![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 6 months ago
Last modified 6 months ago
#17846 closed defect
ChimeraX bug report submission — at Initial Version
| Reported by: | Owned by: | ||
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Window Toolkit | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-15.1.1-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",
"version" : 2,
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"modelCode" : "Mac14,6",
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"captureTime" : "2025-05-29 13:17:10.9756 +0200",
"codeSigningMonitor" : 1,
"incident" : "E4C5B74D-DCCF-4104-8A1A-8362717EB6C7",
"pid" : 86001,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"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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"crashReporterKey" : "381280B0-1E31-C4C4-1B42-E8CED8B17B72",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
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"sleepWakeUUID" : "18182CED-A9FE-496B-964D-D08A650ABB62",
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"path" : "\/Applications\/ChimeraX_Daily.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/scipy\/spatial\/_qhull.cpython-311-darwin.so",
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"uuid" : "b29d2864-b3b5-3815-afd9-30a5d47ea661",
"path" : "\/Applications\/ChimeraX_Daily.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/scipy\/spatial\/_voronoi.cpython-311-darwin.so",
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"path" : "\/Applications\/ChimeraX_Daily.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/scipy\/spatial\/_distance_wrap.cpython-311-darwin.so",
"name" : "_distance_wrap.cpython-311-darwin.so"
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"size" : 131072,
"uuid" : "0b06b6ba-a609-3db4-b7ff-fd4afbf3de00",
"path" : "\/Applications\/ChimeraX_Daily.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/scipy\/spatial\/_hausdorff.cpython-311-darwin.so",
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"name" : "_ufuncs.cpython-311-darwin.so"
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"path" : "\/Applications\/ChimeraX_Daily.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/scipy\/special\/_ufuncs_cxx.cpython-311-darwin.so",
"name" : "_ufuncs_cxx.cpython-311-darwin.so"
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"size" : 524288,
"uuid" : "e9edcc9d-eeb6-39fc-becf-421a649b475d",
"path" : "\/Applications\/ChimeraX_Daily.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/scipy\/special\/_special_ufuncs.cpython-311-darwin.so",
"name" : "_special_ufuncs.cpython-311-darwin.so"
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{
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"base" : 13226049536,
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"uuid" : "a7317978-002e-3af8-93d3-cc91ee124c4d",
"path" : "\/Applications\/ChimeraX_Daily.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/scipy\/special\/_gufuncs.cpython-311-darwin.so",
"name" : "_gufuncs.cpython-311-darwin.so"
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{
"source" : "P",
"arch" : "arm64",
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"size" : 131072,
"uuid" : "fc89a288-1442-3ff7-adf6-f5280d1da110",
"path" : "\/Applications\/ChimeraX_Daily.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/scipy\/special\/_specfun.cpython-311-darwin.so",
"name" : "_specfun.cpython-311-darwin.so"
},
{
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"uuid" : "a44a91c2-b0f9-330e-8fd4-169c9ee598f1",
"path" : "\/Applications\/ChimeraX_Daily.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/scipy\/special\/_comb.cpython-311-darwin.so",
"name" : "_comb.cpython-311-darwin.so"
},
{
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"arch" : "arm64",
"base" : 13147160576,
"size" : 65536,
"uuid" : "69ffb2d0-66c0-31f6-9e66-824d8de2f2a3",
"path" : "\/Applications\/ChimeraX_Daily.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/scipy\/special\/_ellip_harm_2.cpython-311-darwin.so",
"name" : "_ellip_harm_2.cpython-311-darwin.so"
},
{
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"size" : 425984,
"uuid" : "36df0cfc-cf6e-3bb7-bc89-122d9c5277e0",
