Opened 3 weeks ago

Closed 3 weeks ago

#18999 closed defect (can't reproduce)

Crash creating sequence viewer for FASTA file

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

Description (last modified by pett)

The following bug report has been submitted:
Platform:        macOS-14.7.7-arm64-arm-64bit
ChimeraX Version: 1.10.1 (2025-07-24 20:15:27 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault

Current thread 0x00000002008c0f80 (most recent call first):
  File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seq_view/seq_canvas.py", line 2297 in _layout_line
  File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seq_view/seq_canvas.py", line 2348 in layout_lines
  File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seq_view/seq_canvas.py", line 1652 in __init__
  File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seq_view/seq_canvas.py", line 1657 in __init__
  File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seq_view/seq_canvas.py", line 1657 in __init__
  File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seq_view/seq_canvas.py", line 1657 in __init__
  File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seq_view/seq_canvas.py", line 1657 in __init__
  File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seq_view/seq_canvas.py", line 1657 in __init__
  File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seq_view/seq_canvas.py", line 1657 in __init__
  File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seq_view/seq_canvas.py", line 1657 in __init__
  File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seq_view/seq_canvas.py", line 1657 in __init__
  File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seq_view/seq_canvas.py", line 1657 in __init__
  File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seq_view/seq_canvas.py", line 1657 in __init__
  File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seq_view/seq_canvas.py", line 1657 in __init__
  File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seq_view/seq_canvas.py", line 1657 in __init__
  File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seq_view/seq_canvas.py", line 1657 in __init__
  File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seq_view/seq_canvas.py", line 1657 in __init__
  File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seq_view/seq_canvas.py", line 1657 in __init__
  File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seq_view/seq_canvas.py", line 1657 in __init__
  File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seq_view/seq_canvas.py", line 1657 in __init__
  File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seq_view/seq_canvas.py", line 1657 in __init__
  File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seq_view/seq_canvas.py", line 1657 in __init__
  File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seq_view/seq_canvas.py", line 1657 in __init__
  File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seq_view/seq_canvas.py", line 1657 in __init__
  File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seq_view/seq_canvas.py", line 1657 in __init__
  File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seq_view/seq_canvas.py", line 1657 in __init__
  File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seq_view/seq_canvas.py", line 1657 in __init__
  File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seq_view/seq_canvas.py", line 1657 in __init__
  File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seq_view/seq_canvas.py", line 1657 in __init__
  File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seq_view/seq_canvas.py", line 1657 in __init__
  File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seq_view/seq_canvas.py", line 1657 in __init__
  File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seq_view/seq_canvas.py", line 1657 in __init__
  File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seq_view/seq_canvas.py", line 1657 in __init__
  File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seq_view/seq_canvas.py", line 1657 in __init__
  File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seq_view/seq_canvas.py", line 1657 in __init__
  File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seq_view/seq_canvas.py", line 1657 in __init__
  File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seq_view/seq_canvas.py", line 1657 in __init__
  File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seq_view/seq_canvas.py", line 1657 in __init__
  File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seq_view/seq_canvas.py", line 1657 in __init__
  File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seq_view/seq_canvas.py", line 1657 in __init__
  File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seq_view/seq_canvas.py", line 1657 in __init__
  File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seq_view/seq_canvas.py", line 1657 in __init__
  File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seq_view/seq_canvas.py", line 1657 in __init__
  File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seq_view/seq_canvas.py", line 1657 in __init__
  File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seq_view/seq_canvas.py", line 1657 in __init__
  File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seq_view/seq_canvas.py", line 1657 in __init__
  File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seq_view/seq_canvas.py", line 1657 in __init__
  File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seq_view/seq_canvas.py", line 1657 in __init__
  File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seq_view/seq_canvas.py", line 1657 in __init__
  File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seq_view/seq_canvas.py", line 1657 in __init__
  File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seq_view/seq_canvas.py", line 1657 in __init__
  File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seq_view/seq_canvas.py", line 1657 in __init__
  File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seq_view/seq_canvas.py", line 1657 in __init__
  File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seq_view/seq_canvas.py", line 1657 in __init__
  File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seq_view/seq_canvas.py", line 1657 in __init__
  File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seq_view/seq_canvas.py", line 1657 in __init__
  File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seq_view/seq_canvas.py", line 1657 in __init__
  File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seq_view/seq_canvas.py", line 1657 in __init__
  File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seq_view/seq_canvas.py", line 1657 in __init__
  File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seq_view/seq_canvas.py", line 1657 in __init__
  File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seq_view/seq_canvas.py", line 1657 in __init__
  File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seq_view/seq_canvas.py", line 1657 in __init__
  File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seq_view/seq_canvas.py", line 1657 in __init__
  File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seq_view/seq_canvas.py", line 1657 in __init__
  File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seq_view/seq_canvas.py", line 1657 in __init__
  File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seq_view/seq_canvas.py", line 1657 in __init__
  File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seq_view/seq_canvas.py", line 1657 in __init__
  File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seq_view/seq_canvas.py", line 1657 in __init__
  File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seq_view/seq_canvas.py", line 1657 in __init__
  File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seq_view/seq_canvas.py", line 1657 in __init__
  File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seq_view/seq_canvas.py", line 1657 in __init__
  File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seq_view/seq_canvas.py", line 1657 in __init__
  File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seq_view/seq_canvas.py", line 1657 in __init__
  File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seq_view/seq_canvas.py", line 1657 in __init__
  File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seq_view/seq_canvas.py", line 1657 in __init__
  File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seq_view/seq_canvas.py", line 1657 in __init__
  File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seq_view/seq_canvas.py", line 1657 in __init__
  File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seq_view/seq_canvas.py", line 1657 in __init__
  File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seq_view/seq_canvas.py", line 1657 in __init__
  File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seq_view/seq_canvas.py", line 1657 in __init__
  File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seq_view/seq_canvas.py", line 1657 in __init__
  File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seq_view/seq_canvas.py", line 1657 in __init__
  File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seq_view/seq_canvas.py", line 1657 in __init__
  File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seq_view/seq_canvas.py", line 1657 in __init__
  File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seq_view/seq_canvas.py", line 1657 in __init__
  File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seq_view/seq_canvas.py", line 1657 in __init__
  File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seq_view/seq_canvas.py", line 1657 in __init__
  File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seq_view/seq_canvas.py", line 1657 in __init__
  File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seq_view/seq_canvas.py", line 1657 in __init__
  File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seq_view/seq_canvas.py", line 1657 in __init__
  File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seq_view/seq_canvas.py", line 1657 in __init__
  File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seq_view/seq_canvas.py", line 1657 in __init__
  File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seq_view/seq_canvas.py", line 1657 in __init__
  File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seq_view/seq_canvas.py", line 1657 in __init__
  File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seq_view/seq_canvas.py", line 1657 in __init__
  File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seq_view/seq_canvas.py", line 1657 in __init__
  File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seq_view/seq_canvas.py", line 1657 in __init__
  File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seq_view/seq_canvas.py", line 1657 in __init__
  File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seq_view/seq_canvas.py", line 1657 in __init__
  File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seq_view/seq_canvas.py", line 1657 in __init__
  ...

Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, psutil._psutil_osx, psutil._psutil_posix, chimerax.surface._surface, chimerax.pdb_lib._load_libs, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, PIL._imaging, PIL._imagingmath, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.pdb._pdbio (total: 48)


{"app_name":"ChimeraX","timestamp":"2025-09-30 12:37:30.00 +0100","app_version":"1.10.1","slice_uuid":"9cf8124a-d876-34ad-b7ee-c011183ebc15","build_version":"1.10.1.0","platform":1,"bundleID":"edu.ucsf.cgl.ChimeraX","share_with_app_devs":0,"is_first_party":0,"bug_type":"309","os_version":"macOS 14.7.7 (23H723)","roots_installed":0,"name":"ChimeraX","incident_id":"9663BF96-B568-468E-8DA7-2A77260CDC9A"}
{
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  "captureTime" : "2025-09-30 12:37:05.8714 +0100",
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  "pid" : 20276,
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  "cpuType" : "ARM-64",
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  "procLaunch" : "2025-09-29 13:28:28.6722 +0100",
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===== Log before crash start =====
UCSF ChimeraX version: 1.10.1 (2025-07-24)  
© 2016-2025 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/lue81154/Downloads/cryosparc_P1_J293_002_volume_map_sharp.mrc

Opened cryosparc_P1_J293_002_volume_map_sharp.mrc as #1, grid size
256,256,256, pixel 0.825, shown at level 0.129, step 1, values float32  

> surface dust #1 size 8.25

> volume #1 level 0.04414

> surface dust #1 size 8.25

> set bgColor white

> volume #1 color #5249e0

> volume #1 color #ff7e79

> volume #1 color #7a81ff

> volume #1 color #93f79e

> volume #1 color #91999f

> lighting flat

> lighting full

> lighting soft

> volume #1 color #7a9f77

> volume #1 color #8cb688

> volume #1 level 0.02799

> surface dust #1 size 8.25

> volume #1 level 0.2258

> volume #1 level 0.1281

> volume #1 level 0.05658

> surface dust #1 size 8.25

Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps,
got 0 atomic models, 1 maps.  

> open "/Users/lue81154/Library/CloudStorage/OneDrive-
> DiamondLightSourceLtd/-DATA-EXPERIMENTS/Part II - SatBC-
> MsmK/fold_satbc_msmk/fold_satbc_msmk_model_0.cif"

Chain information for fold_satbc_msmk_model_0.cif #2  
---  
Chain | Description  
A B | .  
C | .  
D | .  
  
Computing secondary structure  

> fitmap #2 inMap #1

Fit molecule fold_satbc_msmk_model_0.cif (#2) to map
cryosparc_P1_J293_002_volume_map_sharp.mrc (#1) using 11098 atoms  
average map value = 4.975e-05, steps = 2000  
shifted from previous position = 5.47  
rotated from previous position = 6.78 degrees  
atoms outside contour = 11098, contour level = 0.056583  
  
Position of fold_satbc_msmk_model_0.cif (#2) relative to
cryosparc_P1_J293_002_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.99302503 0.04562548 -0.10871796 1.52316334  
-0.04613111 0.99893310 -0.00213899 -0.01219094  
0.10850438 0.00713935 0.99407033 -4.96204129  
Axis 0.03931678 -0.92047576 -0.38881688  
Axis point 39.15170121 0.00000000 10.77495349  
Rotation angle (degrees) 6.77637961  
Shift along axis 2.00043278  
  

> fitmap #2 inMap #1

Fit molecule fold_satbc_msmk_model_0.cif (#2) to map
cryosparc_P1_J293_002_volume_map_sharp.mrc (#1) using 11098 atoms  
average map value = 6.177e-05, steps = 2000  
shifted from previous position = 2.38  
rotated from previous position = 6.22 degrees  
atoms outside contour = 11098, contour level = 0.056583  
  
Position of fold_satbc_msmk_model_0.cif (#2) relative to
cryosparc_P1_J293_002_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.98453975 0.05470475 -0.16639973 2.60570171  
-0.04027753 0.99522804 0.08887556 -1.90477708  
0.17046760 -0.08079935 0.98204494 -4.00582795  
Axis -0.43622582 -0.86606925 -0.24419476  
Axis point 23.19703237 0.00000000 17.41329869  
Rotation angle (degrees) 11.21438317  
Shift along axis 1.49119668  
  

> fitmap #2 inMap #1

Fit molecule fold_satbc_msmk_model_0.cif (#2) to map
cryosparc_P1_J293_002_volume_map_sharp.mrc (#1) using 11098 atoms  
average map value = 6.224e-05, steps = 872  
shifted from previous position = 0.321  
rotated from previous position = 0.295 degrees  
atoms outside contour = 11098, contour level = 0.056583  
  
Position of fold_satbc_msmk_model_0.cif (#2) relative to
cryosparc_P1_J293_002_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.98488529 0.05827305 -0.16311105 2.43057972  
-0.04432879 0.99514575 0.08786287 -1.70544267  
0.16743930 -0.07930434 0.98268759 -3.84834079  
Axis -0.43491921 -0.85999339 -0.26693940  
Axis point 22.41492126 0.00000000 16.65548097  
Rotation angle (degrees) 11.08014550  
Shift along axis 1.43683738  
  

> fitmap #2 inMap #1

Fit molecule fold_satbc_msmk_model_0.cif (#2) to map
cryosparc_P1_J293_002_volume_map_sharp.mrc (#1) using 11098 atoms  
average map value = 6.039e-05, steps = 2000  
shifted from previous position = 0.739  
rotated from previous position = 0.655 degrees  
atoms outside contour = 11098, contour level = 0.056583  
  
Position of fold_satbc_msmk_model_0.cif (#2) relative to
cryosparc_P1_J293_002_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.98659771 0.05683128 -0.15295479 1.91589777  
-0.04297338 0.99479130 0.09243138 -1.98792582  
0.15741109 -0.08461961 0.98390105 -3.43738878  
Axis -0.47723679 -0.83658395 -0.26902110  
Axis point 20.60741837 0.00000000 15.94162423  
Rotation angle (degrees) 10.69004922  
Shift along axis 1.67346002  
  

