734,-0.9906,417.88

> ui mousemode right ""rotate selected models""

> view matrix models
> #4,-0.26951,0.20848,0.94016,27.463,-0.57613,0.74739,-0.33089,211.78,-0.77165,-0.63083,-0.081311,483.09

> view matrix models
> #4,0.82866,0.5176,0.2131,-97.897,-0.55557,0.71411,0.4259,88.3,0.068268,-0.47132,0.87932,148.74

> view matrix models
> #4,0.82021,0.57192,-0.013074,-68.93,-0.5682,0.8118,-0.13464,165.6,-0.066392,0.11786,0.99081,42.625

> ui mousemode right ""translate selected models""

> view matrix models
> #4,0.82021,0.57192,-0.013074,-78.158,-0.5682,0.8118,-0.13464,147.62,-0.066392,0.11786,0.99081,-34.52

> view clip false

> view matrix models
> #4,0.82021,0.57192,-0.013074,-76.385,-0.5682,0.8118,-0.13464,151.05,-0.066392,0.11786,0.99081,-26.909

> volume #8 level 0.2388

> view matrix models
> #4,0.82021,0.57192,-0.013074,-108.18,-0.5682,0.8118,-0.13464,87.979,-0.066392,0.11786,0.99081,-19.852

> view matrix models
> #4,0.82021,0.57192,-0.013074,-110.27,-0.5682,0.8118,-0.13464,84.568,-0.066392,0.11786,0.99081,-19.136

> ui mousemode right ""rotate selected models""

> view matrix models
> #4,-0.61067,-0.777,0.15278,361.06,0.79188,-0.59875,0.12007,73.451,-0.0018165,0.19431,0.98094,-42.933

> ui mousemode right ""translate selected models""

> view matrix models
> #4,-0.61067,-0.777,0.15278,395.53,0.79188,-0.59875,0.12007,129.86,-0.0018165,0.19431,0.98094,-49.726

> view matrix models
> #4,-0.61067,-0.777,0.15278,393.9,0.79188,-0.59875,0.12007,127.25,-0.0018165,0.19431,0.98094,-47.354

> fitmap #4 inMap #8

Fit molecule ABCA2_prestate_AFassembly_KP.pdb (#4) to map
cryosparc_P46_J2062_006_volume_map_sharp.mrc z flip (#8) using 16648 atoms  
average map value = 0.04328, steps = 104  
shifted from previous position = 1.3  
rotated from previous position = 3.92 degrees  
atoms outside contour = 14690, contour level = 0.23884  
  
Position of ABCA2_prestate_AFassembly_KP.pdb (#4) relative to
cryosparc_P46_J2062_006_volume_map_sharp.mrc z flip (#8) coordinates:  
Matrix rotation and translation  
-0.63653544 -0.74318084 0.20616714 381.58838144  
0.77029866 -0.62587209 0.12216427 135.72234129  
0.03824411 0.23657216 0.97086097 -60.69411689  
Axis 0.07492044 0.10996503 0.99110777  
Axis point 160.89438429 160.82999010 0.00000000  
Rotation angle (degrees) 130.22367799  
Shift along axis -16.64093163  
  

> view matrix models
> #4,-0.63654,-0.74318,0.20617,381.91,0.7703,-0.62587,0.12216,135.85,0.038244,0.23657,0.97086,-61.897

> hide #!8 models

> select clear

Drag select of 2 residues  

> select clear

> ui mousemode right ""translate selected atoms""

> ui mousemode right rotate

> ui mousemode right select

> select clear

> select #4/A:2008

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select clear

> select add #4

16648 atoms, 17044 bonds, 6 pseudobonds, 2095 residues, 2 models selected  

> select subtract #4

Nothing selected  

> select add #4

16648 atoms, 17044 bonds, 6 pseudobonds, 2095 residues, 2 models selected  

> show #!8 models

> show #!7 models

> select add #7

16648 atoms, 17044 bonds, 6 pseudobonds, 2095 residues, 4 models selected  

> select subtract #4

2 models selected  
Drag select of 7 cryosparc_P46_J2062_006_volume_map_sharp.mrc , 8
cryosparc_P46_J2062_006_volume_map_sharp.mrc z flip  

> ui mousemode right ""translate selected models""

> ui mousemode right ""rotate selected models""

> view matrix models
> #7,0.024512,0.31983,-0.94716,270.67,-0.90385,-0.39773,-0.15769,415.93,-0.42715,0.85995,0.27933,48.347,#8,0.024512,0.31983,-0.94716,270.67,-0.90385,-0.39773,-0.15769,415.93,-0.42715,0.85995,0.27933,48.347

> volume #7 level 0.416

> view matrix models
> #7,0.13035,-0.96198,0.24001,272.48,-0.95092,-0.18982,-0.24437,402.51,0.28064,-0.19638,-0.93951,322.15,#8,0.13035,-0.96198,0.24001,272.48,-0.95092,-0.18982,-0.24437,402.51,0.28064,-0.19638,-0.93951,322.15

> view matrix models
> #7,0.13436,-0.93993,0.31381,255.04,-0.97135,-0.18757,-0.14594,388.61,0.19603,-0.28521,-0.9382,352.6,#8,0.13436,-0.93993,0.31381,255.04,-0.97135,-0.18757,-0.14594,388.61,0.19603,-0.28521,-0.9382,352.6

> view matrix models
> #7,0.43232,-0.88371,0.1793,215.82,-0.90104,-0.43108,0.047888,385.6,0.034974,-0.18226,-0.98263,370.57,#8,0.43232,-0.88371,0.1793,215.82,-0.90104,-0.43108,0.047888,385.6,0.034974,-0.18226,-0.98263,370.57

> view matrix models
> #7,0.48439,-0.70562,0.51717,116.35,-0.75974,-0.6324,-0.15125,430.88,0.43378,-0.31965,-0.84241,300.03,#8,0.48439,-0.70562,0.51717,116.35,-0.75974,-0.6324,-0.15125,430.88,0.43378,-0.31965,-0.84241,300.03

> view matrix models
> #7,0.93664,0.34649,0.051379,-68.846,-0.3282,0.91937,-0.21691,91.338,-0.12239,0.18631,0.97484,-7.1783,#8,0.93664,0.34649,0.051379,-68.846,-0.3282,0.91937,-0.21691,91.338,-0.12239,0.18631,0.97484,-7.1783

> view matrix models
> #7,0.9895,0.048116,-0.13627,7.2551,-0.044354,0.99855,0.030513,-15.859,0.13754,-0.024149,0.9902,-18.532,#8,0.9895,0.048116,-0.13627,7.2551,-0.044354,0.99855,0.030513,-15.859,0.13754,-0.024149,0.9902,-18.532

> view matrix models
> #7,0.99058,-0.030802,-0.1334,20.535,0.034474,0.99909,0.025302,-28.978,0.1325,-0.029662,0.99074,-16.758,#8,0.99058,-0.030802,-0.1334,20.535,0.034474,0.99909,0.025302,-28.978,0.1325,-0.029662,0.99074,-16.758

> view matrix models
> #7,0.99914,-0.01119,-0.039887,-0.70647,0.01701,0.98873,0.14872,-45.516,0.037774,-0.14927,0.98807,21.619,#8,0.99914,-0.01119,-0.039887,-0.70647,0.01701,0.98873,0.14872,-45.516,0.037774,-0.14927,0.98807,21.619

> ui mousemode right ""translate selected models""

> view matrix models
> #7,0.99914,-0.01119,-0.039887,9.3062,0.01701,0.98873,0.14872,-31.974,0.037774,-0.14927,0.98807,22.407,#8,0.99914,-0.01119,-0.039887,9.3062,0.01701,0.98873,0.14872,-31.974,0.037774,-0.14927,0.98807,22.407

> ui mousemode right ""rotate selected models""