"path" : "\/Applications\/ChimeraX_Daily.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/scipy\/spatial\/_distance_pybind.cpython-311-darwin.so",
"name" : "_distance_pybind.cpython-311-darwin.so"
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"source" : "P",
"arch" : "arm64",
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"size" : 638976,
"uuid" : "945d9dbc-5df0-387d-aef8-bdf9f193154a",
"path" : "\/Applications\/ChimeraX_Daily.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/scipy\/spatial\/transform\/_rotation.cpython-311-darwin.so",
"name" : "_rotation.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "arm64",
"base" : 13138903040,
"size" : 32768,
"uuid" : "f2c2793f-a688-367b-94a7-b0cd3fd9ef60",
"path" : "\/Applications\/ChimeraX_Daily.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/scipy\/optimize\/_direct.cpython-311-darwin.so",
"name" : "_direct.cpython-311-darwin.so"
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"path" : "\/usr\/lib\/system\/libsystem_kernel.dylib",
"name" : "libsystem_kernel.dylib"
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"path" : "\/usr\/lib\/system\/libsystem_platform.dylib",
"name" : "libsystem_platform.dylib"
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"name" : "SkyLight"
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"name" : "CrBrowserMain",
"queue" : "com.apple.main-thread"
}
},
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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
> show #8 models
> show #9/M atoms
> show #9/N atoms
> hide #!9 models
> show #!9 models
> hide #8 models
> show #8 models
> hide #8 models
> hide #!9 models
> open "/Users/zxc755/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/Type
> I-F_HNH/Manuscript/halfcleaved_HNH_center_main_model_temp2.pdb"
Chain information for halfcleaved_HNH_center_main_model_temp2.pdb #10
---
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
> hide #10 atoms
> show #10 cartoons
> cartoon style nucleic xsection oval width 1.6 thickness 1.6
> color #10/L light gray
> color #10/K dim gray
> color #10/J dark red
> color #10/I rebecca purple
> color #10/B forest green
> color #10/C,D,E,F,G,H khaki
> color #10/A steel blue
> color #10/A:232-350 dark turquoise
> show #10/K atoms
> style stick
Changed 131055 atom styles
> show #10 & nucleic atoms
> select #10
24166 atoms, 24925 bonds, 3 pseudobonds, 2803 residues, 2 models selected
> nucleotides sel ladder
> select clear
> show #!4 models
> volume #4 level 0.06
> show #10/M,N,O atoms
> select clear
> select #10/K:4
4 atoms, 3 bonds, 1 residue, 1 model selected
> select add #10/K:3
25 atoms, 26 bonds, 2 residues, 1 model selected
> select add #10/K:2
45 atoms, 47 bonds, 3 residues, 1 model selected
> select add #10/K:1
54 atoms, 56 bonds, 4 residues, 1 model selected
> hide sel cartoons
> nucleotides sel atoms
> style nucleic & sel stick
Changed 54 atom styles
> select clear
> color zone #4 near #10 distance 10
> transparency 50
> volume #4 level 0.05
> cartoon style nucleic xsection oval width 1 thickness 1
> color #10/L light gray
> color #10/K dim gray
> color #10/J dark red
> color #10/I rebecca purple
> color #10/B forest green
> color #10/C,D,E,F,G,H khaki
> color #10/A steel blue
> color #10/A:232-350 dark turquoise
> color zone #4 near #10 distance 10
> hide #!10 models
> hide #!4 models
> show #!10 models
> select #10/M:1@MG
1 atom, 1 residue, 1 model selected
> color sel red
> select #10/O:1@O
1 atom, 1 residue, 1 model selected
> color sel blue
> select clear
> color zone #4 near #10 distance 10
> show #!4 models
> hide #!10 models
> color zone #4 near #10 distance 5
> volume #4 level 0.09
> lighting soft
> lighting full
> lighting soft
> color zone #4 near #10 distance 4
> color zone #4 near #10 distance 3
> volume #4 level 0.07
> surface zone #4 nearAtoms #10 distance 2.5
> surface zone #4 nearAtoms #10 distance 3
> select add #4
2 models selected
> ui tool show "Color Actions"
> color sel navajo white
> set bgColor white
> lighting simple
> transparency sel 50
> show #!10 models
> volume #4 level 0.05
> volume #4 level 0.09
> volume #4 level 0.08
> color #10 byhetero
> select clear
> select #10/K:1@N9
1 atom, 1 residue, 1 model selected
> select up
9 atoms, 9 bonds, 1 residue, 1 model selected
> select add #10/K:2@OP2
10 atoms, 9 bonds, 2 residues, 1 model selected
