Opened 6 months ago

Closed 6 months ago

#17846 closed defect (duplicate)

Crash on Mac waking from sleep

Reported by: guillermo.montoya@… Owned by: Tom Goddard
Priority: normal Milestone:
Component: Window Toolkit Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description (last modified by Eric Pettersen) 

The following bug report has been submitted:
Platform:        macOS-15.1.1-arm64-arm-64bit
ChimeraX Version: 1.10.dev202412070146 (2024-12-07 01:46:57 UTC)
Description
Last time you used ChimeraX it crashed.
This is a known crash that we are unable to fix. Here is information that may help you avoid this crash. The Qt window toolkit crashed due to a display configuration change, typically when waking from sleep or when an external display is disconnected or connected. This has only been seen on Mac computers. We hope a newer version of Qt will fix it. We update ChimeraX daily builds whenever a new Qt is released. You can check here https://www.cgl.ucsf.edu/chimerax/docs/troubleshoot.html#macdisplay to see if it has been fixed in a newer ChimeraX.
Fatal Python error: Segmentation fault

Current thread 0x00000001fbcfb840 (most recent call first):
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 335 in event_loop
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1054 in init
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1217 in 
  File "", line 88 in _run_code
  File "", line 198 in _run_module_as_main

Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, openmm._openmm, openmm.app.internal.compiled, chimerax.map._map, charset_normalizer.md, requests.packages.charset_normalizer.md, requests.packages.chardet.md, PIL._imaging, kiwisolver._cext, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.surface._surface, chimerax.pdb_lib._load_libs, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.pdb._pdbio, lxml._elementpath, lxml.etree, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw, chimerax.morph._morph, PIL._imagingmath, cython.cimports.libc.math, scipy._lib._ccallback_c, scipy.linalg._fblas, scipy.linalg._flapack, scipy.linalg.cython_lapack, scipy.linalg._cythonized_array_utils, scipy.linalg._solve_toeplitz, scipy.linalg._decomp_lu_cython, scipy.linalg._matfuncs_sqrtm_triu, scipy.linalg.cython_blas, scipy.linalg._matfuncs_expm, scipy.linalg._decomp_update, scipy.sparse._sparsetools, _csparsetools, scipy.sparse._csparsetools, scipy.sparse.linalg._dsolve._superlu, scipy.sparse.linalg._eigen.arpack._arpack, scipy.sparse.linalg._propack._spropack, scipy.sparse.linalg._propack._dpropack, scipy.sparse.linalg._propack._cpropack, scipy.sparse.linalg._propack._zpropack, scipy.sparse.csgraph._tools, scipy.sparse.csgraph._shortest_path, scipy.sparse.csgraph._traversal, scipy.sparse.csgraph._min_spanning_tree, scipy.sparse.csgraph._flow, scipy.sparse.csgraph._matching, scipy.sparse.csgraph._reordering, scipy.optimize._group_columns, scipy._lib.messagestream, scipy.optimize._trlib._trlib, scipy.optimize._lbfgsb, _moduleTNC, scipy.optimize._moduleTNC, scipy.optimize._cobyla, scipy.optimize._slsqp, scipy.optimize._minpack, scipy.optimize._lsq.givens_elimination, scipy.optimize._zeros, scipy.optimize._highs.cython.src._highs_wrapper, scipy.optimize._highs._highs_wrapper, scipy.optimize._highs.cython.src._highs_constants, scipy.optimize._highs._highs_constants, scipy.linalg._interpolative, scipy.optimize._bglu_dense, scipy.optimize._lsap, scipy.spatial._ckdtree, scipy.spatial._qhull, scipy.spatial._voronoi, scipy.spatial._distance_wrap, scipy.spatial._hausdorff, scipy.special._ufuncs_cxx, scipy.special._ufuncs, scipy.special._specfun, scipy.special._comb, scipy.special._ellip_harm_2, scipy.spatial.transform._rotation, scipy.optimize._direct (total: 122)


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  "procRole" : "Background",
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  "captureTime" : "2025-05-29 13:17:10.9756 +0200",
  "codeSigningMonitor" : 1,
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  "translated" : false,
  "cpuType" : "ARM-64",
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  "procLaunch" : "2025-05-28 13:07:52.4229 +0200",
  "procStartAbsTime" : 15381538262332,
  "procExitAbsTime" : 16233811031135,
  "procName" : "ChimeraX",
  "procPath" : "\/Applications\/ChimeraX_Daily.app\/Contents\/MacOS\/ChimeraX",
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  "codeSigningTeamID" : "LWV8X224YF",
  "codeSigningFlags" : 570491649,
  "codeSigningValidationCategory" : 6,
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  "instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRcuD\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkWfg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
  "bootSessionUUID" : "49904D18-A1A3-4815-B7C0-38543277A7AA",
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fault"},"pc":{"value":6823763508},"far":{"value":0}},"frames":[{"imageOffset":3636,"symbol":"mach_msg2_trap","symbolLocation":8,"imageIndex":250},{"imageOffset":79312,"symbol":"mach_msg2_internal","symbolLocation":80,"imageIndex":250},{"imageOffset":39384,"symbol":"mach_msg_overwrite","symbolLocation":480,"imageIndex":250},{"imageOffset":4476,"symbol":"mach_msg","symbolLocation":24,"imageIndex":250},{"imageOffset":71161832,"imageIndex":56},{"imageOffset":70677284,"imageIndex":56},{"imageOffset":70677152,"imageIndex":56},{"imageOffset":70343492,"imageIndex":56},{"imageOffset":70809656,"imageIndex":56},{"imageOffset":70544784,"imageIndex":56},{"imageOffset":70952276,"imageIndex":56},{"imageOffset":70952656,"imageIndex":56},{"imageOffset":71057880,"imageIndex":56},{"imageOffset":29412,"symbol":"_pthread_start","symbolLocation":136,"imageIndex":251},{"imageOffset":8444,"symbol":"thread_start","symbolLocation":8,"imageIndex":251}]},{"id":11307781,"name":"ThreadPoolSingleThreadSharedBackgroundBlocking2","threadState":{"x":[{"value":268451845},{"value":17179869186},{"value":0},{"value":446414605778944},{"value":0},{"value":446414605778944},{"value":32},{"value":0},{"value":18446744073709550527},{"value":32},{"value":0},{"value":0},{"value":0},{"value":103939},{"value":3685357571},{"value":3683258395},{"value":18446744073709551569},{"value":3},{"value":0},{"value":0},{"value":32},{"value":446414605778944},{"value":0},{"value":446414605778944},{"value":14945496368},{"value":0},{"value":17179869186},{"value":17179869186},{"value":2}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6823839184},"cpsr":{"value":4096},"fp":{"value":14945495712},"sp":{"value":14945495632},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6823763508},"far":{"value":0}},"frames":[{"imageOffset":3636,"symbol":"mach_msg2_trap","symbolLocation":8,"imageIndex":250},{"imageOffset":79312,"symbol":"mach_msg2_internal","symbolLocation":80,"imageIndex":250},{"imageOffset":39384,"symbol":"mach_msg_overwrite","symbolLocation":480,"imageIndex":250},{"imageOffset":4476,"symbol":"mach_msg","symbolLocation":24,"imageIndex":250},{"imageOffset":71161832,"imageIndex":56},{"imageOffset":70677284,"imageIndex":56},{"imageOffset":70900888,"imageIndex":56},{"imageOffset":70903324,"imageIndex":56},{"imageOffset":70902760,"imageIndex":56},{"imageOffset":71057880,"imageIndex":56},{"imageOffset":29412,"symbol":"_pthread_start","symbolLocation":136,"imageIndex":251},{"imageOffset":8444,"symbol":"thread_start","symbolLocation":8,"imageIndex":251}]},{"id":11506596,"name":"QFileInfoGatherer","threadState":{"x":[{"value":260},{"value":0},{"value":8448},{"value":0},{"value":0},{"value":160},{"value":0},{"value":0},{"value":20538502536},{"value":0},{"value":0},{"value":2},{"value":2},{"value":0},{"value":0},{"value":0},{"value":305},{"value":8656361480},{"value":0},{"value":105553795934336},{"value":105553795934400},{"value":20538503392},{"value":0},{"value":0},{"value":8448},{"value":8449},{"value":8704},{"value":0},{"value":0}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6824032404},"cpsr":{"value":1610616832},"fp":{"value":20538502656},"sp":{"value":20538502512},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6823777740},"far":{"value":0}},"frames":[{"imageOffset":17868,"symbol":"__psynch_cvwait","symbolLocation":8,"imageIndex":250},{"imageOffset":30868,"symbol":"_pthread_cond_wait","symbolLocation":1204,"imageIndex":251},{"imageOffset":2118012,"imageIndex":45},{"imageOffset":2117824,"symbol":"QWaitCondition::wait(QMutex*, QDeadlineTimer)","symbolLocation":108,"imageIndex":45},{"imageOffset":4264588,"symbol":"QFileInfoGatherer::run()","symbolLocation":136,"imageIndex":50},{"imageOffset":2063036,"imageIndex":45},{"imageOffset":29412,"symbol":"_pthread_start","symbolLocation":136,"imageIndex":251},{"imageOffset":8444,"symbol":"thread_start","symbolLocation":8,"imageIndex":251}]},{"id":11699742,"frames":[{"imageOffset":8424,"symbol":"start_wqthread","symbolLocation":0,"imageIndex":251}],"threadState":{"x":[{"value":13196619776},{"value":131495},{"value":13196083200},{"value":0},{"value":409604},{"value":18446744073709551615},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0}],"flavor":"ARM_THREAD_STATE64","lr":{"value":0},"cpsr":{"value":4096},"fp":{"value":0},"sp":{"value":13196619776},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6824009960},"far":{"value":0}}},{"id":11752627,"frames":[{"imageOffset":8424,"symbol":"start_wqthread","symbolLocation":0,"imageIndex":251}],"threadState":{"x":[{"value":13195620352},{"value":158831},{"value":13195083776},{"value":0},{"value":409604},{"value":18446744073709551615},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0}],"flavor":"ARM_THREAD_STATE64","lr":{"value":0},"cpsr":{"value":4096},"fp":{"value":0},"sp":{"value":13195620352},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6824009960},"far":{"value":0}}},{"id":11752628,"frames":[{"imageOffset":8424,"symbol":"start_wqthread","symbolLocation":0,"imageIndex":251}],"threadState":{"x":[{"value":13197619200},{"value":0},{"value":13197082624},{"value":0},{"value":278530},{"value":18446744073709551615},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0}],"flavor":"ARM_THREAD_STATE64","lr":{"value":0},"cpsr":{"value":4096},"fp":{"value":0},"sp":{"value":13197619200},"esr":{"value":0,"description":" Address size fault"},"pc":{"value":6824009960},"far":{"value":0}}}],
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[deleted to fit within ticket limits]

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===== Log before crash start =====
UCSF ChimeraX version: 1.10.dev202412070146 (2024-12-07)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open /Users/gmontoya/Downloads/cas8_movment.cxs

Opened halfcleaved_HNH_center_sharp.mrc as #13, grid size 420,420,420, pixel
0.725, shown at level 0.02, step 1, values float32  
Opened post_HNH_cent_sharp.mrc as #5, grid size 420,420,420, pixel 0.725,
shown at level 0.00328, step 2, values float32  
Opened apo_HNH_cent_sharp.mrc as #9, grid size 420,420,420, pixel 0.725, shown
at level 0.00199, step 2, values float32  
Opened apo_HNH_cent_sharp.mrc zone as #21, grid size 420,420,420, pixel 0.725,
shown at level 0.00199, step 2, values float32  
Opened apo_HNH_in_sharp.mrc as #23, grid size 420,420,420, pixel 0.725, shown
at level 0.00173, step 2, values float32  
Opened apo_HNH_in_sharp.mrc zone as #24, grid size 420,420,420, pixel 0.725,
shown at level 0.00173, step 2, values float32  
Opened apo_HNH_out_sharp.mrc as #26, grid size 420,420,420, pixel 0.725, shown
at level 0.00214, step 2, values float32  
Opened apo_HNH_out_sharp.mrc zone as #27, grid size 420,420,420, pixel 0.725,
shown at level 0.00214, step 2, values float32  
Opened post_HNH_in_sharp.mrc as #2, grid size 420,420,420, pixel 0.725, shown
at level 0.0257, step 2, values float32  
Opened post_HNH_out_sharp.mrc as #6, grid size 420,420,420, pixel 0.725, shown
at level 0.00342, step 2, values float32  
Opened halfcleaved_HNH_in_sharp.mrc as #12, grid size 420,420,420, pixel
0.725, shown at level 0.00277, step 2, values float32  
Opened halfcleaved_HNH_out_sharp.mrc as #16, grid size 420,420,420, pixel
0.725, shown at level 0.0029, step 2, values float32  
Opened post_HNH_in_sharp.mrc zone as #17, grid size 420,420,420, pixel 0.725,
shown at level 0.0257, step 2, values float32  
Opened post_HNH_out_sharp.mrc zone as #18, grid size 420,420,420, pixel 0.725,
shown at level 0.00342, step 2, values float32  
Opened post_HNH_cent_sharp.mrc zone as #19, grid size 420,420,420, pixel
0.725, shown at level 0.00328, step 2, values float32  
Opened halfcleaved_HNH_center.mrc zone as #20, grid size 420,420,420, pixel
0.725, shown at level 0.02, step 1, values float32  
Opened halfcleaved_HNH_in_sharp.mrc zone as #28, grid size 420,420,420, pixel
0.725, shown at level 0.00277, step 2, values float32  
Opened halfcleaved_HNH_out_sharp.mrc zone as #29, grid size 420,420,420, pixel
0.725, shown at level 0.0029, step 2, values float32  
Log from Wed May 28 12:25:00 2025UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open "/Users/zxc755/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/Type
> I-F_HNH/Manuscript/figures/structure/cas8_movement/cas8_movement.cxs"

Opened halfcleaved_HNH_center_sharp3Å.mrc as #13, grid size 420,420,420,
pixel 0.725, shown at level 0.02, step 1, values float32  
Opened post_HNH_cent_sharp.mrc as #5, grid size 420,420,420, pixel 0.725,
shown at level 0.00328, step 2, values float32  
Opened apo_HNH_cent_sharp.mrc as #9, grid size 420,420,420, pixel 0.725, shown
at level 0.00199, step 2, values float32  
Opened apo_HNH_cent_sharp.mrc zone as #10, grid size 420,420,420, pixel 0.725,
shown at level 0.02, step 2, values float32  
Opened apo_HNH_cent_sharp.mrc zone as #21, grid size 420,420,420, pixel 0.725,
shown at level 0.00199, step 2, values float32  
Opened apo_HNH_in_sharp.mrc as #23, grid size 420,420,420, pixel 0.725, shown
at level 0.00173, step 2, values float32  
Opened apo_HNH_in_sharp.mrc zone as #24, grid size 420,420,420, pixel 0.725,
shown at level 0.00173, step 2, values float32  
Opened apo_HNH_out_sharp.mrc as #26, grid size 420,420,420, pixel 0.725, shown
at level 0.00214, step 2, values float32  
Opened apo_HNH_out_sharp.mrc zone as #27, grid size 420,420,420, pixel 0.725,
shown at level 0.00214, step 2, values float32  
Opened post_HNH_in_sharp.mrc as #2, grid size 420,420,420, pixel 0.725, shown
at level 0.0257, step 2, values float32  
Opened post_HNH_out_sharp.mrc as #6, grid size 420,420,420, pixel 0.725, shown
at level 0.00342, step 2, values float32  
Opened halfcleaved_HNH_in_sharp.mrc as #12, grid size 420,420,420, pixel
0.725, shown at level 0.00277, step 2, values float32  
Opened halfcleaved_HNH_out_sharp.mrc as #16, grid size 420,420,420, pixel
0.725, shown at level 0.0029, step 2, values float32  
Opened post_HNH_in_sharp.mrc zone as #17, grid size 420,420,420, pixel 0.725,
shown at level 0.0257, step 2, values float32  
Opened post_HNH_out_sharp.mrc zone as #18, grid size 420,420,420, pixel 0.725,
shown at level 0.00342, step 2, values float32  
Opened post_HNH_cent_sharp.mrc zone as #19, grid size 420,420,420, pixel
0.725, shown at level 0.00328, step 2, values float32  
Opened halfcleaved_HNH_center_sharp3Å.mrc zone as #20, grid size 420,420,420,
pixel 0.725, shown at level 0.02, step 1, values float32  
Opened halfcleaved_HNH_in_sharp.mrc zone as #28, grid size 420,420,420, pixel
0.725, shown at level 0.00277, step 2, values float32  
Opened halfcleaved_HNH_out_sharp.mrc zone as #29, grid size 420,420,420, pixel
0.725, shown at level 0.0029, step 2, values float32  
Log from Sat May 17 13:40:51 2025UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open "/Users/zxc755/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/Type
> I-F_HNH/Manuscript/figures/structure/HNH/HNH_cat_session.cxs"

Opened halfcleaved_HNH_center_sharp3Å.mrc as #13, grid size 420,420,420,
pixel 0.725, shown at level 0.05, step 1, values float32  
Opened halfcleaved_HNH_center_sharp3Å.mrc zone as #40, grid size 420,420,420,
pixel 0.725, shown at level 0.02, step 1, values float32  
Opened halfcleaved_HNH_center_sharp3Å.mrc zone as #39, grid size 420,420,420,
pixel 0.725, shown at level 0.04, step 1, values float32  
Log from Wed May 14 12:43:12 2025UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open "/Users/zxc755/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/Type I-F_HNH/Manuscript/chimerax_session.cxs"