> view matrix models
> #7,0.94123,0.33535,-0.040315,-41.73,-0.32834,0.93644,0.1236,42.686,0.0792,-0.1031,0.99151,6.3139,#8,0.94123,0.33535,-0.040315,-41.73,-0.32834,0.93644,0.1236,42.686,0.0792,-0.1031,0.99151,6.3139

> fitmap #4 inMap #7

Fit molecule ABCA2_prestate_AFassembly_KP.pdb (#4) to map
cryosparc_P46_J2062_006_volume_map_sharp.mrc (#7) using 16648 atoms  
average map value = 0.02928, steps = 160  
shifted from previous position = 2.33  
rotated from previous position = 3.29 degrees  
atoms outside contour = 16198, contour level = 0.41602  
  
Position of ABCA2_prestate_AFassembly_KP.pdb (#4) relative to
cryosparc_P46_J2062_006_volume_map_sharp.mrc (#7) coordinates:  
Matrix rotation and translation  
-0.83468538 -0.48060079 0.26892985 352.62994843  
0.50845385 -0.86011224 0.04100839 241.98098325  
0.21160118 0.17096752 0.96228640 -78.65361860  
Axis 0.13006289 0.05737445 0.98984434  
Axis point 148.62017221 171.27266560 0.00000000  
Rotation angle (degrees) 150.02638805  
Shift along axis -18.10724296  
  

> select subtract #8

2 models selected  

> hide #!8 models

> volume #7 level 0.2483

> view matrix models
> #7,0.99641,0.036093,0.076602,-18.647,-0.032467,0.99832,-0.048065,9.042,-0.078208,0.045406,0.9959,7.0756

> view matrix models
> #7,0.24838,-0.96574,0.075193,291.41,-0.95417,-0.2573,-0.15283,412.63,0.16694,-0.033788,-0.98539,319.9

> view matrix models
> #7,0.33858,-0.93886,-0.062498,294.47,-0.93906,-0.34135,0.040517,391.47,-0.059374,0.044971,-0.99722,348.01

> ui mousemode right ""translate selected models""

> view matrix models
> #7,0.33858,-0.93886,-0.062498,291.64,-0.93906,-0.34135,0.040517,387.97,-0.059374,0.044971,-0.99722,348.89

> fitmap #4 inMap #7

Fit molecule ABCA2_prestate_AFassembly_KP.pdb (#4) to map
cryosparc_P46_J2062_006_volume_map_sharp.mrc (#7) using 16648 atoms  
average map value = 0.03195, steps = 108  
shifted from previous position = 3.17  
rotated from previous position = 0.953 degrees  
atoms outside contour = 15542, contour level = 0.24828  
  
Position of ABCA2_prestate_AFassembly_KP.pdb (#4) relative to
cryosparc_P46_J2062_006_volume_map_sharp.mrc (#7) coordinates:  
Matrix rotation and translation  
-0.94487543 0.32609552 -0.02953353 275.52549565  
0.32532240 0.92474838 -0.19749904 -12.40087953  
-0.03709248 -0.19621990 -0.97985815 404.77293890  
Axis 0.16600780 0.98100666 -0.10033616  
Axis point 139.20871589 0.00000000 201.48063422  
Rotation angle (degrees) 179.77925907  
Shift along axis -7.03932379  
  

> fitmap #4 inMap #7

Fit molecule ABCA2_prestate_AFassembly_KP.pdb (#4) to map
cryosparc_P46_J2062_006_volume_map_sharp.mrc (#7) using 16648 atoms  
average map value = 0.03195, steps = 48  
shifted from previous position = 0.00226  
rotated from previous position = 0.00598 degrees  
atoms outside contour = 15540, contour level = 0.24828  
  
Position of ABCA2_prestate_AFassembly_KP.pdb (#4) relative to
cryosparc_P46_J2062_006_volume_map_sharp.mrc (#7) coordinates:  
Matrix rotation and translation  
-0.94488105 0.32607696 -0.02955863 275.53615969  
0.32530545 0.92473344 -0.19759688 -12.37930533  
-0.03709794 -0.19632112 -0.97983766 404.78909009  
Axis 0.16599939 0.98100285 -0.10038727  
Axis point 139.21116120 0.00000000 201.49018113  
Rotation angle (degrees) 179.77983170  
Shift along axis -7.04097239  
  

> show #!8 models

> hide #!7 models

> select subtract #7

Nothing selected  

> fitmap #4 inMap #8

Fit molecule ABCA2_prestate_AFassembly_KP.pdb (#4) to map
cryosparc_P46_J2062_006_volume_map_sharp.mrc z flip (#8) using 16648 atoms  
average map value = 0.03643, steps = 284  
shifted from previous position = 3.3  
rotated from previous position = 5.75 degrees  
atoms outside contour = 15032, contour level = 0.23884  
  
Position of ABCA2_prestate_AFassembly_KP.pdb (#4) relative to
cryosparc_P46_J2062_006_volume_map_sharp.mrc z flip (#8) coordinates:  
Matrix rotation and translation  
-0.81158526 -0.54451465 0.21173859 369.58350744  
0.55685816 -0.83060610 -0.00160249 235.05291648  
0.17674393 0.11660780 0.97732506 -66.17966127  
Axis 0.10666382 0.03157647 0.99379362  
Axis point 152.49055520 175.11475331 0.00000000  
Rotation angle (degrees) 146.34949687  
Shift along axis -18.92559461  
  

> fitmap #4 inMap #8

Fit molecule ABCA2_prestate_AFassembly_KP.pdb (#4) to map
cryosparc_P46_J2062_006_volume_map_sharp.mrc z flip (#8) using 16648 atoms  
average map value = 0.03643, steps = 60  
shifted from previous position = 0.00963  
rotated from previous position = 0.0269 degrees  
atoms outside contour = 15029, contour level = 0.23884  
  
Position of ABCA2_prestate_AFassembly_KP.pdb (#4) relative to
cryosparc_P46_J2062_006_volume_map_sharp.mrc z flip (#8) coordinates:  
Matrix rotation and translation  
-0.81183990 -0.54418567 0.21160813 369.58140481  
0.55649068 -0.83085219 -0.00168479 235.17189765  
0.17673191 0.11639017 0.97735318 -66.13942804  
Axis 0.10661004 0.03148979 0.99380214  
Axis point 152.49560503 175.12618747 0.00000000  
Rotation angle (degrees) 146.37393851  
Shift along axis -18.92290342  
  

> volume #8 level 0.1687

> select add #4

16648 atoms, 17044 bonds, 6 pseudobonds, 2095 residues, 2 models selected  

> view matrix models
> #4,-0.58464,-0.79552,0.15921,392.57,0.80952,-0.58497,0.049739,129.93,0.053562,0.15796,0.98599,-52.482

> ui mousemode right ""rotate selected models""

> view matrix models
> #4,-0.59451,-0.79986,0.082386,407.89,0.80316,-0.58578,0.10861,121.36,-0.038616,0.13074,0.99066,-32.323

> view matrix models
> #4,-0.6871,-0.72123,0.087877,408.11,0.72602,-0.67687,0.1214,149.57,-0.028075,0.14721,0.98871,-36.9

> ui mousemode right ""translate selected atoms""

> fitmap #4 inMap #8

Fit molecule ABCA2_prestate_AFassembly_KP.pdb (#4) to map
cryosparc_P46_J2062_006_volume_map_sharp.mrc z flip (#8) using 16648 atoms  
average map value = 0.03592, steps = 256  
shifted from previous position = 1.11  
rotated from previous position = 5.81 degrees  
atoms outside contour = 14442, contour level = 0.16866  
  