> fitmap #2 inMap #1

Fit molecule fold_satbc_msmk_model_0.cif (#2) to map
cryosparc_P1_J293_002_volume_map_sharp.mrc (#1) using 11098 atoms  
average map value = 6.063e-05, steps = 2000  
shifted from previous position = 0.997  
rotated from previous position = 0.96 degrees  
atoms outside contour = 11098, contour level = 0.056583  
  
Position of fold_satbc_msmk_model_0.cif (#2) relative to
cryosparc_P1_J293_002_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.98451929 0.05725520 -0.16566115 2.41458466  
-0.04413743 0.99566994 0.08181235 -1.55752934  
0.16962801 -0.07323398 0.98278335 -4.14179098  
Axis -0.40475220 -0.87528051 -0.26468792  
Axis point 23.72589514 0.00000000 15.97981300  
Rotation angle (degrees) 11.04222732  
Shift along axis 1.48224864  
  

> fitmap #2 inMap #1

Fit molecule fold_satbc_msmk_model_0.cif (#2) to map
cryosparc_P1_J293_002_volume_map_sharp.mrc (#1) using 11098 atoms  
average map value = 6.238e-05, steps = 500  
shifted from previous position = 0.33  
rotated from previous position = 0.372 degrees  
atoms outside contour = 11098, contour level = 0.056583  
  
Position of fold_satbc_msmk_model_0.cif (#2) relative to
cryosparc_P1_J293_002_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.98495493 0.05847519 -0.16261744 2.41080790  
-0.04462826 0.99516090 0.08753920 -1.69835768  
0.16694939 -0.07896483 0.98279828 -3.85217705  
Axis -0.43432321 -0.85967005 -0.26894377  
Axis point 22.45194350 0.00000000 16.61778061  
Rotation angle (degrees) 11.05096972  
Shift along axis 1.44897644  
  

> fitmap #2 inMap #1

Fit molecule fold_satbc_msmk_model_0.cif (#2) to map
cryosparc_P1_J293_002_volume_map_sharp.mrc (#1) using 11098 atoms  
average map value = 6.1e-05, steps = 2000  
shifted from previous position = 0.0994  
rotated from previous position = 0.194 degrees  
atoms outside contour = 11098, contour level = 0.056583  
  
Position of fold_satbc_msmk_model_0.cif (#2) relative to
cryosparc_P1_J293_002_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.98527448 0.05589453 -0.16158588 2.48814393  
-0.04185789 0.99515123 0.08900535 -1.74740667  
0.16577730 -0.08093105 0.98283674 -3.82943659  
Axis -0.44535350 -0.85792298 -0.25618045  
Axis point 22.75067453 0.00000000 17.10657923  
Rotation angle (degrees) 10.99878708  
Shift along axis 1.37206351  
  

> fitmap #2 inMap #1

Fit molecule fold_satbc_msmk_model_0.cif (#2) to map
cryosparc_P1_J293_002_volume_map_sharp.mrc (#1) using 11098 atoms  
average map value = 5.977e-05, steps = 2000  
shifted from previous position = 0.174  
rotated from previous position = 0.484 degrees  
atoms outside contour = 11098, contour level = 0.056583  
  
Position of fold_satbc_msmk_model_0.cif (#2) relative to
cryosparc_P1_J293_002_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.98433654 0.05369553 -0.16792368 2.59331881  
-0.04005117 0.99569319 0.08361208 -1.60841353  
0.17169006 -0.07557688 0.98224776 -3.80223730  
Axis -0.41175625 -0.87844082 -0.24248407  
Axis point 22.06169163 0.00000000 16.49247704  
Rotation angle (degrees) 11.14571471  
Shift along axis 1.26706285  
  

> fitmap #2 inMap #1

Fit molecule fold_satbc_msmk_model_0.cif (#2) to map
cryosparc_P1_J293_002_volume_map_sharp.mrc (#1) using 11098 atoms  
average map value = 6.12e-05, steps = 2000  
shifted from previous position = 0.404  
rotated from previous position = 0.384 degrees  
atoms outside contour = 11098, contour level = 0.056583  
  
Position of fold_satbc_msmk_model_0.cif (#2) relative to
cryosparc_P1_J293_002_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.98456380 0.05763632 -0.16526399 2.37545344  
-0.04492401 0.99580961 0.07965587 -1.50705225  
0.16916254 -0.07100196 0.98302734 -4.12463264  
Axis -0.39556841 -0.87807299 -0.26928322  
Axis point 23.58389214 0.00000000 15.74766558  
Rotation angle (degrees) 10.97800107  
Shift along axis 1.49434190  
  

> fitmap #2 inMap #1

Fit molecule fold_satbc_msmk_model_0.cif (#2) to map
cryosparc_P1_J293_002_volume_map_sharp.mrc (#1) using 11098 atoms  
average map value = 6.12e-05, steps = 2000  
shifted from previous position = 0.228  
rotated from previous position = 0.432 degrees  
atoms outside contour = 11098, contour level = 0.056583  
  
Position of fold_satbc_msmk_model_0.cif (#2) relative to
cryosparc_P1_J293_002_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.98531643 0.05987235 -0.15989633 2.26636707  
-0.04672524 0.99530559 0.08475576 -1.57529909  
0.16422023 -0.07604005 0.98348850 -3.95163605  
Axis -0.42630286 -0.85929984 -0.28261219  
Axis point 23.08944222 0.00000000 16.06421392  
Rotation angle (degrees) 10.87070809  
Shift along axis 1.50427602  
  

> fitmap #2 inMap #1

Fit molecule fold_satbc_msmk_model_0.cif (#2) to map
cryosparc_P1_J293_002_volume_map_sharp.mrc (#1) using 11098 atoms  
average map value = 6.212e-05, steps = 2000  
shifted from previous position = 0.215  
rotated from previous position = 0.245 degrees  
atoms outside contour = 11098, contour level = 0.056583  
  
Position of fold_satbc_msmk_model_0.cif (#2) relative to
cryosparc_P1_J293_002_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.98516780 0.06289516 -0.15965152 2.08101835  
-0.05020908 0.99534278 0.08229095 -1.47893362  
0.16408369 -0.07305443 0.98373756 -3.96524820  
Axis -0.41263741 -0.85992428 -0.30043403  
Axis point 22.72209833 0.00000000 15.07043993  
Rotation angle (degrees) 10.84978264  
Shift along axis 1.60436040  
  

> fitmap #2 inMap #1

Fit molecule fold_satbc_msmk_model_0.cif (#2) to map
cryosparc_P1_J293_002_volume_map_sharp.mrc (#1) using 11098 atoms  
average map value = 6.224e-05, steps = 372  
shifted from previous position = 0.447  
rotated from previous position = 0.504 degrees  
atoms outside contour = 11098, contour level = 0.056583  
  
Position of fold_satbc_msmk_model_0.cif (#2) relative to
cryosparc_P1_J293_002_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.98487570 0.05822839 -0.16318487 2.43345926  
-0.04426570 0.99514237 0.08793295 -1.70883975  
0.16751237 -0.07937954 0.98266907 -3.84749506  
Axis -0.43511518 -0.86001580 -0.26654756  
Axis point 22.40712271 0.00000000 16.66538286  
Rotation angle (degrees) 11.08483908  
Shift along axis 1.43633455  
  

> fitmap #2 inMap #1

Fit molecule fold_satbc_msmk_model_0.cif (#2) to map
cryosparc_P1_J293_002_volume_map_sharp.mrc (#1) using 11098 atoms  
average map value = 6.003e-05, steps = 2000  
shifted from previous position = 0.392  
rotated from previous position = 0.406 degrees  
atoms outside contour = 11098, contour level = 0.056583  
  
Position of fold_satbc_msmk_model_0.cif (#2) relative to
cryosparc_P1_J293_002_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.98581683 0.05677119 -0.15793100 2.51529865  
-0.04253113 0.99483823 0.09213035 -1.89522981  
0.16234615 -0.08410667 0.98314282 -3.52933818  
Axis -0.46523713 -0.84547973 -0.26214202  
Axis point 21.41705519 0.00000000 18.00171785  
Rotation angle (degrees) 10.91809645  
Shift along axis 1.35735589  
  

> fitmap #2 inMap #1

Fit molecule fold_satbc_msmk_model_0.cif (#2) to map
cryosparc_P1_J293_002_volume_map_sharp.mrc (#1) using 11098 atoms  
average map value = 6.226e-05, steps = 1160  
shifted from previous position = 0.389  
rotated from previous position = 0.403 degrees  
atoms outside contour = 11098, contour level = 0.056583  
  
Position of fold_satbc_msmk_model_0.cif (#2) relative to
cryosparc_P1_J293_002_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.98489937 0.05842320 -0.16297229 2.42714509  
-0.04448713 0.99513626 0.08789038 -1.70049515  
0.16731447 -0.07931301 0.98270815 -3.83710349  
Axis -0.43515873 -0.85959478 -0.26783146  
Axis point 22.35977329 0.00000000 16.64813934  
Rotation angle (degrees) 11.07639730  
Shift along axis 1.43324040  
  

> fitmap #2 inMap #1

Fit molecule fold_satbc_msmk_model_0.cif (#2) to map
cryosparc_P1_J293_002_volume_map_sharp.mrc (#1) using 11098 atoms  
average map value = 6.073e-05, steps = 2000  
shifted from previous position = 0.349  
rotated from previous position = 0.555 degrees  
atoms outside contour = 11098, contour level = 0.056583  
  
Position of fold_satbc_msmk_model_0.cif (#2) relative to
cryosparc_P1_J293_002_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.98591762 0.06186005 -0.15536983 2.14771284  
-0.04924152 0.99526569 0.08379428 -1.53110205  
0.15981778 -0.07496361 0.98429606 -3.94126668  
Axis -0.42908971 -0.85188686 -0.30028455  
Axis point 23.29398875 0.00000000 16.03751858  
Rotation angle (degrees) 10.66077201  
Shift along axis 1.56626572  
  

> fitmap #2 inMap #1

Fit molecule fold_satbc_msmk_model_0.cif (#2) to map
cryosparc_P1_J293_002_volume_map_sharp.mrc (#1) using 11098 atoms  
average map value = 6.25e-05, steps = 2000  
shifted from previous position = 0.19  
rotated from previous position = 0.161 degrees  
atoms outside contour = 11098, contour level = 0.056583  
  
Position of fold_satbc_msmk_model_0.cif (#2) relative to
cryosparc_P1_J293_002_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.98548863 0.06257374 -0.15778685 1.96390432  
-0.04995222 0.99531941 0.08272877 -1.52608331  
0.16222497 -0.07364646 0.98400166 -3.88317571  
Axis -0.41864437 -0.85672872 -0.30125204  
Axis point 22.32156915 0.00000000 14.78498469  
Rotation angle (degrees) 10.76398309  
Shift along axis 1.65507653  
  

> fitmap #2 inMap #1

Fit molecule fold_satbc_msmk_model_0.cif (#2) to map
cryosparc_P1_J293_002_volume_map_sharp.mrc (#1) using 11098 atoms  
average map value = 6.231e-05, steps = 1980  
shifted from previous position = 0.506  
rotated from previous position = 0.516 degrees  
atoms outside contour = 11098, contour level = 0.056583  
  
Position of fold_satbc_msmk_model_0.cif (#2) relative to
cryosparc_P1_J293_002_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.98491014 0.05838088 -0.16292236 2.42304272  
-0.04443505 0.99513163 0.08796910 -1.71233231  
0.16726491 -0.07940220 0.98270939 -3.84461396  
Axis -0.43563844 -0.85942013 -0.26761201  
Axis point 22.39578540 0.00000000 16.66161983  
Rotation angle (degrees) 11.07529730  
Shift along axis 1.44490720  
  

> fitmap #2 inMap #1

Fit molecule fold_satbc_msmk_model_0.cif (#2) to map
cryosparc_P1_J293_002_volume_map_sharp.mrc (#1) using 11098 atoms  
average map value = 6.221e-05, steps = 828  
shifted from previous position = 0.0196  
rotated from previous position = 0.0173 degrees  
atoms outside contour = 11098, contour level = 0.056583  
  
Position of fold_satbc_msmk_model_0.cif (#2) relative to
cryosparc_P1_J293_002_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.98488645 0.05839488 -0.16306050 2.42793825  
-0.04448262 0.99515267 0.08770664 -1.69399693  
0.16739171 -0.07912772 0.98270994 -3.84845241  
Axis -0.43422875 -0.86008570 -0.26776480  
Axis point 22.41573434 0.00000000 16.62870925  
Rotation angle (degrees) 11.07561062  
Shift along axis 1.43318204  
  

> fitmap #2 inMap #1

Fit molecule fold_satbc_msmk_model_0.cif (#2) to map
cryosparc_P1_J293_002_volume_map_sharp.mrc (#1) using 11098 atoms  
average map value = 6.228e-05, steps = 1408  
shifted from previous position = 0.0186  
rotated from previous position = 0.0322 degrees  
atoms outside contour = 11098, contour level = 0.056583  
  
Position of fold_satbc_msmk_model_0.cif (#2) relative to
cryosparc_P1_J293_002_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.98494952 0.05860953 -0.16260186 2.41307180  
-0.04476890 0.99515647 0.08751771 -1.68689768  
0.16694367 -0.07892102 0.98280277 -3.84237201  
Axis -0.43412188 -0.85955308 -0.26964180  
Axis point 22.40334840 0.00000000 16.60721509  
Rotation angle (degrees) 11.05176906  
Shift along axis 1.43847495  
  