Opened halfcleaved_HNH_center_sharp3Å.mrc as #13, grid size 420,420,420,
pixel 0.725, shown at level 0.05, step 1, values float32  
Opened halfcleaved_HNH_center_sharp3Å.mrc 0 as #22.1, grid size 420,420,420,
pixel 0.725, shown at level 0.02, step 1, values float32  
Opened halfcleaved_HNH_center_sharp3Å.mrc 1 as #22.2, grid size 420,420,420,
pixel 0.725, shown at level 0.02, step 1, values float32  
Opened halfcleaved_HNH_center_sharp3Å.mrc 2 as #22.3, grid size 420,420,420,
pixel 0.725, shown at level 0.02, step 1, values float32  
Opened halfcleaved_HNH_center_sharp3Å.mrc 3 as #22.4, grid size 420,420,420,
pixel 0.725, shown at level 0.02, step 1, values float32  
Opened halfcleaved_HNH_center_sharp3Å.mrc 4 as #22.5, grid size 420,420,420,
pixel 0.725, shown at level 0.02, step 1, values float32  
Opened halfcleaved_HNH_center_sharp3Å.mrc 5 as #22.6, grid size 420,420,420,
pixel 0.725, shown at level 0.02, step 1, values float32  
Opened halfcleaved_HNH_center_sharp3Å.mrc 6 as #22.7, grid size 420,420,420,
pixel 0.725, shown at level 0.02, step 1, values float32  
Opened halfcleaved_HNH_center_sharp3Å.mrc 7 as #22.8, grid size 420,420,420,
pixel 0.725, shown at level 0.02, step 1, values float32  
Opened halfcleaved_HNH_center_sharp3Å.mrc 8 as #22.9, grid size 420,420,420,
pixel 0.725, shown at level 0.02, step 1, values float32  
Opened halfcleaved_HNH_center_sharp3Å.mrc 9 as #22.10, grid size 420,420,420,
pixel 0.725, shown at level 0.02, step 1, values float32  
Opened halfcleaved_HNH_in_sharp.mrc as #9, grid size 420,420,420, pixel 0.725,
shown at level 0.002, step 1, values float32  
Opened halfcleaved_HNH_out_sharp.mrc as #10, grid size 420,420,420, pixel
0.725, shown at level 0.05, step 1, values float32  
Opened halfcleaved_HNH_in_sharp.mrc 0 as #7.1, grid size 420,420,420, pixel
0.725, shown at level 0.02, step 1, values float32  
Opened halfcleaved_HNH_in_sharp.mrc 1 as #7.2, grid size 420,420,420, pixel
0.725, shown at level 0.02, step 1, values float32  
Opened halfcleaved_HNH_in_sharp.mrc 2 as #7.3, grid size 420,420,420, pixel
0.725, shown at level 0.02, step 1, values float32  
Opened halfcleaved_HNH_in_sharp.mrc 3 as #7.4, grid size 420,420,420, pixel
0.725, shown at level 0.02, step 1, values float32  
Opened halfcleaved_HNH_in_sharp.mrc 4 as #7.5, grid size 420,420,420, pixel
0.725, shown at level 0.02, step 1, values float32  
Opened halfcleaved_HNH_in_sharp.mrc 5 as #7.6, grid size 420,420,420, pixel
0.725, shown at level 0.02, step 1, values float32  
Opened halfcleaved_HNH_in_sharp.mrc 6 as #7.7, grid size 420,420,420, pixel
0.725, shown at level 0.02, step 1, values float32  
Opened halfcleaved_HNH_in_sharp.mrc 7 as #7.8, grid size 420,420,420, pixel
0.725, shown at level 0.02, step 1, values float32  
Opened halfcleaved_HNH_in_sharp.mrc 8 as #7.9, grid size 420,420,420, pixel
0.725, shown at level 0.02, step 1, values float32  
Opened halfcleaved_HNH_out_sharp.mrc 0 as #8.1, grid size 420,420,420, pixel
0.725, shown at level 0.05, step 1, values float32  
Opened halfcleaved_HNH_out_sharp.mrc 1 as #8.2, grid size 420,420,420, pixel
0.725, shown at level 0.05, step 1, values float32  
Opened halfcleaved_HNH_out_sharp.mrc 2 as #8.3, grid size 420,420,420, pixel
0.725, shown at level 0.05, step 1, values float32  
Opened halfcleaved_HNH_out_sharp.mrc 3 as #8.4, grid size 420,420,420, pixel
0.725, shown at level 0.05, step 1, values float32  
Opened halfcleaved_HNH_out_sharp.mrc 4 as #8.5, grid size 420,420,420, pixel
0.725, shown at level 0.05, step 1, values float32  
Opened halfcleaved_HNH_out_sharp.mrc 5 as #8.6, grid size 420,420,420, pixel
0.725, shown at level 0.05, step 1, values float32  
Opened halfcleaved_HNH_out_sharp.mrc 6 as #8.7, grid size 420,420,420, pixel
0.725, shown at level 0.05, step 1, values float32  
Opened halfcleaved_HNH_out_sharp.mrc 7 as #8.8, grid size 420,420,420, pixel
0.725, shown at level 0.05, step 1, values float32  
Opened halfcleaved_HNH_out_sharp.mrc 8 as #8.9, grid size 420,420,420, pixel
0.725, shown at level 0.05, step 1, values float32  
Opened apo_HNH_cent_sharp.mrc as #17, grid size 420,420,420, pixel 0.725,
shown at level 0.05, step 1, values float32  
Opened apo_HNH_in_sharp.mrc as #18, grid size 420,420,420, pixel 0.725, shown
at level 0.05, step 1, values float32  
Opened apo_HNH_out_sharp.mrc as #19, grid size 420,420,420, pixel 0.725, shown
at level 0.05, step 1, values float32  
Opened post_HNH_cent_sharp.mrc as #24, grid size 420,420,420, pixel 0.725,
shown at level 0.05, step 1, values float32  
Opened post_HNH_in_sharp.mrc as #25, grid size 420,420,420, pixel 0.725, shown
at level 0.05, step 1, values float32  
Opened post_HNH_out_sharp.mrc as #26, grid size 420,420,420, pixel 0.725,
shown at level 0.05, step 1, values float32  
Opened apo_HNH_cent_sharp.mrc 0 as #27.1, grid size 420,420,420, pixel 0.725,
shown at level 0.05, step 1, values float32  
Opened apo_HNH_cent_sharp.mrc 1 as #27.2, grid size 420,420,420, pixel 0.725,
shown at level 0.05, step 1, values float32  
Opened apo_HNH_cent_sharp.mrc 2 as #27.3, grid size 420,420,420, pixel 0.725,
shown at level 0.05, step 1, values float32  
Opened apo_HNH_cent_sharp.mrc 3 as #27.4, grid size 420,420,420, pixel 0.725,
shown at level 0.05, step 1, values float32  
Opened apo_HNH_cent_sharp.mrc 4 as #27.5, grid size 420,420,420, pixel 0.725,
shown at level 0.05, step 1, values float32  
Opened apo_HNH_cent_sharp.mrc 5 as #27.6, grid size 420,420,420, pixel 0.725,
shown at level 0.05, step 1, values float32  
Opened apo_HNH_in_sharp.mrc 0 as #28.1, grid size 420,420,420, pixel 0.725,
shown at level 0.05, step 1, values float32  
Opened apo_HNH_in_sharp.mrc 1 as #28.2, grid size 420,420,420, pixel 0.725,
shown at level 0.05, step 1, values float32  
Opened apo_HNH_in_sharp.mrc 2 as #28.3, grid size 420,420,420, pixel 0.725,
shown at level 0.05, step 1, values float32  
Opened apo_HNH_in_sharp.mrc 3 as #28.4, grid size 420,420,420, pixel 0.725,
shown at level 0.05, step 1, values float32  
Opened apo_HNH_in_sharp.mrc 4 as #28.5, grid size 420,420,420, pixel 0.725,
shown at level 0.05, step 1, values float32  
Opened apo_HNH_in_sharp.mrc 5 as #28.6, grid size 420,420,420, pixel 0.725,
shown at level 0.05, step 1, values float32  
Opened apo_HNH_out_sharp.mrc 0 as #29.1, grid size 420,420,420, pixel 0.725,
shown at level 0.05, step 1, values float32  
Opened apo_HNH_out_sharp.mrc 1 as #29.2, grid size 420,420,420, pixel 0.725,
shown at level 0.05, step 1, values float32  
Opened apo_HNH_out_sharp.mrc 2 as #29.3, grid size 420,420,420, pixel 0.725,
shown at level 0.05, step 1, values float32  
Opened apo_HNH_out_sharp.mrc 3 as #29.4, grid size 420,420,420, pixel 0.725,
shown at level 0.05, step 1, values float32  
Opened apo_HNH_out_sharp.mrc 4 as #29.5, grid size 420,420,420, pixel 0.725,
shown at level 0.05, step 1, values float32  
Opened apo_HNH_out_sharp.mrc 5 as #29.6, grid size 420,420,420, pixel 0.725,
shown at level 0.05, step 1, values float32  
Opened post_HNH_cent_sharp.mrc 0 as #30.1, grid size 420,420,420, pixel 0.725,
shown at level 0.05, step 1, values float32  
Opened post_HNH_cent_sharp.mrc 1 as #30.2, grid size 420,420,420, pixel 0.725,
shown at level 0.05, step 1, values float32  
Opened post_HNH_cent_sharp.mrc 2 as #30.3, grid size 420,420,420, pixel 0.725,
shown at level 0.05, step 1, values float32  
Opened post_HNH_cent_sharp.mrc 3 as #30.4, grid size 420,420,420, pixel 0.725,
shown at level 0.05, step 1, values float32  
Opened post_HNH_cent_sharp.mrc 4 as #30.5, grid size 420,420,420, pixel 0.725,
shown at level 0.05, step 1, values float32  
Opened post_HNH_cent_sharp.mrc 5 as #30.6, grid size 420,420,420, pixel 0.725,
shown at level 0.05, step 1, values float32  
Opened post_HNH_cent_sharp.mrc 6 as #30.7, grid size 420,420,420, pixel 0.725,
shown at level 0.05, step 1, values float32  
Opened post_HNH_cent_sharp.mrc 7 as #30.8, grid size 420,420,420, pixel 0.725,
shown at level 0.05, step 1, values float32  
Opened post_HNH_in_sharp.mrc 0 as #31.1, grid size 420,420,420, pixel 0.725,
shown at level 0.05, step 1, values float32  
Opened post_HNH_in_sharp.mrc 1 as #31.2, grid size 420,420,420, pixel 0.725,
shown at level 0.05, step 1, values float32  
Opened post_HNH_in_sharp.mrc 2 as #31.3, grid size 420,420,420, pixel 0.725,
shown at level 0.05, step 1, values float32  
Opened post_HNH_in_sharp.mrc 3 as #31.4, grid size 420,420,420, pixel 0.725,
shown at level 0.05, step 1, values float32  
Opened post_HNH_in_sharp.mrc 4 as #31.5, grid size 420,420,420, pixel 0.725,
shown at level 0.05, step 1, values float32  
Opened post_HNH_in_sharp.mrc 5 as #31.6, grid size 420,420,420, pixel 0.725,
shown at level 0.05, step 1, values float32  
Opened post_HNH_in_sharp.mrc 6 as #31.7, grid size 420,420,420, pixel 0.725,
shown at level 0.05, step 1, values float32  
Opened post_HNH_in_sharp.mrc 7 as #31.8, grid size 420,420,420, pixel 0.725,
shown at level 0.05, step 1, values float32  
Opened post_HNH_out_sharp.mrc 0 as #33.1, grid size 420,420,420, pixel 0.725,
shown at level 0.05, step 1, values float32  
Opened post_HNH_out_sharp.mrc 1 as #33.2, grid size 420,420,420, pixel 0.725,
shown at level 0.05, step 1, values float32  
Opened post_HNH_out_sharp.mrc 2 as #33.3, grid size 420,420,420, pixel 0.725,
shown at level 0.05, step 1, values float32  
Opened post_HNH_out_sharp.mrc 3 as #33.4, grid size 420,420,420, pixel 0.725,
shown at level 0.05, step 1, values float32  
Opened post_HNH_out_sharp.mrc 4 as #33.5, grid size 420,420,420, pixel 0.725,
shown at level 0.05, step 1, values float32  
Opened post_HNH_out_sharp.mrc 5 as #33.6, grid size 420,420,420, pixel 0.725,
shown at level 0.05, step 1, values float32  
Opened post_HNH_out_sharp.mrc 6 as #33.7, grid size 420,420,420, pixel 0.725,
shown at level 0.05, step 1, values float32  
Opened post_HNH_out_sharp.mrc 7 as #33.8, grid size 420,420,420, pixel 0.725,
shown at level 0.05, step 1, values float32  
Opened halfcleaved_HNH_center_sharp3Å.mrc 1 0 as #34.1, grid size
420,420,420, pixel 0.725, shown at level 0.05, step 1, values float32  
Opened halfcleaved_HNH_center_sharp3Å.mrc 1 1 as #34.2, grid size
420,420,420, pixel 0.725, shown at level 0.05, step 1, values float32  
Opened halfcleaved_HNH_center_sharp3Å.mrc 1 2 as #34.3, grid size
420,420,420, pixel 0.725, shown at level 0.05, step 1, values float32  
Opened halfcleaved_HNH_center_sharp3Å.mrc 1 3 as #34.4, grid size
420,420,420, pixel 0.725, shown at level 0.05, step 1, values float32  
Opened halfcleaved_HNH_center_sharp3Å.mrc 1 4 as #34.5, grid size
420,420,420, pixel 0.725, shown at level 0.05, step 1, values float32  
Opened halfcleaved_HNH_center_sharp3Å.mrc 1 5 as #34.6, grid size
420,420,420, pixel 0.725, shown at level 0.05, step 1, values float32  
Opened halfcleaved_HNH_center_sharp3Å.mrc 1 6 as #34.7, grid size
420,420,420, pixel 0.725, shown at level 0.05, step 1, values float32  
Opened halfcleaved_HNH_center_sharp3Å.mrc 1 7 as #34.8, grid size
420,420,420, pixel 0.725, shown at level 0.05, step 1, values float32  
Opened halfcleaved_HNH_center_sharp3Å.mrc 1 8 as #34.9, grid size
420,420,420, pixel 0.725, shown at level 0.05, step 1, values float32  
Opened halfcleaved_HNH_center_sharp3Å.mrc 1 9 as #34.10, grid size
420,420,420, pixel 0.725, shown at level 0.05, step 1, values float32  
Opened halfcleaved_HNH_center_sharp3Å.mrc 1 10 as #34.11, grid size
420,420,420, pixel 0.725, shown at level 0.05, step 1, values float32  
Opened halfcleaved_HNH_center_sharp3Å.mrc 1 11 as #34.12, grid size
420,420,420, pixel 0.725, shown at level 0.05, step 1, values float32  
Opened halfcleaved_HNH_center_sharp3Å.mrc 1 12 as #34.13, grid size
420,420,420, pixel 0.725, shown at level 0.05, step 1, values float32  
Log from Mon May 12 14:04:47 2025UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open "/Users/zxc755/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/Type I-F_HNH/Manuscript/chimerax_session.cxs"

Opened halfcleaved_HNH_center_sharp3Å.mrc as #13, grid size 420,420,420,
pixel 0.725, shown at level 0.03, step 1, values float32  
Opened halfcleaved_HNH_center_sharp3Å.mrc 0 as #22.1, grid size 420,420,420,
pixel 0.725, shown at level 0.02, step 1, values float32  
Opened halfcleaved_HNH_center_sharp3Å.mrc 1 as #22.2, grid size 420,420,420,
pixel 0.725, shown at level 0.02, step 1, values float32  
Opened halfcleaved_HNH_center_sharp3Å.mrc 2 as #22.3, grid size 420,420,420,
pixel 0.725, shown at level 0.02, step 1, values float32  
Opened halfcleaved_HNH_center_sharp3Å.mrc 3 as #22.4, grid size 420,420,420,
pixel 0.725, shown at level 0.02, step 1, values float32  
Opened halfcleaved_HNH_center_sharp3Å.mrc 4 as #22.5, grid size 420,420,420,
pixel 0.725, shown at level 0.02, step 1, values float32  
Opened halfcleaved_HNH_center_sharp3Å.mrc 5 as #22.6, grid size 420,420,420,
pixel 0.725, shown at level 0.02, step 1, values float32  
Opened halfcleaved_HNH_center_sharp3Å.mrc 6 as #22.7, grid size 420,420,420,
pixel 0.725, shown at level 0.02, step 1, values float32  
Opened halfcleaved_HNH_center_sharp3Å.mrc 7 as #22.8, grid size 420,420,420,
pixel 0.725, shown at level 0.02, step 1, values float32  
Opened halfcleaved_HNH_center_sharp3Å.mrc 8 as #22.9, grid size 420,420,420,
pixel 0.725, shown at level 0.02, step 1, values float32  
Opened halfcleaved_HNH_center_sharp3Å.mrc 9 as #22.10, grid size 420,420,420,
pixel 0.725, shown at level 0.02, step 1, values float32  
Opened halfcleaved_HNH_in_sharp.mrc as #9, grid size 420,420,420, pixel 0.725,
shown at level 0.00277, step 1, values float32  
Opened halfcleaved_HNH_out_sharp.mrc as #10, grid size 420,420,420, pixel
0.725, shown at level 0.0029, step 1, values float32  
Opened halfcleaved_HNH_in_sharp.mrc 0 as #7.1, grid size 420,420,420, pixel
0.725, shown at level 0.002, step 1, values float32  
Opened halfcleaved_HNH_in_sharp.mrc 1 as #7.2, grid size 420,420,420, pixel
0.725, shown at level 0.002, step 1, values float32  
Opened halfcleaved_HNH_in_sharp.mrc 2 as #7.3, grid size 420,420,420, pixel
0.725, shown at level 0.002, step 1, values float32  
Opened halfcleaved_HNH_in_sharp.mrc 3 as #7.4, grid size 420,420,420, pixel
0.725, shown at level 0.002, step 1, values float32  
Opened halfcleaved_HNH_in_sharp.mrc 4 as #7.5, grid size 420,420,420, pixel
0.725, shown at level 0.002, step 1, values float32  
Opened halfcleaved_HNH_in_sharp.mrc 5 as #7.6, grid size 420,420,420, pixel
0.725, shown at level 0.002, step 1, values float32  
Opened halfcleaved_HNH_in_sharp.mrc 6 as #7.7, grid size 420,420,420, pixel
0.725, shown at level 0.002, step 1, values float32  
Opened halfcleaved_HNH_in_sharp.mrc 7 as #7.8, grid size 420,420,420, pixel
0.725, shown at level 0.002, step 1, values float32  
Opened halfcleaved_HNH_in_sharp.mrc 8 as #7.9, grid size 420,420,420, pixel
0.725, shown at level 0.002, step 1, values float32  
Opened halfcleaved_HNH_out_sharp.mrc 0 as #8.1, grid size 420,420,420, pixel
0.725, shown at level 0.002, step 1, values float32  
Opened halfcleaved_HNH_out_sharp.mrc 1 as #8.2, grid size 420,420,420, pixel
0.725, shown at level 0.002, step 1, values float32  
Opened halfcleaved_HNH_out_sharp.mrc 2 as #8.3, grid size 420,420,420, pixel
0.725, shown at level 0.002, step 1, values float32  
Opened halfcleaved_HNH_out_sharp.mrc 3 as #8.4, grid size 420,420,420, pixel
0.725, shown at level 0.002, step 1, values float32  
Opened halfcleaved_HNH_out_sharp.mrc 4 as #8.5, grid size 420,420,420, pixel
0.725, shown at level 0.002, step 1, values float32  
Opened halfcleaved_HNH_out_sharp.mrc 5 as #8.6, grid size 420,420,420, pixel
0.725, shown at level 0.002, step 1, values float32  
Opened halfcleaved_HNH_out_sharp.mrc 6 as #8.7, grid size 420,420,420, pixel
0.725, shown at level 0.002, step 1, values float32  
Opened halfcleaved_HNH_out_sharp.mrc 7 as #8.8, grid size 420,420,420, pixel
0.725, shown at level 0.002, step 1, values float32  
Opened halfcleaved_HNH_out_sharp.mrc 8 as #8.9, grid size 420,420,420, pixel
0.725, shown at level 0.002, step 1, values float32  
Opened apo_HNH_cent_sharp.mrc as #17, grid size 420,420,420, pixel 0.725,
shown at level 0.00199, step 1, values float32  
Opened apo_HNH_in_sharp.mrc as #18, grid size 420,420,420, pixel 0.725, shown
at level 0.00173, step 1, values float32  
Opened apo_HNH_out_sharp.mrc as #19, grid size 420,420,420, pixel 0.725, shown
at level 0.00214, step 1, values float32  
Opened post_HNH_cent_sharp.mrc as #24, grid size 420,420,420, pixel 0.725,
shown at level 0.00328, step 1, values float32  
Opened post_HNH_in_sharp.mrc as #25, grid size 420,420,420, pixel 0.725, shown
at level 0.0257, step 1, values float32  
Opened post_HNH_out_sharp.mrc as #26, grid size 420,420,420, pixel 0.725,
shown at level 0.00342, step 1, values float32  
Opened apo_HNH_cent_sharp.mrc 0 as #27.1, grid size 420,420,420, pixel 0.725,
shown at level 0.00199, step 1, values float32  
Opened apo_HNH_cent_sharp.mrc 1 as #27.2, grid size 420,420,420, pixel 0.725,
shown at level 0.00199, step 1, values float32  
Opened apo_HNH_cent_sharp.mrc 2 as #27.3, grid size 420,420,420, pixel 0.725,
shown at level 0.00199, step 1, values float32  
Opened apo_HNH_cent_sharp.mrc 3 as #27.4, grid size 420,420,420, pixel 0.725,
shown at level 0.00199, step 1, values float32  
Opened apo_HNH_cent_sharp.mrc 4 as #27.5, grid size 420,420,420, pixel 0.725,
shown at level 0.00199, step 1, values float32  
Opened apo_HNH_cent_sharp.mrc 5 as #27.6, grid size 420,420,420, pixel 0.725,
shown at level 0.00199, step 1, values float32  
Opened apo_HNH_in_sharp.mrc 0 as #28.1, grid size 420,420,420, pixel 0.725,
shown at level 0.00173, step 1, values float32  
Opened apo_HNH_in_sharp.mrc 1 as #28.2, grid size 420,420,420, pixel 0.725,
shown at level 0.00173, step 1, values float32  
Opened apo_HNH_in_sharp.mrc 2 as #28.3, grid size 420,420,420, pixel 0.725,
shown at level 0.00173, step 1, values float32  
Opened apo_HNH_in_sharp.mrc 3 as #28.4, grid size 420,420,420, pixel 0.725,
shown at level 0.00173, step 1, values float32  
Opened apo_HNH_in_sharp.mrc 4 as #28.5, grid size 420,420,420, pixel 0.725,
shown at level 0.00173, step 1, values float32  
Opened apo_HNH_in_sharp.mrc 5 as #28.6, grid size 420,420,420, pixel 0.725,
shown at level 0.00173, step 1, values float32  
Opened apo_HNH_out_sharp.mrc 0 as #29.1, grid size 420,420,420, pixel 0.725,
shown at level 0.00214, step 1, values float32  
Opened apo_HNH_out_sharp.mrc 1 as #29.2, grid size 420,420,420, pixel 0.725,
shown at level 0.00214, step 1, values float32  
Opened apo_HNH_out_sharp.mrc 2 as #29.3, grid size 420,420,420, pixel 0.725,
shown at level 0.00214, step 1, values float32  
Opened apo_HNH_out_sharp.mrc 3 as #29.4, grid size 420,420,420, pixel 0.725,
shown at level 0.00214, step 1, values float32  
Opened apo_HNH_out_sharp.mrc 4 as #29.5, grid size 420,420,420, pixel 0.725,
shown at level 0.00214, step 1, values float32  
Opened apo_HNH_out_sharp.mrc 5 as #29.6, grid size 420,420,420, pixel 0.725,
shown at level 0.00214, step 1, values float32  
Opened post_HNH_cent_sharp.mrc 0 as #30.1, grid size 420,420,420, pixel 0.725,
shown at level 0.00328, step 1, values float32  
Opened post_HNH_cent_sharp.mrc 1 as #30.2, grid size 420,420,420, pixel 0.725,
shown at level 0.00328, step 1, values float32  
Opened post_HNH_cent_sharp.mrc 2 as #30.3, grid size 420,420,420, pixel 0.725,
shown at level 0.00328, step 1, values float32  
Opened post_HNH_cent_sharp.mrc 3 as #30.4, grid size 420,420,420, pixel 0.725,
shown at level 0.00328, step 1, values float32  
Opened post_HNH_cent_sharp.mrc 4 as #30.5, grid size 420,420,420, pixel 0.725,
shown at level 0.00328, step 1, values float32  
Opened post_HNH_cent_sharp.mrc 5 as #30.6, grid size 420,420,420, pixel 0.725,
shown at level 0.00328, step 1, values float32  
Opened post_HNH_cent_sharp.mrc 6 as #30.7, grid size 420,420,420, pixel 0.725,
shown at level 0.00328, step 1, values float32  
Opened post_HNH_cent_sharp.mrc 7 as #30.8, grid size 420,420,420, pixel 0.725,
shown at level 0.00328, step 1, values float32  
Opened post_HNH_in_sharp.mrc 0 as #31.1, grid size 420,420,420, pixel 0.725,
shown at level 0.0257, step 1, values float32  
Opened post_HNH_in_sharp.mrc 1 as #31.2, grid size 420,420,420, pixel 0.725,
shown at level 0.07, step 1, values float32  
Opened post_HNH_in_sharp.mrc 2 as #31.3, grid size 420,420,420, pixel 0.725,
shown at level 0.0257, step 1, values float32  
Opened post_HNH_in_sharp.mrc 3 as #31.4, grid size 420,420,420, pixel 0.725,
shown at level 0.0257, step 1, values float32  
Opened post_HNH_in_sharp.mrc 4 as #31.5, grid size 420,420,420, pixel 0.725,
shown at level 0.0257, step 1, values float32  
Opened post_HNH_in_sharp.mrc 5 as #31.6, grid size 420,420,420, pixel 0.725,
shown at level 0.0257, step 1, values float32  
Opened post_HNH_in_sharp.mrc 6 as #31.7, grid size 420,420,420, pixel 0.725,
shown at level 0.0257, step 1, values float32  
Opened post_HNH_in_sharp.mrc 7 as #31.8, grid size 420,420,420, pixel 0.725,
shown at level 0.0257, step 1, values float32  
Opened post_HNH_out_sharp.mrc 0 as #33.1, grid size 420,420,420, pixel 0.725,
shown at level 0.00342, step 1, values float32  
Opened post_HNH_out_sharp.mrc 1 as #33.2, grid size 420,420,420, pixel 0.725,
shown at level 0.00342, step 1, values float32  
Opened post_HNH_out_sharp.mrc 2 as #33.3, grid size 420,420,420, pixel 0.725,
shown at level 0.00342, step 1, values float32  
Opened post_HNH_out_sharp.mrc 3 as #33.4, grid size 420,420,420, pixel 0.725,
shown at level 0.00342, step 1, values float32  
Opened post_HNH_out_sharp.mrc 4 as #33.5, grid size 420,420,420, pixel 0.725,
shown at level 0.00342, step 1, values float32  
Opened post_HNH_out_sharp.mrc 5 as #33.6, grid size 420,420,420, pixel 0.725,
shown at level 0.00342, step 1, values float32  
Opened post_HNH_out_sharp.mrc 6 as #33.7, grid size 420,420,420, pixel 0.725,
shown at level 0.00342, step 1, values float32  
Opened post_HNH_out_sharp.mrc 7 as #33.8, grid size 420,420,420, pixel 0.725,
shown at level 0.00342, step 1, values float32  
Log from Thu May 1 15:38:06 2025UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open "/Users/zxc755/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/Type I-F_HNH/Manuscript/chimerax_session.cxs"