> select up
29 atoms, 31 bonds, 2 residues, 1 model selected
> select down
10 atoms, 9 bonds, 2 residues, 1 model selected
> select add #10/K:2@OP1
11 atoms, 12 bonds, 2 residues, 1 model selected
> select add #10/K:2@O2
12 atoms, 17 bonds, 2 residues, 1 model selected
> select add #10/K:2@O4
13 atoms, 20 bonds, 2 residues, 1 model selected
> select add #10/K:2@C5
14 atoms, 21 bonds, 2 residues, 1 model selected
> select add #10/K:2@C7
15 atoms, 24 bonds, 2 residues, 1 model selected
> select add #10/K:3@N6
16 atoms, 25 bonds, 3 residues, 1 model selected
> select up
28 atoms, 27 bonds, 3 residues, 1 model selected
> select up
50 atoms, 55 bonds, 3 residues, 1 model selected
> hide #!4 models
> select subtract #10/K:3@OP1
49 atoms, 53 bonds, 3 residues, 1 model selected
> select subtract #10/K:3@P
48 atoms, 51 bonds, 3 residues, 1 model selected
> select subtract #10/K:3@OP2
47 atoms, 51 bonds, 3 residues, 1 model selected
> select add #10/K:4@P
48 atoms, 51 bonds, 4 residues, 1 model selected
> select add #10/K:4@OP1
49 atoms, 52 bonds, 4 residues, 1 model selected
> select add #10/K:4@OP2
50 atoms, 54 bonds, 4 residues, 1 model selected
> select subtract #10/K:2@O3'
49 atoms, 53 bonds, 4 residues, 1 model selected
> select subtract #10/K:2@C4'
48 atoms, 50 bonds, 4 residues, 1 model selected
> select subtract #10/K:2@O4'
47 atoms, 48 bonds, 4 residues, 1 model selected
> select subtract #10/K:2@C3'
46 atoms, 48 bonds, 4 residues, 1 model selected
> select subtract #10/K:2@C2'
45 atoms, 47 bonds, 4 residues, 1 model selected
> select subtract #10/K:2@C1'
44 atoms, 46 bonds, 4 residues, 1 model selected
> select subtract #10/K:2@C5'
43 atoms, 46 bonds, 4 residues, 1 model selected
> hide sel atoms
> show #10/K:3 atoms
> hide sel atoms
> select #10/K:3@C5'
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select #10/K:3@C4'
1 atom, 1 residue, 1 model selected
> select add #10/K:3@O3'
2 atoms, 1 residue, 1 model selected
> select add #10/K:3@C2'
3 atoms, 1 residue, 1 model selected
> select add #10/K:3@O4'
4 atoms, 1 residue, 1 model selected
> hide sel atoms
> select #10/K:3@C3'
1 atom, 1 residue, 1 model selected
> select add #10/K:3@C1'
2 atoms, 1 residue, 1 model selected
> select add #10/K:3@C8
3 atoms, 1 residue, 1 model selected
> select up
21 atoms, 23 bonds, 1 residue, 1 model selected
> select down
3 atoms, 1 residue, 1 model selected
> select add #10/K:3@N3
4 atoms, 1 residue, 1 model selected
> select add #10/K:3@C4
5 atoms, 1 residue, 1 model selected
> select add #10/K:3@C5
6 atoms, 1 residue, 1 model selected
> select add #10/K:3@N7
7 atoms, 1 residue, 1 model selected
> select add #10/K:3@C6
8 atoms, 1 residue, 1 model selected
> select add #10/K:3@N6
9 atoms, 1 residue, 1 model selected
> select add #10/K:3@N1
10 atoms, 1 residue, 1 model selected
> select add #10/K:3@C2
11 atoms, 1 residue, 1 model selected
> hide sel atoms
> select #10/K:3@N9
1 atom, 1 residue, 1 model selected
> hide sel atoms
> show #!4 models
> select #10/K:2@C5'
1 atom, 1 residue, 1 model selected
> hide sel atoms
> volume #4 level 0.07
> show #10/A:305,304,280,328
> volume #4 level 0.09
> select #10/K:4@O5'
1 atom, 1 residue, 1 model selected
> hide sel atoms
> color #10/M red
> color #10/O blue
> color #10/O dark blue
> color #10/O blue
> volume #4 level 0.07
> show #10/K:2 atoms
> volume #4 level 0.06
> show #10/K:1-2 atoms
> show #!5 models
> hide #!5 models
> show #!2 models
> hide #!2 models
> hide #!4 models
> hide #!10 models
> show #!10 models
> select #10/K:1@O5'
1 atom, 1 residue, 1 model selected
> select add #10/K:1@C5'
2 atoms, 1 residue, 1 model selected
> select add #10/K:1@C4'
3 atoms, 1 residue, 1 model selected
> select add #10/K:1@O4'
4 atoms, 1 residue, 1 model selected
> select add #10/K:1@C1'
5 atoms, 1 residue, 1 model selected
> select add #10/K:1@N9
6 atoms, 1 residue, 1 model selected
> select add #10/K:1@C2'
7 atoms, 1 residue, 1 model selected
> select add #10/K:1@C3'
8 atoms, 1 residue, 1 model selected
> select add #10/K:1@O3'
9 atoms, 1 residue, 1 model selected
> select add #10/K:2@P
10 atoms, 2 residues, 1 model selected
> select add #10/K:2@OP2
11 atoms, 2 residues, 1 model selected
> select add #10/K:2@OP1
12 atoms, 2 residues, 1 model selected
> select add #10/K:2@O5'
13 atoms, 2 residues, 1 model selected