> fitmap #2 inMap #1

Fit molecule fold_satbc_msmk_model_0.cif (#2) to map
cryosparc_P1_J293_002_volume_map_sharp.mrc (#1) using 11098 atoms  
average map value = 6.224e-05, steps = 792  
shifted from previous position = 0.0381  
rotated from previous position = 0.0568 degrees  
atoms outside contour = 11098, contour level = 0.056583  
  
Position of fold_satbc_msmk_model_0.cif (#2) relative to
cryosparc_P1_J293_002_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.98486844 0.05818892 -0.16324278 2.43851702  
-0.04420035 0.99513453 0.08805455 -1.71246401  
0.16757232 -0.07950676 0.98264856 -3.84735483  
Axis -0.43555638 -0.85991585 -0.26614915  
Axis point 22.40909379 0.00000000 16.68808419  
Rotation angle (degrees) 11.09014506  
Shift along axis 1.43443353  
  

> fitmap #2 inMap #1

Fit molecule fold_satbc_msmk_model_0.cif (#2) to map
cryosparc_P1_J293_002_volume_map_sharp.mrc (#1) using 11098 atoms  
average map value = 6.154e-05, steps = 2000  
shifted from previous position = 0.349  
rotated from previous position = 0.31 degrees  
atoms outside contour = 11098, contour level = 0.056583  
  
Position of fold_satbc_msmk_model_0.cif (#2) relative to
cryosparc_P1_J293_002_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.98480142 0.05471131 -0.16484182 2.40675128  
-0.04000967 0.99502629 0.09122448 -2.04394925  
0.16901296 -0.08324273 0.98209229 -3.78464540  
Axis -0.44917187 -0.85952065 -0.24386241  
Axis point 21.88071147 0.00000000 16.93920045  
Rotation angle (degrees) 11.19856983  
Shift along axis 1.59870438  
  

> fitmap #2 inMap #1

Fit molecule fold_satbc_msmk_model_0.cif (#2) to map
cryosparc_P1_J293_002_volume_map_sharp.mrc (#1) using 11098 atoms  
average map value = 6.223e-05, steps = 1940  
shifted from previous position = 0.364  
rotated from previous position = 0.336 degrees  
atoms outside contour = 11098, contour level = 0.056583  
  
Position of fold_satbc_msmk_model_0.cif (#2) relative to
cryosparc_P1_J293_002_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.98490009 0.05836762 -0.16298785 2.42384054  
-0.04445897 0.99515268 0.08771852 -1.69764645  
0.16731772 -0.07914770 0.98272093 -3.85133116  
Axis -0.43445405 -0.85998585 -0.26772002  
Axis point 22.43417492 0.00000000 16.62592670  
Rotation angle (degrees) 11.07193484  
Shift along axis 1.43798303  
  

> fitmap #2 inMap #1

Fit molecule fold_satbc_msmk_model_0.cif (#2) to map
cryosparc_P1_J293_002_volume_map_sharp.mrc (#1) using 11098 atoms  
average map value = 6.042e-05, steps = 2000  
shifted from previous position = 0.3  
rotated from previous position = 0.374 degrees  
atoms outside contour = 11098, contour level = 0.056583  
  
Position of fold_satbc_msmk_model_0.cif (#2) relative to
cryosparc_P1_J293_002_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.98531585 0.06191452 -0.15912031 2.25291691  
-0.04888632 0.99522113 0.08452831 -1.48060285  
0.16359342 -0.07550828 0.98363392 -3.77284246  
Axis -0.42464413 -0.85629477 -0.29400107  
Axis point 22.10131782 0.00000000 15.90951618  
Rotation angle (degrees) 10.86153218  
Shift along axis 1.42036425  
  

> transparency 50

> transparency 0

> ui mousemode right select

> select clear

> select /D:274

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

> select up

82 atoms, 82 bonds, 11 residues, 1 model selected  

> select up

2199 atoms, 2261 bonds, 279 residues, 1 model selected  

> select up

11098 atoms, 11364 bonds, 1397 residues, 1 model selected  

> ui mousemode right "translate selected models"

> view matrix models
> #2,0.98532,0.061915,-0.15912,89.871,-0.048886,0.99522,0.084528,69.504,0.16359,-0.075508,0.98363,105.21

> view matrix models
> #2,0.98532,0.061915,-0.15912,113.37,-0.048886,0.99522,0.084528,93.421,0.16359,-0.075508,0.98363,114.31

> ui mousemode right select

> select clear

> fitmap #2 inMap #1

Fit molecule fold_satbc_msmk_model_0.cif (#2) to map
cryosparc_P1_J293_002_volume_map_sharp.mrc (#1) using 11098 atoms  
average map value = 0.03484, steps = 208  
shifted from previous position = 5.86  
rotated from previous position = 10.6 degrees  
atoms outside contour = 7641, contour level = 0.056583  
  
Position of fold_satbc_msmk_model_0.cif (#2) relative to
cryosparc_P1_J293_002_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.97937155 0.06933339 -0.18980053 112.80532812  
-0.08833111 0.99169052 -0.09352826 92.18899772  
0.18173875 0.10836421 0.97735778 120.16103059  
Axis 0.44737028 -0.82328796 -0.34936625  
Axis point -431.89302090 0.00000000 800.17153571  
Rotation angle (degrees) 13.04072584  
Shift along axis -67.41254830  
  

> fitmap #2 inMap #1

Fit molecule fold_satbc_msmk_model_0.cif (#2) to map
cryosparc_P1_J293_002_volume_map_sharp.mrc (#1) using 11098 atoms  
average map value = 0.03484, steps = 64  
shifted from previous position = 0.00155  
rotated from previous position = 0.0042 degrees  
atoms outside contour = 7644, contour level = 0.056583  
  
Position of fold_satbc_msmk_model_0.cif (#2) relative to
cryosparc_P1_J293_002_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.97936601 0.06933179 -0.18982971 112.80488507  
-0.08832052 0.99169767 -0.09346238 92.18986644  
0.18177376 0.10829974 0.97735841 120.16233998  
Axis 0.44709108 -0.82344789 -0.34934673  
Axis point -431.75505163 0.00000000 800.05128098  
Rotation angle (degrees) 13.04044059  
Shift along axis -67.45781466  
  

> fitmap #2 inMap #1

Fit molecule fold_satbc_msmk_model_0.cif (#2) to map
cryosparc_P1_J293_002_volume_map_sharp.mrc (#1) using 11098 atoms  
average map value = 0.03484, steps = 44  
shifted from previous position = 0.0157  
rotated from previous position = 0.0177 degrees  
atoms outside contour = 7643, contour level = 0.056583  
  
Position of fold_satbc_msmk_model_0.cif (#2) relative to
cryosparc_P1_J293_002_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.97938965 0.06939069 -0.18968616 112.81105326  
-0.08841073 0.99166593 -0.09371358 92.17699091  
0.18160246 0.10855240 0.97736223 120.16914907  
Axis 0.44818919 -0.82271646 -0.34966281  
Axis point -432.33462837 0.00000000 800.70071251  
Rotation angle (degrees) 13.04098480  
Shift along axis -67.29351451  
  

> fitmap #2 inMap #1

Fit molecule fold_satbc_msmk_model_0.cif (#2) to map
cryosparc_P1_J293_002_volume_map_sharp.mrc (#1) using 11098 atoms  
average map value = 0.03484, steps = 40  
shifted from previous position = 0.0128  
rotated from previous position = 0.0146 degrees  
atoms outside contour = 7643, contour level = 0.056583  
  
Position of fold_satbc_msmk_model_0.cif (#2) relative to
cryosparc_P1_J293_002_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.97937062 0.06932128 -0.18980975 112.80655664  
-0.08831815 0.99169255 -0.09351892 92.18784590  
0.18175006 0.10835333 0.97735688 120.16377198  
Axis 0.44732638 -0.82333509 -0.34931138  
Axis point -431.89847105 0.00000000 800.13135195  
Rotation angle (degrees) 13.04069946  
Shift along axis -67.41471289  
  

> fitmap #2 inMap #1

Fit molecule fold_satbc_msmk_model_0.cif (#2) to map
cryosparc_P1_J293_002_volume_map_sharp.mrc (#1) using 11098 atoms  
average map value = 0.03484, steps = 100  
shifted from previous position = 0.0124  
rotated from previous position = 0.013 degrees  
atoms outside contour = 7643, contour level = 0.056583  
  
Position of fold_satbc_msmk_model_0.cif (#2) relative to
cryosparc_P1_J293_002_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.97938770 0.06938174 -0.18969953 112.81097495  
-0.08839944 0.99166883 -0.09369354 92.17758102  
0.18161849 0.10853163 0.97736156 120.16949011  
Axis 0.44809994 -0.82278374 -0.34961888  
Axis point -432.29682656 0.00000000 800.64006032  
Rotation angle (degrees) 13.04095007  
Shift along axis -67.30514681  
  

> fitmap #2 inMap #1

Fit molecule fold_satbc_msmk_model_0.cif (#2) to map
cryosparc_P1_J293_002_volume_map_sharp.mrc (#1) using 11098 atoms  
average map value = 0.03484, steps = 40  
shifted from previous position = 0.0134  
rotated from previous position = 0.014 degrees  
atoms outside contour = 7643, contour level = 0.056583  
  
Position of fold_satbc_msmk_model_0.cif (#2) relative to
cryosparc_P1_J293_002_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.97936934 0.06932504 -0.18981502 112.80607418  
-0.08831896 0.99169430 -0.09349964 92.18858762  
0.18175660 0.10833495 0.97735770 120.16341053  
Axis 0.44724841 -0.82337134 -0.34932578  
Axis point -431.85372088 0.00000000 800.11130854  
Rotation angle (degrees) 13.04053684  
Shift along axis -67.42928026  
  

> volume #1 level 0.09233

> select clear

> select #2

11098 atoms, 11364 bonds, 1397 residues, 1 model selected  

> ui mousemode right "translate selected models"

> view matrix models
> #2,0.97937,0.069325,-0.18982,112.04,-0.088319,0.99169,-0.0935,107.68,0.18176,0.10833,0.97736,111.73

> volume #1 level 0.07326

> volume #1 level 0.0542

> view matrix models
> #2,0.97937,0.069325,-0.18982,99.918,-0.088319,0.99169,-0.0935,103.63,0.18176,0.10833,0.97736,124.26

> ui mousemode right select

> select clear

> fitmap #2 inMap #1

Fit molecule fold_satbc_msmk_model_0.cif (#2) to map
cryosparc_P1_J293_002_volume_map_sharp.mrc (#1) using 11098 atoms  
average map value = 0.03674, steps = 340  
shifted from previous position = 14.1  
rotated from previous position = 8.6 degrees  
atoms outside contour = 7486, contour level = 0.0542  
  
Position of fold_satbc_msmk_model_0.cif (#2) relative to
cryosparc_P1_J293_002_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.96331238 0.02941717 -0.26676559 111.02289505  
-0.08949008 0.97229758 -0.21593734 100.96010841  
0.25302327 0.23188799 0.93925885 116.26684344  
Axis 0.64312794 -0.74647573 -0.17076429  
Axis point -319.20522822 0.00000000 517.49881252  
Rotation angle (degrees) 20.37493161  
Shift along axis -23.81656931  
  

> volume #1 level 0.19

> select #2

11098 atoms, 11364 bonds, 1397 residues, 1 model selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #2,0.1466,0.98681,0.068601,107.57,-0.811,0.080195,0.57952,95.636,0.56638,-0.14059,0.81207,117.58

> ui mousemode right "translate selected models"

> view matrix models
> #2,0.1466,0.98681,0.068601,105.39,-0.811,0.080195,0.57952,104.58,0.56638,-0.14059,0.81207,119.66

> ui mousemode right select

> select clear

> fitmap #2 inMap #1

Fit molecule fold_satbc_msmk_model_0.cif (#2) to map
cryosparc_P1_J293_002_volume_map_sharp.mrc (#1) using 11098 atoms  
average map value = 0.04474, steps = 276  
shifted from previous position = 4.33  
rotated from previous position = 15.7 degrees  
atoms outside contour = 9893, contour level = 0.19002  
  
Position of fold_satbc_msmk_model_0.cif (#2) relative to
cryosparc_P1_J293_002_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.04001344 0.99131990 -0.12523491 108.01215903  
-0.83874460 0.03479515 0.54341218 107.12887042  
0.54305287 0.12678389 0.83007194 121.08926906  
Axis -0.20911755 -0.33543259 -0.91856128  
Axis point 65.24582338 -4.69877707 0.00000000  
Rotation angle (degrees) 95.02400898  
Shift along axis -169.74966695  
  
Drag select of 21 residues  

> delete sel

Drag select of 6 residues  
Drag select of 21 residues  

> delete sel

> fitmap #2 inMap #1

Fit molecule fold_satbc_msmk_model_0.cif (#2) to map
cryosparc_P1_J293_002_volume_map_sharp.mrc (#1) using 10704 atoms  
average map value = 0.04627, steps = 84  
shifted from previous position = 0.0736  
rotated from previous position = 0.144 degrees  
atoms outside contour = 9507, contour level = 0.19002  
  