Opened halfcleaved_HNH_center_sharp3Å.mrc as #13, grid size 420,420,420,
pixel 0.725, shown at level 0.03, step 1, values float32  
Opened halfcleaved_HNH_center_sharp3Å.mrc 0 as #22.1, grid size 420,420,420,
pixel 0.725, shown at level 0.02, step 1, values float32  
Opened halfcleaved_HNH_center_sharp3Å.mrc 1 as #22.2, grid size 420,420,420,
pixel 0.725, shown at level 0.02, step 1, values float32  
Opened halfcleaved_HNH_center_sharp3Å.mrc 2 as #22.3, grid size 420,420,420,
pixel 0.725, shown at level 0.02, step 1, values float32  
Opened halfcleaved_HNH_center_sharp3Å.mrc 3 as #22.4, grid size 420,420,420,
pixel 0.725, shown at level 0.02, step 1, values float32  
Opened halfcleaved_HNH_center_sharp3Å.mrc 4 as #22.5, grid size 420,420,420,
pixel 0.725, shown at level 0.02, step 1, values float32  
Opened halfcleaved_HNH_center_sharp3Å.mrc 5 as #22.6, grid size 420,420,420,
pixel 0.725, shown at level 0.02, step 1, values float32  
Opened halfcleaved_HNH_center_sharp3Å.mrc 6 as #22.7, grid size 420,420,420,
pixel 0.725, shown at level 0.02, step 1, values float32  
Opened halfcleaved_HNH_center_sharp3Å.mrc 7 as #22.8, grid size 420,420,420,
pixel 0.725, shown at level 0.02, step 1, values float32  
Opened halfcleaved_HNH_center_sharp3Å.mrc 8 as #22.9, grid size 420,420,420,
pixel 0.725, shown at level 0.02, step 1, values float32  
Opened halfcleaved_HNH_center_sharp3Å.mrc 9 as #22.10, grid size 420,420,420,
pixel 0.725, shown at level 0.02, step 1, values float32  
Log from Fri Apr 25 19:29:02 2025UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/figures/chimera_session.cxs" format session

Opened halfcleaved_HNH_center_main_map_2p4Å.mrc as #4, grid size 420,420,420,
pixel 0.725, shown at level 0.05, step 1, values float32  
Opened halfcleaved_HNH_center_sharp3Å.mrc as #13, grid size 420,420,420,
pixel 0.725, shown at level 0.02, step 1, values float32  
Opened halfcleaved_HNH_in_sharp3Å.mrc as #14, grid size 420,420,420, pixel
0.725, shown at level 0.02, step 1, values float32  
Opened post_HNH_in_sharp_4p5.mrc as #18, grid size 420,420,420, pixel 0.725,
shown at level 0.0257, step 1, values float32  
Opened post_HNH_cent_sharp.mrc as #19, grid size 420,420,420, pixel 0.725,
shown at level 0.01, step 1, values float32  
Opened halfcleaved_HNH_center_sharp3Å.mrc 0 as #22.1, grid size 420,420,420,
pixel 0.725, shown at level 0.02, step 1, values float32  
Opened halfcleaved_HNH_center_sharp3Å.mrc 1 as #22.2, grid size 420,420,420,
pixel 0.725, shown at level 0.02, step 1, values float32  
Opened halfcleaved_HNH_center_sharp3Å.mrc 2 as #22.3, grid size 420,420,420,
pixel 0.725, shown at level 0.02, step 1, values float32  
Opened halfcleaved_HNH_center_sharp3Å.mrc 3 as #22.4, grid size 420,420,420,
pixel 0.725, shown at level 0.02, step 1, values float32  
Opened halfcleaved_HNH_center_sharp3Å.mrc 4 as #22.5, grid size 420,420,420,
pixel 0.725, shown at level 0.02, step 1, values float32  
Opened halfcleaved_HNH_center_sharp3Å.mrc 5 as #22.6, grid size 420,420,420,
pixel 0.725, shown at level 0.02, step 1, values float32  
Opened halfcleaved_HNH_center_sharp3Å.mrc 6 as #22.7, grid size 420,420,420,
pixel 0.725, shown at level 0.02, step 1, values float32  
Opened halfcleaved_HNH_center_sharp3Å.mrc 7 as #22.8, grid size 420,420,420,
pixel 0.725, shown at level 0.02, step 1, values float32  
Opened halfcleaved_HNH_center_sharp3Å.mrc 8 as #22.9, grid size 420,420,420,
pixel 0.725, shown at level 0.02, step 1, values float32  
Opened halfcleaved_HNH_center_sharp3Å.mrc 9 as #22.10, grid size 420,420,420,
pixel 0.725, shown at level 0.02, step 1, values float32  
Opened halfcleaved_HNH_center_sharp3Å.mrc 5 copy as #28, grid size
420,420,420, pixel 0.725, shown at level 0.02, step 1, values float32  
Opened halfcleaved_HNH_center_sharp3Å.mrc 8 copy as #31, grid size
420,420,420, pixel 0.725, shown at level 0.02, step 1, values float32  
Opened halfcleaved_HNH_center_sharp3Å.mrc 5 copy as #23, grid size
420,420,420, pixel 0.725, shown at level 0.02, step 1, values float32  
Opened halfcleaved_HNH_center_sharp3Å.mrc 8 copy as #24, grid size
420,420,420, pixel 0.725, shown at level 0.02, step 1, values float32  
Opened J620_abinitio_map.mrc as #29, grid size 128,128,128, pixel 2.38, shown
at level 0.218, step 1, values float32  
Opened half_hetref_J623_map.mrc as #30, grid size 128,128,128, pixel 2.38,
shown at level 0.33, step 1, values float32  
Log from Wed Apr 23 13:09:57 2025UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open "/Users/zxc755/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/Type I-F_HNH/Manuscript/figures/chimera_session.cxs"

Opened halfcleaved_HNH_center_main_map_2p4Å.mrc as #4, grid size 420,420,420,
pixel 0.725, shown at level 0.05, step 1, values float32  
Opened halfcleaved_HNH_center_sharp3Å.mrc as #13, grid size 420,420,420,
pixel 0.725, shown at level 0.02, step 1, values float32  
Opened halfcleaved_HNH_in_sharp3Å.mrc as #14, grid size 420,420,420, pixel
0.725, shown at level 0.02, step 1, values float32  
Opened post_HNH_in_sharp_4p5.mrc as #18, grid size 420,420,420, pixel 0.725,
shown at level 0.0257, step 1, values float32  
Opened post_HNH_cent_sharp.mrc as #19, grid size 420,420,420, pixel 0.725,
shown at level 0.01, step 1, values float32  
Opened halfcleaved_HNH_center_sharp3Å.mrc 0 as #22.1, grid size 420,420,420,
pixel 0.725, shown at level 0.02, step 1, values float32  
Opened halfcleaved_HNH_center_sharp3Å.mrc 1 as #22.2, grid size 420,420,420,
pixel 0.725, shown at level 0.02, step 1, values float32  
Opened halfcleaved_HNH_center_sharp3Å.mrc 2 as #22.3, grid size 420,420,420,
pixel 0.725, shown at level 0.02, step 1, values float32  
Opened halfcleaved_HNH_center_sharp3Å.mrc 3 as #22.4, grid size 420,420,420,
pixel 0.725, shown at level 0.02, step 1, values float32  
Opened halfcleaved_HNH_center_sharp3Å.mrc 4 as #22.5, grid size 420,420,420,
pixel 0.725, shown at level 0.02, step 1, values float32  
Opened halfcleaved_HNH_center_sharp3Å.mrc 5 as #22.6, grid size 420,420,420,
pixel 0.725, shown at level 0.02, step 1, values float32  
Opened halfcleaved_HNH_center_sharp3Å.mrc 6 as #22.7, grid size 420,420,420,
pixel 0.725, shown at level 0.02, step 1, values float32  
Opened halfcleaved_HNH_center_sharp3Å.mrc 7 as #22.8, grid size 420,420,420,
pixel 0.725, shown at level 0.02, step 1, values float32  
Opened halfcleaved_HNH_center_sharp3Å.mrc 8 as #22.9, grid size 420,420,420,
pixel 0.725, shown at level 0.02, step 1, values float32  
Opened halfcleaved_HNH_center_sharp3Å.mrc 9 as #22.10, grid size 420,420,420,
pixel 0.725, shown at level 0.02, step 1, values float32  
Opened halfcleaved_HNH_center_sharp3Å.mrc 5 copy as #28, grid size
420,420,420, pixel 0.725, shown at level 0.02, step 1, values float32  
Opened halfcleaved_HNH_center_sharp3Å.mrc 8 copy as #31, grid size
420,420,420, pixel 0.725, shown at level 0.02, step 1, values float32  
Opened halfcleaved_HNH_center_sharp3Å.mrc 5 copy as #23, grid size
420,420,420, pixel 0.725, shown at level 0.02, step 1, values float32  
Opened halfcleaved_HNH_center_sharp3Å.mrc 8 copy as #24, grid size
420,420,420, pixel 0.725, shown at level 0.02, step 1, values float32  
Log from Mon Mar 31 18:07:43 2025UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open "/Users/zxc755/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/Type I-F_HNH/Manuscript/figures/chimera_session.cxs"

Opened halfcleaved_HNH_center_main_map_2p4Å.mrc as #4, grid size 420,420,420,
pixel 0.725, shown at level 0.05, step 1, values float32  
Opened halfcleaved_HNH_center_sharp3Å.mrc as #13, grid size 420,420,420,
pixel 0.725, shown at level 0.02, step 1, values float32  
Opened halfcleaved_HNH_in_sharp3Å.mrc as #14, grid size 420,420,420, pixel
0.725, shown at level 0.02, step 1, values float32  
Opened post_HNH_in_sharp_4p5.mrc as #18, grid size 420,420,420, pixel 0.725,
shown at level 0.0257, step 1, values float32  
Opened post_HNH_cent_sharp.mrc as #19, grid size 420,420,420, pixel 0.725,
shown at level 0.01, step 1, values float32  
Opened halfcleaved_HNH_center_sharp3Å.mrc 0 as #22.1, grid size 420,420,420,
pixel 0.725, shown at level 0.02, step 1, values float32  
Opened halfcleaved_HNH_center_sharp3Å.mrc 1 as #22.2, grid size 420,420,420,
pixel 0.725, shown at level 0.02, step 1, values float32  
Opened halfcleaved_HNH_center_sharp3Å.mrc 2 as #22.3, grid size 420,420,420,
pixel 0.725, shown at level 0.02, step 1, values float32  
Opened halfcleaved_HNH_center_sharp3Å.mrc 3 as #22.4, grid size 420,420,420,
pixel 0.725, shown at level 0.02, step 1, values float32  
Opened halfcleaved_HNH_center_sharp3Å.mrc 4 as #22.5, grid size 420,420,420,
pixel 0.725, shown at level 0.02, step 1, values float32  
Opened halfcleaved_HNH_center_sharp3Å.mrc 5 as #22.6, grid size 420,420,420,
pixel 0.725, shown at level 0.02, step 1, values float32  
Opened halfcleaved_HNH_center_sharp3Å.mrc 6 as #22.7, grid size 420,420,420,
pixel 0.725, shown at level 0.02, step 1, values float32  
Opened halfcleaved_HNH_center_sharp3Å.mrc 7 as #22.8, grid size 420,420,420,
pixel 0.725, shown at level 0.02, step 1, values float32  
Opened halfcleaved_HNH_center_sharp3Å.mrc 8 as #22.9, grid size 420,420,420,
pixel 0.725, shown at level 0.02, step 1, values float32  
Opened halfcleaved_HNH_center_sharp3Å.mrc 9 as #22.10, grid size 420,420,420,
pixel 0.725, shown at level 0.02, step 1, values float32  
Opened halfcleaved_HNH_center_sharp3Å.mrc 5 copy as #28, grid size
420,420,420, pixel 0.725, shown at level 0.02, step 1, values float32  
Opened halfcleaved_HNH_center_sharp3Å.mrc 8 copy as #31, grid size
420,420,420, pixel 0.725, shown at level 0.02, step 1, values float32  
Opened halfcleaved_HNH_center_sharp3Å.mrc 5 copy as #23, grid size
420,420,420, pixel 0.725, shown at level 0.02, step 1, values float32  
Opened halfcleaved_HNH_center_sharp3Å.mrc 8 copy as #24, grid size
420,420,420, pixel 0.725, shown at level 0.02, step 1, values float32  
Log from Thu Mar 27 17:05:34 2025UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open "/Users/zxc755/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/Type I-F_HNH/Manuscript/figures/chimera_session.cxs"

Opened halfcleaved_HNH_center_main_map_2p4Å.mrc as #4, grid size 420,420,420,
pixel 0.725, shown at level 0.05, step 1, values float32  
Opened halfcleaved_HNH_center_sharp3Å.mrc as #13, grid size 420,420,420,
pixel 0.725, shown at level 0.02, step 1, values float32  
Opened halfcleaved_HNH_in_sharp3Å.mrc as #14, grid size 420,420,420, pixel
0.725, shown at level 0.02, step 1, values float32  
Opened post_HNH_in_sharp_4p5.mrc as #18, grid size 420,420,420, pixel 0.725,
shown at level 0.0257, step 1, values float32  
Opened post_HNH_cent_sharp.mrc as #19, grid size 420,420,420, pixel 0.725,
shown at level 0.01, step 1, values float32  
Log from Wed Mar 26 12:19:53 2025UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open "/Users/zxc755/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/Type I-F_HNH/Manuscript/figures/chimera_session.cxs"

Opened halfcleaved_HNH_center_main_map_2p4Å.mrc as #4, grid size 420,420,420,
pixel 0.725, shown at level 0.05, step 1, values float32  
Log from Tue Mar 25 00:19:58 2025UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open "/Users/zxc755/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/Type I-F_HNH/Manuscript/figures/chimera_session.cxs"

Opened halfcleaved_HNH_center_main_map_2p4Å.mrc as #4, grid size 420,420,420,
pixel 0.725, shown at level 0.09, step 1, values float32  
Log from Mon Mar 24 13:31:18 2025UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open "/Users/zxc755/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/Type I-F_HNH/Manuscript/figures/chimera_session.cxs"

Opened halfcleaved_HNH_center_main_map_2p4Å.mrc as #4, grid size 420,420,420,
pixel 0.725, shown at level 0.09, step 1, values float32  
Log from Mon Mar 24 00:43:04 2025 Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 1imp

Summary of feedback from opening 1imp fetched from pdb  
---  
note | Fetching compressed mmCIF 1imp from http://files.rcsb.org/download/1imp.cif  
  
1imp title:  
Colicin E9 immunity protein IM9, NMR, 21 structures [more info...]  
  
Chain information for 1imp  
---  
Chain | Description | UniProt  
1.1/A 1.2/A 1.3/A 1.4/A 1.5/A 1.6/A 1.7/A 1.8/A 1.9/A 1.10/A 1.11/A 1.12/A 1.13/A 1.14/A 1.15/A 1.16/A 1.17/A 1.18/A 1.19/A 1.20/A 1.21/A | IM9 | IMM9_ECOLI 1-86  
  

> hide #1.1 models

> show #1.1 models

> hide models

> show #1.1 models

> open 1fsj

Summary of feedback from opening 1fsj fetched from pdb  
---  
note | Fetching compressed mmCIF 1fsj from http://files.rcsb.org/download/1fsj.cif  
  
1fsj title:  
Crystal structure of the E9 DNAse domain [more info...]  
  