Position of ABCA2_prestate_AFassembly_KP.pdb (#4) relative to
cryosparc_P46_J2062_006_volume_map_sharp.mrc z flip (#8) coordinates:  
Matrix rotation and translation  
-0.83741059 -0.52597334 0.14864598 385.87429527  
0.53754252 -0.84176719 0.04976059 230.78913601  
0.09895256 0.12157357 0.98763775 -55.10658740  
Axis 0.06729763 0.04656887 0.99664556  
Axis point 161.20589953 172.81879546 0.00000000  
Rotation angle (degrees) 147.75452852  
Shift along axis -18.20572215  
  

> fitmap #4 inMap #8

Fit molecule ABCA2_prestate_AFassembly_KP.pdb (#4) to map
cryosparc_P46_J2062_006_volume_map_sharp.mrc z flip (#8) using 16648 atoms  
average map value = 0.03592, steps = 48  
shifted from previous position = 0.0117  
rotated from previous position = 0.00322 degrees  
atoms outside contour = 14444, contour level = 0.16866  
  
Position of ABCA2_prestate_AFassembly_KP.pdb (#4) relative to
cryosparc_P46_J2062_006_volume_map_sharp.mrc z flip (#8) coordinates:  
Matrix rotation and translation  
-0.83741494 -0.52595394 0.14869008 385.85965478  
0.53753155 -0.84177238 0.04979117 230.79068013  
0.09897533 0.12162148 0.98762957 -55.12786336  
Axis 0.06731563 0.04659008 0.99664335  
Axis point 161.20042254 172.81705420 0.00000000  
Rotation angle (degrees) 147.75548033  
Shift along axis -18.21587647  
  

> select clear

> select :696-1250

20003 atoms, 20432 bonds, 7 pseudobonds, 2599 residues, 11 models selected  

> fitmap #4 inMap #8

Fit molecule ABCA2_prestate_AFassembly_KP.pdb (#4) to map
cryosparc_P46_J2062_006_volume_map_sharp.mrc z flip (#8) using 16648 atoms  
average map value = 0.03592, steps = 76  
shifted from previous position = 0.0118  
rotated from previous position = 0.00772 degrees  
atoms outside contour = 14445, contour level = 0.16866  
  
Position of ABCA2_prestate_AFassembly_KP.pdb (#4) relative to
cryosparc_P46_J2062_006_volume_map_sharp.mrc z flip (#8) coordinates:  
Matrix rotation and translation  
-0.83740000 -0.52596309 0.14874189 385.84861903  
0.53753468 -0.84177773 0.04966675 230.81379175  
0.09908472 0.12154485 0.98762804 -55.12085539  
Axis 0.06735962 0.04653556 0.99664293  
Axis point 161.19226713 172.82615864 0.00000000  
Rotation angle (degrees) 147.75504768  
Shift along axis -18.20414628  
  

> fitmap #4 inMap #8

Fit molecule ABCA2_prestate_AFassembly_KP.pdb (#4) to map
cryosparc_P46_J2062_006_volume_map_sharp.mrc z flip (#8) using 16648 atoms  
average map value = 0.03592, steps = 76  
shifted from previous position = 0.0018  
rotated from previous position = 0.00122 degrees  
atoms outside contour = 14443, contour level = 0.16866  
  
Position of ABCA2_prestate_AFassembly_KP.pdb (#4) relative to
cryosparc_P46_J2062_006_volume_map_sharp.mrc z flip (#8) coordinates:  
Matrix rotation and translation  
-0.83740917 -0.52595229 0.14872845 385.85168654  
0.53752323 -0.84178442 0.04967738 230.81368227  
0.09906935 0.12154528 0.98762952 -55.11823955  
Axis 0.06735150 0.04653837 0.99664334  
Axis point 161.19435933 172.82510072 0.00000000  
Rotation angle (degrees) 147.75581888  
Shift along axis -18.20384539  
  

> fitmap #4 inMap #8

Fit molecule ABCA2_prestate_AFassembly_KP.pdb (#4) to map
cryosparc_P46_J2062_006_volume_map_sharp.mrc z flip (#8) using 16648 atoms  
average map value = 0.03592, steps = 60  
shifted from previous position = 0.00515  
rotated from previous position = 0.00378 degrees  
atoms outside contour = 14443, contour level = 0.16866  
  
Position of ABCA2_prestate_AFassembly_KP.pdb (#4) relative to
cryosparc_P46_J2062_006_volume_map_sharp.mrc z flip (#8) coordinates:  
Matrix rotation and translation  
-0.83739693 -0.52597931 0.14870182 385.86333664  
0.53755188 -0.84176331 0.04972510 230.79366263  
0.09901735 0.12157458 0.98763113 -55.11585561  
Axis 0.06733074 0.04655972 0.99664375  
Axis point 161.20032094 172.82069211 0.00000000  
Rotation angle (degrees) 147.75394193  
Shift along axis -18.20472196  
  

> select :1-695

28486 atoms, 29132 bonds, 16 pseudobonds, 3662 residues, 12 models selected  

> fitmap #4 inMap #8

Fit molecule ABCA2_prestate_AFassembly_KP.pdb (#4) to map
cryosparc_P46_J2062_006_volume_map_sharp.mrc z flip (#8) using 16648 atoms  
average map value = 0.03592, steps = 64  
shifted from previous position = 0.0117  
rotated from previous position = 0.00313 degrees  
atoms outside contour = 14446, contour level = 0.16866  
  
Position of ABCA2_prestate_AFassembly_KP.pdb (#4) relative to
cryosparc_P46_J2062_006_volume_map_sharp.mrc z flip (#8) coordinates:  
Matrix rotation and translation  
-0.83741458 -0.52595453 0.14869007 385.85998091  
0.53753031 -0.84177425 0.04977294 230.79450845  
0.09898516 0.12160600 0.98763049 -55.12632492  
Axis 0.06731827 0.04658090 0.99664360  
Axis point 161.20012216 172.81865507 0.00000000  
Rotation angle (degrees) 147.75551146  
Shift along axis -18.21525695  
  

> fitmap #4 inMap #8

Fit molecule ABCA2_prestate_AFassembly_KP.pdb (#4) to map
cryosparc_P46_J2062_006_volume_map_sharp.mrc z flip (#8) using 16648 atoms  
average map value = 0.03592, steps = 76  
shifted from previous position = 0.00831  
rotated from previous position = 0.00281 degrees  
atoms outside contour = 14443, contour level = 0.16866  
  
Position of ABCA2_prestate_AFassembly_KP.pdb (#4) relative to
cryosparc_P46_J2062_006_volume_map_sharp.mrc z flip (#8) coordinates:  
Matrix rotation and translation  
-0.83740416 -0.52596964 0.14869526 385.86389810  
0.53754139 -0.84176998 0.04972549 230.79652252  
0.09901309 0.12157018 0.98763210 -55.11859559  
Axis 0.06732754 0.04655845 0.99664403  
Axis point 161.20093908 172.82097225 0.00000000  
Rotation angle (degrees) 147.75463680  
Shift along axis -18.20882247  
  

> fitmap #4 inMap #8

Fit molecule ABCA2_prestate_AFassembly_KP.pdb (#4) to map
cryosparc_P46_J2062_006_volume_map_sharp.mrc z flip (#8) using 16648 atoms  
average map value = 0.03592, steps = 64  
shifted from previous position = 0.00878  
rotated from previous position = 0.00306 degrees  
atoms outside contour = 14445, contour level = 0.16866  
  
Position of ABCA2_prestate_AFassembly_KP.pdb (#4) relative to
cryosparc_P46_J2062_006_volume_map_sharp.mrc z flip (#8) coordinates:  
Matrix rotation and translation  
-0.83743183 -0.52593333 0.14866789 385.86002564  
0.53750187 -0.84179500 0.04972917 230.81217293  
0.09899365 0.12155406 0.98763604 -55.11091584  
Axis 0.06731385 0.04655441 0.99664514  
Axis point 161.19903036 172.82302008 0.00000000  
Rotation angle (degrees) 147.75725418  
Shift along axis -18.20697787  
  