Position of fold_satbc_msmk_model_0.cif (#2) relative to
cryosparc_P1_J293_002_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.04053584 0.99106331 -0.12708408 107.96193853  
-0.83789379 0.03557242 0.54467292 107.18957168  
0.54432604 0.12856173 0.82896384 121.11219110  
Axis -0.20886589 -0.33701250 -0.91804009  
Axis point 65.10837813 -4.77916232 0.00000000  
Rotation angle (degrees) 95.04854692  
Shift along axis -169.85963937  
  

> volume #1 level 0.08518

> surface dust #1 size 8.25

> volume #1 level 0.03514

> surface dust #1 size 8.25

> volume #1 level 0.1066

> transparency 50

> lighting shadows true intensity 0.5

> lighting shadows false

> lighting shadows true

> graphics silhouettes false

> lighting soft

> lighting simple

> volume style surface

> transparency 0

> volume #1 color #c0a1bf

> set color model #2 black

Expected a keyword  

> color model #2 black

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword  

> color bymodel #2 black

Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword  

> fitmap #2 inMap #1

Fit molecule fold_satbc_msmk_model_0.cif (#2) to map
cryosparc_P1_J293_002_volume_map_sharp.mrc (#1) using 10704 atoms  
average map value = 0.04627, steps = 136  
shifted from previous position = 0.00633  
rotated from previous position = 0.00339 degrees  
atoms outside contour = 8074, contour level = 0.10662  
  
Position of fold_satbc_msmk_model_0.cif (#2) relative to
cryosparc_P1_J293_002_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.04051584 0.99106725 -0.12705968 107.96693449  
-0.83786679 0.03558213 0.54471382 107.19256472  
0.54436909 0.12852863 0.82894070 121.11516649  
Axis -0.20890298 -0.33702177 -0.91802825  
Axis point 65.10762210 -4.77817623 0.00000000  
Rotation angle (degrees) 95.04835791  
Shift along axis -169.86798640  
  

> fitmap #2 inMap #1

Fit molecule fold_satbc_msmk_model_0.cif (#2) to map
cryosparc_P1_J293_002_volume_map_sharp.mrc (#1) using 10704 atoms  
average map value = 0.04627, steps = 60  
shifted from previous position = 0.0113  
rotated from previous position = 0.0144 degrees  
atoms outside contour = 8080, contour level = 0.10662  
  
Position of fold_satbc_msmk_model_0.cif (#2) relative to
cryosparc_P1_J293_002_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.04048358 0.99108005 -0.12697017 107.96731452  
-0.83799243 0.03553029 0.54452391 107.18145286  
0.54417807 0.12844432 0.82907918 121.11931011  
Axis -0.20884887 -0.33687918 -0.91809290  
Axis point 65.12036569 -4.77928495 0.00000000  
Rotation angle (degrees) 95.04493851  
Shift along axis -169.85482968  
  

> fitmap #2 inMap #1

Fit molecule fold_satbc_msmk_model_0.cif (#2) to map
cryosparc_P1_J293_002_volume_map_sharp.mrc (#1) using 10704 atoms  
average map value = 0.04627, steps = 120  
shifted from previous position = 0.00693  
rotated from previous position = 0.00746 degrees  
atoms outside contour = 8078, contour level = 0.10662  
  
Position of fold_satbc_msmk_model_0.cif (#2) relative to
cryosparc_P1_J293_002_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.04052830 0.99106584 -0.12706673 107.96436291  
-0.83795290 0.03555524 0.54458310 107.18215524  
0.54423560 0.12854696 0.82902551 121.11310864  
Axis -0.20882774 -0.33695762 -0.91806892  
Axis point 65.11454376 -4.78377176 0.00000000  
Rotation angle (degrees) 95.04705048  
Shift along axis -169.85197815  
  

> volume #1 level 0.1829

> lighting full

> lighting soft

> lighting full

> lighting shadows false

> lighting soft

> lighting shadows true intensity 0.5

> lighting shadows false

> volume #1 level 0.2687

Drag select of 2 residues  

> volume #1 level 0.2091

> open /Users/lue81154/Downloads/cryosparc_P1_J293_002_volume_map.mrc

Opened cryosparc_P1_J293_002_volume_map.mrc as #3, grid size 256,256,256,
pixel 0.825, shown at level 0.0698, step 1, values float32  

> surface dust #3 size 8.25

> fitmap #2 inMap #3

Fit molecule fold_satbc_msmk_model_0.cif (#2) to map
cryosparc_P1_J293_002_volume_map.mrc (#3) using 10704 atoms  
average map value = 0.03807, steps = 128  
shifted from previous position = 0.395  
rotated from previous position = 0.744 degrees  
atoms outside contour = 8390, contour level = 0.069838  
  
Position of fold_satbc_msmk_model_0.cif (#2) relative to
cryosparc_P1_J293_002_volume_map.mrc (#3) coordinates:  
Matrix rotation and translation  
-0.04822578 0.99145979 -0.12116832 108.04086104  
-0.83279945 0.02706425 0.55291284 106.89122864  
0.55147018 0.12757356 0.82438197 121.34784791  
Axis -0.21370655 -0.33795904 -0.91657689  
Axis point 64.23463281 -4.32153914 0.00000000  
Rotation angle (degrees) 95.64645420  
Shift along axis -170.43853014  
  

> fitmap #2 inMap #3

Fit molecule fold_satbc_msmk_model_0.cif (#2) to map
cryosparc_P1_J293_002_volume_map.mrc (#3) using 10704 atoms  
average map value = 0.03807, steps = 76  
shifted from previous position = 0.00392  
rotated from previous position = 0.00754 degrees  
atoms outside contour = 8393, contour level = 0.069838  
  
Position of fold_satbc_msmk_model_0.cif (#2) relative to
cryosparc_P1_J293_002_volume_map.mrc (#3) coordinates:  
Matrix rotation and translation  
-0.04818901 0.99146413 -0.12114745 108.04029347  
-0.83286906 0.02706716 0.55280783 106.88714561  
0.55136825 0.12753923 0.82445546 121.34873633  
Axis -0.21366984 -0.33789545 -0.91660890  
Axis point 64.24231364 -4.32315146 0.00000000  
Rotation angle (degrees) 95.64319657  
Shift along axis -170.43096304  
  

> fitmap #2 inMap #3

Fit molecule fold_satbc_msmk_model_0.cif (#2) to map
cryosparc_P1_J293_002_volume_map.mrc (#3) using 10704 atoms  
average map value = 0.03807, steps = 56  
shifted from previous position = 0.00494  
rotated from previous position = 0.00414 degrees  
atoms outside contour = 8393, contour level = 0.069838  
  
Position of fold_satbc_msmk_model_0.cif (#2) relative to
cryosparc_P1_J293_002_volume_map.mrc (#3) coordinates:  
Matrix rotation and translation  
-0.04816147 0.99146541 -0.12114790 108.04334748  
-0.83290696 0.02708161 0.55275002 106.88951389  
0.55131340 0.12752619 0.82449415 121.35159795  
Axis -0.21364649 -0.33786676 -0.91662491  
Axis point 64.24938114 -4.32445947 0.00000000  
Rotation angle (degrees) 95.64087409  
Shift along axis -170.43139390  
  

> fitmap #2 inMap #3

Fit molecule fold_satbc_msmk_model_0.cif (#2) to map
cryosparc_P1_J293_002_volume_map.mrc (#3) using 10704 atoms  
average map value = 0.03807, steps = 48  
shifted from previous position = 0.00551  
rotated from previous position = 0.00893 degrees  
atoms outside contour = 8389, contour level = 0.069838  
  
Position of fold_satbc_msmk_model_0.cif (#2) relative to
cryosparc_P1_J293_002_volume_map.mrc (#3) coordinates:  
Matrix rotation and translation  
-0.04820688 0.99146297 -0.12114984 108.04354484  
-0.83282297 0.02706426 0.55287740 106.89523084  
0.55143630 0.12754887 0.82440845 121.35021150  
Axis -0.21370067 -0.33793197 -0.91658824  
Axis point 64.24045409 -4.31989443 0.00000000  
Rotation angle (degrees) 95.64514789  
Shift along axis -170.44047125  
  

> fitmap #2 inMap #3

Fit molecule fold_satbc_msmk_model_0.cif (#2) to map
cryosparc_P1_J293_002_volume_map.mrc (#3) using 10704 atoms  
average map value = 0.03807, steps = 60  
shifted from previous position = 0.00252  
rotated from previous position = 0.00386 degrees  
atoms outside contour = 8389, contour level = 0.069838  
  
Position of fold_satbc_msmk_model_0.cif (#2) relative to
cryosparc_P1_J293_002_volume_map.mrc (#3) coordinates:  
Matrix rotation and translation  
-0.04822228 0.99145798 -0.12118447 108.04194820  
-0.83279272 0.02707773 0.55292231 106.89354245  
0.55148064 0.12758472 0.82437324 121.35113099  
Axis -0.21370562 -0.33797227 -0.91657223  
Axis point 64.23424051 -4.32241658 0.00000000  
Rotation angle (degrees) 95.64621704  
Shift along axis -170.44330163  
  

> fitmap #2 inMap #3

Fit molecule fold_satbc_msmk_model_0.cif (#2) to map
cryosparc_P1_J293_002_volume_map.mrc (#3) using 10704 atoms  
average map value = 0.03807, steps = 60  
shifted from previous position = 0.0135  
rotated from previous position = 0.0195 degrees  
atoms outside contour = 8395, contour level = 0.069838  
  
Position of fold_satbc_msmk_model_0.cif (#2) relative to
cryosparc_P1_J293_002_volume_map.mrc (#3) coordinates:  
Matrix rotation and translation  
-0.04814012 0.99147575 -0.12107170 108.04511403  
-0.83296370 0.02704381 0.55266637 106.87930692  
0.55122954 0.12745376 0.82456142 121.35041825  
Axis -0.21364031 -0.33778549 -0.91665630  
Axis point 64.25450616 -4.32531351 0.00000000  
Rotation angle (degrees) 95.63941119  
Shift along axis -170.42169683  
  

> volume #3 color #ffd8c1

> lighting soft

> lighting shadows true intensity 0.5

> lighting shadows false

> lighting shadows true

> lighting shadows false

> lighting shadows true

> lighting shadows false

> lighting soft

> lighting full

> lighting soft

> volume #3 color #ffc2ea

> volume #3 level 0.04236

> volume #3 level 0.08816

> volume #3 level 0.1042

> graphics silhouettes true

> volume #3 level 0.07289

> volume #3 level 0.04465

> fitmap #2 inMap #3

Fit molecule fold_satbc_msmk_model_0.cif (#2) to map
cryosparc_P1_J293_002_volume_map.mrc (#3) using 10704 atoms  
average map value = 0.03807, steps = 48  
shifted from previous position = 0.0122  
rotated from previous position = 0.0085 degrees  
atoms outside contour = 6703, contour level = 0.044649  
  
Position of fold_satbc_msmk_model_0.cif (#2) relative to
cryosparc_P1_J293_002_volume_map.mrc (#3) coordinates:  
Matrix rotation and translation  
-0.04813338 0.99146976 -0.12112345 108.05062166  
-0.83288883 0.02709560 0.55277664 106.88819918  
0.55134324 0.12748938 0.82447989 121.35763839  
Axis -0.21367807 -0.33786900 -0.91661673  
Axis point 64.24826557 -4.32734422 0.00000000  
Rotation angle (degrees) 95.64007300  
Shift along axis -170.44069830  
  

> fitmap #2 inMap #3

Fit molecule fold_satbc_msmk_model_0.cif (#2) to map
cryosparc_P1_J293_002_volume_map.mrc (#3) using 10704 atoms  
average map value = 0.03807, steps = 104  
shifted from previous position = 0.00622  
rotated from previous position = 0.00852 degrees  
atoms outside contour = 6702, contour level = 0.044649  
  
Position of fold_satbc_msmk_model_0.cif (#2) relative to
cryosparc_P1_J293_002_volume_map.mrc (#3) coordinates:  
Matrix rotation and translation  
-0.04812003 0.99147177 -0.12111234 108.04748386  
-0.83297047 0.02708165 0.55265430 106.88236703  
0.55122106 0.12747675 0.82456354 121.35748400  
Axis -0.21362207 -0.33780064 -0.91665497  
Axis point 64.25581316 -4.32916158 0.00000000  
Rotation angle (degrees) 95.63768223  
Shift along axis -170.42919991  
  

> fitmap #2 inMap #3

Fit molecule fold_satbc_msmk_model_0.cif (#2) to map
cryosparc_P1_J293_002_volume_map.mrc (#3) using 10704 atoms  
average map value = 0.03807, steps = 60  
shifted from previous position = 0.013  
rotated from previous position = 0.00722 degrees  
atoms outside contour = 6702, contour level = 0.044649  
  
Position of fold_satbc_msmk_model_0.cif (#2) relative to
cryosparc_P1_J293_002_volume_map.mrc (#3) coordinates:  
Matrix rotation and translation  
-0.04815980 0.99148021 -0.12102737 108.04275893  
-0.83301268 0.02699137 0.55259509 106.87671027  
0.55115380 0.12743020 0.82461569 121.34641748  
Axis -0.21361653 -0.33772546 -0.91668397  
Axis point 64.26039582 -4.32180527 0.00000000  
Rotation angle (degrees) 95.63992484  
Shift along axis -170.41102032  
  