Chain information for 1fsj #2  
---  
Chain | Description | UniProt  
B C D E | COLICIN E9 | CEA9_ECOLI 2-134 202-334 402-434 602-734  
  
Non-standard residues in 1fsj #2  
---  
PO4 — phosphate ion  
ZN — zinc ion  
  
1fsj mmCIF Assemblies  
---  
1| author_defined_assembly  
2| author_defined_assembly  
3| author_defined_assembly  
4| author_defined_assembly  
  

> hide #!1 models

Drag select of 49 atoms, 132 residues, 4 pseudobonds, 43 bonds  

> hide #2 cartoons

> show sel cartoons

Drag select of 60 atoms, 4 pseudobonds, 55 bonds  

> hide sel atoms

Drag select of 141 atoms, 8 pseudobonds, 127 bonds  

> hide sel atoms

> select clear

> open "/Users/zxc755/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/Type
> I-F_HNH/Manuscript/IFhnh_Manuscript/maps_and_models/NTS_cleaved/halfcleaved_HNH_center_main_model_refined2.pdb"

Chain information for halfcleaved_HNH_center_main_model_refined2.pdb #3  
---  
Chain | Description  
Aa | No description available  
Ba | No description available  
Ca | No description available  
DA | No description available  
Da | No description available  
Db | No description available  
Dc | No description available  
Dd | No description available  
De | No description available  
Df | No description available  
EA | No description available  
FA | No description available  
  

> open "/Users/zxc755/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/Type
> I-F_HNH/Manuscript/IFhnh_Manuscript/maps_and_models/NTS_cleaved/halfcleaved_HNH_center_main_map_2p4Å.mrc"

Opened halfcleaved_HNH_center_main_map_2p4Å.mrc as #4, grid size 420,420,420,
pixel 0.725, shown at level 0.0319, step 2, values float32  

> volume #4 level 0.07

> volume #4 step 1

> hide #!4 models

> style stick

Changed 56061 atom styles  

> color #3/DA light gray

> color #3/EA dim gray

> color #3/FA dark red

> color #3/Ca rebecca purple

> color #3/Ba forest green

> color #3/Da,Db,Dc,Dd,De,Df khaki

> color #3/Aa steel blue

> color #3/Aa:232-350 dark turquoise

> hide #3 atoms

> show #3 cartoons

Drag select of 49 atoms, 132 residues, 4 pseudobonds, 43 bonds  

> ui mousemode right "rotate selected models"

> view matrix models #2,1,0,0,82.662,0,1,0,181.25,0,0,1,114.9

> view matrix models
> #2,1,0.0013443,-0.0025868,85.9,-0.0013444,1,-6.0428e-05,181.66,0.0025868,6.3905e-05,1,96.743

> mmaker sel to #3/Aa:230-350

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker halfcleaved_HNH_center_main_model_refined2.pdb, chain Aa (#3) with
1fsj, chain E (#2), sequence alignment score = 97  
RMSD between 11 pruned atom pairs is 1.284 angstroms; (across all 97 pairs:
16.295)  
  

> color #2 yellow

> color #2 byhetero

> hide #!3 models

> select subtract #2/E:700

1046 atoms, 43 bonds, 4 pseudobonds, 135 residues, 2 models selected  

> select subtract #2/E:701

1038 atoms, 39 bonds, 4 pseudobonds, 134 residues, 2 models selected  

> select subtract #2/E:702

1028 atoms, 32 bonds, 3 pseudobonds, 133 residues, 2 models selected  

> select subtract #2/E:703

1018 atoms, 25 bonds, 3 pseudobonds, 132 residues, 2 models selected  

> select subtract #2/E:719

1010 atoms, 25 bonds, 3 pseudobonds, 131 residues, 2 models selected  

> select subtract #2/E:720

999 atoms, 25 bonds, 3 pseudobonds, 130 residues, 2 models selected  

> select subtract #2/E:721

992 atoms, 25 bonds, 3 pseudobonds, 129 residues, 2 models selected  

> select subtract #2/E:722

985 atoms, 25 bonds, 3 pseudobonds, 128 residues, 2 models selected  

> select clear

> select add #2/E:700

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

> select add #2/E:701

17 atoms, 15 bonds, 2 residues, 1 model selected  

> select add #2/E:702

27 atoms, 25 bonds, 3 residues, 1 model selected  

> select add #2/E:703

37 atoms, 35 bonds, 4 residues, 1 model selected  

> select add #2/E:719

45 atoms, 43 bonds, 5 residues, 1 model selected  

> select add #2/E:720

56 atoms, 53 bonds, 6 residues, 1 model selected  

> select add #2/E:721

63 atoms, 59 bonds, 7 residues, 1 model selected  

> select add #2/E:722

70 atoms, 65 bonds, 8 residues, 1 model selected  

> hide #!2 models

> show #!3 models

> mmaker sel to #3/Aa:300-325

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker halfcleaved_HNH_center_main_model_refined2.pdb, chain Aa (#3) with
1fsj, chain E (#2), sequence alignment score = 33.3  
RMSD between 6 pruned atom pairs is 0.986 angstroms; (across all 8 pairs:
2.082)  
  

> show #!2 models

> view matrix models
> #2,0.97297,-0.22873,-0.031935,103.66,0.22967,0.94372,0.23802,167.46,-0.024305,-0.23892,0.97073,110.17

> view matrix models
> #2,0.97551,-0.19874,-0.094297,106.33,0.21196,0.96388,0.16128,171.49,0.058839,-0.17731,0.98239,106.64

> view matrix models
> #2,0.97749,-0.14562,0.15266,94.724,0.17631,0.96123,-0.21202,189.82,-0.11586,0.23416,0.96527,111.65

> select clear

> select #2/E:702

10 atoms, 10 bonds, 1 residue, 1 model selected  

> view matrix models
> #2,0.98567,-0.047376,0.16189,94.269,0.055707,0.99733,-0.047316,185.39,-0.15921,0.055656,0.98567,112.54

> select #2/E:700

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

> select add #2/E:701

17 atoms, 15 bonds, 2 residues, 1 model selected  

> select add #2/E:702

27 atoms, 25 bonds, 3 residues, 1 model selected  

> select add #2/E:703

37 atoms, 35 bonds, 4 residues, 1 model selected  

> select add #2/E:704

45 atoms, 42 bonds, 5 residues, 1 model selected  

> select add #2/E:706

52 atoms, 49 bonds, 6 residues, 1 model selected  

> select add #2/E:707

60 atoms, 56 bonds, 7 residues, 1 model selected  

> select add #2/E:708

66 atoms, 61 bonds, 8 residues, 1 model selected  

> select add #2/E:709

75 atoms, 69 bonds, 9 residues, 1 model selected  

> select add #2/E:710

79 atoms, 72 bonds, 10 residues, 1 model selected  

> mmaker sel to #3/Aa:300-314

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker halfcleaved_HNH_center_main_model_refined2.pdb, chain Aa (#3) with
1fsj, chain E (#2), sequence alignment score = 46.3  
RMSD between 10 pruned atom pairs is 0.499 angstroms; (across all 10 pairs:
0.499)  
  

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> select #3/Aa:280

11 atoms, 10 bonds, 1 residue, 1 model selected  

> show #3/Aa:305,280,328,304

> select #3/Aa:332

7 atoms, 6 bonds, 1 residue, 1 model selected  

> show sel atoms

> show #!4 models

> transparency 50

> hide #!4 models

> hide #!3 models

> hide #!2 models

> select clear

> show #!3 models

> show #!2 models

> combine #2

> hide #!2 models

> hide #!3 models

> show #5 cartoons

> select #5/C:273

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

> select up

72 atoms, 72 bonds, 10 residues, 1 model selected  

> select up

1047 atoms, 1071 bonds, 132 residues, 1 model selected  

> delete sel

> select #5/D:407

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

> select add #5/B:6

17 atoms, 15 bonds, 2 residues, 1 model selected  

> select up

86 atoms, 84 bonds, 10 residues, 1 model selected  

> select up

2111 atoms, 2159 bonds, 266 residues, 1 model selected  

> delete sel

> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Structure/1fsj_E9_nuclease_HNH_like.pdb" models #5

> select #5/E:904@ZN

1 atom, 1 residue, 1 model selected  

> select up

3 atoms, 1 bond, 2 residues, 1 model selected  

> select up

6 atoms, 4 bonds, 2 residues, 1 model selected  

> select #5

1388 atoms, 1087 bonds, 7 pseudobonds, 457 residues, 2 models selected  

> select subtract #5/E:804@P

1387 atoms, 1083 bonds, 7 pseudobonds, 457 residues, 2 models selected  

> select subtract #5/E:804@O2

1386 atoms, 1083 bonds, 7 pseudobonds, 457 residues, 2 models selected  

> select subtract #5/E:804@O3

1385 atoms, 1083 bonds, 6 pseudobonds, 457 residues, 2 models selected  

> select subtract #5/E:804@O1

1384 atoms, 1083 bonds, 6 pseudobonds, 457 residues, 2 models selected  

> select subtract #5/E:804@O4

1383 atoms, 1083 bonds, 6 pseudobonds, 456 residues, 2 models selected  

> select subtract #5/E:904@ZN

1382 atoms, 1083 bonds, 3 pseudobonds, 455 residues, 2 models selected  

> delete sel

> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Structure/zn_phosphate_from_1fsj.pdb" models #5

> hide #!5 models

> show #!3 models

> hide #!3 models

> show #!4 models

> hide #!4 models

> show #!2 models

> hide #!2 models

> open "/Users/zxc755/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/Type
> I-F_HNH/Manuscript/IFhnh_Manuscript/maps_and_models/NTS_cleaved/halfcleaved_HNH_center_main_model_refined_with_water.pdb"

Chain information for halfcleaved_HNH_center_main_model_refined_with_water.pdb
#6  
---  
Chain | Description  
Aa | No description available  
Ba | No description available  
Ca | No description available  
DA | No description available  
Da | No description available  
Db | No description available  
Dc | No description available  
Dd | No description available  
De | No description available  
Df | No description available  
EA | No description available  
FA | No description available  
  

> style stick

Changed 80248 atom styles  

> hide #6 atoms

> show #6 cartoons

> show #6/B atoms

> show #6/D atoms

> show #6/C atoms

> show #6/A atoms

> color #6/DA light gray

> color #6/EA dim gray

> color #6/FA dark red

> color #6/Ca rebecca purple

> color #6/Ba forest green

> color #6/Da,Db,Dc,Dd,De,Df khaki

> color #6/Aa steel blue

> color #6/Aa:232-350 dark turquoise

> color #6 byhetero

> show #6/Aa:305,280,328

> show #6/Aa:304,280,328

> show #!5 models

> hide #!5 models

> show #!2 models

> select #6/Aa:303

7 atoms, 6 bonds, 1 residue, 1 model selected  

> show #!3 models

> hide #!3 models

> show #!4 models

> volume #4 level 0.09

> hide #!2 models

> show #!2 models

> hide #!4 models

> select #6/Aa:332

7 atoms, 6 bonds, 1 residue, 1 model selected  

> show sel atoms

> lighting soft

> lighting simple

> lighting full

> lighting soft

> lighting simple

> lighting soft

> lighting simple

> select #6/Aa:302

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

> select add #2/E:700

18 atoms, 16 bonds, 2 residues, 2 models selected  

> show sel atoms

> select #2/E:723

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select add #6/Aa:324

13 atoms, 11 bonds, 2 residues, 2 models selected  

> show sel atoms

> open 1v14

Summary of feedback from opening 1v14 fetched from pdb  
---  
note | Fetching compressed mmCIF 1v14 from http://files.rcsb.org/download/1v14.cif  
  
1v14 title:  
Crystal Structure of the Colicin E9, mutant His103Ala, in complex with Mg+2
and dsDNA (resolution 2.9A) [more info...]  
  
Chain information for 1v14 #7  
---  
Chain | Description | UniProt  
A B C D | COLICIN E9 | CEA9_ECOLI 2-134  
E F G H I J K L | 5'-D(*GP*CP*GP*AP*TP*CP*GP*CP)-3' |   
  
Non-standard residues in 1v14 #7  
---  
MG — magnesium ion  
  
1v14 mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
2| author_and_software_defined_assembly  
3| author_and_software_defined_assembly  
4| author_and_software_defined_assembly  
  

> hide #!2 models

> hide #!6 models

> view

> select add #7

5341 atoms, 5524 bonds, 73 pseudobonds, 623 residues, 5 models selected  

> select clear

> select add #7

5328 atoms, 5513 bonds, 73 pseudobonds, 621 residues, 3 models selected  

> hide sel atoms

> show sel cartoons

> select clear

> select add #7/G:8

19 atoms, 20 bonds, 1 residue, 1 model selected  

> select add #7/H:12

40 atoms, 43 bonds, 2 residues, 1 model selected  

> select add #7/J:11

62 atoms, 67 bonds, 3 residues, 1 model selected  

> select add #7/I:8

81 atoms, 87 bonds, 4 residues, 1 model selected  

> select add #7/C:80

87 atoms, 92 bonds, 5 residues, 1 model selected  

> select add #7/B:123

94 atoms, 98 bonds, 6 residues, 1 model selected  

> select add #7/E:5

114 atoms, 119 bonds, 7 residues, 1 model selected  

> select add #7/F:12

135 atoms, 142 bonds, 8 residues, 1 model selected  

> select add #7/A:53

146 atoms, 153 bonds, 9 residues, 1 model selected  

> select up

1143 atoms, 1247 bonds, 77 residues, 1 model selected  

> select up

3979 atoms, 4147 bonds, 438 residues, 1 model selected  

> hide sel cartoons

> select clear

> select #7/D:100

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

> select add #7/D:101

17 atoms, 15 bonds, 2 residues, 1 model selected  

> select add #7/D:102

27 atoms, 25 bonds, 3 residues, 1 model selected  

> select add #7/D:103

32 atoms, 29 bonds, 4 residues, 1 model selected  

> select add #7/D:104

40 atoms, 36 bonds, 5 residues, 1 model selected  

> select add #7/D:105

49 atoms, 44 bonds, 6 residues, 1 model selected  

> select add #7/D:106

56 atoms, 51 bonds, 7 residues, 1 model selected  

> select add #7/D:107

64 atoms, 58 bonds, 8 residues, 1 model selected  

> show #!6 models

> mmaker sel to #6/Aa:300-310

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker halfcleaved_HNH_center_main_model_refined_with_water.pdb, chain Aa
(#6) with 1v14, chain D (#7), sequence alignment score = 23.8  
RMSD between 8 pruned atom pairs is 0.406 angstroms; (across all 8 pairs:
0.406)  
  

> color #7 yellow

> color #7 byhetero

> select clear

> select #7/K:6

19 atoms, 20 bonds, 1 residue, 1 model selected  

> show #!4 models

> hide #!4 models

> show #!4 models

> show sel atoms

> select #7/K:5

20 atoms, 21 bonds, 1 residue, 1 model selected  

> show sel atoms

> view sel

> select #7/D:5

11 atoms, 10 bonds, 1 residue, 1 model selected  

> hide #!4 models

> select #7/D:102

10 atoms, 10 bonds, 1 residue, 1 model selected  

> select add #7/D:6

18 atoms, 17 bonds, 2 residues, 1 model selected  

> select subtract #7/D:6

10 atoms, 10 bonds, 1 residue, 1 model selected  

> select add #7/D:5

21 atoms, 20 bonds, 2 residues, 1 model selected  

> select add #7/D:103

26 atoms, 24 bonds, 3 residues, 1 model selected  

> select add #7/D:100

35 atoms, 32 bonds, 4 residues, 1 model selected  

> select add #7/D:127

45 atoms, 42 bonds, 5 residues, 1 model selected  

> show sel atoms

> style stick

Changed 85576 atom styles  

> select add #7/K:4

66 atoms, 65 bonds, 6 residues, 1 model selected  

> select #7/K:5

20 atoms, 21 bonds, 1 residue, 1 model selected  

> select add #7/K:6

39 atoms, 41 bonds, 2 residues, 1 model selected  

> hide sel cartoons

> select clear

> show #!4 models

> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Structure/1v14_E9_nuclease_his103_mut_with_dsDNA.pdb" models #7

> hide #!4 models

> hide #!6 models

> hide #!7 models

> show #!7 models

> show #7 cartoons

> view

> select #7/H:12

21 atoms, 23 bonds, 1 residue, 1 model selected  

> select add #7/G:8

40 atoms, 43 bonds, 2 residues, 1 model selected  

> select add #7/F:13

60 atoms, 64 bonds, 3 residues, 1 model selected  

> select add #7/E:7

82 atoms, 88 bonds, 4 residues, 1 model selected  

> select add #7/A:102

92 atoms, 98 bonds, 5 residues, 1 model selected  

> select add #7/J:12

113 atoms, 121 bonds, 6 residues, 1 model selected  

> select add #7/I:7

135 atoms, 145 bonds, 7 residues, 1 model selected  

> select add #7/C:78

141 atoms, 150 bonds, 8 residues, 1 model selected  

> select up

956 atoms, 1055 bonds, 56 residues, 1 model selected  

> select up

2934 atoms, 3079 bonds, 306 residues, 1 model selected  

> select up

2956 atoms, 3079 bonds, 328 residues, 1 model selected  

> select up

5328 atoms, 5513 bonds, 621 residues, 1 model selected  

> select down

2956 atoms, 3079 bonds, 328 residues, 1 model selected  

> delete sel

> select #7/B:89

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

> select up

42 atoms, 42 bonds, 5 residues, 1 model selected  

> select up

1045 atoms, 1068 bonds, 132 residues, 1 model selected  

> delete sel

> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Structure/1v14_E9_nuclease_his103_mut_with_dsDNA.pdb" models #7

> hide #!7 models

> open 1emv

Summary of feedback from opening 1emv fetched from pdb  
---  
note | Fetching compressed mmCIF 1emv from http://files.rcsb.org/download/1emv.cif  
  
1emv title:  
Crystal structure of colicin E9 DNAse domain with its cognate immunity protein
IM9 (1.7 angstroms) [more info...]  
  
Chain information for 1emv #8  
---  
Chain | Description | UniProt  
A | IMMUNITY PROTEIN IM9 | IMM9_ECOLI 1-86  
B | COLICIN E9 | CEA9_ECOLI 2-134  
  
Non-standard residues in 1emv #8  
---  
PO4 — phosphate ion  
  

> view

> select #8/A:71

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select up

121 atoms, 123 bonds, 16 residues, 1 model selected  

> select up

651 atoms, 664 bonds, 83 residues, 1 model selected  

> delete sel

> mmaker #8/B:100-110 to #6/Aa:300-310

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker halfcleaved_HNH_center_main_model_refined_with_water.pdb, chain Aa
(#6) with 1emv, chain B (#8), sequence alignment score = 35.4  
RMSD between 9 pruned atom pairs is 0.264 angstroms; (across all 9 pairs:
0.264)  
  

> view

> show #!6 models

> hide #!6 models

> show #!6 models

> hide #8 models

> show #8 models

> hide #!6 models

> show #!6 models

> hide #!6 models

> show #!6 models

> hide #!6 models

> select #8/B:127

10 atoms, 10 bonds, 1 residue, 1 model selected  

> show sel atoms

> show #!6 models

> hide #!6 models

> show #!6 models

> select #8/B:100

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

> show sel atoms

> hide #8 models

> hide #!6 models

> show #!5 models

> hide #!5 models

> show #!2 models

> show #!6 models

> select #6/Aa:303

7 atoms, 6 bonds, 1 residue, 1 model selected  

> show sel atoms

> select #2/E:704

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

> select #6/Aa:306

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

> select #2/E:706

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

> select #6/Ba:128

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select clear

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> show #!4 models

> lighting simple

> lighting soft

> lighting simple

> hide #!4 models

> hide #!2 models

> hide #!6 models

> show #8 models

> set chain

Expected a keyword  

> set chain #8/B A

Expected a keyword  

> set chain #8/B to A

Expected a keyword  

> set chain A #8/B

Expected a keyword  

> open "/Users/zxc755/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/Type
> I-F_HNH/Manuscript/halfcleaved_HNH_center_main_model_refined2.pdb"

Chain information for halfcleaved_HNH_center_main_model_refined2.pdb #9  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
F | No description available  
G | No description available  
H | No description available  
I | No description available  
J | No description available  
K | No description available  
L | No description available  
  

> color #9/L light gray

> color #9/K dim gray

> color #9/J dark red

> color #9/I rebecca purple

> color #9/B forest green

> color #9/C,D,E,F,G,H khaki

> color #9/A steel blue

> color #9/A:232-350 dark turquoise

> style stick

Changed 106889 atom styles  

> hide #9 atoms

> show #9 cartoons

> hide #!9 models

> show #!3 models

> hide #!3 models

> show #!6 models

> hide #!6 models

> show #!9 models

> hide #!9 models

> show #!9 models

> hide #!9 models

> show #!9 models

> hide #8 models

> show #8 models

> hide #8 models

> show #8 models

> hide #8 models

[deleted to fit within ticket limits]


> distance style radius 0.04

[Repeated 2 time(s)]

> distance style radius 0.05

[Repeated 2 time(s)]

> distance style radius 50

[Repeated 2 time(s)]

> distance style radius 0.01

[Repeated 4 time(s)]

> distance style radius 0.02

[Repeated 2 time(s)]

> distance style radius 0.03

[Repeated 2 time(s)]

> distance style radius 0.04

[Repeated 2 time(s)]

> distance style radius 0.05

[Repeated 2 time(s)]