> select clear

> hide #!4 models

> show #!1 models

> mmaker #1 to #4

Computing secondary structure  
Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker ABCA2_prestate_AFassembly_KP.pdb, chain A (#4) with
ABCA2_open_prestate.pdb, chain A (#1), sequence alignment score = 7586.6  
RMSD between 1565 pruned atom pairs is 0.357 angstroms; (across all 1615
pairs: 3.615)  
  

> fitmap #1 inMap #8

Fit molecule ABCA2_open_prestate.pdb (#1) to map
cryosparc_P46_J2062_006_volume_map_sharp.mrc z flip (#8) using 13098 atoms  
average map value = 0.03457, steps = 84  
shifted from previous position = 0.395  
rotated from previous position = 1.37 degrees  
atoms outside contour = 11443, contour level = 0.16866  
  
Position of ABCA2_open_prestate.pdb (#1) relative to
cryosparc_P46_J2062_006_volume_map_sharp.mrc z flip (#8) coordinates:  
Matrix rotation and translation  
-0.96942267 -0.24398361 0.02630124 381.19198340  
0.24070458 -0.96626739 -0.09158979 319.94616690  
0.04776043 -0.08245838 0.99544945 -1.89642114  
Axis 0.01881798 -0.04422305 0.99884443  
Axis point 170.91422326 183.44084467 0.00000000  
Rotation angle (degrees) 165.95850997  
Shift along axis -8.86996016  
  

> fitmap #1 inMap #8

Fit molecule ABCA2_open_prestate.pdb (#1) to map
cryosparc_P46_J2062_006_volume_map_sharp.mrc z flip (#8) using 13098 atoms  
average map value = 0.03457, steps = 80  
shifted from previous position = 0.000858  
rotated from previous position = 0.00382 degrees  
atoms outside contour = 11444, contour level = 0.16866  
  
Position of ABCA2_open_prestate.pdb (#1) relative to
cryosparc_P46_J2062_006_volume_map_sharp.mrc z flip (#8) coordinates:  
Matrix rotation and translation  
-0.96943767 -0.24392221 0.02631760 381.18068120  
0.24064148 -0.96628201 -0.09160141 319.96128109  
0.04777383 -0.08246875 0.99544795 -1.89652700  
Axis 0.01882540 -0.04422831 0.99884406  
Axis point 170.91285228 183.44149462 0.00000000  
Rotation angle (degrees) 165.96218544  
Shift along axis -8.86980035  
  

> select clear

> select :1-600

23746 atoms, 24218 bonds, 16 pseudobonds, 3092 residues, 12 models selected  

> select :50-600

21292 atoms, 21686 bonds, 16 pseudobonds, 2804 residues, 12 models selected  

> delete atoms (#!1 & sel)

> delete bonds (#!1 & sel)

> select clear

> fitmap #1 inMap #8

Fit molecule ABCA2_open_prestate.pdb (#1) to map
cryosparc_P46_J2062_006_volume_map_sharp.mrc z flip (#8) using 9438 atoms  
average map value = 0.044, steps = 60  
shifted from previous position = 0.0879  
rotated from previous position = 0.219 degrees  
atoms outside contour = 7792, contour level = 0.16866  
  
Position of ABCA2_open_prestate.pdb (#1) relative to
cryosparc_P46_J2062_006_volume_map_sharp.mrc z flip (#8) coordinates:  
Matrix rotation and translation  
-0.96874696 -0.24649917 0.02770470 381.23096588  
0.24297503 -0.96546483 -0.09402587 319.90129200  
0.04992520 -0.08435572 0.99518422 -1.88014581  
Axis 0.01973203 -0.04534114 0.99877667  
Axis point 170.73445827 183.66331210 0.00000000  
Rotation angle (degrees) 165.81598822  
Shift along axis -8.86007504  
  

> show #!8 models

> hide #!8 models

> hide #!1 models

> show #!8 models

> volume #8 level 0.289

> volume #8 level 0.08845

> view #8 clip false

> surface dust #8 size 6.8

> volume #8 level 0.1185

> open /Users/arne/Downloads/250610_BicA_nd_BAY981.pdb

Chain information for 250610_BicA_nd_BAY981.pdb #9  
---  
Chain | Description  
A B | No description available  
C D | No description available  
  

> hide #!8 models

> view #9 clip false

> color #9 bychain

> hide #9 models

> show #!8 models

> volume #8 level 0.1959

> show #!4 models

> hide #!4 models

> show #!1 models

> hide #!1 models

> show #!2 models

> hide #!2 models

> show #!1 models

> hide #!8 models

> show #!8 models

> hide #!8 models

> show #!8 models

> fitmap #1 inMap #8

Fit molecule ABCA2_open_prestate.pdb (#1) to map
cryosparc_P46_J2062_006_volume_map_sharp.mrc z flip (#8) using 9438 atoms  
average map value = 0.044, steps = 60  
shifted from previous position = 0.000603  
rotated from previous position = 0.001 degrees  
atoms outside contour = 8008, contour level = 0.19595  
  
Position of ABCA2_open_prestate.pdb (#1) relative to
cryosparc_P46_J2062_006_volume_map_sharp.mrc z flip (#8) coordinates:  
Matrix rotation and translation  
-0.96874679 -0.24649965 0.02770624 381.23027856  
0.24297451 -0.96546327 -0.09404325 319.90432126  
0.04993097 -0.08437219 0.99518254 -1.87773749  
Axis 0.01973390 -0.04534977 0.99877624  
Axis point 170.73389227 183.66485011 0.00000000  
Rotation angle (degrees) 165.81598308  
Shift along axis -8.85986654  
  

> fitmap #1 inMap #8

Fit molecule ABCA2_open_prestate.pdb (#1) to map
cryosparc_P46_J2062_006_volume_map_sharp.mrc z flip (#8) using 9438 atoms  
average map value = 0.044, steps = 40  
shifted from previous position = 0.000519  
rotated from previous position = 0.00332 degrees  
atoms outside contour = 8006, contour level = 0.19595  
  
Position of ABCA2_open_prestate.pdb (#1) relative to
cryosparc_P46_J2062_006_volume_map_sharp.mrc z flip (#8) coordinates:  
Matrix rotation and translation  
-0.96873504 -0.24654560 0.02770825 381.23556328  
0.24301840 -0.96544887 -0.09407758 319.90017345  
0.04994530 -0.08440262 0.99517924 -1.87399091  
Axis 0.01973818 -0.04536653 0.99877539  
Axis point 170.73296682 183.66771487 0.00000000  
Rotation angle (degrees) 165.81331289  
Shift along axis -8.85955869  
  

> open /Users/arne/Downloads/cryosparc_P79_J479_003_volume_map.mrc

Opened cryosparc_P79_J479_003_volume_map.mrc as #10, grid size 384,384,384,
pixel 0.68, shown at level 0.0258, step 2, values float32  

> open /Users/arne/Downloads/cryosparc_P79_J479_003_volume_map_sharp.mrc

Opened cryosparc_P79_J479_003_volume_map_sharp.mrc as #11, grid size
384,384,384, pixel 0.68, shown at level 0.0257, step 2, values float32  

> hide #!1 models

> volume #11 level 0.03838

> volume #11 step 1

> view #1 clip false

> view #11 clip false

> open /Users/arne/Downloads/cryosparc_P46_J2097_009_volume_map_sharp.mrc

Opened cryosparc_P46_J2097_009_volume_map_sharp.mrc as #12, grid size
336,336,336, pixel 1.36, shown at level 0.0529, step 2, values float32  