> select add #10/K:2@C5'
14 atoms, 2 residues, 1 model selected
> hide sel atoms
> show #!4 models
> hide #!4 models
> ui tool show Distances
> select #10/O:1@O
1 atom, 1 residue, 1 model selected
> select #10/K:3@OP2
1 atom, 1 residue, 1 model selected
> select add #10/O:1@O
2 atoms, 2 residues, 1 model selected
> distance #10/K:3@OP2 #10/O:1@O
Distance between halfcleaved_HNH_center_main_model_temp2.pdb #10/K DA 3 OP2
and /O HOH 1 O: 2.479Å
> select #10/A:304@ND1
1 atom, 1 residue, 1 model selected
> select add #10/M:1@MG
2 atoms, 2 residues, 1 model selected
> distance #10/A:304@ND1 #10/M:1@MG
Distance between halfcleaved_HNH_center_main_model_temp2.pdb #10/A HIS 304 ND1
and /M MG 1 MG: 2.377Å
> select #10/A:328@NE2
1 atom, 1 residue, 1 model selected
> select add #10/M:1@MG
2 atoms, 2 residues, 1 model selected
> distance #10/A:328@NE2 #10/M:1@MG
Distance between halfcleaved_HNH_center_main_model_temp2.pdb #10/A HIS 328 NE2
and /M MG 1 MG: 2.352Å
> select #10/M:1@MG
1 atom, 1 residue, 1 model selected
> select add #10/K:3@OP1
2 atoms, 2 residues, 1 model selected
> distance #10/M:1@MG #10/K:3@OP1
Distance between halfcleaved_HNH_center_main_model_temp2.pdb #10/M MG 1 MG and
/K DA 3 OP1: 3.166Å
> select #10/A:280@NH2
1 atom, 1 residue, 1 model selected
> select add #10/K:3@OP2
2 atoms, 2 residues, 1 model selected
> distance #10/A:280@NH2 #10/K:3@OP2
Distance between halfcleaved_HNH_center_main_model_temp2.pdb #10/A ARG 280 NH2
and /K DA 3 OP2: 2.389Å
> select #10/A:280@NH1
1 atom, 1 residue, 1 model selected
> select add #10/K:3@O5'
2 atoms, 2 residues, 1 model selected
> distance #10/A:280@NH1 #10/K:3@O5'
Distance between halfcleaved_HNH_center_main_model_temp2.pdb #10/A ARG 280 NH1
and /K DA 3 O5': 2.765Å
> select #10/A:238
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #10/A:319
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> select #10/A:305@ND1
1 atom, 1 residue, 1 model selected
> select add #10/K:3@OP2
2 atoms, 2 residues, 1 model selected
> distance #10/A:305@ND1 #10/K:3@OP2
Distance between halfcleaved_HNH_center_main_model_temp2.pdb #10/A HIS 305 ND1
and /K DA 3 OP2: 3.592Å
> select #10/A:309
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel cartoons
> show sel atoms
> select #10/A:309@N
1 atom, 1 residue, 1 model selected
> select add #10/O:1@O
2 atoms, 2 residues, 1 model selected
> distance #10/A:309@N #10/O:1@O
Distance between halfcleaved_HNH_center_main_model_temp2.pdb #10/A LEU 309 N
and /O HOH 1 O: 3.104Å
> select #10/A:309@N
1 atom, 1 residue, 1 model selected
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel atoms
> show sel cartoons
> select clear
> view
> select #10/A:305@ND1
1 atom, 1 residue, 1 model selected
> select add #10/K:3@OP1
2 atoms, 2 residues, 1 model selected
> distance #10/A:305@ND1 #10/K:3@OP1
Distance between halfcleaved_HNH_center_main_model_temp2.pdb #10/A HIS 305 ND1
and /K DA 3 OP1: 3.734Å
> delete sel
> ~distance #10/A:305@ND1 #10/K:3@OP1
> open "/Users/zxc755/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/Type
> I-F_HNH/Manuscript/halfcleaved_HNH_center_main_model_temp2.pdb"
Chain information for halfcleaved_HNH_center_main_model_temp2.pdb #12
---
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
> style stick
Changed 155221 atom styles
> hide #12 atoms
> color #12/L light gray
> color #12/K dim gray
> color #12/J dark red
> color #12/I rebecca purple
> color #12/B forest green
> color #12/C,D,E,F,G,H khaki
> color #12/A steel blue
> color #12/A:232-350 dark turquoise
> hide #!11 models
> show #!11 models
> close #11
> show #12 cartoons
> cartoon style nucleic xsection oval width 1 thickness 1
> show #12/K:2-3 atoms
> hide #12/K:1-3 cartoons
> select clear
> select #12/K:2@OP1
1 atom, 1 residue, 1 model selected
> select add #12/K:2@OP2
2 atoms, 1 residue, 1 model selected
> select add #12/K:2@P
3 atoms, 1 residue, 1 model selected
> select add #12/K:2@C5'
4 atoms, 1 residue, 1 model selected
> select add #12/K:3@C5'
5 atoms, 2 residues, 1 model selected
> select add #12/K:3@C4'
6 atoms, 2 residues, 1 model selected
> select add #12/K:3@C3'
7 atoms, 2 residues, 1 model selected
> select add #12/K:4
11 atoms, 3 bonds, 3 residues, 1 model selected
> select add #12/K:3@O4'
12 atoms, 3 bonds, 3 residues, 1 model selected