> color #11 teal

> select clear

> show #!20 models

> show #!19 models

> show #!18 models

> show #!16 models

> select #32/A:47

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

> select add #32/A:48

14 atoms, 12 bonds, 2 residues, 1 model selected  

> select add #32/A:49

21 atoms, 19 bonds, 3 residues, 1 model selected  

> select add #32/A:50

25 atoms, 22 bonds, 4 residues, 1 model selected  

> select add #32/A:51

33 atoms, 29 bonds, 5 residues, 1 model selected  

> select add #32/A:52

41 atoms, 36 bonds, 6 residues, 1 model selected  

> select add #32/A:53

45 atoms, 39 bonds, 7 residues, 1 model selected  

> select add #32/A:54

50 atoms, 43 bonds, 8 residues, 1 model selected  

> select subtract #32/A:47

42 atoms, 36 bonds, 7 residues, 1 model selected  

> hide sel cartoons

> select #32/A:78

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

> select add #32/A:77

15 atoms, 14 bonds, 2 residues, 1 model selected  

> select add #32/A:76

24 atoms, 22 bonds, 3 residues, 1 model selected  

> select add #32/A:75

33 atoms, 30 bonds, 4 residues, 1 model selected  

> select add #32/A:74

47 atoms, 45 bonds, 5 residues, 1 model selected  

> select add #32/A:73

51 atoms, 48 bonds, 6 residues, 1 model selected  

> select add #32/A:55

63 atoms, 60 bonds, 7 residues, 1 model selected  

> select add #32/A:56

71 atoms, 67 bonds, 8 residues, 1 model selected  

> select add #32/A:57

79 atoms, 74 bonds, 9 residues, 1 model selected  

> select add #32/A:58

87 atoms, 81 bonds, 10 residues, 1 model selected  

> select add #32/A:59

93 atoms, 86 bonds, 11 residues, 1 model selected  

> select add #32/A:60

99 atoms, 91 bonds, 12 residues, 1 model selected  

> select add #32/A:61

107 atoms, 98 bonds, 13 residues, 1 model selected  

> select add #32/A:62

115 atoms, 105 bonds, 14 residues, 1 model selected  

> select add #32/A:63

123 atoms, 112 bonds, 15 residues, 1 model selected  

> select add #32/A:64

129 atoms, 117 bonds, 16 residues, 1 model selected  

> select add #32/A:65

133 atoms, 120 bonds, 17 residues, 1 model selected  

> select add #32/A:66

145 atoms, 132 bonds, 18 residues, 1 model selected  

> select add #32/A:67

153 atoms, 139 bonds, 19 residues, 1 model selected  

> select add #32/A:68

161 atoms, 146 bonds, 20 residues, 1 model selected  

> select add #32/A:69

168 atoms, 152 bonds, 21 residues, 1 model selected  

> select add #32/A:70

173 atoms, 156 bonds, 22 residues, 1 model selected  

> select add #32/A:71

181 atoms, 163 bonds, 23 residues, 1 model selected  

> select add #32/A:72

186 atoms, 167 bonds, 24 residues, 1 model selected  

> hide sel cartoons

> select #32/A:21

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

> select add #32/A:22

17 atoms, 15 bonds, 2 residues, 1 model selected  

> select add #32/A:23

29 atoms, 27 bonds, 3 residues, 1 model selected  

> select add #32/A:25

38 atoms, 35 bonds, 4 residues, 1 model selected  

> select add #32/A:24

46 atoms, 42 bonds, 5 residues, 1 model selected  

> select add #32/A:26

50 atoms, 45 bonds, 6 residues, 1 model selected  

> select add #32/A:27

58 atoms, 52 bonds, 7 residues, 1 model selected  

> select add #32/A:29

67 atoms, 60 bonds, 8 residues, 1 model selected  

> select add #32/A:28

78 atoms, 71 bonds, 9 residues, 1 model selected  

> hide sel cartoons

> select add #32/A:30

84 atoms, 76 bonds, 10 residues, 1 model selected  

> select add #32/A:31

92 atoms, 83 bonds, 11 residues, 1 model selected  

> select add #32/A:32

100 atoms, 90 bonds, 12 residues, 1 model selected  

> select add #32/A:33

109 atoms, 98 bonds, 13 residues, 1 model selected  

> select add #32/A:34

117 atoms, 105 bonds, 14 residues, 1 model selected  

> select add #32/A:35

127 atoms, 115 bonds, 15 residues, 1 model selected  

> select subtract #32/A:35

117 atoms, 105 bonds, 14 residues, 1 model selected  

> select add #32/A:35

127 atoms, 115 bonds, 15 residues, 1 model selected  

> select add #32/A:36

135 atoms, 122 bonds, 16 residues, 1 model selected  

> select add #32/A:37

140 atoms, 126 bonds, 17 residues, 1 model selected  

> select add #32/A:38

147 atoms, 132 bonds, 18 residues, 1 model selected  

> select add #32/A:39

157 atoms, 142 bonds, 19 residues, 1 model selected  

> hide sel cartoons

> select #32/A:47

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

> select add #32/A:41

13 atoms, 11 bonds, 2 residues, 1 model selected  

> select add #32/A:40

20 atoms, 17 bonds, 3 residues, 1 model selected  

> select add #32/A:79

28 atoms, 24 bonds, 4 residues, 1 model selected  

> select add #32/A:80

35 atoms, 30 bonds, 5 residues, 1 model selected  

> select add #32/A:81

42 atoms, 36 bonds, 6 residues, 1 model selected  

> select add #32/A:86

54 atoms, 48 bonds, 7 residues, 1 model selected  

> hide sel cartoons

> select clear

> select add #32/B:94

5 atoms, 4 bonds, 1 residue, 1 model selected  

> select add #32/B:90

14 atoms, 12 bonds, 2 residues, 1 model selected  

> select add #32/B:91

23 atoms, 20 bonds, 3 residues, 1 model selected  

> select add #32/B:92

31 atoms, 27 bonds, 4 residues, 1 model selected  

> select add #32/B:93

39 atoms, 34 bonds, 5 residues, 1 model selected  

> select add #32/B:97

47 atoms, 41 bonds, 6 residues, 1 model selected  

> select add #32/B:98

55 atoms, 48 bonds, 7 residues, 1 model selected  

> select add #32/B:99

64 atoms, 56 bonds, 8 residues, 1 model selected  

> select add #32/B:100

69 atoms, 60 bonds, 9 residues, 1 model selected  

> hide sel cartoons

> turn y 45

> turn y -45

[Repeated 1 time(s)]

> turn y 45

> turn y 10

> turn y -10

> turn y -20

[Repeated 2 time(s)]

> turn y 40

> cd "/Users/zxc755/Library/CloudStorage/OneDrive-UniversityofCopenhagen/Type
> I-F_HNH/Manuscript/figures/structure/PAM"

Current working directory is: /Users/zxc755/Library/CloudStorage/OneDrive-
UniversityofCopenhagen/Type I-F_HNH/Manuscript/figures/structure/PAM  

> save PAM_with_map.tif supersample 3

> turn y -40

> save PAM_with_map_rotate_40degree.tif supersample 3

> turn y 40

> close #1-10

> show #!12 models

> hide #!12 models

> close #12

> show #!14 models

> hide #!14 models

> close #14

> show #!15 models

> hide #!15 models

> show #!15 models

> hide #!15 models

> show #!39 models

> hide #!39 models

> show #!39 models

> hide #!39 models

> show #!40 models

> hide #!40 models

> close #39-40

> save PAM_session.cxs includeMaps true

> select /A:85

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

> select add /A:84

14 atoms, 12 bonds, 2 residues, 1 model selected  

> select add /A:83

22 atoms, 19 bonds, 3 residues, 1 model selected  

> select hid car

Expected an objects specifier or a keyword  

> hide sel cartoons

> show sel

> show sel cartoons

> hide sel cartoons

> show sel cartoons

> select /A:84@CB

1 atom, 1 residue, 1 model selected  

> hide sel

> select clear

> turn y 180

[Repeated 14 time(s)]

> save PAM_with_map_front.tif supersample 3

> turn y 180

> save PAM_with_map_back.tif supersample 3

> hide #!18 models

> hide #!19 models

> hide #!20 models

> hide #!16 models

> hide #32

> show #32 cartoons

> hide #32 & nucleic cartoons

> show #32 & nucle

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

> show #32 & nucleic

> color #32/L dark orange

> color #32/K dim gray

> color #32/J dark red

> color #32/I rebecca purple

> color #32/B forest green

> color #32/C,D,E,F,G,H salmon

> color #32/A steel blue

> color #32/A:232-350 dark turquoise

> color #32/O blue

> color #32/M red

> select /K:3@P

1 atom, 1 residue, 1 model selected  

> select add /K:2@O3'

2 atoms, 2 residues, 1 model selected  

> select add /K:3@OP1

3 atoms, 2 residues, 1 model selected  

> select add /K:3@OP2

4 atoms, 2 residues, 1 model selected  

> select add /K:3@O5'

5 atoms, 2 residues, 1 model selected  

> color sel byhetero

> select clear

> color #32/a byhetero

> select clear

> show #32/a:319,328,280,304,305

> select /A:280@CB

1 atom, 1 residue, 1 model selected  

> select add /A:280@CG

2 atoms, 1 residue, 1 model selected  

> select add /A:280@CD

3 atoms, 1 residue, 1 model selected  

> select add /A:280@NE

4 atoms, 1 residue, 1 model selected  

> select add /A:280@CZ

5 atoms, 1 residue, 1 model selected  

> select add /A:280@NH1

6 atoms, 1 residue, 1 model selected  

> select add /A:280@NH2

7 atoms, 1 residue, 1 model selected  

> select add /A:305@CE1

8 atoms, 2 residues, 1 model selected  

> select add /A:305@NE2

9 atoms, 2 residues, 1 model selected  

> select add /A:305@CD2

10 atoms, 2 residues, 1 model selected  

> select add /A:305@CG

11 atoms, 2 residues, 1 model selected  

> select add /A:305@ND1

12 atoms, 2 residues, 1 model selected  

> select add /A:305@CB

13 atoms, 2 residues, 1 model selected  

> select add /A:319@ND2

14 atoms, 3 residues, 1 model selected  

> select add /A:319@OD1

15 atoms, 3 residues, 1 model selected  

> select add /A:319@CG

16 atoms, 3 residues, 1 model selected  

> select add /A:319@CB

17 atoms, 3 residues, 1 model selected  

> select add /A:304@ND1

18 atoms, 4 residues, 1 model selected  

> select add /A:304@CE1

19 atoms, 4 residues, 1 model selected  

> select add /A:304@NE2

20 atoms, 4 residues, 1 model selected  

> select add /A:304@CD2

21 atoms, 4 residues, 1 model selected  

> select add /A:304@CG

22 atoms, 4 residues, 1 model selected  

> select add /A:304@CB

23 atoms, 4 residues, 1 model selected  

> select add /A:328@NE2

24 atoms, 5 residues, 1 model selected  

> select add /A:328@CD2

25 atoms, 5 residues, 1 model selected  

> select add /A:328@CG

26 atoms, 5 residues, 1 model selected  

> select add /A:328@ND1

27 atoms, 5 residues, 1 model selected  

> select add /A:328@CE1

28 atoms, 5 residues, 1 model selected  

> select add /A:328@CB

29 atoms, 5 residues, 1 model selected  

> show #32/m,o

> select add /M:2@MG

30 atoms, 6 residues, 1 model selected  

> volume zone #13 nearAtoms sel range 1 newMap true

Opened halfcleaved_HNH_center_sharp3Å.mrc zone as #1, grid size 420,420,420,
pixel 0.725, shown at step 1, values float32  

> transparency #1 90

> select /K:3@P

1 atom, 1 residue, 1 model selected  

> select add /K:3@OP2

2 atoms, 1 residue, 1 model selected  

> select add /K:3@OP1

3 atoms, 1 residue, 1 model selected  

> select add /K:3@O5'

4 atoms, 1 residue, 1 model selected  

> select add /K:2@O3'

5 atoms, 2 residues, 1 model selected  

> select add /K:2@C3'

6 atoms, 2 residues, 1 model selected  

> select add /K:2@C2'

7 atoms, 2 residues, 1 model selected  

> select add /K:2@C1'

8 atoms, 2 residues, 1 model selected  

> select add /K:2@O4'

9 atoms, 2 residues, 1 model selected  

> select add /K:2@C4'

10 atoms, 2 residues, 1 model selected  

> select add /K:2@C5'

11 atoms, 2 residues, 1 model selected  

> select add /K:2@O5'

12 atoms, 2 residues, 1 model selected  

> volume zone #13 nearAtoms sel range 1 newMap true

Opened halfcleaved_HNH_center_sharp3Å.mrc zone as #2, grid size 420,420,420,
pixel 0.725, shown at step 1, values float32  

> transparency #2 90

> select /O:1@O

1 atom, 1 residue, 1 model selected  

> volume zone #13 nearAtoms sel range 1 newMap true

Opened halfcleaved_HNH_center_sharp3Å.mrc zone as #3, grid size 420,420,420,
pixel 0.725, shown at step 1, values float32  

> transparency #3 90

> color #1 turquoise

> color #2 dim gray

> color #3 blue

> select clear

> hide #32/b-l cartoons

> hide #32/j-l

> show #32/k:1-3

> hide #32/a:1-232 cartoons

> show #32/a:225-232 cartoons

> select /A:232

12 atoms, 12 bonds, 1 residue, 1 model selected  

> select /A:231

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

> select add /A:230

18 atoms, 16 bonds, 2 residues, 1 model selected  

> select add /A:229

26 atoms, 23 bonds, 3 residues, 1 model selected  

> select add /A:228

34 atoms, 30 bonds, 4 residues, 1 model selected  

> select add /A:226

43 atoms, 38 bonds, 5 residues, 1 model selected  

> select add /A:227

48 atoms, 42 bonds, 6 residues, 1 model selected  

> select add /A:225

53 atoms, 46 bonds, 7 residues, 1 model selected  

> hide sel cartoons

> select clear

> hide #32/a:324-350 cartoons

> hide #32/a:282-301 cartoons

> show #32/a:300-320 cartoons

> show #32/a:300-330 cartoons

> select add /A:301

12 atoms, 12 bonds, 1 residue, 1 model selected  

> select add /A:300

16 atoms, 15 bonds, 2 residues, 1 model selected  

> hide sel cartoons

> select /A:278

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

> hide #32/a:252-278 cartoons

> hide #32/a:232-251 cartoons

> hide #32/a:310-318 cartoons

> select /A:306

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

> select add /A:307

15 atoms, 13 bonds, 2 residues, 1 model selected  

> show sel

> hide sel

> select clear

> graphics silhouettes false

> lighting soft

> lighting shadows true intensity 0.5

> lighting shadows false

> lighting shadows true

> lighting shadows false

> lighting soft

> lighting full

> lighting shadows false

> lighting simple

> lighting soft

> lighting full

> lighting flat

> graphics silhouettes false

> lighting soft

> lighting full

[Repeated 1 time(s)]

> lighting soft

> lighting full

> lighting shadows false

> lighting soft

> lighting shadows true intensity 0.5

> lighting shadows false

> lighting shadows true

> lighting shadows false

> lighting shadows true

> lighting shadows false

> lighting simple

> lighting shadows true

> lighting shadows false

> lighting soft

> lighting full

> lighting flat

> lighting shadows true intensity 0.5

> lighting shadows false

> lighting shadows true

> lighting shadows false

> lighting shadows true

> lighting shadows false

> lighting shadows true

> lighting shadows false

> lighting shadows true

> lighting shadows false

> lighting shadows true

> lighting shadows false

> graphics silhouettes false

> lighting full

> lighting flat

> lighting simple

> graphics silhouettes false

> lighting soft

> lighting flat

> hide cd "/Users/zxc755/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/Type I-F_HNH/Manuscript/figures/structure/HNH"

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

> cd "/Users/zxc755/Library/CloudStorage/OneDrive-UniversityofCopenhagen/Type
> I-F_HNH/Manuscript/figures/structure/HNH"

Current working directory is: /Users/zxc755/Library/CloudStorage/OneDrive-
UniversityofCopenhagen/Type I-F_HNH/Manuscript/figures/structure/HNH  

> select /A:307

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select add /A:306

15 atoms, 13 bonds, 2 residues, 1 model selected  

> hide sel cartoons

> open "/Users/zxc755/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/Type
> I-F_HNH/Manuscript/IFhnh_Manuscript/maps_and_models/post_cleavage/postcleavage_HNH_center_refined.pdb"

Summary of feedback from opening /Users/zxc755/Library/CloudStorage/OneDrive-
UniversityofCopenhagen/Type
I-F_HNH/Manuscript/IFhnh_Manuscript/maps_and_models/post_cleavage/postcleavage_HNH_center_refined.pdb  
---  
warning | Ignored bad PDB record found on line 59  
SSBOND 1 CYS Aa 295 CYS Ca 140  
  
Chain information for postcleavage_HNH_center_refined.pdb #4  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
F | No description available  
G | No description available  
H | No description available  
I | No description available  
J | No description available  
K | No description available  
L | No description available  
  

> open "/Users/zxc755/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/Type
> I-F_HNH/Manuscript/IFhnh_Manuscript/maps_and_models/post_cleavage/post_HNH_cent_sharp.mrc"

Opened post_HNH_cent_sharp.mrc as #5, grid size 420,420,420, pixel 0.725,
shown at level 0.00328, step 2, values float32  

> hide #!4 models

> show #!4 models

> hide #!5 models

> hide #!4 models

> style #4 stick

Changed 23513 atom styles  

> hide #4

> show #4/a:279-330 cartoons

Computing secondary structure  

> show #!4 models

> hide #!4 models

> show #!4 models

> combine #4

> hide #!4 models

> mmaker #6/a:232-350 to #32/a:232-350

Computing secondary structure  
Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker halfcleaved_HNH_center_main_model_temp_editing.pdb, chain A (#32)
with copy of postcleavage_HNH_center_refined.pdb, chain A (#6), sequence
alignment score = 542.1  
RMSD between 110 pruned atom pairs is 0.556 angstroms; (across all 111 pairs:
0.605)  
  

> show #6/A:280,319,328,304,305

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!6 models

> save half_HNH_minimal_with_map.tif supersample 3

> show #!6 models

> hide #!2 models

> hide #!1 models

> hide #!3 models

> hide #32/k,m,o

> hide #4,6/a:282-301

> hide #4,6/a:282-301 cartoons

> select #6/A:307

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select add #6/A:306

15 atoms, 13 bonds, 2 residues, 1 model selected  

> hide sel cartoons

> select #6/A:318

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

> select add #6/A:317

17 atoms, 15 bonds, 2 residues, 1 model selected  

> select add #6/A:316

23 atoms, 20 bonds, 3 residues, 1 model selected  

> select add #6/A:315

31 atoms, 27 bonds, 4 residues, 1 model selected  

> select add #6/A:314

36 atoms, 31 bonds, 5 residues, 1 model selected  

> select add #6/A:313

40 atoms, 34 bonds, 6 residues, 1 model selected  

> select add #6/A:312

44 atoms, 37 bonds, 7 residues, 1 model selected  

> select add #6/A:311

53 atoms, 45 bonds, 8 residues, 1 model selected  

> select add #6/A:310

59 atoms, 50 bonds, 9 residues, 1 model selected  

> hide sel cartoons

Drag select of 4 residues  

> hide sel cartoons

> save minimal_HNH_superimposition.tif supersample 3

> color #4,6 salmon

> save minimal_HNH_superimposition.tif supersample 3

> hide #!6 models

> hide #!32 models

> show #!4 models

> show #4/a:280,319,328,304,305

> color #4/a byhetero

> select clear

> select #4/A:305@CE1

1 atom, 1 residue, 1 model selected  

> select add #4/A:305@ND1

2 atoms, 1 residue, 1 model selected  

> select add #4/A:305@CG

3 atoms, 1 residue, 1 model selected  

> select add #4/A:305@CD2

4 atoms, 1 residue, 1 model selected  

> select add #4/A:305@NE2

5 atoms, 1 residue, 1 model selected  

> select add #4/A:305@CB

6 atoms, 1 residue, 1 model selected  

> select add #4/A:319@ND2

7 atoms, 2 residues, 1 model selected  

> select add #4/A:319@OD1

8 atoms, 2 residues, 1 model selected  

> select add #4/A:319@CB

9 atoms, 2 residues, 1 model selected  

> select add #4/A:280@NE

10 atoms, 3 residues, 1 model selected  

> select add #4/A:280@CZ

11 atoms, 3 residues, 1 model selected  

> select add #4/A:280@NH1

12 atoms, 3 residues, 1 model selected  

> select add #4/A:280@NH2

13 atoms, 3 residues, 1 model selected  

> select add #4/A:280@CD

14 atoms, 3 residues, 1 model selected  

> select add #4/A:280@CG

15 atoms, 3 residues, 1 model selected  

> select add #4/A:280@CB

16 atoms, 3 residues, 1 model selected  

> select add #4/A:304@ND1

17 atoms, 4 residues, 1 model selected  

> select add #4/A:304@CE1

18 atoms, 4 residues, 1 model selected  

> select add #4/A:304@NE2

19 atoms, 4 residues, 1 model selected  

> select add #4/A:304@CD2

20 atoms, 4 residues, 1 model selected  

> select add #4/A:304@CG

21 atoms, 4 residues, 1 model selected  

> select add #4/A:304@CB

22 atoms, 4 residues, 1 model selected  

> select add #4/A:328@NE2

23 atoms, 5 residues, 1 model selected  

> select add #4/A:328@CD2

24 atoms, 5 residues, 1 model selected  

> select add #4/A:328@CG

25 atoms, 5 residues, 1 model selected  

> select add #4/A:328@CB

26 atoms, 5 residues, 1 model selected  

> select add #4/A:328@ND1

27 atoms, 5 residues, 1 model selected  

> select add #4/A:328@CE1

28 atoms, 5 residues, 1 model selected  

> volume zone #5 nearAtoms sel range 1 newMap true

Opened post_HNH_cent_sharp.mrc zone as #7, grid size 420,420,420, pixel 0.725,
shown at step 1, values float32  