> hide #!11 models

> hide #!12 models

> show #!12 models

> view #12 clip false

> volume #12 level 0.07397

> volume #12 level 0.1372

> volume #12 step 1

> volume #12 level 0.2809

> volume #12 level 0.2658

> volume #12 level 0.4095

> volume #12 level 0.2885

> surface dust #12 size 13.6

> open /Users/arne/Downloads/cryosparc_P79_J593_005_volume_map_sharp.mrc

Opened cryosparc_P79_J593_005_volume_map_sharp.mrc as #13, grid size
384,384,384, pixel 0.68, shown at level 0.0263, step 2, values float32  

> view #13 clip false

> volume #13 level 0.05006

> volume #13 step 1

> open /Users/arne/Downloads/cryosparc_P46_J2103_002_volume_map_sharp.mrc

Opened cryosparc_P46_J2103_002_volume_map_sharp.mrc as #14, grid size
672,672,672, pixel 0.68, shown at step 1, values float32  

> view #14 clip false

> volume #14 region 0,0,0,671,671,671 step 4

> volume #14 change image level -0.003196,0 level 0.0229,0.8 level 0.2268,1

> volume #14 level 0.0245

> volume #14 step 1

> volume #14 level 0.0344

> surface dust #12 size 13.6

> surface dust #14 size 6.8

> volume #14 level 0.03902

> hide #!14 models

> show #!14 models

> hide #!12 models

> show #!12 models

> hide #!12 models

> show #!12 models

> hide #!12 models

> show #!12 models

> hide #!12 models

> show #!12 models

> hide #!14 models

> show #!14 models

> hide #!14 models

> show #!14 models

> hide #!14 models

> show #!14 models

> hide #!14 models

> show #!14 models

> hide #!12 models

> show #!12 models

> hide #!12 models

> show #!12 models

> hide #!12 models

> show #!12 models

> hide #!14 models

> hide #!12 models

> open /Users/arne/Downloads/cryosparc_P46_J2103_002_volume_map_sharp.mrc

Opened cryosparc_P46_J2103_002_volume_map_sharp.mrc as #15, grid size
672,672,672, pixel 0.68, shown at step 1, values float32  

> volume #15 region 0,0,0,671,671,671 step 4

> volume #15 change image level -0.003196,0 level 0.0229,0.8 level 0.2268,1

> volume #15 level 0.01864

> volume #15 step 1

> close #15

> open /Users/arne/Downloads/cryosparc_P79_J593_008_volume_map_sharp.mrc

Opened cryosparc_P79_J593_008_volume_map_sharp.mrc as #15, grid size
384,384,384, pixel 0.68, shown at level 0.0247, step 2, values float32  

> view #15 clip false

> surface dust #15 size 6.8

> volume #15 level 0.04265

> surface dust #15 size 6.8

> volume #15 step 1

> volume #15 level 0.05365

> open /Users/arne/Downloads/cryosparc_P79_J592_007_volume_map_sharp.mrc

Opened cryosparc_P79_J592_007_volume_map_sharp.mrc as #16, grid size
384,384,384, pixel 0.68, shown at level 0.0325, step 2, values float32  

> hide #!15 models

> volume #16 step 1

> volume #16 level 0.06526

> close #16

> show #!8 models

> view #8 clip false

> show #!1 models

> hide #!8 models

> select add #1

9438 atoms, 9707 bonds, 5 pseudobonds, 1156 residues, 2 models selected  

> show #!8 models

> ui mousemode right ""translate selected models""

> view matrix models
> #1,-0.83232,-0.55241,-0.04559,422.89,0.55182,-0.83356,0.025805,215.25,-0.052257,-0.0036795,0.99863,2.9155

> view matrix models
> #1,-0.83232,-0.55241,-0.04559,421.45,0.55182,-0.83356,0.025805,212.85,-0.052257,-0.0036795,0.99863,2.1251

> view matrix models
> #1,-0.83232,-0.55241,-0.04559,421.87,0.55182,-0.83356,0.025805,213.31,-0.052257,-0.0036795,0.99863,1.8801

> ui mousemode right ""translate selected atoms""

> fitmap #1 inMap #8

Fit molecule ABCA2_open_prestate.pdb (#1) to map
cryosparc_P46_J2062_006_volume_map_sharp.mrc z flip (#8) using 9438 atoms  
average map value = 0.04593, steps = 92  
shifted from previous position = 2.93  
rotated from previous position = 2.78 degrees  
atoms outside contour = 7963, contour level = 0.19595  
  
Position of ABCA2_open_prestate.pdb (#1) relative to
cryosparc_P46_J2062_006_volume_map_sharp.mrc z flip (#8) coordinates:  
Matrix rotation and translation  
-0.96309458 -0.26344591 0.05518290 374.81147584  
0.26024438 -0.96374090 -0.05896094 305.68075451  
0.06871503 -0.04242391 0.99673392 -13.85242441  
Axis 0.03155162 -0.02581845 0.99916861  
Axis point 167.24147083 177.69585781 0.00000000  
Rotation angle (degrees) 164.80749036  
Shift along axis -9.90720459  
  

> fitmap #1 inMap #8

Fit molecule ABCA2_open_prestate.pdb (#1) to map
cryosparc_P46_J2062_006_volume_map_sharp.mrc z flip (#8) using 9438 atoms  
average map value = 0.04593, steps = 28  
shifted from previous position = 0.00788  
rotated from previous position = 0.00468 degrees  
atoms outside contour = 7963, contour level = 0.19595  
  
Position of ABCA2_open_prestate.pdb (#1) relative to
cryosparc_P46_J2062_006_volume_map_sharp.mrc z flip (#8) coordinates:  
Matrix rotation and translation  
-0.96311093 -0.26337758 0.05522375 374.79079351  
0.26017399 -0.96375966 -0.05896506 305.70185975  
0.06875248 -0.04242211 0.99673142 -13.86206918  
Axis 0.03157127 -0.02581882 0.99916798  
Axis point 167.23558545 177.69808429 0.00000000  
Rotation angle (degrees) 164.81160205  
Shift along axis -9.91077348  
  

> select clear

> open emdb:16467

Summary of feedback from opening 16467 fetched from emdb  
---  
notes | Fetching compressed map 16467 from ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-16467/map/emd_16467.map.gz  
Fetching map header 16467 from
ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-16467/header/emd-16467.xml  
  
Opened emdb 16467 as #16, grid size 432,432,432, pixel 0.924, shown at level
0.18, step 2, values float32, fit PDB 8c80  

> hide #!8 models

> hide #!1 models

> open 8c80

Summary of feedback from opening 8c80 fetched from pdb  
---  
notes | Fetching compressed mmCIF 8c80 from http://files.rcsb.org/download/8c80.cif  
Fetching CCD Q7G from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/G/Q7G/Q7G.cif  
Fetching CCD Z8A from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/A/Z8A/Z8A.cif  
  
8c80 title:  
Cryo-EM structure of the yeast SPT-Orm1-Monomer complex [more info...]  
  