> select add #12/K:3@C2'
13 atoms, 3 bonds, 3 residues, 1 model selected
> select add #12/K:3@C1'
14 atoms, 3 bonds, 3 residues, 1 model selected
> select add #12/K:3@N9
15 atoms, 3 bonds, 3 residues, 1 model selected
> select add #12/K:3@C8
16 atoms, 3 bonds, 3 residues, 1 model selected
> select add #12/K:3@C4
17 atoms, 3 bonds, 3 residues, 1 model selected
> select add #12/K:3@C5
18 atoms, 3 bonds, 3 residues, 1 model selected
> select add #12/K:3@N7
19 atoms, 3 bonds, 3 residues, 1 model selected
> select add #12/K:3@C6
20 atoms, 3 bonds, 3 residues, 1 model selected
> select add #12/K:3@N6
21 atoms, 3 bonds, 3 residues, 1 model selected
> select add #12/K:3@N1
22 atoms, 3 bonds, 3 residues, 1 model selected
> select add #12/K:3@C2
23 atoms, 3 bonds, 3 residues, 1 model selected
> select add #12/K:3@N3
24 atoms, 3 bonds, 3 residues, 1 model selected
> hide sel atoms
> hide sel cartoons
> select #12/K:3@O3'
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select clear
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> select #12/K:2@O5'
1 atom, 1 residue, 1 model selected
> hide sel atoms
> show #12/M,O atoms
> select #12/O:1@O
1 atom, 1 residue, 1 model selected
> color sel blue
> select #12/M:1@MG
1 atom, 1 residue, 1 model selected
> color sel red
> select clear
> show #12/A:304-305,328,280
> select #12/A:319
8 atoms, 7 bonds, 1 residue, 1 model selected
> select ~sel & ##selected
24158 atoms, 24918 bonds, 3 pseudobonds, 2802 residues, 2 models selected
> show #12/A:304-305,328,280,319
> color #12 byhetero
> select #12/O:1@O
1 atom, 1 residue, 1 model selected
> select add #12/M:1@MG
2 atoms, 2 residues, 1 model selected
> select #12/M:1@MG
1 atom, 1 residue, 1 model selected
> select #12/O:1@O
1 atom, 1 residue, 1 model selected
> color sel blue
> select #12/M:1@MG
1 atom, 1 residue, 1 model selected
> color sel red
> select clear
> select #12/A:305@ND1
1 atom, 1 residue, 1 model selected
> select add #12/K:3@OP2
2 atoms, 2 residues, 1 model selected
> distance #12/A:305@ND1 #12/K:3@OP2
Distance between halfcleaved_HNH_center_main_model_temp2.pdb #12/A HIS 305 ND1
and /K DA 3 OP2: 3.159Å
> select #12/A:280@NH2
1 atom, 1 residue, 1 model selected
> select add #12/K:3@OP2
2 atoms, 2 residues, 1 model selected
> distance #12/A:280@NH2 #12/K:3@OP2
Distance between halfcleaved_HNH_center_main_model_temp2.pdb #12/A ARG 280 NH2
and /K DA 3 OP2: 2.389Å
> select #12/A:280@NH1
1 atom, 1 residue, 1 model selected
> select add #12/K:3@O5'
2 atoms, 2 residues, 1 model selected
> distance #12/A:280@NH1 #12/K:3@O5'
Distance between halfcleaved_HNH_center_main_model_temp2.pdb #12/A ARG 280 NH1
and /K DA 3 O5': 2.765Å
> view
> select #12/K:3@OP1
1 atom, 1 residue, 1 model selected
> select add #12/M:1@MG
2 atoms, 2 residues, 1 model selected
> distance #12/K:3@OP1 #12/M:1@MG
Distance between halfcleaved_HNH_center_main_model_temp2.pdb #12/K DA 3 OP1
and /M MG 1 MG: 3.166Å
> select #12/M:1@MG
1 atom, 1 residue, 1 model selected
> select add #12/A:304@ND1
2 atoms, 2 residues, 1 model selected
> distance #12/M:1@MG #12/A:304@ND1
Distance between halfcleaved_HNH_center_main_model_temp2.pdb #12/M MG 1 MG and
/A HIS 304 ND1: 2.377Å
> select #12/A:328@NE2
1 atom, 1 residue, 1 model selected
> select add #12/M:1@MG
2 atoms, 2 residues, 1 model selected
> distance #12/A:328@NE2 #12/M:1@MG
Distance between halfcleaved_HNH_center_main_model_temp2.pdb #12/A HIS 328 NE2
and /M MG 1 MG: 2.352Å
> select clear
> color sel maroon
> color sel teal
> color sel cornflower blue
> color sel dark salmon
> color sel dark khaki
> color sel peru
> select #12/O:1@O
1 atom, 1 residue, 1 model selected
> select add #12/K:3@OP2
2 atoms, 2 residues, 1 model selected
> color sel indigo
> color sel red
> select #12/O:1@O
1 atom, 1 residue, 1 model selected
> color sel blue
> select #12/K:3@OP2
1 atom, 1 residue, 1 model selected
> select add #12/O:1@O
2 atoms, 2 residues, 1 model selected
> distance #12/K:3@OP2 #12/O:1@O
Distance between halfcleaved_HNH_center_main_model_temp2.pdb #12/K DA 3 OP2
and /O HOH 1 O: 2.479Å
> color sel indigo
> select clear
> color sel dark blue
[Repeated 1 time(s)]
> select clear
> select #12/A:309
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #12/O:1@O
9 atoms, 7 bonds, 2 residues, 1 model selected
Exactly two atoms must be selected!