> close #7

> volume zone #5 nearAtoms sel range 1.5 newMap true

Opened post_HNH_cent_sharp.mrc zone as #7, grid size 420,420,420, pixel 0.725,
shown at step 1, values float32  

> transparency #7 90

> volume #7 level 0.02

> volume #7 level 0.06

> volume #7 level 0.04

> volume #7 level 0.09

> color #7 salmon

> color #7 charcoal

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

> color #7 coal

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

> color #7 dim gray

> color #7 light slate gray

> volume #7 level .03

> select clear

> save post_HNH_minimal_with_map.tif supersample 3

> hide #!11 models

> hide #!7 models

> hide #!4 models

> show #!32 models

> show #!3 models

> show #!2 models

> show #!1 models

> show #32/m,o

> select clear

> show #32/k:1-3

> select clear

> save HNH_cat_session.cxs includeMaps true

> show #32 cartoons

> select #32/a:1-100

763 atoms, 777 bonds, 1 pseudobond, 98 residues, 2 models selected  

> select #32/a:1-90

693 atoms, 706 bonds, 1 pseudobond, 88 residues, 2 models selected  

> select #32/a:1-80

608 atoms, 619 bonds, 78 residues, 1 model selected  

> select #32/a:1-40

309 atoms, 313 bonds, 38 residues, 1 model selected  

> select #32/a:1-30

229 atoms, 231 bonds, 28 residues, 1 model selected  

> select #32/a:1-35

272 atoms, 275 bonds, 33 residues, 1 model selected  

> select #32/a:80-150

584 atoms, 593 bonds, 1 pseudobond, 71 residues, 2 models selected  

> select #32/a:80-135

456 atoms, 461 bonds, 1 pseudobond, 56 residues, 2 models selected  

> open "/Users/zxc755/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/Type I-F_HNH/Manuscript/apo_HNH_center_refined-
> coot-0.pdb"

Chain information for apo_HNH_center_refined-coot-0.pdb #8  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
F | No description available  
G | No description available  
H | No description available  
I | No description available  
J | No description available  
  

> open "/Users/zxc755/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/Type
> I-F_HNH/Manuscript/IFhnh_Manuscript/maps_and_models/apo/apo_HNH_cent_sharp.mrc"

Opened apo_HNH_cent_sharp.mrc as #9, grid size 420,420,420, pixel 0.725, shown
at level 0.00199, step 2, values float32  

> hide #!1 models

> hide #!2 models

> hide #!3 models

> hide #!32 models

> style stick

Changed 94148 atom styles  

> hide #8

> show #8 cartoons

Computing secondary structure  

> transparency #9 90

> color #8/L dark orange

> color #8/K dim gray

> color #8/J dark red

> color #8/I rebecca purple

> color #8/B forest green

> color #8/C,D,E,F,G,H salmon

> color #8/A steel blue

> color #8/A:232-350 dark turquoise

> color #8/O blue

> color #8/M red

> hide #!9 models

> show #!9 models

> hide #!9 models

> show #!9 models

> hide #!9 models

> volume zone #9 nearAtoms #8/A range 3 newMap true

Opened apo_HNH_cent_sharp.mrc zone as #10, grid size 420,420,420, pixel 0.725,
shown at step 1, values float32  

> show #!9 models

> hide #!9 models

> hide #!10 models

> show #!10 models

> transparency #10 90

> volume #10 level 0.02

> hide #!10 models

> show #!9 models

> hide #!9 models

> show #!9 models

> show #!10 models

> hide #!9 models

> hide #8 cartoons

> show #8/a cartoons

> surface dust #10 size 5

> combine #8

> hide #!8 models

> fitmap #12/A:232-350 inMap #9

Fit molecule copy of apo_HNH_center_refined-coot-0.pdb (#12) to map
apo_HNH_cent_sharp.mrc (#9) using 897 atoms  
average map value = 0.1137, steps = 76  
shifted from previous position = 1.81  
rotated from previous position = 3.94 degrees  
atoms outside contour = 144, contour level = 0.0019908  
  
Position of copy of apo_HNH_center_refined-coot-0.pdb (#12) relative to
apo_HNH_cent_sharp.mrc (#9) coordinates:  
Matrix rotation and translation  
0.99849050 0.04622093 0.02967081 -7.99164150  
-0.04495289 0.99810294 -0.04206845 14.50694265  
-0.03155897 0.04067116 0.99867407 0.51270662  
Axis 0.60172121 0.44529167 -0.66305876  
Axis point 301.29448148 199.80947793 0.00000000  
Rotation angle (degrees) 3.94233491  
Shift along axis 1.31112589  
  

> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/apo_HNH_center_refined-coot-0_HNH_fit.pdb" models #12

> fitmap #12/A:80-135 inMap #9

Fit molecule copy of apo_HNH_center_refined-coot-0.pdb (#12) to map
apo_HNH_cent_sharp.mrc (#9) using 456 atoms  
average map value = 0.05565, steps = 96  
shifted from previous position = 6.74  
rotated from previous position = 5.58 degrees  
atoms outside contour = 120, contour level = 0.0019908  
  
Position of copy of apo_HNH_center_refined-coot-0.pdb (#12) relative to
apo_HNH_cent_sharp.mrc (#9) coordinates:  
Matrix rotation and translation  
0.99481363 0.04551028 0.09096513 -18.50883752  
-0.04872161 0.99825385 0.03339856 1.51076745  
-0.08928631 -0.03765731 0.99529387 16.74468113  
Axis -0.32980050 0.83662351 -0.43737025  
Axis point 176.51077727 0.00000000 213.37405101  
Rotation angle (degrees) 6.18421935  
Shift along axis 0.04454214  
  

> show #!8 models

> hide #!8 models

> show #!8 models

> hide #!8 models

> show #!8 models

> hide #!8 models

> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/apo_HNH_center_refined-coot-0_N-ter_fit.pdb"

> hide #!12 models

> show #!8 models

> fitmap #8/A:80-135 inMap #9

Fit molecule apo_HNH_center_refined-coot-0.pdb (#8) to map
apo_HNH_cent_sharp.mrc (#9) using 456 atoms  
average map value = 0.05868, steps = 176  
shifted from previous position = 2.5  
rotated from previous position = 13.2 degrees  
atoms outside contour = 119, contour level = 0.0019908  
  
Position of apo_HNH_center_refined-coot-0.pdb (#8) relative to
apo_HNH_cent_sharp.mrc (#9) coordinates:  
Matrix rotation and translation  
0.97387880 0.10270175 -0.20251527 8.86888724  
-0.10753121 0.99411722 -0.01296093 14.32149660  
0.19999281 0.03439909 0.97919333 -23.07565390  
Axis 0.10373066 -0.88159654 -0.46046443  
Axis point 120.86155715 0.00000000 28.75781651  
Rotation angle (degrees) 13.19604193  
Shift along axis -1.08028845  
  

> fitmap #8/A inMap #9

Fit molecule apo_HNH_center_refined-coot-0.pdb (#8) to map
apo_HNH_cent_sharp.mrc (#9) using 2728 atoms  
average map value = 0.05474, steps = 136  
shifted from previous position = 1.91  
rotated from previous position = 11.7 degrees  
atoms outside contour = 1271, contour level = 0.0019908  
  
Position of apo_HNH_center_refined-coot-0.pdb (#8) relative to
apo_HNH_cent_sharp.mrc (#9) coordinates:  
Matrix rotation and translation  
0.96863084 -0.03548685 -0.24595725 34.61064363  
-0.01015117 0.98327484 -0.18184486 22.60765338  
0.24829668 0.17863729 0.95207010 -47.86311464  
Axis 0.58876206 -0.80724652 0.04137982  
Axis point 214.60251744 0.00000000 112.99623949  
Rotation angle (degrees) 17.82650237  
Shift along axis 0.14691702  
  

> show #!9 models

> hide #!9 models

> fitmap #8/A inMap #10

Fit molecule apo_HNH_center_refined-coot-0.pdb (#8) to map
apo_HNH_cent_sharp.mrc zone (#10) using 2728 atoms  
average map value = 0.04338, steps = 68  
shifted from previous position = 0.747  
rotated from previous position = 1.19 degrees  
atoms outside contour = 1886, contour level = 0.02  
  
Position of apo_HNH_center_refined-coot-0.pdb (#8) relative to
apo_HNH_cent_sharp.mrc zone (#10) coordinates:  
Matrix rotation and translation  
0.96913985 -0.02068010 -0.24564259 32.81429654  
-0.02062424 0.98617920 -0.16439353 21.97080178  
0.24564729 0.16438651 0.95531905 -46.25105779  
Axis 0.55616727 -0.83107037 0.00009450  
Axis point 207.83659879 0.00000000 107.50533490  
Rotation angle (degrees) 17.19211508  
Shift along axis -0.01341541  
  

> select clear

> select #8/A:231

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

> ui mousemode right "rotate selected models"

> view matrix models
> #8,0.98518,0.053245,-0.16304,14.087,-0.04686,0.99799,0.042762,-2.3863,0.16499,-0.034489,0.98569,-19.98

> fitmap #8/A inMap #10

Fit molecule apo_HNH_center_refined-coot-0.pdb (#8) to map
apo_HNH_cent_sharp.mrc zone (#10) using 2728 atoms  
average map value = 0.1094, steps = 112  
shifted from previous position = 5.82  
rotated from previous position = 10.7 degrees  
atoms outside contour = 1095, contour level = 0.02  
  
Position of apo_HNH_center_refined-coot-0.pdb (#8) relative to
apo_HNH_cent_sharp.mrc zone (#10) coordinates:  
Matrix rotation and translation  
0.99997652 -0.00466439 0.00502091 0.20988985  
0.00473618 0.99988534 -0.01438311 1.27122337  
-0.00495325 0.01440656 0.99988395 -0.80414690  
Axis 0.90290151 0.31280943 0.29482049  
Axis point 0.00000000 63.62884067 80.26210486  
Rotation angle (degrees) 0.91349740  
Shift along axis 0.35008153  
  

> fitmap #8/A:80-135 inMap #10

Fit molecule apo_HNH_center_refined-coot-0.pdb (#8) to map
apo_HNH_cent_sharp.mrc zone (#10) using 456 atoms  
average map value = 0.05864, steps = 96  
shifted from previous position = 1.63  
rotated from previous position = 12.7 degrees  
atoms outside contour = 227, contour level = 0.02  
  
Position of apo_HNH_center_refined-coot-0.pdb (#8) relative to
apo_HNH_cent_sharp.mrc zone (#10) coordinates:  
Matrix rotation and translation  
0.97694589 0.10504409 -0.18585603 6.38549743  
-0.10761365 0.99418567 -0.00376302 13.31326798  
0.18438012 0.02367691 0.98256978 -20.25353573  
Axis 0.06413527 -0.86535176 -0.49704425  
Axis point 114.59977050 0.00000000 20.50228547  
Rotation angle (degrees) 12.35231087  
Shift along axis -1.04422077  
  

> fitmap #8/A:1-135 inMap #10

Fit molecule apo_HNH_center_refined-coot-0.pdb (#8) to map
apo_HNH_cent_sharp.mrc zone (#10) using 1057 atoms  
average map value = 0.07052, steps = 108  
shifted from previous position = 2.65  
rotated from previous position = 10.5 degrees  
atoms outside contour = 524, contour level = 0.02  
  
Position of apo_HNH_center_refined-coot-0.pdb (#8) relative to
apo_HNH_cent_sharp.mrc zone (#10) coordinates:  
Matrix rotation and translation  
0.99946033 0.02326146 -0.02319395 -0.64828860  
-0.02335695 0.99971976 -0.00385462 3.15728544  
0.02309779 0.00439427 0.99972355 -2.67969831  
Axis 0.12457993 -0.69912699 -0.70406057  
Axis point 122.81669961 28.56907646 0.00000000  
Rotation angle (degrees) 1.89722763  
Shift along axis -0.40143729  
  

> fitmap #8/A:232-350 inMap #10

Fit molecule apo_HNH_center_refined-coot-0.pdb (#8) to map
apo_HNH_cent_sharp.mrc zone (#10) using 897 atoms  
average map value = 0.1135, steps = 88  
shifted from previous position = 3.95  
rotated from previous position = 3.77 degrees  
atoms outside contour = 263, contour level = 0.02  
  
Position of apo_HNH_center_refined-coot-0.pdb (#8) relative to
apo_HNH_cent_sharp.mrc zone (#10) coordinates:  
Matrix rotation and translation  
0.99894847 0.03136930 0.03343540 -6.87861474  
-0.03015042 0.99888397 -0.03635608 10.87881307  
-0.03453855 0.03530975 0.99877941 1.73316127  
Axis 0.61586393 0.58413756 -0.52867281  
Axis point 0.00000000 -57.34675321 281.67474684  
Rotation angle (degrees) 3.33553382  
Shift along axis 1.20215737  
  

> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/apo_HNH_center_refined-coot-0_HNH_fit.pdb" models #8

> hide #!10 models

Drag select of 129 residues  

> show #!10 models

> fitmap sel inMap #10

Fit molecule apo_HNH_center_refined-coot-0.pdb (#8) to map
apo_HNH_cent_sharp.mrc zone (#10) using 1033 atoms  
average map value = 0.06563, steps = 304  
shifted from previous position = 5.04  
rotated from previous position = 19.6 degrees  
atoms outside contour = 527, contour level = 0.02  
  
Position of apo_HNH_center_refined-coot-0.pdb (#8) relative to
apo_HNH_cent_sharp.mrc zone (#10) coordinates:  
Matrix rotation and translation  
0.97550451 -0.21809449 0.02873560 32.60163060  
0.20802092 0.95705305 0.20193255 -41.53482359  
-0.07154187 -0.19100851 0.97897779 42.51583633  
Axis -0.66798838 0.17046879 0.72438382  
Axis point 228.05641713 129.81114836 0.00000000  
Rotation angle (degrees) 17.10493668  
Shift along axis 1.93988222  
  

> hide #!10 models

Drag select of 92 residues  

> show #!10 models

> fitmap #8/a inMap #10

Fit molecule apo_HNH_center_refined-coot-0.pdb (#8) to map
apo_HNH_cent_sharp.mrc zone (#10) using 2728 atoms  
average map value = 0.1094, steps = 152  
shifted from previous position = 8.19  
rotated from previous position = 17.4 degrees  
atoms outside contour = 1095, contour level = 0.02  
  
Position of apo_HNH_center_refined-coot-0.pdb (#8) relative to
apo_HNH_cent_sharp.mrc zone (#10) coordinates:  
Matrix rotation and translation  
0.99997611 -0.00472570 0.00504416 0.21355520  
0.00479823 0.99988385 -0.01446572 1.27948594  
-0.00497521 0.01448958 0.99988264 -0.80934348  
Axis 0.90243179 0.31226729 0.29682657  
Axis point 0.00000000 63.71907535 80.33882755  
Rotation angle (degrees) 0.91923153  
Shift along axis 0.35202596  
  

> fitmap sel inMap #10

Fit molecule apo_HNH_center_refined-coot-0.pdb (#8) to map
apo_HNH_cent_sharp.mrc zone (#10) using 751 atoms  
average map value = 0.04893, steps = 116  
shifted from previous position = 0.796  
rotated from previous position = 3.08 degrees  
atoms outside contour = 429, contour level = 0.02  
  
Position of apo_HNH_center_refined-coot-0.pdb (#8) relative to
apo_HNH_cent_sharp.mrc zone (#10) coordinates:  
Matrix rotation and translation  
0.99892100 0.03260019 -0.03307674 -0.59088395  
-0.03287494 0.99942906 -0.00779691 4.45668233  
0.03280367 0.00887590 0.99942240 -4.33104269  
Axis 0.17667979 -0.69812691 -0.69383217  
Axis point 136.11302865 -0.00000000 -21.17869303  
Rotation angle (degrees) 2.70443076  
Shift along axis -0.21071038  
  

> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/apo_HNH_center_refined-coot-0_N-ter_fit.pdb" models #8

> show #!9 models

> hide #!9 models

> show #!9 models

> hide #!9 models

> show #!9 models

> hide #!9 models

> show #!9 models

> hide #!9 models

> show #!9 models

> hide #!10 models

> fitmap sel inMap #9

Fit molecule apo_HNH_center_refined-coot-0.pdb (#8) to map
apo_HNH_cent_sharp.mrc (#9) using 751 atoms  
average map value = 0.04893, steps = 64  
shifted from previous position = 0.00612  
rotated from previous position = 0.0147 degrees  
atoms outside contour = 222, contour level = 0.0019908  
  
Position of apo_HNH_center_refined-coot-0.pdb (#8) relative to
apo_HNH_cent_sharp.mrc (#9) coordinates:  
Matrix rotation and translation  
0.99891180 0.03266370 -0.03329126 -0.57577626  
-0.03294448 0.99942580 -0.00792044 4.48398773  
0.03301344 0.00900858 0.99941431 -4.37110048  
Axis 0.17857319 -0.69940507 -0.69205792  
Axis point 136.52172827 0.00000000 -20.61037254  
Rotation angle (degrees) 2.71688308  
Shift along axis -0.21388724  
  
Drag select of 2 residues, 9 apo_HNH_cent_sharp.mrc  

> hide #!9 models

Drag select of 92 residues  

> show #!9 models

> view matrix models
> #8,0.99891,0.032664,-0.033291,-3.0428,-0.032944,0.99943,-0.0079204,1.8123,0.033013,0.0090086,0.99941,-4.4427

> fitmap sel inMap #9

Fit molecule apo_HNH_center_refined-coot-0.pdb (#8) to map
apo_HNH_cent_sharp.mrc (#9) using 751 atoms  
average map value = 0.04941, steps = 112  
shifted from previous position = 1.87  
rotated from previous position = 13.6 degrees  
atoms outside contour = 241, contour level = 0.0019908  
  
Position of apo_HNH_center_refined-coot-0.pdb (#8) relative to
apo_HNH_cent_sharp.mrc (#9) coordinates:  
Matrix rotation and translation  
0.99824896 -0.04930729 -0.03267722 10.31067123  
0.05510661 0.97598361 0.21075875 -27.44944198  
0.02150049 -0.21219043 0.97699179 35.29516095  
Axis -0.96343154 -0.12341082 0.23784331  
Axis point 0.00000000 148.42617946 146.07203449  
Rotation angle (degrees) 12.67975067  
Shift along axis 1.84865039  
  

> view matrix models
> #8,0.99825,-0.049307,-0.032677,9.4603,0.055107,0.97598,0.21076,-22.821,0.0215,-0.21219,0.97699,34.178

> fitmap sel inMap #9

Fit molecule apo_HNH_center_refined-coot-0.pdb (#8) to map
apo_HNH_cent_sharp.mrc (#9) using 751 atoms  
average map value = 0.0484, steps = 320  
shifted from previous position = 4.25  
rotated from previous position = 13 degrees  
atoms outside contour = 234, contour level = 0.0019908  
  
Position of apo_HNH_center_refined-coot-0.pdb (#8) relative to
apo_HNH_cent_sharp.mrc (#9) coordinates:  
Matrix rotation and translation  
0.97609557 0.09991348 -0.19301485 8.78155338  
-0.06675455 0.98296459 0.17124380 -9.35267581  
0.20683633 -0.15426570 0.96613706 4.94968795  
Axis -0.60072274 -0.73791918 -0.30758327  
Axis point -16.25369823 0.00000000 47.83281120  
Rotation angle (degrees) 15.71970747  
Shift along axis 0.10379886  
  

> view matrix models
> #8,0.94061,-0.031443,-0.33802,47.216,-0.0044741,0.99447,-0.10496,14.912,0.33945,0.10024,0.93527,-47.508

> fitmap sel inMap #9

Fit molecule apo_HNH_center_refined-coot-0.pdb (#8) to map
apo_HNH_cent_sharp.mrc (#9) using 751 atoms  
average map value = 0.04895, steps = 140  
shifted from previous position = 4.05  
rotated from previous position = 13.8 degrees  
atoms outside contour = 235, contour level = 0.0019908  
  