Chain information for 8c80 #17  
---  
Chain | Description | UniProt  
A | Protein ORM1 | ORM1_YEAST 1-222  
B | Serine palmitoyltransferase 1 | LCB1_YEAST -21-558  
C | Serine palmitoyltransferase 2 | LCB2_YEAST 1-561  
D | Serine palmitoyltransferase-regulating protein TSC3 | TSC3_YEAST 1-80  
  
Non-standard residues in 8c80 #17  
---  
ERG — ergosterol  
PLP — pyridoxal-5'-phosphate (VITAMIN B6 Phosphate)  
Q7G — 2-{[(4-O-alpha-D-glucopyranosyl-alpha-D-
glucopyranosyl)oxy]methyl}-4-{[(3beta,9beta,14beta,17beta,25R)-spirost-5-en-3-yl]oxy}butyl
4-O-alpha-D-glucopyranosyl-alpha-D-glucopyranoside  
Z8A — N-[(2S,3S,4R)-1,3,4-trihydroxyoctadecan-2-yl]hexacosanamide  
  

> volume #16 step 1

> volume #16 level 0.1235

> hide #!16 models

Drag select of 27 residues  

> select clear

> show #!16 models

> surface #17 resolution 3.5

4 Gaussian surfaces, threshold level 0.428 - 0.430  

> hide #!16 models

> show #!16 models

> open emdb:16469

Summary of feedback from opening 16469 fetched from emdb  
---  
notes | Fetching compressed map 16469 from ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-16469/map/emd_16469.map.gz  
Fetching map header 16469 from
ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-16469/header/emd-16469.xml  
  
Opened emdb 16469 as #18, grid size 432,432,432, pixel 0.924, shown at level
0.13, step 2, values float32, fit PDB 8c82  

> hide #!16 models

> hide #!17 models

> volume #18 step 1

> volume #18 level 0.1214

> open emdb:16468

Summary of feedback from opening 16468 fetched from emdb  
---  
notes | Fetching compressed map 16468 from ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-16468/map/emd_16468.map.gz  
Fetching map header 16468 from
ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-16468/header/emd-16468.xml  
  
Opened emdb 16468 as #19, grid size 432,432,432, pixel 0.924, shown at level
0.14, step 2, values float32, fit PDB 8c81  

> volume #18 level 0.08701

> hide #!18 models

> volume #19 step 1

> volume #19 level 0.1652

> ui tool show ""Map Filter""

> volume gaussian #19 sDev 0.7

Opened emdb 16468 gaussian as #20, grid size 432,432,432, pixel 0.924, shown
at step 1, values float32  

> volume #20 level 0.08351

> volume gaussian #19 sDev 3.88 modelId #20

Opened emdb 16468 gaussian as #20, grid size 432,432,432, pixel 0.924, shown
at step 1, values float32  

> volume gaussian #19 sDev 3.88 modelId #20

Opened emdb 16468 gaussian as #20, grid size 432,432,432, pixel 0.924, shown
at step 1, values float32  

> volume #20 level 0.03785

> volume gaussian #18 sDev 3.88

Opened emdb 16469 gaussian as #21, grid size 432,432,432, pixel 0.924, shown
at step 1, values float32  

> volume #21 level 0.04255

> open emdb:14760

Summary of feedback from opening 14760 fetched from emdb  
---  
notes | Fetching compressed map 14760 from ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-14760/map/emd_14760.map.gz  
Fetching map header 14760 from
ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-14760/header/emd-14760.xml  
  
Opened emdb 14760 as #22, grid size 400,400,400, pixel 0.573, shown at level
0.09, step 2, values float32, fit PDB 7zka  

> hide #!21 models

> view #22 clip false

> volume gaussian #22 sDev 3.88

Opened emdb 14760 gaussian as #23, grid size 400,400,400, pixel 0.573, shown
at step 1, values float32  

> volume #23 level 0.02262

> hide #!23 models

> show #!22 models

> hide #!22 models

> show #!21 models

> lighting soft

> lighting full

> hide #!21 models

> open /Users/arne/Downloads/cryosparc_P46_J2120_003_volume_map_sharp.mrc

Opened cryosparc_P46_J2120_003_volume_map_sharp.mrc as #24, grid size
672,672,672, pixel 0.68, shown at step 1, values float32  

> volume #24 region 0,0,0,671,671,671 step 4

> volume #24 change image level -0.01109,0 level 0.02893,0.8 level 0.4332,1

> volume #24 level 0.04809

> volume #24 step 1

> view #24 clip false

> volume #24 level 0.07671

> open /Users/arne/Downloads/cryosparc_P46_J2120_003_volume_map.mrc

Opened cryosparc_P46_J2120_003_volume_map.mrc as #25, grid size 672,672,672,
pixel 0.68, shown at step 1, values float32  

> volume #25 region 0,0,0,671,671,671 step 4

> volume #25 step 1

> volume #25 change image level -0.003069,0 level 0.02136,0.8 level 0.1826,1

> volume #25 level 0.01264

> volume #25 level 0.03001

> show #!1 models

> select add #1

9438 atoms, 9707 bonds, 5 pseudobonds, 1156 residues, 2 models selected  

> ui mousemode right ""translate selected models""

> view matrix models
> #1,-0.82203,-0.56938,-0.0079789,523.09,0.56837,-0.82126,0.049843,213.41,-0.034932,0.036438,0.99873,41.191

> view matrix models
> #1,-0.82203,-0.56938,-0.0079789,512.27,0.56837,-0.82126,0.049843,259.21,-0.034932,0.036438,0.99873,36.708

> view matrix models
> #1,-0.82203,-0.56938,-0.0079789,505.71,0.56837,-0.82126,0.049843,287.07,-0.034932,0.036438,0.99873,44.33

> ui mousemode right ""rotate selected models""

> view matrix models
> #1,-0.81357,-0.58005,-0.040612,511.67,0.55921,-0.76136,-0.32804,342.21,0.15936,-0.2896,0.94379,77.61

> view matrix models
> #1,0.94373,0.24841,-0.21832,111.23,-0.29827,0.92448,-0.23743,179.49,0.14285,0.28919,0.94655,-19.208

> ui mousemode right ""translate selected models""

> view matrix models
> #1,0.94373,0.24841,-0.21832,103.23,-0.29827,0.92448,-0.23743,154.13,0.14285,0.28919,0.94655,-21.969

> view matrix models
> #1,0.94373,0.24841,-0.21832,74.869,-0.29827,0.92448,-0.23743,167.23,0.14285,0.28919,0.94655,-7.7555

> ui mousemode right ""rotate selected models""

> view matrix models
> #1,0.92186,0.28313,-0.26459,80.358,-0.23841,0.95265,0.18873,80.383,0.3055,-0.1109,0.94571,34.148

> ui mousemode right ""translate selected models""

> view matrix models
> #1,0.92186,0.28313,-0.26459,82.049,-0.23841,0.95265,0.18873,75.778,0.3055,-0.1109,0.94571,21.537

> view matrix models
> #1,0.92186,0.28313,-0.26459,82.374,-0.23841,0.95265,0.18873,74.642,0.3055,-0.1109,0.94571,19.407

> view matrix models
> #1,0.92186,0.28313,-0.26459,82.049,-0.23841,0.95265,0.18873,76.558,0.3055,-0.1109,0.94571,20.636

> ui mousemode right ""rotate selected models""

> view matrix models
> #1,0.92881,0.27088,-0.25286,81.017,-0.26337,0.96259,0.063739,100.13,0.26066,0.0073941,0.9654,4.4155

> ui mousemode right ""translate selected models""

> view matrix models
> #1,0.92881,0.27088,-0.25286,81.423,-0.26337,0.96259,0.063739,96.824,0.26066,0.0073941,0.9654,3.9273

> view matrix models
> #1,0.92881,0.27088,-0.25286,68.366,-0.26337,0.96259,0.063739,94.303,0.26066,0.0073941,0.9654,5.1192

> view matrix models
> #1,0.92881,0.27088,-0.25286,68.101,-0.26337,0.96259,0.063739,94.337,0.26066,0.0073941,0.9654,6.0277

> view matrix models
> #1,0.92881,0.27088,-0.25286,67.503,-0.26337,0.96259,0.063739,95.548,0.26066,0.0073941,0.9654,11.392

> flip #25

Unknown command: flip #25  

> volume flip #25

Opened cryosparc_P46_J2120_003_volume_map.mrc z flip as #26, grid size
672,672,672, pixel 0.68, shown at step 1, values float32  

> view matrix models
> #1,0.92881,0.27088,-0.25286,62.72,-0.26337,0.96259,0.063739,134.84,0.26066,0.0073941,0.9654,11.691

> view matrix models
> #1,0.92881,0.27088,-0.25286,57.543,-0.26337,0.96259,0.063739,147.26,0.26066,0.0073941,0.9654,28.501