> vop gaussian #3 sdev 2.47

Opened cryosparc_P1_J293_002_volume_map.mrc gaussian as #4, grid size
256,256,256, pixel 0.825, shown at step 1, values float32  

> volume #4 level 0.03309

> volume #4 level 0.07431

> volume #3 level 0.04694

> reflect #2

Unknown command: reflect #2  

> reflect

Unknown command: reflect  

> vop zflip

> volume zflip

Expected a density maps specifier or a keyword  

> vop zflip #1

> volume zflip #1

Expected a density maps specifier or a keyword  

> volume

> volume zflip

Expected a density maps specifier or a keyword  

> volume #1 zflip

Expected a keyword  

> ui tool show "Show Volume Menu"

> toolshed show

> ui tool show "Map Coordinates"

> volume flip #3

Opened cryosparc_P1_J293_002_volume_map.mrc z flip as #5, grid size
256,256,256, pixel 0.825, shown at step 1, values float32  

> fitmap #2 inMap #5

Fit molecule fold_satbc_msmk_model_0.cif (#2) to map
cryosparc_P1_J293_002_volume_map.mrc z flip (#5) using 10704 atoms  
average map value = 0.03724, steps = 260  
shifted from previous position = 19.5  
rotated from previous position = 13.9 degrees  
atoms outside contour = 6862, contour level = 0.046939  
  
Position of fold_satbc_msmk_model_0.cif (#2) relative to
cryosparc_P1_J293_002_volume_map.mrc z flip (#5) coordinates:  
Matrix rotation and translation  
-0.25095334 0.94582559 -0.20600091 109.37712155  
-0.76270586 -0.06215750 0.64375167 101.56659655  
0.59607230 0.31866973 0.73698535 102.95052203  
Axis -0.16973581 -0.41878840 -0.89207961  
Axis point 60.52754386 -8.14162985 0.00000000  
Rotation angle (degrees) 106.74201072  
Shift along axis -152.94018839  
  

> select #2

10704 atoms, 10946 bonds, 1355 residues, 1 model selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #2,0.54217,0.28891,0.78904,121.28,-0.82959,0.034755,0.5573,100.52,0.13358,-0.95673,0.25852,97.742

> view matrix models
> #2,-0.017679,-0.99365,0.11113,114.28,-0.69251,0.092339,0.71548,102.38,-0.7212,-0.064308,-0.68974,85.416

> ui mousemode right select

> select clear

> fitmap #2 inMap #5

Fit molecule fold_satbc_msmk_model_0.cif (#2) to map
cryosparc_P1_J293_002_volume_map.mrc z flip (#5) using 10704 atoms  
average map value = 0.04085, steps = 228  
shifted from previous position = 9.37  
rotated from previous position = 31.3 degrees  
atoms outside contour = 6622, contour level = 0.046939  
  
Position of fold_satbc_msmk_model_0.cif (#2) relative to
cryosparc_P1_J293_002_volume_map.mrc z flip (#5) coordinates:  
Matrix rotation and translation  
0.45065228 -0.89232871 -0.02572948 108.21532117  
-0.72537550 -0.38283127 0.57207570 106.45404206  
-0.52032962 -0.23914369 -0.81979717 88.45472581  
Axis -0.84093333 0.51271672 0.17306849  
Axis point 0.00000000 100.29717673 37.43448874  
Rotation angle (degrees) 151.16213046  
Shift along axis -21.11237724  
  
Drag select of 5 residues, 5 cryosparc_P1_J293_002_volume_map.mrc z flip  

> select clear

> fitmap #2 inMap #5

Fit molecule fold_satbc_msmk_model_0.cif (#2) to map
cryosparc_P1_J293_002_volume_map.mrc z flip (#5) using 10704 atoms  
average map value = 0.04085, steps = 44  
shifted from previous position = 0.00464  
rotated from previous position = 0.00825 degrees  
atoms outside contour = 6621, contour level = 0.046939  
  
Position of fold_satbc_msmk_model_0.cif (#2) relative to
cryosparc_P1_J293_002_volume_map.mrc z flip (#5) coordinates:  
Matrix rotation and translation  
0.45071298 -0.89229824 -0.02572296 108.21728572  
-0.72528607 -0.38284730 0.57217836 106.45852669  
-0.52040170 -0.23923171 -0.81972573 88.45609312  
Axis -0.84094718 0.51268614 0.17309178  
Axis point 0.00000000 100.30112085 37.43178235  
Rotation angle (degrees) 151.15523490  
Shift along axis -21.11418745  
  

> fitmap #2 inMap #5

Fit molecule fold_satbc_msmk_model_0.cif (#2) to map
cryosparc_P1_J293_002_volume_map.mrc z flip (#5) using 10704 atoms  
average map value = 0.04085, steps = 44  
shifted from previous position = 0.00332  
rotated from previous position = 0.0015 degrees  
atoms outside contour = 6623, contour level = 0.046939  
  
Position of fold_satbc_msmk_model_0.cif (#2) relative to
cryosparc_P1_J293_002_volume_map.mrc z flip (#5) coordinates:  
Matrix rotation and translation  
0.45069969 -0.89230522 -0.02571362 108.21627302  
-0.72528400 -0.38282692 0.57219462 106.45846649  
-0.52041611 -0.23923826 -0.81971467 88.45287993  
Axis -0.84094212 0.51269326 0.17309526  
Axis point 0.00000000 100.30154181 37.42968942  
Rotation angle (degrees) 151.15415791  
Shift along axis -21.11231027  
  

> fitmap #2 inMap #5

Fit molecule fold_satbc_msmk_model_0.cif (#2) to map
cryosparc_P1_J293_002_volume_map.mrc z flip (#5) using 10704 atoms  
average map value = 0.04085, steps = 56  
shifted from previous position = 0.00598  
rotated from previous position = 0.00842 degrees  
atoms outside contour = 6618, contour level = 0.046939  
  
Position of fold_satbc_msmk_model_0.cif (#2) relative to
cryosparc_P1_J293_002_volume_map.mrc z flip (#5) coordinates:  
Matrix rotation and translation  
0.45071701 -0.89229707 -0.02569310 108.21695735  
-0.72535728 -0.38286496 0.57207626 106.46159704  
-0.52029895 -0.23920782 -0.81979792 88.45792517  
Axis -0.84095244 0.51269340 0.17304471  
Axis point 0.00000000 100.30030751 37.43235192  
Rotation angle (degrees) 151.16033169  
Shift along axis -21.11597953  
  

> fitmap #2 inMap #5

Fit molecule fold_satbc_msmk_model_0.cif (#2) to map
cryosparc_P1_J293_002_volume_map.mrc z flip (#5) using 10704 atoms  
average map value = 0.04085, steps = 40  
shifted from previous position = 0.0122  
rotated from previous position = 0.00712 degrees  
atoms outside contour = 6626, contour level = 0.046939  
  
Position of fold_satbc_msmk_model_0.cif (#2) relative to
cryosparc_P1_J293_002_volume_map.mrc z flip (#5) coordinates:  
Matrix rotation and translation  
0.45070788 -0.89229967 -0.02576281 108.21679676  
-0.72528949 -0.38286927 0.57215932 106.45843508  
-0.52040136 -0.23919122 -0.81973776 88.44596700  
Axis -0.84094738 0.51268221 0.17310246  
Axis point 0.00000000 100.29798846 37.42882166  
Rotation angle (degrees) 151.15755727  
Shift along axis -21.11507127  
  

> fitmap #2 inMap #5

Fit molecule fold_satbc_msmk_model_0.cif (#2) to map
cryosparc_P1_J293_002_volume_map.mrc z flip (#5) using 10704 atoms  
average map value = 0.04085, steps = 44  
shifted from previous position = 0.00904  
rotated from previous position = 0.00561 degrees  
atoms outside contour = 6622, contour level = 0.046939  
  
Position of fold_satbc_msmk_model_0.cif (#2) relative to
cryosparc_P1_J293_002_volume_map.mrc z flip (#5) coordinates:  
Matrix rotation and translation  
0.45073464 -0.89228627 -0.02575873 108.21665842  
-0.72523101 -0.38286680 0.57223510 106.46354839  
-0.52045968 -0.23924515 -0.81968500 88.45347294  
Axis -0.84095205 0.51266778 0.17312247  
Axis point 0.00000000 100.30290630 37.43028649  
Rotation angle (degrees) 151.15268821  
Shift along axis -21.11130636  
  

> fitmap #2 inMap #5

Fit molecule fold_satbc_msmk_model_0.cif (#2) to map
cryosparc_P1_J293_002_volume_map.mrc z flip (#5) using 10704 atoms  
average map value = 0.04085, steps = 44  
shifted from previous position = 0.00955  
rotated from previous position = 0.0059 degrees  
atoms outside contour = 6628, contour level = 0.046939  
  
Position of fold_satbc_msmk_model_0.cif (#2) relative to
cryosparc_P1_J293_002_volume_map.mrc z flip (#5) coordinates:  
Matrix rotation and translation  
0.45065513 -0.89232600 -0.02577343 108.21576540  
-0.72528609 -0.38282124 0.57219577 106.46232878  
-0.52045178 -0.23916985 -0.81971199 88.44403964  
Axis -0.84092968 0.51270314 0.17312642  
Axis point 0.00000000 100.30214518 37.42836566  
Rotation angle (degrees) 151.15630694  
Shift along axis -21.10627876  
  

> fitmap #2 inMap #5

Fit molecule fold_satbc_msmk_model_0.cif (#2) to map
cryosparc_P1_J293_002_volume_map.mrc z flip (#5) using 10704 atoms  
average map value = 0.04085, steps = 44  
shifted from previous position = 0.0106  
rotated from previous position = 0.00181 degrees  
atoms outside contour = 6623, contour level = 0.046939  
  
Position of fold_satbc_msmk_model_0.cif (#2) relative to
cryosparc_P1_J293_002_volume_map.mrc z flip (#5) coordinates:  
Matrix rotation and translation  
0.45063902 -0.89233488 -0.02574774 108.21699916  
-0.72529921 -0.38279452 0.57219701 106.45179447  
-0.52044744 -0.23917948 -0.81971193 88.44384973  
Axis -0.84092408 0.51271499 0.17311854  
Axis point 0.00000000 100.29873848 37.42859209  
Rotation angle (degrees) 151.15567381  
Shift along axis -21.11157897  
  

> fitmap #2 inMap #5

Fit molecule fold_satbc_msmk_model_0.cif (#2) to map
cryosparc_P1_J293_002_volume_map.mrc z flip (#5) using 10704 atoms  
average map value = 0.04085, steps = 48  
shifted from previous position = 0.00277  
rotated from previous position = 0.0155 degrees  
atoms outside contour = 6619, contour level = 0.046939  
  
Position of fold_satbc_msmk_model_0.cif (#2) relative to
cryosparc_P1_J293_002_volume_map.mrc z flip (#5) coordinates:  
Matrix rotation and translation  
0.45063703 -0.89233728 -0.02569914 108.21594726  
-0.72545113 -0.38283118 0.57197985 106.44979121  
-0.52023738 -0.23911184 -0.81986500 88.44670054  
Axis -0.84093235 0.51273266 0.17302602  
Axis point 0.00000000 100.29260786 37.43112172  
Rotation angle (degrees) 151.16705990  
Shift along axis -21.11842530  
  

> fitmap #2 inMap #5

Fit molecule fold_satbc_msmk_model_0.cif (#2) to map
cryosparc_P1_J293_002_volume_map.mrc z flip (#5) using 10704 atoms  
average map value = 0.04085, steps = 44  
shifted from previous position = 0.0156  
rotated from previous position = 0.0162 degrees  
atoms outside contour = 6624, contour level = 0.046939  
  
Position of fold_satbc_msmk_model_0.cif (#2) relative to
cryosparc_P1_J293_002_volume_map.mrc z flip (#5) coordinates:  
Matrix rotation and translation  
0.45066043 -0.89232385 -0.02575531 108.21602169  
-0.72528289 -0.38281350 0.57220501 106.46615830  
-0.52045165 -0.23919027 -0.81970611 88.44858193  
Axis -0.84093048 0.51270355 0.17312134  
Axis point 0.00000000 100.30531566 37.42918742  
Rotation angle (degrees) 151.15518342  
Shift along axis -21.10423712  
  

> fitmap #2 inMap #5

Fit molecule fold_satbc_msmk_model_0.cif (#2) to map
cryosparc_P1_J293_002_volume_map.mrc z flip (#5) using 10704 atoms  
average map value = 0.04085, steps = 40  
shifted from previous position = 0.0043  
rotated from previous position = 0.00843 degrees  
atoms outside contour = 6628, contour level = 0.046939  
  
Position of fold_satbc_msmk_model_0.cif (#2) relative to
cryosparc_P1_J293_002_volume_map.mrc z flip (#5) coordinates:  
Matrix rotation and translation  
0.45057422 -0.89236414 -0.02586736 108.21438215  
-0.72528639 -0.38279989 0.57220967 106.46489946  
-0.52052141 -0.23906168 -0.81969932 88.44448858  
Axis -0.84090621 0.51272323 0.17318092  
Axis point 0.00000000 100.30412102 37.43405990  
Rotation angle (degrees) 151.15909227  
Shift along axis -21.09422098  
  