Position of apo_HNH_center_refined-coot-0.pdb (#8) relative to
apo_HNH_cent_sharp.mrc (#9) coordinates:  
Matrix rotation and translation  
0.98211439 0.09352479 -0.16341495 5.31498086  
-0.09144608 0.99560485 0.02021373 8.63776478  
0.16458720 -0.00490854 0.98635032 -14.18520647  
Axis -0.06656667 -0.86911010 -0.49011888  
Axis point 90.73511369 0.00000000 22.22348540  
Rotation angle (degrees) 10.87692740  
Shift along axis -0.90853175  
  

> view matrix models
> #8,0.98211,0.093525,-0.16341,-3.653,-0.091446,0.9956,0.020214,15.181,0.16459,-0.0049085,0.98635,-17.989

> fitmap sel inMap #9

Fit molecule apo_HNH_center_refined-coot-0.pdb (#8) to map
apo_HNH_cent_sharp.mrc (#9) using 751 atoms  
average map value = 0.04278, steps = 204  
shifted from previous position = 11.5  
rotated from previous position = 49.1 degrees  
atoms outside contour = 286, contour level = 0.0019908  
  
Position of apo_HNH_center_refined-coot-0.pdb (#8) relative to
apo_HNH_cent_sharp.mrc (#9) coordinates:  
Matrix rotation and translation  
0.51617442 0.50434421 -0.69224337 52.94424808  
-0.36241786 0.86093017 0.35700496 22.73796343  
0.77602659 0.06660453 0.62717348 -56.46806541  
Axis -0.16790288 -0.84892009 -0.50114200  
Axis point 81.93964639 0.00000000 19.23832231  
Rotation angle (degrees) 59.85838174  
Shift along axis 0.10631310  
  

> view matrix models
> #8,0.75563,0.53552,0.37715,-102.7,-0.65339,0.65658,0.37681,98.385,-0.045843,-0.53116,0.84603,110.59

> fitmap sel inMap #9

Fit molecule apo_HNH_center_refined-coot-0.pdb (#8) to map
apo_HNH_cent_sharp.mrc (#9) using 751 atoms  
average map value = 0.02767, steps = 144  
shifted from previous position = 7.5  
rotated from previous position = 13 degrees  
atoms outside contour = 399, contour level = 0.0019908  
  
Position of apo_HNH_center_refined-coot-0.pdb (#8) relative to
apo_HNH_cent_sharp.mrc (#9) coordinates:  
Matrix rotation and translation  
0.84445830 0.49866537 0.19550710 -85.59391132  
-0.52302025 0.68898866 0.50174140 57.10323282  
0.11549889 -0.52595387 0.84263428 92.00315528  
Axis -0.70809886 0.05512697 -0.70395811  
Axis point 0.00000000 175.17228734 -5.33803959  
Rotation angle (degrees) 46.52479336  
Shift along axis -1.00948880  
  

> view matrix models
> #8,0.22325,-0.12434,0.9668,1.3433,-0.96716,-0.1519,0.2038,273.03,0.12152,-0.98054,-0.15417,271.04

> fitmap sel inMap #9

Fit molecule apo_HNH_center_refined-coot-0.pdb (#8) to map
apo_HNH_cent_sharp.mrc (#9) using 751 atoms  
average map value = 0.02054, steps = 72  
shifted from previous position = 0.557  
rotated from previous position = 6.62 degrees  
atoms outside contour = 451, contour level = 0.0019908  
  
Position of apo_HNH_center_refined-coot-0.pdb (#8) relative to
apo_HNH_cent_sharp.mrc (#9) coordinates:  
Matrix rotation and translation  
0.32093819 -0.07334501 0.94425589 -15.53284174  
-0.93429007 -0.18794079 0.30295267 264.15586909  
0.15524413 -0.97943798 -0.12884289 264.10267667  
Axis -0.73936752 0.45490792 -0.49638136  
Axis point 0.00000000 230.80804800 33.94290972  
Rotation angle (degrees) 119.86266478  
Shift along axis 0.55543077  
  

> view matrix models
> #8,0.51797,0.29889,0.80148,-77.363,-0.84718,0.3088,0.43234,159.71,-0.11827,-0.90294,0.41316,217.23

> fitmap sel inMap #9

Fit molecule apo_HNH_center_refined-coot-0.pdb (#8) to map
apo_HNH_cent_sharp.mrc (#9) using 751 atoms  
average map value = 0.03756, steps = 156  
shifted from previous position = 8.79  
rotated from previous position = 28.4 degrees  
atoms outside contour = 345, contour level = 0.0019908  
  
Position of apo_HNH_center_refined-coot-0.pdb (#8) relative to
apo_HNH_cent_sharp.mrc (#9) coordinates:  
Matrix rotation and translation  
0.82035985 0.09006159 0.56471110 -54.91363732  
-0.57114524 0.17797173 0.80132339 101.29105575  
-0.02833415 -0.97990559 0.19743911 248.32489572  
Axis -0.89491213 0.29795349 -0.33219874  
Axis point 0.00000000 193.91338679 71.34026782  
Rotation angle (degrees) 84.38258802  
Shift along axis -3.17031318  
  

> fitmap #8/a:1-232 inMap #9

Fit molecule apo_HNH_center_refined-coot-0.pdb (#8) to map
apo_HNH_cent_sharp.mrc (#9) using 1843 atoms  
average map value = 0.07444, steps = 132  
shifted from previous position = 5.34  
rotated from previous position = 8.06 degrees  
atoms outside contour = 740, contour level = 0.0019908  
  
Position of apo_HNH_center_refined-coot-0.pdb (#8) relative to
apo_HNH_cent_sharp.mrc (#9) coordinates:  
Matrix rotation and translation  
0.85556495 0.03689190 0.51637932 -43.24932520  
-0.51768413 0.06757577 0.85289897 100.05195461  
-0.00342966 -0.99703184 0.07691381 261.90564432  
Axis -0.92496541 0.25990449 -0.27728802  
Axis point 0.00000000 184.53788363 82.42044866  
Rotation angle (degrees) 89.99843794  
Shift along axis -6.61521397  
  

> fitmap #8/a:1-232 inMap #10

Fit molecule apo_HNH_center_refined-coot-0.pdb (#8) to map
apo_HNH_cent_sharp.mrc zone (#10) using 1843 atoms  
average map value = 0.04496, steps = 204  
shifted from previous position = 3.49  
rotated from previous position = 15.1 degrees  
atoms outside contour = 1324, contour level = 0.02  
  
Position of apo_HNH_center_refined-coot-0.pdb (#8) relative to
apo_HNH_cent_sharp.mrc zone (#10) coordinates:  
Matrix rotation and translation  
0.85917065 0.12276216 0.49674464 -53.18821240  
-0.50867642 0.31010579 0.80317040 65.81149160  
-0.05544446 -0.94274272 0.32888002 229.17603074  
Axis -0.90136454 0.28507929 -0.32599351  
Axis point 0.00000000 186.58673918 75.48977018  
Rotation angle (degrees) 75.57702649  
Shift along axis -8.00643664  
  

> view matrix models
> #8,0.85917,0.12276,0.49674,-64.07,-0.50868,0.31011,0.80317,70.614,-0.055444,-0.94274,0.32888,227.33

> fitmap #8/a:1-232 inMap #10

Fit molecule apo_HNH_center_refined-coot-0.pdb (#8) to map
apo_HNH_cent_sharp.mrc zone (#10) using 1843 atoms  
average map value = 0.03523, steps = 100  
shifted from previous position = 1.41  
rotated from previous position = 6.44 degrees  
atoms outside contour = 1400, contour level = 0.02  
  
Position of apo_HNH_center_refined-coot-0.pdb (#8) relative to
apo_HNH_cent_sharp.mrc zone (#10) coordinates:  
Matrix rotation and translation  
0.80480185 0.18549600 0.56381310 -75.67146644  
-0.59351183 0.26133077 0.76121609 93.91370671  
-0.00613918 -0.94725786 0.32041356 222.16366887  
Axis -0.87065314 0.29045262 -0.39698914  
Axis point 0.00000000 190.88011217 63.74735928  
Rotation angle (degrees) 78.85614004  
Shift along axis 4.96451775  
  

> view matrix models
> #8,0.95413,0.18283,0.2371,-44.561,-0.29249,0.73836,0.60767,1.8038,-0.063966,-0.64915,0.75797,133.99

> fitmap #8/a:1-232 inMap #10

Fit molecule apo_HNH_center_refined-coot-0.pdb (#8) to map
apo_HNH_cent_sharp.mrc zone (#10) using 1843 atoms  
average map value = 0.04793, steps = 112  
shifted from previous position = 1.31  
rotated from previous position = 8.5 degrees  
atoms outside contour = 1301, contour level = 0.02  
  
Position of apo_HNH_center_refined-coot-0.pdb (#8) relative to
apo_HNH_cent_sharp.mrc zone (#10) coordinates:  
Matrix rotation and translation  
0.93571186 0.27776002 0.21746882 -53.80939596  
-0.35134002 0.78914218 0.50380035 13.01747719  
-0.03167822 -0.54781747 0.83599791 104.83057724  
Axis -0.84096032 0.19923852 -0.50308027  
Axis point 0.00000000 173.44882492 44.82069031  
Rotation angle (degrees) 38.70040585  
Shift along axis -4.89304496  
  

> view matrix models
> #8,-0.34192,-0.82356,0.4526,255.51,0.043806,-0.49507,-0.86775,319.8,0.93871,-0.27688,0.20535,9.9731

> fitmap #8/a:1-232 inMap #10

Fit molecule apo_HNH_center_refined-coot-0.pdb (#8) to map
apo_HNH_cent_sharp.mrc zone (#10) using 1843 atoms  
average map value = 0.01904, steps = 240  
shifted from previous position = 15.2  
rotated from previous position = 14.3 degrees  
atoms outside contour = 1658, contour level = 0.02  
  
Position of apo_HNH_center_refined-coot-0.pdb (#8) relative to
apo_HNH_cent_sharp.mrc zone (#10) coordinates:  
Matrix rotation and translation  
-0.25816560 -0.79737188 0.54548016 216.97863355  
0.22288946 -0.59854746 -0.76945515 298.39643581  
0.94003766 -0.07706507 0.33225015 -41.78946055  
Axis 0.53482557 -0.30476959 0.78808445  
Axis point 53.68514190 192.65985646 0.00000000  
Rotation angle (degrees) 139.66131452  
Shift along axis -7.83006181  
  

> hide #!8 models

> show #!10 models

> hide #!10 models

> show #!10 models

> hide #!9 models

> show #!8 models

> view matrix models
> #8,0.99221,0.12413,0.010984,-16.454,-0.11883,0.91586,0.38351,-21.706,0.037546,-0.38183,0.92347,54.561

> fitmap #8/a:1-232 inMap #10

Fit molecule apo_HNH_center_refined-coot-0.pdb (#8) to map
apo_HNH_cent_sharp.mrc zone (#10) using 1843 atoms  
average map value = 0.1142, steps = 192  
shifted from previous position = 7.86  
rotated from previous position = 24.2 degrees  
atoms outside contour = 781, contour level = 0.02  
  
Position of apo_HNH_center_refined-coot-0.pdb (#8) relative to
apo_HNH_cent_sharp.mrc zone (#10) coordinates:  
Matrix rotation and translation  
0.99991970 -0.01233620 -0.00289962 2.01037916  
0.01231916 0.99990715 -0.00582431 -0.62951411  
0.00297120 0.00578812 0.99997883 -0.74339140  
Axis 0.41653941 -0.21058730 0.88439126  
Axis point 46.90450042 152.10806215 0.00000000  
Rotation angle (degrees) 0.79868134  
Shift along axis 0.31252097  
  

> fitmap sel inMap #9

Fit molecule apo_HNH_center_refined-coot-0.pdb (#8) to map
apo_HNH_cent_sharp.mrc (#9) using 751 atoms  
average map value = 0.04894, steps = 72  
shifted from previous position = 1.03  
rotated from previous position = 3.1 degrees  
atoms outside contour = 222, contour level = 0.0019908  
  
Position of apo_HNH_center_refined-coot-0.pdb (#8) relative to
apo_HNH_cent_sharp.mrc (#9) coordinates:  
Matrix rotation and translation  
0.99892404 0.03249695 -0.03308647 -0.57194403  
-0.03277317 0.99943206 -0.00784060 4.44583961  
0.03281289 0.00891651 0.99942174 -4.34188516  
Axis 0.17778779 -0.69917177 -0.69249573  
Axis point 136.25073516 0.00000000 -20.62446803  
Rotation angle (degrees) 2.70116337  
Shift along axis -0.20335325  
  

> open "/Users/zxc755/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/Type I-F_HNH/Manuscript/apo_HNH_center_refined-
> coot-0.pdb"

Chain information for apo_HNH_center_refined-coot-0.pdb #14  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
F | No description available  
G | No description available  
H | No description available  
I | No description available  
J | No description available  
  

> style stick

Changed 140210 atom styles  

> hide #!8 models

> hide #14

> show #14/A cartoons

Computing secondary structure  

> hide #14/a:1-231 cartoons

> hide #!10 models

> select up

1257 atoms, 1283 bonds, 157 residues, 1 model selected  

> select up

2728 atoms, 2786 bonds, 340 residues, 1 model selected  

> select down

1257 atoms, 1283 bonds, 157 residues, 1 model selected  

> select down

751 atoms, 92 residues, 1 model selected  

> show #14/A cartoons

> show #!9 models

> hide #!9 models

> show #!9 models

> hide #!9 models

> volume zone #9 nearAtoms #14/a range 2.5 newMap true

Opened apo_HNH_cent_sharp.mrc zone as #21, grid size 420,420,420, pixel 0.725,
shown at step 1, values float32  

> transparency #21 90

> surface dust #21

> open "/Users/zxc755/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/Type
> I-F_HNH/Manuscript/IFhnh_Manuscript/maps_and_models/apo/apo_HNH_inwards_refined.pdb"

Chain information for apo_HNH_inwards_refined.pdb #22  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D E | No description available  
F G | No description available  
H | No description available  
I | No description available  
J | No description available  
  

> open "/Users/zxc755/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/Type
> I-F_HNH/Manuscript/IFhnh_Manuscript/maps_and_models/apo/apo_HNH_in_sharp.mrc"

Opened apo_HNH_in_sharp.mrc as #23, grid size 420,420,420, pixel 0.725, shown
at level 0.00173, step 2, values float32  

> hide #!23 models

> hide #!21 models

> hide #!14 models

> hide #22

> show #22/a cartoons

Computing secondary structure  

> volume zone #23 nearAtoms #22/a range 2.5 newMap true

Opened apo_HNH_in_sharp.mrc zone as #24, grid size 420,420,420, pixel 0.725,
shown at step 1, values float32  

> transparency #24 90

> hide #!24 models

> hide #!22 models

> show #!21 models

> show #!14 models

> hide #!14 models

> hide #!21 models

> show #!22 models

> show #!24 models

> hide #!24 models

> hide #!22 models

> open "/Users/zxc755/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/Type
> I-F_HNH/Manuscript/IFhnh_Manuscript/maps_and_models/apo/apo_HNH_outwards_refined.pdb"

Summary of feedback from opening /Users/zxc755/Library/CloudStorage/OneDrive-
UniversityofCopenhagen/Type
I-F_HNH/Manuscript/IFhnh_Manuscript/maps_and_models/apo/apo_HNH_outwards_refined.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 1 1 ILE a 6 ALA a 9 1 4  
Start residue of secondary structure not found: HELIX 2 2 GLU a 16 SER a 30 1
15  
Start residue of secondary structure not found: HELIX 3 3 ALA a 41 THR a 44 1
4  
Start residue of secondary structure not found: HELIX 4 4 ALA a 84 TYR a 86 5
3  
Start residue of secondary structure not found: HELIX 5 5 ARG a 88 VAL a 93 1
6  
155 messages similar to the above omitted  
  
Chain information for apo_HNH_outwards_refined.pdb #25  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
F G | No description available  
H | No description available  
I | No description available  
J | No description available  
  

> open "/Users/zxc755/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/Type
> I-F_HNH/Manuscript/IFhnh_Manuscript/maps_and_models/apo/apo_HNH_out_sharp.mrc"

Opened apo_HNH_out_sharp.mrc as #26, grid size 420,420,420, pixel 0.725, shown
at level 0.00214, step 2, values float32  

> hide #!26 models

> style stick

Changed 185894 atom styles  

> hide #25

> show #25/a cartoons

Computing secondary structure  

> volume zone #26 nearAtoms #25/a range 2.5 newMap true

Opened apo_HNH_out_sharp.mrc zone as #27, grid size 420,420,420, pixel 0.725,
shown at step 1, values float32  

> transparency #27 90

> show #!24 models

> show #!21 models

> hide #!21 models

> hide #!24 models

> hide #!27 models

> show #!22 models

> show #!14 models

> hide #!14 models

> show #!14 models

> hide #!14 models

> show #!14 models

> hide #!14 models

> show #!14 models

> hide #!14 models

> show #!14 models

> morph #14,22,25

Computed 101 frame morph #28  

> coordset #28 1,101

> close #28

> morph #22,14,25

Computed 101 frame morph #28  

> coordset #28 1,101

> close #28

> show #!27 models

> volume zone #26 nearAtoms #25/a range 1 newMap true

Opened apo_HNH_out_sharp.mrc zone as #28, grid size 420,420,420, pixel 0.725,
shown at step 1, values float32  

> hide #!27 models

> close #28

> volume zone #26 nearAtoms #25/a range 1.5 newMap true

Opened apo_HNH_out_sharp.mrc zone as #28, grid size 420,420,420, pixel 0.725,
shown at step 1, values float32  

> close #28

> volume zone #26 nearAtoms #25/a range 2 newMap true

Opened apo_HNH_out_sharp.mrc zone as #28, grid size 420,420,420, pixel 0.725,
shown at step 1, values float32  

> show #!27 models

> hide #!27 models

> show #!27 models

> hide #!27 models

> hide #!28 models

> show #!27 models

> close #28

> show #!1 models

> hide #!1 models

> show #!5 models

> hide #!5 models

> show #!6 models

> hide #!6 models

> select ~sel & ##selected

22280 atoms, 22901 bonds, 1 pseudobond, 2652 residues, 2 models selected  

> show #!7 models

> hide #!7 models

> show #!12 models

> hide #!12 models

> show #!15 models

> hide #!15 models

> show #!16 models

> show #!17 models

> show #!15 models

> show #!18 models

> show #!19 models

> show #!20 models

> show #!21 models

> hide #!21 models

> show #!21 models

> hide #!21 models

> show #!22 models

> hide #!22 models

> close #1-3,6,7,12,15-20

> hide #!27 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #4

> show #4/a cartoons

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> select clear

> show #!8 models

> hide #!8 models

> open "/Users/zxc755/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/Type
> I-F_HNH/Manuscript/IFhnh_Manuscript/maps_and_models/post_cleavage/postcleavage_HNH_inwards_refined.pdb"

Chain information for postcleavage_HNH_inwards_refined.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
F | No description available  
G | No description available  
H | No description available  
I | No description available  
J | No description available  
K | No description available  
L | No description available  
  

> open "/Users/zxc755/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/Type
> I-F_HNH/Manuscript/IFhnh_Manuscript/maps_and_models/post_cleavage/post_HNH_in_sharp.mrc"

Opened post_HNH_in_sharp.mrc as #2, grid size 420,420,420, pixel 0.725, shown
at level 0.0257, step 2, values float32  

> hide #!1 models

> hide #!2 models

> hide #!4 models

> open "/Users/zxc755/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/Type
> I-F_HNH/Manuscript/IFhnh_Manuscript/maps_and_models/post_cleavage/postcleavage_HNH_outwards.pdb"

Chain information for postcleavage_HNH_outwards.pdb #3  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D E | No description available  
F | No description available  
G | No description available  
H | No description available  
I | No description available  
J | No description available  
K | No description available  
L | No description available  
  

> open "/Users/zxc755/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/Type
> I-F_HNH/Manuscript/IFhnh_Manuscript/maps_and_models/post_cleavage/post_HNH_out_sharp.mrc"

Opened post_HNH_out_sharp.mrc as #6, grid size 420,420,420, pixel 0.725, shown
at level 0.00342, step 2, values float32  

> hide #!3 models

> hide #!6 models

> open "/Users/zxc755/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/Type
> I-F_HNH/Manuscript/IFhnh_Manuscript/maps_and_models/NTS_cleaved/halfcleaved_HNH_inwards_refined.pdb"