> view matrix models
> #1,0.92881,0.27088,-0.25286,58.389,-0.26337,0.96259,0.063739,145.79,0.26066,0.0073941,0.9654,25.027

> ui mousemode right ""rotate selected models""

> view matrix models
> #1,0.90363,0.31275,-0.29265,62.121,-0.22165,0.9261,0.30529,104.19,0.36651,-0.211,0.90617,55.012

> view matrix models
> #1,0.9154,0.29275,-0.27629,60.846,-0.24374,0.94934,0.19835,121.94,0.32036,-0.11422,0.94038,40.217

> view matrix models
> #1,0.91189,0.29864,-0.28154,61.303,-0.2376,0.94345,0.23119,116.37,0.33466,-0.14393,0.93128,44.493

> view matrix models
> #1,0.91522,0.29306,-0.27657,60.872,-0.24343,0.94906,0.20007,121.64,0.32112,-0.11578,0.93994,40.435

> view matrix models
> #1,0.90965,0.30244,-0.28473,61.562,-0.23346,0.9392,0.25178,112.93,0.34357,-0.16256,0.92495,47.289

> view matrix models
> #1,0.9211,0.28333,-0.26702,59.955,-0.25288,0.95687,0.14298,131.52,0.29602,-0.064177,0.95302,33.508

> view matrix models
> #1,0.89926,0.32032,-0.29786,62.454,-0.21247,0.91512,0.34267,98.095,0.38234,-0.24486,0.89099,60.772

> view matrix models
> #1,0.88065,0.31619,-0.35281,75.534,-0.2253,0.93461,0.27522,108.29,0.41676,-0.16288,0.8943,40.478

> view matrix models
> #1,-0.94094,-0.29432,-0.16735,447.41,0.30664,-0.95037,-0.052675,398.58,-0.14354,-0.10088,0.98449,106.64

> view matrix models
> #1,-0.8619,-0.45237,-0.22912,471.94,0.46812,-0.88351,-0.016583,354.6,-0.19493,-0.12155,0.97326,120.49

> view matrix models
> #1,-0.86536,-0.47871,-0.14828,463.39,0.47065,-0.87795,0.087661,335.66,-0.17215,0.006071,0.98505,92.933

> dssp

Computing secondary structure  

> ui mousemode right ""translate selected models""

> view matrix models
> #1,-0.86536,-0.47871,-0.14828,449.57,0.47065,-0.87795,0.087661,316.02,-0.17215,0.006071,0.98505,84.857

> view matrix models
> #1,-0.86536,-0.47871,-0.14828,452.05,0.47065,-0.87795,0.087661,290.14,-0.17215,0.006071,0.98505,80.117

> view matrix models
> #1,-0.86536,-0.47871,-0.14828,452.47,0.47065,-0.87795,0.087661,284,-0.17215,0.006071,0.98505,81.768

> view matrix models
> #1,-0.86536,-0.47871,-0.14828,473.39,0.47065,-0.87795,0.087661,285.57,-0.17215,0.006071,0.98505,89.475

> view matrix models
> #1,-0.86536,-0.47871,-0.14828,471.03,0.47065,-0.87795,0.087661,243.46,-0.17215,0.006071,0.98505,88.498

> view matrix models
> #1,-0.86536,-0.47871,-0.14828,476.71,0.47065,-0.87795,0.087661,216.77,-0.17215,0.006071,0.98505,92.721

> view matrix models
> #1,-0.86536,-0.47871,-0.14828,476.94,0.47065,-0.87795,0.087661,215.64,-0.17215,0.006071,0.98505,93.001

> ui mousemode right ""rotate selected models""

> view matrix models
> #1,-0.85418,-0.49118,-0.17064,481.01,0.45962,-0.86667,0.19397,197.59,-0.24317,0.087258,0.96605,93.952

> view matrix models
> #1,-0.87553,-0.46743,-0.12227,472.29,0.47383,-0.88017,-0.028108,235.04,-0.094478,-0.082544,0.9921,94.247

> view matrix models
> #1,-0.87539,-0.46759,-0.1227,472.37,0.47385,-0.88021,-0.026247,234.72,-0.095729,-0.081118,0.9921,94.204

> view matrix models
> #1,-0.86899,-0.47467,-0.13978,475.41,0.47273,-0.87985,0.048976,222.14,-0.14623,-0.023517,0.98897,93.14

> ui mousemode right ""translate selected models""

> view matrix models
> #1,-0.86899,-0.47467,-0.13978,459.87,0.47273,-0.87985,0.048976,292.31,-0.14623,-0.023517,0.98897,87.045

> view matrix models
> #1,-0.86899,-0.47467,-0.13978,472.64,0.47273,-0.87985,0.048976,288.71,-0.14623,-0.023517,0.98897,88.675

> view matrix models
> #1,-0.86899,-0.47467,-0.13978,470.24,0.47273,-0.87985,0.048976,289.36,-0.14623,-0.023517,0.98897,89.058

> hide #!1 models

> show #!4 models

> mmaker #4 to #1

Computing secondary structure  
Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker ABCA2_open_prestate.pdb, chain A (#1) with
ABCA2_prestate_AFassembly_KP.pdb, chain A (#4), sequence alignment score =
6855.8  
RMSD between 1083 pruned atom pairs is 0.419 angstroms; (across all 1133
pairs: 4.315)  
  

> select clear

> hide #4,26 target a

> select add #4

16648 atoms, 17044 bonds, 6 pseudobonds, 2095 residues, 2 models selected  

> view matrix models
> #4,-0.68362,-0.7298,0.0074217,433.3,0.71998,-0.67269,0.17065,250.43,-0.11955,0.12201,0.9853,42.796

> ui mousemode right ""play coordinates""

> ui mousemode right ""rotate selected models""

> view matrix models
> #4,-0.4357,-0.80862,0.39536,340,-0.86323,0.49981,0.070933,322.48,-0.25496,-0.31038,-0.91579,465.89

> view matrix models
> #4,-0.44891,-0.7951,0.4078,337.68,-0.87544,0.48282,-0.02231,343.41,-0.17916,-0.36702,-0.9128,462.83

> view matrix models
> #4,0.93612,0.35133,-0.015556,-41.588,0.35159,-0.934,0.063461,380.2,0.0077672,-0.064877,-0.99786,389.06

> view matrix models
> #4,0.93188,0.36188,-0.025371,-41.16,0.36211,-0.92369,0.12517,366.1,0.021861,-0.12583,-0.99181,396.9

> ui mousemode right ""translate selected models""

> view matrix models
> #4,0.93188,0.36188,-0.025371,-37.581,0.36211,-0.92369,0.12517,306.09,0.021861,-0.12583,-0.99181,421.33

> view matrix models
> #4,0.93188,0.36188,-0.025371,6.8863,0.36211,-0.92369,0.12517,314.04,0.021861,-0.12583,-0.99181,438.05

> view matrix models
> #4,0.93188,0.36188,-0.025371,7.0224,0.36211,-0.92369,0.12517,314.1,0.021861,-0.12583,-0.99181,438.7

> ui mousemode right ""rotate selected models""

> fitmap #4 inMap #26

Fit molecule ABCA2_prestate_AFassembly_KP.pdb (#4) to map
cryosparc_P46_J2120_003_volume_map.mrc z flip (#26) using 16648 atoms  
average map value = 0.02473, steps = 452  
shifted from previous position = 3.96  
rotated from previous position = 10.6 degrees  
atoms outside contour = 11760, contour level = 0.030005  
  
Position of ABCA2_prestate_AFassembly_KP.pdb (#4) relative to
cryosparc_P46_J2120_003_volume_map.mrc z flip (#26) coordinates:  
Matrix rotation and translation  
0.89074781 0.41221908 -0.19142563 35.88726921  
0.44298552 -0.88161985 0.16281973 283.89082033  
-0.10164724 -0.22983010 -0.96790803 477.50196589  
Axis -0.97201087 -0.22224783 0.07616282  
Axis point 0.00000000 163.15274299 225.97441810  
Rotation angle (degrees) 168.34734294  
Shift along axis -61.60903631  
  