> fitmap #2 inMap #5

Fit molecule fold_satbc_msmk_model_0.cif (#2) to map
cryosparc_P1_J293_002_volume_map.mrc z flip (#5) using 10704 atoms  
average map value = 0.04085, steps = 44  
shifted from previous position = 0.0129  
rotated from previous position = 0.0103 degrees  
atoms outside contour = 6621, contour level = 0.046939  
  
Position of fold_satbc_msmk_model_0.cif (#2) relative to
cryosparc_P1_J293_002_volume_map.mrc z flip (#5) coordinates:  
Matrix rotation and translation  
0.45064791 -0.89233119 -0.02572006 108.21569615  
-0.72532751 -0.38279876 0.57215830 106.45910259  
-0.52040030 -0.23918647 -0.81973982 88.45631882  
Axis -0.84092798 0.51271724 0.17309295  
Axis point 0.00000000 100.30292212 37.43320511  
Rotation angle (degrees) 151.15705355  
Shift along axis -21.10702369  
  

> fitmap #2 inMap #5

Fit molecule fold_satbc_msmk_model_0.cif (#2) to map
cryosparc_P1_J293_002_volume_map.mrc z flip (#5) using 10704 atoms  
average map value = 0.04085, steps = 48  
shifted from previous position = 0.00884  
rotated from previous position = 0.0136 degrees  
atoms outside contour = 6621, contour level = 0.046939  
  
Position of fold_satbc_msmk_model_0.cif (#2) relative to
cryosparc_P1_J293_002_volume_map.mrc z flip (#5) coordinates:  
Matrix rotation and translation  
0.45082081 -0.89224472 -0.02568971 108.21553075  
-0.72533322 -0.38295659 0.57204543 106.46747995  
-0.52024256 -0.23925639 -0.81981953 88.45798233  
Axis -0.84098577 0.51264758 0.17301847  
Axis point 0.00000000 100.29781223 37.42991132  
Rotation angle (degrees) 151.16089246  
Shift along axis -21.12256184  
  

> fitmap #2 inMap #5

Fit molecule fold_satbc_msmk_model_0.cif (#2) to map
cryosparc_P1_J293_002_volume_map.mrc z flip (#5) using 10704 atoms  
average map value = 0.04085, steps = 36  
shifted from previous position = 0.0165  
rotated from previous position = 0.0174 degrees  
atoms outside contour = 6628, contour level = 0.046939  
  
Position of fold_satbc_msmk_model_0.cif (#2) relative to
cryosparc_P1_J293_002_volume_map.mrc z flip (#5) coordinates:  
Matrix rotation and translation  
0.45061714 -0.89234412 -0.02581031 108.21556294  
-0.72530111 -0.38281342 0.57218197 106.45995907  
-0.52046375 -0.23911475 -0.81972046 88.44299305  
Axis -0.84091943 0.51271462 0.17314222  
Axis point 0.00000000 100.30086603 37.43076637  
Rotation angle (degrees) 151.15860191  
Shift along axis -21.10377594  
  

> fitmap #2 inMap #5

Fit molecule fold_satbc_msmk_model_0.cif (#2) to map
cryosparc_P1_J293_002_volume_map.mrc z flip (#5) using 10704 atoms  
average map value = 0.04085, steps = 44  
shifted from previous position = 0.00804  
rotated from previous position = 0.00476 degrees  
atoms outside contour = 6624, contour level = 0.046939  
  
Position of fold_satbc_msmk_model_0.cif (#2) relative to
cryosparc_P1_J293_002_volume_map.mrc z flip (#5) coordinates:  
Matrix rotation and translation  
0.45065975 -0.89232398 -0.02576240 108.21560272  
-0.72527069 -0.38281176 0.57222164 106.46546422  
-0.52046924 -0.23919255 -0.81969428 88.44896720  
Axis -0.84092967 0.51270198 0.17312992  
Axis point 0.00000000 100.30524272 37.42955496  
Rotation angle (degrees) 151.15441743  
Shift along axis -21.10349398  
  

> volume #3 level 0.192

> volume #5 level 0.0416

> surface dust #5 size 8.25

> fitmap #2 inMap #5

Fit molecule fold_satbc_msmk_model_0.cif (#2) to map
cryosparc_P1_J293_002_volume_map.mrc z flip (#5) using 10704 atoms  
average map value = 0.04085, steps = 44  
shifted from previous position = 0.0112  
rotated from previous position = 0.004 degrees  
atoms outside contour = 6169, contour level = 0.041596  
  
Position of fold_satbc_msmk_model_0.cif (#2) relative to
cryosparc_P1_J293_002_volume_map.mrc z flip (#5) coordinates:  
Matrix rotation and translation  
0.45067247 -0.89231615 -0.02581144 108.21689345  
-0.72527721 -0.38285904 0.57218172 106.45771232  
-0.52044913 -0.23914609 -0.81972060 88.44092169  
Axis -0.84093652 0.51268906 0.17313488  
Axis point 0.00000000 100.29770417 37.42897483  
Rotation angle (degrees) 151.15803371  
Shift along axis -21.11162546  
  

> fitmap #2 inMap #5

Fit molecule fold_satbc_msmk_model_0.cif (#2) to map
cryosparc_P1_J293_002_volume_map.mrc z flip (#5) using 10704 atoms  
average map value = 0.04085, steps = 44  
shifted from previous position = 0.0166  
rotated from previous position = 0.0102 degrees  
atoms outside contour = 6172, contour level = 0.041596  
  
Position of fold_satbc_msmk_model_0.cif (#2) relative to
cryosparc_P1_J293_002_volume_map.mrc z flip (#5) coordinates:  
Matrix rotation and translation  
0.45069077 -0.89230988 -0.02570818 108.21563331  
-0.72537113 -0.38285449 0.57206570 106.45821246  
-0.52030237 -0.23917676 -0.81980481 88.45776278  
Axis -0.84094517 0.51270319 0.17305102  
Axis point 0.00000000 100.29851156 37.43397698  
Rotation angle (degrees) 151.16167759  
Shift along axis -21.11424346  
  

> fitmap #2 inMap #5

Fit molecule fold_satbc_msmk_model_0.cif (#2) to map
cryosparc_P1_J293_002_volume_map.mrc z flip (#5) using 10704 atoms  
average map value = 0.04085, steps = 40  
shifted from previous position = 0.0097  
rotated from previous position = 0.01 degrees  
atoms outside contour = 6170, contour level = 0.041596  
  
Position of fold_satbc_msmk_model_0.cif (#2) relative to
cryosparc_P1_J293_002_volume_map.mrc z flip (#5) coordinates:  
Matrix rotation and translation  
0.45066105 -0.89232346 -0.02575799 108.21571823  
-0.72528502 -0.38281683 0.57220007 106.46142217  
-0.52044813 -0.23918640 -0.81970947 88.44806251  
Axis -0.84093096 0.51270298 0.17312070  
Axis point 0.00000000 100.30259091 37.42962796  
Rotation angle (degrees) 151.15554385  
Shift along axis -21.10666965  
  

> fitmap #2 inMap #5

Fit molecule fold_satbc_msmk_model_0.cif (#2) to map
cryosparc_P1_J293_002_volume_map.mrc z flip (#5) using 10704 atoms  
average map value = 0.04085, steps = 48  
shifted from previous position = 0.0057  
rotated from previous position = 0.00983 degrees  
atoms outside contour = 6170, contour level = 0.041596  
  
Position of fold_satbc_msmk_model_0.cif (#2) relative to
cryosparc_P1_J293_002_volume_map.mrc z flip (#5) coordinates:  
Matrix rotation and translation  
0.45064395 -0.89233116 -0.02579050 108.21641792  
-0.72537068 -0.38285976 0.57206275 106.46345685  
-0.52034356 -0.23908894 -0.81980429 88.44335553  
Axis -0.84093273 0.51271033 0.17309035  
Axis point 0.00000000 100.29875771 37.43084772  
Rotation angle (degrees) 151.16474062  
Shift along axis -21.10912211  
  

> volume #5 level 0.06755

> fitmap #2 inMap #5

Fit molecule fold_satbc_msmk_model_0.cif (#2) to map
cryosparc_P1_J293_002_volume_map.mrc z flip (#5) using 10704 atoms  
average map value = 0.04085, steps = 48  
shifted from previous position = 0.00514  
rotated from previous position = 0.00254 degrees  
atoms outside contour = 8098, contour level = 0.067548  
  
Position of fold_satbc_msmk_model_0.cif (#2) relative to
cryosparc_P1_J293_002_volume_map.mrc z flip (#5) coordinates:  
Matrix rotation and translation  
0.45060810 -0.89234975 -0.02577345 108.21428172  
-0.72538635 -0.38281982 0.57206960 106.46112683  
-0.52035275 -0.23908348 -0.81980004 88.43921873  
Axis -0.84092098 0.51272949 0.17309066  
Axis point 0.00000000 100.29836730 37.42871101  
Rotation angle (degrees) 151.16424597  
Shift along axis -21.10589722  
  

> fitmap #2 inMap #5

Fit molecule fold_satbc_msmk_model_0.cif (#2) to map
cryosparc_P1_J293_002_volume_map.mrc z flip (#5) using 10704 atoms  
average map value = 0.04085, steps = 48  
shifted from previous position = 0.0201  
rotated from previous position = 0.00732 degrees  
atoms outside contour = 8093, contour level = 0.067548  
  
Position of fold_satbc_msmk_model_0.cif (#2) relative to
cryosparc_P1_J293_002_volume_map.mrc z flip (#5) coordinates:  
Matrix rotation and translation  
0.45069940 -0.89230581 -0.02569842 108.21551618  
-0.72537889 -0.38286051 0.57205183 106.45968365  
-0.52028408 -0.23918233 -0.81981480 88.45939462  
Axis -0.84094825 0.51270147 0.17304115  
Axis point 0.00000000 100.29892957 37.43421619  
Rotation angle (degrees) 151.16211616  
Shift along axis -21.11449692  
  

> fitmap #2 inMap #5

Fit molecule fold_satbc_msmk_model_0.cif (#2) to map
cryosparc_P1_J293_002_volume_map.mrc z flip (#5) using 10704 atoms  
average map value = 0.04085, steps = 44  
shifted from previous position = 0.0166  
rotated from previous position = 0.0082 degrees  
atoms outside contour = 8097, contour level = 0.067548  
  
Position of fold_satbc_msmk_model_0.cif (#2) relative to
cryosparc_P1_J293_002_volume_map.mrc z flip (#5) coordinates:  
Matrix rotation and translation  
0.45071400 -0.89229670 -0.02575854 108.21755081  
-0.72529008 -0.38287298 0.57215608 106.45744143  
-0.52039523 -0.23919634 -0.81974016 88.44282903  
Axis -0.84094932 0.51268028 0.17309876  
Axis point 0.00000000 100.29706137 37.42707568  
Rotation angle (degrees) 151.15755684  
Shift along axis -21.11750045  
  

> fitmap #2 inMap #5

Fit molecule fold_satbc_msmk_model_0.cif (#2) to map
cryosparc_P1_J293_002_volume_map.mrc z flip (#5) using 10704 atoms  
average map value = 0.04085, steps = 44  
shifted from previous position = 0.0119  
rotated from previous position = 0.0114 degrees  
atoms outside contour = 8097, contour level = 0.067548  
  
Position of fold_satbc_msmk_model_0.cif (#2) relative to
cryosparc_P1_J293_002_volume_map.mrc z flip (#5) coordinates:  
Matrix rotation and translation  
0.45067022 -0.89232124 -0.02567430 108.21602159  
-0.72542063 -0.38283476 0.57201615 106.44809454  
-0.52025117 -0.23916597 -0.81984045 88.45116033  
Axis -0.84094035 0.51272043 0.17302337  
Axis point 0.00000000 100.29292682 37.43126467  
Rotation angle (degrees) 151.16384328  
Shift along axis -21.12098874  
  

> fitmap #2 inMap #5

Fit molecule fold_satbc_msmk_model_0.cif (#2) to map
cryosparc_P1_J293_002_volume_map.mrc z flip (#5) using 10704 atoms  
average map value = 0.04085, steps = 28  
shifted from previous position = 0.0185  
rotated from previous position = 0.0137 degrees  
atoms outside contour = 8099, contour level = 0.067548  
  
Position of fold_satbc_msmk_model_0.cif (#2) relative to
cryosparc_P1_J293_002_volume_map.mrc z flip (#5) coordinates:  
Matrix rotation and translation  
0.45066252 -0.89232198 -0.02578349 108.21645109  
-0.72528448 -0.38283441 0.57218899 106.46349074  
-0.52044762 -0.23916376 -0.81971640 88.43933636  
Axis -0.84093250 0.51269825 0.17312724  
Axis point 0.00000000 100.30147868 37.42626996  
Rotation angle (degrees) 151.15691289  
Shift along axis -21.10782678  
  

> volume #5 level 0.01564

> volume #5 level 0.09274

> volume #5 level 0.08129

> select clear

> ui tool show "Map Eraser"

> volume erase #5 center 58.182,127.44,120.07 radius 25.303

Opened cryosparc_P1_J293_002_volume_map.mrc z flip copy as #7, grid size
256,256,256, pixel 0.825, shown at step 1, values float32  