> select clear
> select #12/A LEU 309 N
Expected a keyword
> select #12/A:309
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel cartoons
> select #12/A:309@N
1 atom, 1 residue, 1 model selected
> select add #12/O:1@O
2 atoms, 2 residues, 1 model selected
> distance #12/A:309@N #12/O:1@O
Distance between halfcleaved_HNH_center_main_model_temp2.pdb #12/A LEU 309 N
and /O HOH 1 O: 3.104Å
> distance style decimalPlaces 2
[Repeated 2 time(s)]
> distance style decimalPlaces 1
[Repeated 2 time(s)]
> select subtract #12/O:1@O
1 atom, 1 residue, 1 model selected
> select ~sel & ##selected
24165 atoms, 24925 bonds, 11 pseudobonds, 2803 residues, 3 models selected
> hide #12/A:309 atoms
> show #12/A:309 cartoons
> select clear
> show #!4 models
> volume #4 level 0.07
> volume #4 level 0.08
> select #12/K:2@N3
1 atom, 1 residue, 1 model selected
> select up
20 atoms, 21 bonds, 1 residue, 1 model selected
> select up
886 atoms, 986 bonds, 45 residues, 1 model selected
> select down
20 atoms, 21 bonds, 1 residue, 1 model selected
> hide sel atoms
> surface dust #4 size 7.25
[Repeated 1 time(s)]
> surface dust #4 1
Expected a keyword
> surface dust #4 size 1
> show (sel-residues & sidechain) target ab
> hide sel atoms
> select clear
> select #12/K:3@O5'
1 atom, 1 residue, 1 model selected
> select up
21 atoms, 23 bonds, 1 residue, 1 model selected
> show #12/K:2 atoms
> select #12/K:2@C2
1 atom, 1 residue, 1 model selected
> select up
20 atoms, 21 bonds, 1 residue, 1 model selected
> hide #!4 models
> select subtract #12/K:2@O3'
19 atoms, 20 bonds, 1 residue, 1 model selected
> hide sel atoms
> show #!4 models
> volume #4 level 0.06
> volume #4 level 0.08
> volume #4 level 0.09
> volume #4 level 0.08
> view matrix models
> #12,0.95038,0.072866,-0.30245,40.949,-0.29386,-0.10887,-0.94963,361.72,-0.10212,0.99138,-0.082056,19.143
> show #!10 models
> hide #!10 models
> mmaker #12 to #10
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_temp2.pdb, chain A (#10) with
halfcleaved_HNH_center_main_model_temp2.pdb, chain A (#12), sequence alignment
score = 1753
RMSD between 340 pruned atom pairs is 0.001 angstroms; (across all 340 pairs:
0.001)
> ui tool show "Side View"
> hide #11.1 models
> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/figures/structure/HNH/HNH_cat_0p8.tif" width 1984 height
> 1210 supersample 3 transparentBackground true
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!4 models
> select #2/E:804@O1
1 atom, 1 residue, 1 model selected
> select up
5 atoms, 4 bonds, 1 residue, 1 model selected
> select add #2/E:731@CG
6 atoms, 4 bonds, 2 residues, 1 model selected
> select up
15 atoms, 14 bonds, 2 residues, 1 model selected
> select up
17 atoms, 15 bonds, 3 residues, 1 model selected
> select up
19 atoms, 16 bonds, 4 residues, 1 model selected
> select add #12/A:319@OD1
20 atoms, 16 bonds, 5 residues, 2 models selected
> select up
39 atoms, 35 bonds, 5 residues, 2 models selected
> select add #2/E:31@O
40 atoms, 35 bonds, 6 residues, 2 models selected
> select add #2/E:298@O
41 atoms, 35 bonds, 7 residues, 2 models selected
> select subtract #2/E:298@O
40 atoms, 35 bonds, 6 residues, 2 models selected
> hide #2.1 models
> show #2.1 models
> hide #2.1 models
> show #2.1 models
> hide #2.1 models
> show #2.1 models
> hide #2.1 models
> show #2.1 models
> hide #2.1 models
> show #2.1 models
> hide #2.1 models
> select add #12
24198 atoms, 24953 bonds, 11 pseudobonds, 2808 residues, 4 models selected
> select subtract #12
32 atoms, 28 bonds, 5 residues, 1 model selected
> hide sel atoms
> select #2/E:701@CB
1 atom, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #12/A:319@OD1
1 atom, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #2/E:298@O
1 atom, 1 residue, 1 model selected
> hide sel atoms
> color sel dark blue
> select clear
> show #!4 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/figures/structure/HNH/HNH_cat_0p8.tif" width 1984 height
> 1210 supersample 3
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> hide #!12 models
> hide #!4 models
> show #!2 models
> select #2/E:904@ZN
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select clear
> hide #!2 models
> show #!12 models
> select #12/M:1@MG
1 atom, 1 residue, 1 model selected
> color sel silver
> color sel metallic
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color sel dark gray
> color sel dim gray
> select clear
> color sel red
> select #12/M:1@MG