> select clear

> open /Users/arne/Downloads/cryosparc_P46_J2121_003_volume_map_sharp.mrc

Opened cryosparc_P46_J2121_003_volume_map_sharp.mrc as #27, grid size
672,672,672, pixel 0.68, shown at step 1, values float32  

> open /Users/arne/Downloads/cryosparc_P46_J2121_003_volume_map.mrc

Opened cryosparc_P46_J2121_003_volume_map.mrc as #28, grid size 672,672,672,
pixel 0.68, shown at step 1, values float32  

> volume #28 region 0,0,0,671,671,671 step 4

> volume flip #28

Opened cryosparc_P46_J2121_003_volume_map.mrc z flip as #29, grid size
672,672,672, pixel 0.68, shown at step 1, values float32  

> volume #29 level 0.01634

> volume #29 level 0.02319

> volume #29 level 0.0289

> hide #!26 models

> show #!26 models

> hide #!4 models

> hide #!26 models

> show #!26 models

> hide #!26 models

> show #!26 models

> hide #!26 models

> show #!26 models

> hide #!26 models

> show #!26 models

> hide #!26 models

> show #!26 models

> hide #!26 models

> show #!26 models

> hide #!26 models

> show #!26 models

> fitmap #26 inMap #29

Fit map cryosparc_P46_J2120_003_volume_map.mrc z flip in map
cryosparc_P46_J2121_003_volume_map.mrc z flip using 287241 points  
correlation = 0.9901, correlation about mean = 0.9591, overlap = 1367  
steps = 64, shift = 0.205, angle = 0.577 degrees  
  
Position of cryosparc_P46_J2120_003_volume_map.mrc z flip (#26) relative to
cryosparc_P46_J2121_003_volume_map.mrc z flip (#29) coordinates:  
Matrix rotation and translation  
0.99994993 0.01000697 0.00001786 -2.37470843  
-0.01000694 0.99994932 -0.00109989 2.54041689  
-0.00002886 0.00109966 0.99999939 -0.42763578  
Axis 0.10924314 0.00232040 -0.99401235  
Axis point 252.60806599 240.44220571 0.00000000  
Rotation angle (degrees) 0.57681976  
Shift along axis 0.17154943  
  

> hide #!26 models

> hide #!29 models

> open /Users/arne/Downloads/cryosparc_P79_J621_012_volume_map_sharp.mrc

Opened cryosparc_P79_J621_012_volume_map_sharp.mrc as #30, grid size
384,384,384, pixel 0.68, shown at level 0.0269, step 2, values float32  

> view #30 clip false

> volume #30 level 0.0425

> volume #30 step 1

> volume #30 level 0.06063

> volume #30 level 0.0969

> hide #!30 models

> open 1PYK

Summary of feedback from opening 1PYK fetched from pdb  
---  
note | Fetching compressed mmCIF 1pyk from http://files.rcsb.org/download/1pyk.cif  
  
1pyk title:  
Crystal structure of cat muscle pyruvate kinase At A resolution of 2.6
angstroms [more info...]  
  
Chain information for 1pyk #31  
---  
Chain | Description  
A | PYRUVATE KINASE  
  
1pyk mmCIF Assemblies  
---  
1| author_defined_assembly  
  

> view #31 clip false

> open /Users/arne/Downloads/1pyk.pdb1.gz

1pyk.pdb1.gz title:  
Crystal structure of cat muscle pyruvate kinase At A resolution of 2.6
angstroms [more info...]  
  
Chain information for 1pyk.pdb1.gz  
---  
Chain | Description  
32.1/A 32.2/A 32.3/A 32.4/A | No description available  
  

> hide #!31 models

> view #32 clip false

> hide #!32 models

> show #!26 models

> view #26 clip false

> show #!29 models

> hide #!26 models

> hide #!29 models

> show #!27 models

> hide #!27 models

> show #!24 models

> hide #!24 models

> show #!25 models

> hide #!25 models

> show #!26 models

> show #!4 models

> hide #!4 models

> hide #!26 models

> show #!26 models

> show #!32 models

> show #!25 models

> hide #!26 models

> show #!24 models

> hide #!25 models

> hide #!24 models

> view #32 clip false

> surface #32.1 resolution 4

1 Gaussian surfaces, threshold level 0.243  

> surface #32 resolution 4

4 Gaussian surfaces, threshold level 0.243  

> surface #32 resolution 5

4 Gaussian surfaces, threshold level 0.125  

> surface #32 resolution 15

4 Gaussian surfaces, threshold level 0.011  

> hide #32.1.2 models

> hide #32.1.1 models

> hide #!32.1 models

> show #!32.1 models

> show #32.1.1 models

> show #32.1.2 models

> hide #32.1.1 models

> hide #!32.1 models

> show #!32.1 models

> hide #!32 models

> show #!30 models

> view #30 clip false

> hide #!30 models

> show #!28 models

> hide #!28 models

> show #!29 models

> show #!26 models

> view #29 clip false

> hide #!29 models

> show #!29 models

> hide #!29 models

> show #!29 models

> hide #!29 models

> show #!29 models

> hide #!29 models

> show #!29 models

> hide #!29 models

> show #!29 models

> hide #!26 models

> show #!26 models

> hide #!26 models

> show #!26 models

> hide #!26 models

> show #!26 models

> hide #!26 models

> show #!26 models

> show #!4 models

> hide #!4 models

> hide #!29 models

> hide #!26 models

> show #!32 models

> view #32 clip false

> hide #32.1.2 models

> show #32.1.2 models

> surface #32.2 resolution 15

1 Gaussian surfaces, threshold level 0.011  

> surface #32.3 resolution 15

1 Gaussian surfaces, threshold level 0.011  

> surface #32.4 resolution 15

1 Gaussian surfaces, threshold level 0.011  

> hide #!32.1 models

> show #!32.1 models

> hide #!32.2 models

> show #!32.2 models

> hide #32.2.1 models

> hide #!32.2 models

> show #!32.2 models

> hide #32.2.2 models

> hide #!32.2 models

> show #32.2.2 models

> hide #!32.3 models

> hide #32.3.1 models

> show #!32.3 models

> hide #32.3.2 models

> show #32.3.2 models

> hide #!32.3 models

> show #32.3.1 models

> hide #32.3.2 models

> hide #!32.3 models

> hide #32.3.1 models

> show #32.3.2 models

> hide #32.4.1 models

> hide #32.4.2 models

> show #32.4.2 models

> select clear

> hide #!32.1-4 cartoons

> select clear

> hide #!32.4 models

> show #!32.4 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 M1 Ultra
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: Mac Studio
      Model Identifier: Mac13,2
      Model Number: Z14K000B9D/A
      Chip: Apple M1 Ultra
      Total Number of Cores: 20 (16 performance and 4 efficiency)
      Memory: 128 GB
      System Firmware Version: 11881.81.4
      OS Loader Version: 11881.81.4

Software:

    System Software Overview:

      System Version: macOS 15.3.2 (24D81)
      Kernel Version: Darwin 24.3.0
      Time since boot: 84 days, 2 hours, 9 minutes

Graphics/Displays:

    Apple M1 Ultra:

      Chipset Model: Apple M1 Ultra
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 64
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        EV2785:
          Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition)
          UI Looks like: 1920 x 1080 @ 60.00Hz
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Rotation: Supported
        EV2785:
          Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition)
          UI Looks like: 1920 x 1080 @ 60.00Hz
          Mirror: Off
          Online: Yes
          Rotation: Supported
        EV2785:
          Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition)
          UI Looks like: 1920 x 1080 @ 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	closed	normal		Window Toolkit		duplicate						all	ChimeraX