> volume erase #7 center 75.618,152.95,117.59 radius 25.238

> volume erase #7 center 127.14,53.565,126.13 radius 25.238

> volume erase #7 center 91.993,50.165,126.17 radius 25.238

> volume erase #7 center 64.916,67.666,113.61 radius 25.238

> volume erase #7 center 147.48,78.13,120.88 radius 25.238

> volume erase #7 center 154.16,121.42,121.24 radius 25.238

> volume erase #7 center 148.8,135.09,117.64 radius 25.238

> surface dust #7 size 8.25

> fitmap #2 inMap #7

Fit molecule fold_satbc_msmk_model_0.cif (#2) to map
cryosparc_P1_J293_002_volume_map.mrc z flip copy (#7) using 10704 atoms  
average map value = 0.04074, steps = 44  
shifted from previous position = 0.0396  
rotated from previous position = 0.164 degrees  
atoms outside contour = 8898, contour level = 0.081288  
  
Position of fold_satbc_msmk_model_0.cif (#2) relative to
cryosparc_P1_J293_002_volume_map.mrc z flip copy (#7) coordinates:  
Matrix rotation and translation  
0.45137065 -0.89188288 -0.02845129 108.19522362  
-0.72462790 -0.38495905 0.57159509 106.45390688  
-0.52074846 -0.23738465 -0.82004243 88.47209375  
Axis -0.84123761 0.51192739 0.17392423  
Axis point 0.00000000 100.17903915 37.56330254  
Rotation angle (degrees) 151.26056235  
Shift along axis -21.13377916  
  

> fitmap #2 inMap #7

Fit molecule fold_satbc_msmk_model_0.cif (#2) to map
cryosparc_P1_J293_002_volume_map.mrc z flip copy (#7) using 10704 atoms  
average map value = 0.04074, steps = 44  
shifted from previous position = 0.00242  
rotated from previous position = 0.00387 degrees  
atoms outside contour = 8898, contour level = 0.081288  
  
Position of fold_satbc_msmk_model_0.cif (#2) relative to
cryosparc_P1_J293_002_volume_map.mrc z flip copy (#7) coordinates:  
Matrix rotation and translation  
0.45142685 -0.89185462 -0.02844541 108.19596896  
-0.72461844 -0.38500770 0.57157431 106.45518051  
-0.52071289 -0.23741192 -0.82005712 88.47414334  
Axis -0.84125573 0.51190344 0.17390703  
Axis point 0.00000000 100.17754103 37.56315997  
Rotation angle (degrees) 151.26098727  
Shift along axis -21.13943034  
  

> fitmap #2 inMap #7

Fit molecule fold_satbc_msmk_model_0.cif (#2) to map
cryosparc_P1_J293_002_volume_map.mrc z flip copy (#7) using 10704 atoms  
average map value = 0.04074, steps = 48  
shifted from previous position = 0.0132  
rotated from previous position = 0.00792 degrees  
atoms outside contour = 8894, contour level = 0.081288  
  
Position of fold_satbc_msmk_model_0.cif (#2) relative to
cryosparc_P1_J293_002_volume_map.mrc z flip copy (#7) coordinates:  
Matrix rotation and translation  
0.45147653 -0.89183343 -0.02832104 108.19603381  
-0.72464461 -0.38499007 0.57155301 106.44718519  
-0.52063340 -0.23752008 -0.82007627 88.48488717  
Axis -0.84126924 0.51190337 0.17384191  
Axis point 0.00000000 100.17594419 37.56307509  
Rotation angle (degrees) 151.25811848  
Shift along axis -21.14894006  
  

> fitmap #2 inMap #7

Fit molecule fold_satbc_msmk_model_0.cif (#2) to map
cryosparc_P1_J293_002_volume_map.mrc z flip copy (#7) using 10704 atoms  
average map value = 0.04074, steps = 44  
shifted from previous position = 0.00735  
rotated from previous position = 0.00989 degrees  
atoms outside contour = 8894, contour level = 0.081288  
  
Position of fold_satbc_msmk_model_0.cif (#2) relative to
cryosparc_P1_J293_002_volume_map.mrc z flip copy (#7) coordinates:  
Matrix rotation and translation  
0.45135561 -0.89189162 -0.02841577 108.19486227  
-0.72464227 -0.38492766 0.57159801 106.44647595  
-0.52074149 -0.23740270 -0.82004163 88.47736955  
Axis -0.84123205 0.51194043 0.17391272  
Axis point 0.00000000 100.17769209 37.56542041  
Rotation angle (degrees) 151.25954064  
Shift along axis -21.13539053  
  

> fitmap #2 inMap #7

Fit molecule fold_satbc_msmk_model_0.cif (#2) to map
cryosparc_P1_J293_002_volume_map.mrc z flip copy (#7) using 10704 atoms  
average map value = 0.04074, steps = 48  
shifted from previous position = 0.0013  
rotated from previous position = 0.0145 degrees  
atoms outside contour = 8895, contour level = 0.081288  
  
Position of fold_satbc_msmk_model_0.cif (#2) relative to
cryosparc_P1_J293_002_volume_map.mrc z flip copy (#7) coordinates:  
Matrix rotation and translation  
0.45135845 -0.89189108 -0.02838784 108.19537805  
-0.72477965 -0.38497526 0.57139173 106.44549709  
-0.52054780 -0.23732755 -0.82018634 88.47909773  
Axis -0.84124172 0.51195204 0.17383176  
Axis point 0.00000000 100.17201954 37.56804512  
Rotation angle (degrees) 151.27083121  
Shift along axis -21.14299855  
  

> fitmap #2 inMap #7

Fit molecule fold_satbc_msmk_model_0.cif (#2) to map
cryosparc_P1_J293_002_volume_map.mrc z flip copy (#7) using 10704 atoms  
average map value = 0.04074, steps = 28  
shifted from previous position = 0.0113  
rotated from previous position = 0.0177 degrees  
atoms outside contour = 8893, contour level = 0.081288  
  
Position of fold_satbc_msmk_model_0.cif (#2) relative to
cryosparc_P1_J293_002_volume_map.mrc z flip copy (#7) coordinates:  
Matrix rotation and translation  
0.45147144 -0.89183345 -0.02840159 108.19682184  
-0.72458297 -0.38500844 0.57161879 106.45220146  
-0.52072360 -0.23749025 -0.82002763 88.48832855  
Axis -0.84126646 0.51188898 0.17389772  
Axis point 0.00000000 100.17922484 37.56723856  
Rotation angle (degrees) 151.25661850  
Shift along axis -21.14273000  
  

> fitmap #2 inMap #7

Fit molecule fold_satbc_msmk_model_0.cif (#2) to map
cryosparc_P1_J293_002_volume_map.mrc z flip copy (#7) using 10704 atoms  
average map value = 0.04074, steps = 48  
shifted from previous position = 0.0101  
rotated from previous position = 0.0123 degrees  
atoms outside contour = 8895, contour level = 0.081288  
  
Position of fold_satbc_msmk_model_0.cif (#2) relative to
cryosparc_P1_J293_002_volume_map.mrc z flip copy (#7) coordinates:  
Matrix rotation and translation  
0.45138175 -0.89187829 -0.02841891 108.19345639  
-0.72471453 -0.38498900 0.57146507 106.46097865  
-0.52061826 -0.23735331 -0.82013416 88.48693552  
Axis -0.84124624 0.51193304 0.17386584  
Axis point 0.00000000 100.18057613 37.57020106  
Rotation angle (degrees) 151.26715179  
Shift along axis -21.13159105  
  

> fitmap #2 inMap #7

Fit molecule fold_satbc_msmk_model_0.cif (#2) to map
cryosparc_P1_J293_002_volume_map.mrc z flip copy (#7) using 10704 atoms  
average map value = 0.04074, steps = 40  
shifted from previous position = 0.00605  
rotated from previous position = 0.00223 degrees  
atoms outside contour = 8893, contour level = 0.081288  
  
Position of fold_satbc_msmk_model_0.cif (#2) relative to
cryosparc_P1_J293_002_volume_map.mrc z flip copy (#7) coordinates:  
Matrix rotation and translation  
0.45137549 -0.89188217 -0.02839659 108.19391644  
-0.72470691 -0.38496490 0.57149097 106.45505738  
-0.52063430 -0.23737781 -0.82011689 88.48633669  
Axis -0.84124263 0.51193884 0.17386622  
Axis point 0.00000000 100.17937136 37.56927861  
Rotation angle (degrees) 151.26505977  
Shift along axis -21.13407146  
  

> fitmap #2 inMap #7

Fit molecule fold_satbc_msmk_model_0.cif (#2) to map
cryosparc_P1_J293_002_volume_map.mrc z flip copy (#7) using 10704 atoms  
average map value = 0.04074, steps = 44  
shifted from previous position = 0.00372  
rotated from previous position = 0.00896 degrees  
atoms outside contour = 8892, contour level = 0.081288  
  
Position of fold_satbc_msmk_model_0.cif (#2) relative to
cryosparc_P1_J293_002_volume_map.mrc z flip copy (#7) coordinates:  
Matrix rotation and translation  
0.45136482 -0.89188976 -0.02832769 108.19536941  
-0.72465674 -0.38488709 0.57160699 106.45303176  
-0.52071338 -0.23747543 -0.82003842 88.48853109  
Axis -0.84123251 0.51195137 0.17387828  
Axis point 0.00000000 100.18492077 37.56599192  
Rotation angle (degrees) 151.25638405  
Shift along axis -21.13245331  
  

> fitmap #2 inMap #7

Fit molecule fold_satbc_msmk_model_0.cif (#2) to map
cryosparc_P1_J293_002_volume_map.mrc z flip copy (#7) using 10704 atoms  
average map value = 0.04074, steps = 48  
shifted from previous position = 0.0183  
rotated from previous position = 0.0122 degrees  
atoms outside contour = 8897, contour level = 0.081288  
  
Position of fold_satbc_msmk_model_0.cif (#2) relative to
cryosparc_P1_J293_002_volume_map.mrc z flip copy (#7) coordinates:  
Matrix rotation and translation  
0.45127226 -0.89193110 -0.02850019 108.19350909  
-0.72468717 -0.38491811 0.57154752 106.46111474  
-0.52075125 -0.23726982 -0.82007389 88.47219317  
Axis -0.84121056 0.51196577 0.17394207  
Axis point 0.00000000 100.18310915 37.56739192  
Rotation angle (degrees) 151.26585995  
Shift along axis -21.12003961  
  

> fitmap #2 inMap #7

Fit molecule fold_satbc_msmk_model_0.cif (#2) to map
cryosparc_P1_J293_002_volume_map.mrc z flip copy (#7) using 10704 atoms  
average map value = 0.04074, steps = 40  
shifted from previous position = 0.0117  
rotated from previous position = 0.00688 degrees  
atoms outside contour = 8896, contour level = 0.081288  
  
Position of fold_satbc_msmk_model_0.cif (#2) relative to
cryosparc_P1_J293_002_volume_map.mrc z flip copy (#7) coordinates:  
Matrix rotation and translation  
0.45132055 -0.89190900 -0.02842714 108.19445159  
-0.72464512 -0.38490085 0.57161245 106.44987177  
-0.52076792 -0.23738086 -0.82003117 88.47382873  
Axis -0.84122084 0.51195396 0.17392711  
Axis point 0.00000000 100.18019149 37.56421870  
Rotation angle (degrees) 151.25940936  
Shift along axis -21.12999707  
  

> fitmap #2 inMap #7

Fit molecule fold_satbc_msmk_model_0.cif (#2) to map
cryosparc_P1_J293_002_volume_map.mrc z flip copy (#7) using 10704 atoms  
average map value = 0.04074, steps = 48  
shifted from previous position = 0.0161  
rotated from previous position = 0.0046 degrees  
atoms outside contour = 8897, contour level = 0.081288  
  
Position of fold_satbc_msmk_model_0.cif (#2) relative to
cryosparc_P1_J293_002_volume_map.mrc z flip copy (#7) coordinates:  
Matrix rotation and translation  
0.45130235 -0.89191724 -0.02845767 108.19513108  
-0.72460740 -0.38488487 0.57167103 106.46620226  
-0.52083618 -0.23737584 -0.81998927 88.47428817  
Axis -0.84121324 0.51195466 0.17396181  
Axis point 0.00000000 100.19010513 37.56359073  
Rotation angle (degrees) 151.25704510  
Shift along axis -21.11816148  
  

> fitmap #2 inMap #7

Fit molecule fold_satbc_msmk_model_0.cif (#2) to map
cryosparc_P1_J293_002_volume_map.mrc z flip copy (#7) using 10704 atoms  
average map value = 0.04074, steps = 36  
shifted from previous position = 0.0143  
rotated from previous position = 0.0142 degrees  
atoms outside contour = 8893, contour level = 0.081288  
  
Position of fold_satbc_msmk_model_0.cif (#2) relative to
cryosparc_P1_J293_002_volume_map.mrc z flip copy (#7) coordinates:  
Matrix rotation and translation  
0.45135737 -0.89189243 -0.02836226 108.19394024  
-0.72472507 -0.38493290 0.57148949 106.45575884  
-0.52062472 -0.23739115 -0.82011911 88.48527495  
Axis -0.84123635 0.51195325 0.17385416  
Axis point 0.00000000 100.18112580 37.56742193  
Rotation angle (degrees) 151.26436429  
Shift along axis -21.13277121  
  