Chain information for halfcleaved_HNH_inwards_refined.pdb #7  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
F | No description available  
G | No description available  
H | No description available  
I | No description available  
J | No description available  
K | No description available  
L | No description available  
  

> open "/Users/zxc755/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/Type
> I-F_HNH/Manuscript/IFhnh_Manuscript/maps_and_models/NTS_cleaved/halfcleaved_HNH_in_sharp.mrc"

Opened halfcleaved_HNH_in_sharp.mrc as #12, grid size 420,420,420, pixel
0.725, shown at level 0.00277, step 2, values float32  

> hide #!7 models

> hide #!12 models

> show #!7 models

> hide #!7 models

> open "/Users/zxc755/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/Type
> I-F_HNH/Manuscript/IFhnh_Manuscript/maps_and_models/NTS_cleaved/halfcleaved_HNH_outwards_refined.pdb"

Summary of feedback from opening /Users/zxc755/Library/CloudStorage/OneDrive-
UniversityofCopenhagen/Type
I-F_HNH/Manuscript/IFhnh_Manuscript/maps_and_models/NTS_cleaved/halfcleaved_HNH_outwards_refined.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 1 1 ASN a 4 ILE a 10 1 7  
Start residue of secondary structure not found: HELIX 2 2 GLU a 16 ILE a 31 1
16  
Start residue of secondary structure not found: HELIX 3 3 ALA a 41 PHE a 43 5
3  
Start residue of secondary structure not found: HELIX 4 4 ALA a 84 TYR a 86 5
3  
Start residue of secondary structure not found: HELIX 5 5 ARG a 88 ALA a 94 1
7  
169 messages similar to the above omitted  
  
Chain information for halfcleaved_HNH_outwards_refined.pdb #15  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
F | No description available  
G | No description available  
H | No description available  
I | No description available  
J | No description available  
K | No description available  
L | No description available  
  

> open "/Users/zxc755/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/Type
> I-F_HNH/Manuscript/IFhnh_Manuscript/maps_and_models/NTS_cleaved/halfcleaved_HNH_out_sharp.mrc"

Opened halfcleaved_HNH_out_sharp.mrc as #16, grid size 420,420,420, pixel
0.725, shown at level 0.0029, step 2, values float32  

> hide #!16 models

> hide #!15 models

> style stick

Changed 234593 atom styles  

> show #!1 models

> hide #!1 models

> volume zone #2 nearAtoms #1/a range 2.5 newMap true

Opened post_HNH_in_sharp.mrc zone as #17, grid size 420,420,420, pixel 0.725,
shown at step 1, values float32  

> show #!1 models

> hide #1

> show #1 cartoons

Computing secondary structure  

> select vol

Expected an objects specifier or a keyword  

> transparency 90

> hide #1 cartoons

> show #1/a cartoons

> hide #!1 models

> hide #!17 models

> show #!3 models

> show #!6 models

> hide #!6 models

> hide #3

> show #3/a cartoons

Computing secondary structure  

> show #!6 models

> hide #!6 models

> volume zone #6 nearAtoms #3/a range 2.5 newMap true

Opened post_HNH_out_sharp.mrc zone as #18, grid size 420,420,420, pixel 0.725,
shown at step 1, values float32  

> hide #!18 models

> hide #!3 models

> show #!4 models

> show #!5 models

> hide #!5 models

> volume zone #5 nearAtoms #4/a range 2.5 newMap true

Opened post_HNH_cent_sharp.mrc zone as #19, grid size 420,420,420, pixel
0.725, shown at step 1, values float32  

> hide #!19 models

> hide #!4 models

> volume zone #13 nearAtoms #32/a range 2.5 newMap true

Opened halfcleaved_HNH_center_sharp3Å.mrc zone as #20, grid size 420,420,420,
pixel 0.725, shown at step 1, values float32  

> show #!32 models

> hide #32 cartoons

> show #32/a cartoons

> transparency 90

> hide #!20 models

> hide #!32 models

> show #!7 models

> volume zone #12 nearAtoms #7/a range 2.5 newMap true

Opened halfcleaved_HNH_in_sharp.mrc zone as #28, grid size 420,420,420, pixel
0.725, shown at step 1, values float32  

> hide #7

> show #7/a cartoons

Computing secondary structure  

> transparency 90

> hide #!28 models

> hide #!7 models

> hide #15

> show #15/a cartoons

Computing secondary structure  

> volume zone #16 nearAtoms #15/a range 2.5 newMap true

Opened halfcleaved_HNH_out_sharp.mrc zone as #29, grid size 420,420,420, pixel
0.725, shown at step 1, values float32  

> hide #!29 models

> show #!27 models

> hide #!27 models

> show #!21 models

> hide #!21 models

> show #!14 models

> hide #!14 models

> show #!14 models

> show #!21 models

> hide #!21 models

> hide #!14 models

> cd "/Users/zxc755/Library/CloudStorage/OneDrive-UniversityofCopenhagen/Type
> I-F_HNH/Manuscript/figures/structure/cas8_movement"

Current working directory is: /Users/zxc755/Library/CloudStorage/OneDrive-
UniversityofCopenhagen/Type I-F_HNH/Manuscript/figures/structure/cas8_movement  

> save cas8_movement.cxs includeMaps true

——— End of log from Sat May 17 13:40:51 2025 ———

opened ChimeraX session  

> rename #1 postcleavage_HNH_inwards.pdb

> rename #4 postcleavage_HNH_center.pdb

> show #!2 models

> hide #!2 models

> show #!1 models

> show #!3 models

> hide #!3 models

> show #!3 models

> show #!4 models

> show #!5 models

> hide #!5 models

> show #!6 models

> hide #!6 models

> show #!7 models

> hide #!7 models

> show #!7 models

> hide #!7 models

> rename #7 halfcleaved_HNH_inwards.pdb

> rename #32 halfcleaved_HNH_center_main_model.pdb

> show #!32 models

> hide #!32 models

> show #!32 models

> hide #!32 models

> show #!29 models

> show #!28 models

> hide #!28 models

> hide #!29 models

> show #!29 models

> hide #!29 models

> hide #!4 models

> hide #!3 models

> hide #!1 models

> show #!5 models

> hide #!5 models

> rename #8 apo_HNH_center.pdb

> show #!10 models

> show #!8 models

> hide #!8 models

> hide #!10 models

> show #!10 models

> hide #!10 models

> show #!1 models

> show #!12 models

> hide #!12 models

> show #!17 models

> rename #22 apo_HNH_inwards.pdb

> show #!22 models

> hide #!22 models

> show #!23 models

> hide #!23 models

> show #!28 models

> hide #!28 models

> show #!28 models

> hide #!28 models

> show #!28 models

> hide #!28 models

> show #!28 models

> rename #15 halfcleaved_HNH_outwards.pdb

> rename #14 apo_HNH_center.pdb

> show #!14 models

> show #!8 models

> hide #!8 models

> show #!15 models

> hide #!15 models

> show #!15 models

> hide #!15 models

> hide #!14 models

> show #!14 models

> hide #!14 models

> show #!14 models

> show #!8 models

> hide #!8 models

> show #!8 models

> hide #!8 models

> hide #!14 models

> hide #!17 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!7 models

> hide #!7 models

> show #!7 models

> rename #20 "halfcleaved_HNH_center.mrc zone"

> show #!13 models

> hide #!13 models

> rename #13 halfcleaved_HNH_center_sharp.mrc

> show #!13 models

> hide #!13 models

> show #!12 models

> hide #!12 models

> show #!17 models

> hide #!17 models

> show #!17 models

> show #!22 models

> show #!24 models

> show #!3 models

> show #!18 models

> show #!4 models

> show #!19 models

> show #!15 models

> show #!29 models

> show #!32 models

> show #!20 models

> show #!27 models

> show #!25 models

> show #!14 models

> show #!21 models

> show #!10 models

> hide #!10 models

> show #!10 models

> hide #!10 models

> show #!10 models

> hide #!10 models

> show #!10 models

> hide #!10 models

> show #!10 models

> hide #!10 models

> show #!10 models

> hide #!10 models

> show #!10 models

> hide #!10 models

> show #!10 models

> hide #!10 models

> show #!10 models

> hide #!10 models

> show #!10 models

> hide #!10 models

> show #!10 models

> hide #!10 models

> show #!10 models

> hide #!10 models

> show #!10 models

> hide #!10 models

> show #!10 models

> hide #!10 models

> show #!10 models

> hide #!10 models

> close #8,10

> hide #!29 models

> show #!29 models

> hide #!29 models

> show #!29 models

> transparency 90

> hide #!32 models

> hide #!29 models

> hide #!28 models

> hide #!27 models

> hide #!25 models

> hide #!24 models

> hide #!22 models

> hide #!21 models

> hide #!20 models

> hide #!19 models

> hide #!18 models

> hide #!17 models

> hide #!15 models

> hide #!14 models

> hide #!7 models

> hide #!4 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> hide #!1 models

> show #!3 models

> show #!18 models

> hide #!18 models

> hide #!3 models

> show #!1 models

> show #!17 models

> hide #!17 models

> hide #!1 models

> show #!4 models

> show #!19 models

> hide #!19 models

> hide #!4 models

> show #!7 models

> show #!28 models

> hide #!7 models

> hide #!28 models

> show #!15 models

> show #!29 models

> hide #!15 models

> hide #!29 models

> show #!32 models

> show #!20 models

> hide #32

> hide #!32 models

> hide #!20 models

> show #!22 models

> show #!24 models

> hide #!22 models

> hide #!24 models

> show #!25 models

> show #!27 models

> hide #!25 models

> hide #!27 models

> show #!21 models

> show #!14 models

> hide #!21 models

> hide #!14 models

> cd "/Users/zxc755/Library/CloudStorage/OneDrive-UniversityofCopenhagen/Type
> I-F_HNH/Manuscript/figures/structure/cas8_movement"

Current working directory is: /Users/zxc755/Library/CloudStorage/OneDrive-
UniversityofCopenhagen/Type I-F_HNH/Manuscript/figures/structure/cas8_movement  

> save cas8_movment.cxs includeMaps true

——— End of log from Wed May 28 12:25:00 2025 ———

opened ChimeraX session  

> show #!14 models

> log metadata #3

No models had metadata

> log chains #3

Chain information for postcleavage_HNH_outwards.pdb #3  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D E | No description available  
F | No description available  
G | No description available  
H | No description available  
I | No description available  
J | No description available  
K | No description available  
L | No description available  
  

> show #!1 models

> show #!3 models

> show #!4 models

> show #!7 models

> show #!15 models

> show #!32 models

> show #!22 models

> show #!25 models

> matchmaker #22/A to #14/A

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker apo_HNH_center.pdb, chain A (#14) with apo_HNH_inwards.pdb, chain A
(#22), sequence alignment score = 1518.4  
RMSD between 77 pruned atom pairs is 1.474 angstroms; (across all 340 pairs:
10.274)  
  

> matchmaker #25/A to #14/A

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker apo_HNH_center.pdb, chain A (#14) with
apo_HNH_outwards_refined.pdb, chain A (#25), sequence alignment score = 1501.9  
RMSD between 82 pruned atom pairs is 1.427 angstroms; (across all 336 pairs:
9.925)  
  

> matchmaker #7/A to #14/A

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker apo_HNH_center.pdb, chain A (#14) with halfcleaved_HNH_inwards.pdb,
chain A (#7), sequence alignment score = 1519  
RMSD between 63 pruned atom pairs is 1.325 angstroms; (across all 340 pairs:
10.974)  
  

> matchmaker #32/A to #14/A

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker apo_HNH_center.pdb, chain A (#14) with
halfcleaved_HNH_center_main_model.pdb, chain A (#32), sequence alignment score
= 1526.2  
RMSD between 181 pruned atom pairs is 1.066 angstroms; (across all 340 pairs:
4.116)  
  

> matchmaker #15/A to #14/A

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker apo_HNH_center.pdb, chain A (#14) with
halfcleaved_HNH_outwards.pdb, chain A (#15), sequence alignment score = 1484.2  
RMSD between 67 pruned atom pairs is 1.302 angstroms; (across all 340 pairs:
10.332)  
  

> matchmaker #1/A to #14/A

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker apo_HNH_center.pdb, chain A (#14) with
postcleavage_HNH_inwards.pdb, chain A (#1), sequence alignment score = 1501.2  
RMSD between 65 pruned atom pairs is 1.199 angstroms; (across all 338 pairs:
10.667)  
  

> matchmaker #3/A to #14/A

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker apo_HNH_center.pdb, chain A (#14) with
postcleavage_HNH_outwards.pdb, chain A (#3), sequence alignment score = 1520.2  
RMSD between 70 pruned atom pairs is 1.370 angstroms; (across all 340 pairs:
10.928)  
  

> matchmaker #4/A to #14/A

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker apo_HNH_center.pdb, chain A (#14) with postcleavage_HNH_center.pdb,
chain A (#4), sequence alignment score = 1511.2  
RMSD between 184 pruned atom pairs is 1.025 angstroms; (across all 340 pairs:
3.799)  
  

> dssp

> graphics silhouettes true

> graphics silhouettes width 1

> lighting multiShadow 600

> save /Users/gmontoya/Downloads/cas8_movment2.cxs

——— End of log from Wed May 28 15:04:16 2025 ———

opened ChimeraX session  




OpenGL version: 4.1 Metal - 89.3
OpenGL renderer: Apple M2 Max
OpenGL vendor: Apple

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

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: Mac14,6
      Model Number: Z176001C0DK/A
      Chip: Apple M2 Max
      Total Number of Cores: 12 (8 performance and 4 efficiency)
      Memory: 64 GB
      System Firmware Version: 11881.41.5
      OS Loader Version: 11881.41.5

Software:

    System Software Overview:

      System Version: macOS 15.1.1 (24B91)
      Kernel Version: Darwin 24.1.0
      Time since boot: 27 days, 1 hour, 36 minutes

Graphics/Displays:

    Apple M2 Max:

      Chipset Model: Apple M2 Max
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 38
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-in Liquid Retina XDR Display
          Resolution: 3456 x 2234 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal


Installed Packages:
    alabaster: 1.0.0
    appdirs: 1.4.4
    appnope: 0.1.4
    asttokens: 3.0.0
    auditwheel: 6.1.0
    autocommand: 2.2.2
    babel: 2.16.0
    backports.tarfile: 1.2.0
    beautifulsoup4: 4.12.3
    biopython: 1.83
    blockdiag: 3.0.0
    blosc2: 2.7.1
    build: 1.2.1
    certifi: 2023.11.17
    cftime: 1.6.4.post1
    charset-normalizer: 3.4.0
    ChimeraX-AddCharge: 1.5.18
    ChimeraX-AddH: 2.2.6
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.5
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.16.1
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.58.8
    ChimeraX-AtomicLibrary: 14.1.11
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.4.7
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.13.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.4.0
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.4
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.3
    ChimeraX-Clipper: 0.23.0
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.7
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.10.dev202412070146
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.4
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2.7
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.3
    ChimeraX-Dssp: 2.0
    ChimeraX-EMalign: 0.1.3
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.4.1
    ChimeraX-Hbonds: 2.5
    ChimeraX-Help: 1.3
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.3
    ChimeraX-ISOLDE: 1.8.dev0
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-KVFinder: 1.5
    ChimeraX-Label: 1.1.14
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.3
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.1.6
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.7.2
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.14.2
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.18
    ChimeraX-ModelPanel: 1.5
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-MutationScores: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.2
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.2
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.14
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.7
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.4
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1.2
    ChimeraX-ProfileGrids: 1.0
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.6.2
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.3.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.2
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.5.6
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.15
    ChimeraX-Shape: 1.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.2.0
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-SimilarStructures: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.19
    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: 2.5.1
    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: 1.42.2
    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: 1.1.4
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    contourpy: 1.3.1
    coverage: 7.6.9
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.0.10
    debugpy: 1.8.9
    decorator: 5.1.1
    DiffFit: 0.6.2
    docutils: 0.21.2
    executing: 2.1.0
    filelock: 3.15.4
    finufft: 2.3.1
    fonttools: 4.55.2
    fsspec: 2024.10.0
    funcparserlib: 2.0.0a0
    glfw: 2.8.0
    grako: 3.16.5
    h5py: 3.12.1
    html2text: 2024.2.26
    idna: 3.10
    ihm: 1.3
    imagecodecs: 2024.6.1
    imagesize: 1.4.1
    importlib_metadata: 8.0.0
    importlib_resources: 6.4.0
    inflect: 7.3.1
    iniconfig: 2.0.0
    ipykernel: 6.29.5
    ipython: 8.26.0
    ipywidgets: 8.1.5
    jaraco.context: 5.3.0
    jaraco.functools: 4.0.1
    jaraco.text: 3.12.1
    jedi: 0.19.1
    Jinja2: 3.1.4
    jupyter_client: 8.6.2
    jupyter_core: 5.7.2
    jupyterlab_widgets: 3.0.13
    kiwisolver: 1.4.7
    line_profiler: 4.1.3
    lxml: 5.2.2
    lz4: 4.3.3
    MarkupSafe: 3.0.2
    matplotlib: 3.10.1
    matplotlib: 3.9.2
    matplotlib-inline: 0.1.7
    more-itertools: 10.3.0
    mpmath: 1.3.0
    mrcfile: 1.5.0
    msgpack: 1.0.8
    narwhals: 1.35.0
    ndindex: 1.9.2
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.10.2
    numpy: 1.26.4
    numpy: 1.26.4
    openvr: 1.26.701
    ordered-set: 4.1.0
    packaging: 23.2
    packaging: 24.1
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pexpect: 4.9.0
    pillow: 10.4.0
    pip: 24.2
    pkginfo: 1.11.1
    platformdirs: 4.3.6
    platformdirs: 4.2.2
    plotly: 6.0.1
    pluggy: 1.5.0
    prompt_toolkit: 3.0.48
    psutil: 6.0.0
    ptyprocess: 0.7.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    pyelftools: 0.31
    Pygments: 2.18.0
    pyKVFinder: 0.7.3
    pynmrstar: 3.3.4
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.3401
    pyparsing: 3.2.0
    pyproject_hooks: 1.2.0
    PyQt6-commercial: 6.7.1
    PyQt6-Qt6: 6.7.3
    PyQt6-WebEngine-commercial: 6.7.0
    PyQt6-WebEngine-Qt6: 6.7.3
    PyQt6-WebEngineSubwheel-Qt6: 6.7.3
    PyQt6_sip: 13.8.0
    pytest: 8.3.4
    pytest-cov: 6.0.0
    python-dateutil: 2.9.0.post0
    pytz: 2024.2
    pyzmq: 26.2.0
    qtconsole: 5.5.2
    QtPy: 2.4.2
    qtshim: 1.0
    RandomWords: 0.4.0
    requests: 2.32.3
    scipy: 1.14.0
    setuptools: 72.1.0
    sfftk-rw: 0.8.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.6
    Sphinx: 8.0.2
    sphinx-autodoc-typehints: 2.2.3
    sphinxcontrib-applehelp: 2.0.0
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 2.0.0
    sphinxcontrib-htmlhelp: 2.1.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 2.0.0
    sphinxcontrib-serializinghtml: 2.0.0
    stack-data: 0.6.3
    superqt: 0.6.3
    sympy: 1.13.3
    tables: 3.10.1
    tcia_utils: 1.5.1
    tifffile: 2024.7.24
    tinyarray: 1.2.4
    toml: 0.10.2
    tomli: 2.0.1
    torch: 2.2.1
    tornado: 6.4.2
    traitlets: 5.14.3
    typeguard: 4.3.0
    typing_extensions: 4.12.2
    typing_extensions: 4.12.2
    tzdata: 2024.2
    urllib3: 2.2.3
    wcwidth: 0.2.13
    webcolors: 24.6.0
    wheel: 0.43.0
    wheel: 0.43.0
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.13
    zipp: 3.19.2

Change History (2)

comment:1 by Eric Pettersen, 6 months ago

Component: Unassigned → Window Toolkit
Description: modified (diff)
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Crash on Mac waking from sleep

Reported by Guillermo Montoya

comment:2 by Tom Goddard, 6 months ago

Resolution: → duplicate
Status: assigned → closed

The ChimeraX Bug Reporter panel explains what we know about this crash

"This is a known crash that we are unable to fix. Here is information that may help you avoid this crash. The Qt window toolkit crashed due to a display configuration change, typically when waking from sleep or when an external display is disconnected or connected. This has only been seen on Mac computers. We hope a newer version of Qt will fix it. We update ChimeraX daily builds whenever a new Qt is released. You can check here ​https://www.cgl.ucsf.edu/chimerax/docs/troubleshoot.html#macdisplay to see if it has been fixed in a newer ChimeraX."

The ChimeraX 1.10 release candidate and daily build uses a newer Qt version (6.8.2) and we have not seen these Mac multi-display crashes with that version. So you may want to update ChimeraX.

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