1 atom, 1 residue, 1 model selected
> color sel red
> color sel dim gray
> select clear
> show #!2 models
> hide #!2 models
> show #!4 models
> color sel red
> color #12/M red
> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/figures/structure/HNH/HNH_cat_0p8.tif" width 1984 height
> 1210 supersample 3
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!4 models
> color sel tan
> color sel dim gray
[Repeated 1 time(s)]
> show #!4 models
> select clear
> hide #!2 models
> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/figures/structure/HNH/HNH_cat_0p8.tif" width 1984 height
> 1210 supersample 3
> hide #!4 models
> show #!2 models
> hide #!11 models
> color #2 yellow
> sle #2/E
Unknown command: sle #2/E
> select #2/E
1109 atoms, 1075 bonds, 4 pseudobonds, 190 residues, 2 models selected
> select clear
> ui tool show "Show Sequence Viewer"
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> hide #!2 models
> open "/Users/zxc755/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/Type
> I-F_HNH/Manuscript/halfcleaved_HNH_center_main_model_temp2.pdb"
Chain information for halfcleaved_HNH_center_main_model_temp2.pdb #13
---
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
> hide #13 atoms
> show #13 cartoons
> cartoon style nucleic xsection oval width 1 thickness 1
> color #13/DA light gray
> color #13/EA dim gray
> color #13/FA dark red
> color #13/Ca rebecca purple
> color #13/Ba forest green
> color #13/Da,Db,Dc,Dd,De,Df khaki
> color #13/Aa steel blue
> color #13/Aa:232-350 dark turquoise
> hide #!12 models
> show #!12 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> show #!13 models
> color #13/L light gray
> color #13/K dim gray
> color #13/J dark red
> color #13/I rebecca purple
> color #13/B forest green
> color #13/C,D,E,F,G,H khaki
> color #13/A steel blue
> color #13/A:232-350 dark turquoise
> color #13 byhetero
> hide #!12 models
> color #13/M red
> show #13/K:2 atoms
> style stick
Changed 179387 atom styles
> select #13/K:3
21 atoms, 23 bonds, 1 residue, 1 model selected
> select add #13/K:4
25 atoms, 26 bonds, 2 residues, 1 model selected
> select add #13/K:2
45 atoms, 47 bonds, 3 residues, 1 model selected
> hide sel cartoons
> show #13/K:3 atoms
> select subtract #13/K:3@O5'
44 atoms, 45 bonds, 3 residues, 1 model selected
> select subtract #13/K:3@OP2
43 atoms, 44 bonds, 3 residues, 1 model selected
> select subtract #13/K:3@OP1
42 atoms, 43 bonds, 3 residues, 1 model selected
> select subtract #13/K:2@O3'
41 atoms, 42 bonds, 3 residues, 1 model selected
> select subtract #13/K:2@C3'
40 atoms, 40 bonds, 3 residues, 1 model selected
> select add #13/K:2@C3'
41 atoms, 40 bonds, 3 residues, 1 model selected
> select subtract #13/K:2@C3'
40 atoms, 40 bonds, 3 residues, 1 model selected
> select add #13/K:2@C3'
41 atoms, 40 bonds, 3 residues, 1 model selected
> hide sel atoms
> select #13/K:2@O3'
1 atom, 1 residue, 1 model selected
> select up
20 atoms, 21 bonds, 1 residue, 1 model selected
> select up
886 atoms, 986 bonds, 45 residues, 1 model selected
> show sel atoms
> select #13/K:4@O5'
1 atom, 1 residue, 1 model selected
> select add #13/K:4@OP1
2 atoms, 1 residue, 1 model selected
> select add #13/K:3@O3'
3 atoms, 2 residues, 1 model selected
> select up
25 atoms, 27 bonds, 2 residues, 1 model selected
> select subtract #13/K:3@O5'
24 atoms, 25 bonds, 2 residues, 1 model selected
> select subtract #13/K:3@P
23 atoms, 23 bonds, 2 residues, 1 model selected
> select subtract #13/K:3@OP1
22 atoms, 23 bonds, 2 residues, 1 model selected
> select subtract #13/K:3@OP2
21 atoms, 23 bonds, 2 residues, 1 model selected
> hide sel atoms
> select up
23 atoms, 24 bonds, 3 residues, 1 model selected
> select up
45 atoms, 49 bonds, 3 residues, 1 model selected
> select down
23 atoms, 24 bonds, 3 residues, 1 model selected
> select #13/K:2@N1
1 atom, 1 residue, 1 model selected
> select up
20 atoms, 21 bonds, 1 residue, 1 model selected
> select subtract #13/K:2@O3'
19 atoms, 20 bonds, 1 residue, 1 model selected
> hide sel atoms
> show #13/A:304-305,328,280
> show #13/M,O
> select #13/O:1@O
1 atom, 1 residue, 1 model selected
> color sel blue
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!4 models
> show #!12 models
> hide #!12 models
> select #13/K:1
9 atoms, 9 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select #13/K:1@O5'
1 atom, 1 residue, 1 model selected
> select add #13/K:1@C5'
2 atoms, 1 residue, 1 model selected