> fitmap #2 inMap #7

Fit molecule fold_satbc_msmk_model_0.cif (#2) to map
cryosparc_P1_J293_002_volume_map.mrc z flip copy (#7) using 10704 atoms  
average map value = 0.04074, steps = 48  
shifted from previous position = 0.00752  
rotated from previous position = 0.014 degrees  
atoms outside contour = 8897, contour level = 0.081288  
  
Position of fold_satbc_msmk_model_0.cif (#2) relative to
cryosparc_P1_J293_002_volume_map.mrc z flip copy (#7) coordinates:  
Matrix rotation and translation  
0.45133012 -0.89190372 -0.02844099 108.19354159  
-0.72459607 -0.38489704 0.57167719 106.46176272  
-0.52082786 -0.23740691 -0.81998555 88.47933718  
Axis -0.84122114 0.51194462 0.17395315  
Axis point 0.00000000 100.18771489 37.56520509  
Rotation angle (degrees) 151.25589427  
Shift along axis -21.12090887  
  

> fitmap #2 inMap #7

Fit molecule fold_satbc_msmk_model_0.cif (#2) to map
cryosparc_P1_J293_002_volume_map.mrc z flip copy (#7) using 10704 atoms  
average map value = 0.04074, steps = 44  
shifted from previous position = 0.0102  
rotated from previous position = 0.00698 degrees  
atoms outside contour = 8892, contour level = 0.081288  
  
Position of fold_satbc_msmk_model_0.cif (#2) relative to
cryosparc_P1_J293_002_volume_map.mrc z flip copy (#7) coordinates:  
Matrix rotation and translation  
0.45135683 -0.89189134 -0.02840520 108.19530580  
-0.72465305 -0.38492702 0.57158477 106.45319526  
-0.52072544 -0.23740477 -0.82005122 88.48551206  
Axis -0.84123279 0.51194225 0.17390378  
Axis point 0.00000000 100.18213761 37.56853458  
Rotation angle (degrees) 151.26000177  
Shift along axis -21.13158610  
  

> fitmap #2 inMap #7

Fit molecule fold_satbc_msmk_model_0.cif (#2) to map
cryosparc_P1_J293_002_volume_map.mrc z flip copy (#7) using 10704 atoms  
average map value = 0.04074, steps = 48  
shifted from previous position = 0.015  
rotated from previous position = 0.0128 degrees  
atoms outside contour = 8896, contour level = 0.081288  
  
Position of fold_satbc_msmk_model_0.cif (#2) relative to
cryosparc_P1_J293_002_volume_map.mrc z flip copy (#7) coordinates:  
Matrix rotation and translation  
0.45131976 -0.89191026 -0.02840012 108.19254560  
-0.72478358 -0.38494587 0.57140655 106.44247139  
-0.52057587 -0.23730313 -0.82017559 88.47497840  
Axis -0.84122940 0.51196705 0.17384716  
Axis point 0.00000000 100.17064769 37.56728458  
Rotation angle (degrees) 151.27074448  
Shift along axis -21.13858840  
  

> fitmap #2 inMap #7

Fit molecule fold_satbc_msmk_model_0.cif (#2) to map
cryosparc_P1_J293_002_volume_map.mrc z flip copy (#7) using 10704 atoms  
average map value = 0.04074, steps = 40  
shifted from previous position = 0.0138  
rotated from previous position = 0.0137 degrees  
atoms outside contour = 8897, contour level = 0.081288  
  
Position of fold_satbc_msmk_model_0.cif (#2) relative to
cryosparc_P1_J293_002_volume_map.mrc z flip copy (#7) coordinates:  
Matrix rotation and translation  
0.45136559 -0.89188558 -0.02844677 108.19459838  
-0.72463368 -0.38495369 0.57159137 106.45695666  
-0.52074479 -0.23738319 -0.82004518 88.47529361  
Axis -0.84123612 0.51193065 0.17392183  
Axis point 0.00000000 100.18099402 37.56452048  
Rotation angle (degrees) 151.26070814  
Shift along axis -21.13083945  
  

> fitmap #2 inMap #7

Fit molecule fold_satbc_msmk_model_0.cif (#2) to map
cryosparc_P1_J293_002_volume_map.mrc z flip copy (#7) using 10704 atoms  
average map value = 0.04074, steps = 48  
shifted from previous position = 0.0169  
rotated from previous position = 0.0118 degrees  
atoms outside contour = 8891, contour level = 0.081288  
  
Position of fold_satbc_msmk_model_0.cif (#2) relative to
cryosparc_P1_J293_002_volume_map.mrc z flip copy (#7) coordinates:  
Matrix rotation and translation  
0.45141226 -0.89186448 -0.02836786 108.19423432  
-0.72473074 -0.38499447 0.57144083 106.44724223  
-0.52056924 -0.23739633 -0.82015283 88.49001916  
Axis -0.84125560 0.51192897 0.17383251  
Axis point 0.00000000 100.17402129 37.57071275  
Rotation angle (degrees) 151.26677221  
Shift along axis -21.14313727  
  

> volume #5 level 0.1767

> volume #7 level 0.03396

Can only have one displayed volume when erasing  

> volume #7 level 0.04312

> surface dust #5 size 8.25

> surface dust #7 size 8.25

> volume #5 level 0.0103

> volume #5 level 0.0477

> volume #7 level 0.008773

> volume erase #7 center 41.631,89.076,115.17 radius 25.238

> volume erase #7 center 49.086,115.96,85.314 radius 25.238

> volume erase #7 center 167.6,116.83,98.538 radius 25.238

> volume erase #7 center 153.43,126.76,142.8 radius 25.238

> volume erase #7 center 149.6,82.517,148.34 radius 25.238

> volume erase #7 center 97.281,49.446,150.61 radius 25.238

> volume erase #7 center 48.491,112.62,140.6 radius 25.238

> volume erase #7 center 120.41,179.47,113.69 radius 25.238

> volume erase #7 center 145.95,159.63,134.61 radius 25.238

> volume erase #7 center 96.103,178.36,120.41 radius 25.238

> volume #7 level 0.07442

> volume erase #7 center 99.515,166.5,119.7 radius 25.238

> volume #7 level 0.04389

> save /Users/lue81154/Downloads/mask_tmds.mrc models #7

> save "/Users/lue81154/OneDrive - Diamond Light Source Ltd/flipmap.mrc"
> models #5

> volume #7 level 0.03244

> open /Users/lue81154/Downloads/cryosparc_P1_J302_mask.mrc

Opened cryosparc_P1_J302_mask.mrc as #8, grid size 256,256,256, pixel 0.825,
shown at level 1, step 1, values float32  

> volume #8 level 0.7588

> volume #7 level 0.01793

> volume #8 level 1

> volume #8 level 0.9505

Desktop color scheme is dark  
Desktop color scheme is light  

> open /Users/lue81154/Downloads/sequence.fasta


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

Log:
UCSF ChimeraX version: 1.10.1 (2025-07-24)  
© 2016-2025 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 4.1 Metal - 88.1
OpenGL renderer: Apple M3
OpenGL vendor: Apple

Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.8.1, Qt 6.8.2
Qt runtime version: 6.8.2
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Air
      Model Identifier: Mac15,12
      Model Number: MXCV3B/A
      Chip: Apple M3
      Total Number of Cores: 8 (4 performance and 4 efficiency)
      Memory: 16 GB
      System Firmware Version: 11881.140.96
      OS Loader Version: 10151.140.19.700.2

Software:

    System Software Overview:

      System Version: macOS 14.7.7 (23H723)
      Kernel Version: Darwin 23.6.0
      Time since boot: 13 days, 12 minutes

Graphics/Displays:

    Apple M3:

      Chipset Model: Apple M3
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 10
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-in Liquid Retina Display
          Resolution: 2560 x 1664 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal


Installed Packages:
    alabaster: 1.0.0
    appdirs: 1.4.4
    appnope: 0.1.4
    asttokens: 3.0.0
    babel: 2.17.0
    beautifulsoup4: 4.13.3
    blockdiag: 3.0.0
    blosc2: 3.6.1
    build: 1.2.2.post1
    certifi: 2023.11.17
    cftime: 1.6.4.post1
    charset-normalizer: 3.4.2
    ChimeraX-AddCharge: 1.5.19
    ChimeraX-AddH: 2.2.7
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.6.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.20.2
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Aniso: 1.1.4
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.60.7
    ChimeraX-AtomicLibrary: 14.1.19
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.3
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 3.0.0
    ChimeraX-Boltz: 1.0
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.2
    ChimeraX-BuildStructure: 2.13.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.5.1
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.5
    ChimeraX-ChemGroup: 2.0.2
    ChimeraX-Clashes: 2.3
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.8
    ChimeraX-CommandLine: 1.3
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.10.1
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.5
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.4
    ChimeraX-Dicom: 1.2.7
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.4
    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: 2.5.1
    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: 1.6.2
    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: 2.2.2
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.10.1
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.16
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.19
    ChimeraX-ModelPanel: 1.5.1
    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: 1.14.1
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.10
    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: 1.1.3
    ChimeraX-ProfileGrids: 1.1.3
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.6.3
    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: 2.0.3
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.5.7
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.17.1
    ChimeraX-Shape: 1.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.2.1
    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: 1.19.1
    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: 2.5.2
    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: 1.45.2
    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: 1.1.5
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    contourpy: 1.3.2
    coverage: 7.10.0
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.0.12
    debugpy: 1.8.15
    decorator: 5.2.1
    docutils: 0.21.2
    executing: 2.2.0
    filelock: 3.18.0
    fonttools: 4.59.0
    funcparserlib: 2.0.0a0
    glfw: 2.9.0
    grako: 3.16.5
    h5py: 3.14.0
    html2text: 2024.2.26
    idna: 3.10
    ihm: 2.2
    imagecodecs: 2024.6.1
    imagesize: 1.4.1
    iniconfig: 2.1.0
    ipykernel: 6.29.5
    ipython: 8.26.0
    ipywidgets: 8.1.7
    jedi: 0.19.1
    Jinja2: 3.1.6
    jupyter_client: 8.6.3
    jupyter_core: 5.8.1
    jupyterlab_widgets: 3.0.15
    kiwisolver: 1.4.8
    line_profiler: 4.2.0
    lxml: 5.3.1
    lz4: 4.3.2
    MarkupSafe: 3.0.2
    matplotlib: 3.10.1
    matplotlib-inline: 0.1.7
    msgpack: 1.1.0
    ndindex: 1.10.0
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.11.0
    numpy: 1.26.4
    OpenMM: 8.2.0
    openvr: 1.26.701
    packaging: 24.2
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pexpect: 4.9.0
    pickleshare: 0.7.5
    pillow: 10.4.0
    pip: 25.0.1
    pkginfo: 1.11.1
    platformdirs: 4.3.8
    pluggy: 1.6.0
    prompt_toolkit: 3.0.51
    psutil: 7.0.0
    ptyprocess: 0.7.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    Pygments: 2.18.0
    pynmrstar: 3.3.5
    pynrrd: 1.0.0
    PyOpenGL: 3.1.9
    PyOpenGL-accelerate: 3.1.9
    pyopenxr: 1.1.4501
    pyparsing: 3.2.3
    pyproject_hooks: 1.2.0
    PyQt6-commercial: 6.8.1
    PyQt6-Qt6: 6.8.2
    PyQt6-WebEngine-commercial: 6.8.0
    PyQt6-WebEngine-Qt6: 6.8.2
    PyQt6_sip: 13.10.0
    pytest: 8.4.1
    pytest-cov: 6.2.1
    python-dateutil: 2.9.0.post0
    pytz: 2025.2
    pyzmq: 27.0.0
    qtconsole: 5.5.2
    QtPy: 2.4.3
    qtshim: 1.1
    RandomWords: 0.4.0
    requests: 2.32.3
    roman-numerals-py: 3.1.0
    scipy: 1.14.0
    setuptools: 78.1.0
    sfftk-rw: 0.8.1
    six: 1.16.0
    snowballstemmer: 3.0.1
    sortedcontainers: 2.4.0
    soupsieve: 2.7
    Sphinx: 8.2.3
    sphinx-autodoc-typehints: 3.1.0
    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: 0.7.1
    tables: 3.10.2
    tcia_utils: 1.5.1
    tifffile: 2025.3.13
    tinyarray: 1.2.4
    tornado: 6.5.1
    traitlets: 5.14.3
    typing_extensions: 4.14.1
    tzdata: 2025.2
    urllib3: 2.5.0
    wcwidth: 0.2.13
    webcolors: 24.11.1
    wheel: 0.45.1
    wheel-filename: 1.4.2
    widgetsnbextension: 4.0.14

Change History (2)

comment:1 by pett, 3 weeks ago

Component: UnassignedSequence
Description: modified (diff)
Owner: set to pett
Platform: all
Project: ChimeraX
Status: newaccepted
Summary: ChimeraX bug report submissionCrash creating sequence viewer for FASTA file

comment:2 by pett, 3 weeks ago

Resolution: can't reproduce
Status: acceptedclosed
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