> hide sel atoms
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> select Mg
6 atoms, 6 residues, 6 models selected
> select Zn
5 atoms, 5 residues, 2 models selected
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> select add #2
4547 atoms, 4317 bonds, 16 pseudobonds, 856 residues, 3 models selected
> select subtract #2
1 atom, 1 residue, 1 model selected
> hide #!4 models
> select add #5
6 atoms, 4 bonds, 1 pseudobond, 2 residues, 2 models selected
> select subtract #5
Nothing selected
> select add #5
6 atoms, 4 bonds, 1 pseudobond, 2 residues, 2 models selected
> select subtract #5
Nothing selected
> hide #!5 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> select Zn
5 atoms, 5 residues, 2 models selected
> select add #5
10 atoms, 4 bonds, 1 pseudobond, 6 residues, 3 models selected
> select subtract #5
4 atoms, 4 residues, 1 model selected
> show sel atoms
> show #!2 models
> select water
Expected an objects specifier or a keyword
> ui tool show "Check Waters"
> hbonds #13/O interModel false reveal true restrict any name "water H-bonds"
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: halfcleaved_HNH_center_main_model_temp2.pdb #13/K DG 1 N9
2 hydrogen bonds found
> show #4 models
> select #13/O
1 atom, 1 residue, 1 model selected
> display #13/O : view #13/O @ select add #13/K:3@N7
2 atoms, 2 residues, 1 model selected
> select up
22 atoms, 23 bonds, 2 residues, 1 model selected
> hide #!2 models
> hide #!4 models
> select subtract #13/K:3@O5'
21 atoms, 21 bonds, 2 residues, 1 model selected
> select subtract #13/K:3@OP2
20 atoms, 20 bonds, 2 residues, 1 model selected
> select subtract #13/K:3@OP1
19 atoms, 19 bonds, 2 residues, 1 model selected
> hide sel atoms
> select #13/K:3@O5'
1 atom, 1 residue, 1 model selected
> select up
21 atoms, 23 bonds, 1 residue, 1 model selected
> show sel atoms
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
21 atoms, 23 bonds, 1 residue, 1 model selected
> select subtract #13/K:3@P
20 atoms, 20 bonds, 1 residue, 1 model selected
> select subtract #13/K:3@OP1
19 atoms, 20 bonds, 1 residue, 1 model selected
> select subtract #13/K:3@OP2
18 atoms, 20 bonds, 1 residue, 1 model selected
> select subtract #13/K:3@O5'
17 atoms, 19 bonds, 1 residue, 1 model selected
> hide sel atoms
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
20 atoms, 21 bonds, 1 residue, 1 model selected
> select subtract #13/K:2@O3'
19 atoms, 20 bonds, 1 residue, 1 model selected
> hide sel atoms
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
9 atoms, 9 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #13/A:308@CD
1 atom, 1 residue, 1 model selected
> select up
7 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel atoms
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> hide sel cartoons
> select #13/A:309@N
1 atom, 1 residue, 1 model selected
> show #13/O atoms
> show #!11 models
> hide #!11 models
> close #11
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel atoms
> show sel cartoons
> hide sel
> select #13/O:1@O
1 atom, 1 residue, 1 model selected
> select add #13/K:3@OP2
2 atoms, 2 residues, 1 model selected
> distance #13/O:1@O #13/K:3@OP2
Distance between halfcleaved_HNH_center_main_model_temp2.pdb #13/O HOH 1 O and
/K DA 3 OP2: 2.5Å
> select #13/A:309
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel atoms
> hide sel cartoons
> show sel atoms
> select #13/A:309@N
1 atom, 1 residue, 1 model selected
> select add #13/O:1@O
2 atoms, 2 residues, 1 model selected
> distance #13/A:309@N #13/O:1@O
Distance between halfcleaved_HNH_center_main_model_temp2.pdb #13/A LEU 309 N
and /O HOH 1 O: 3.1Å
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel atoms
> show sel cartoons
> hide #11.1 models
> select #13/M:2@MG
1 atom, 1 residue, 1 model selected
> select add #13/K:2@O3'
2 atoms, 2 residues, 1 model selected
> distance #13/M:2@MG #13/K:2@O3'
Distance between halfcleaved_HNH_center_main_model_temp2.pdb #13/M MG 2 MG and
/K DT 2 O3': 2.9Å
> select #13/A:304@ND1
1 atom, 1 residue, 1 model selected
> select add #13/M:2@MG
2 atoms, 2 residues, 1 model selected
> distance #13/A:304@ND1 #13/M:2@MG
Distance between halfcleaved_HNH_center_main_model_temp2.pdb #13/A HIS 304 ND1
and /M MG 2 MG: 2.6Å
> select #13/A:328@NE2
1 atom, 1 residue, 1 model selected
> select add #13/M:2@MG
2 atoms, 2 residues, 1 model selected
> distance #13/A:328@NE2 #13/M:2@MG
Distance between halfcleaved_HNH_center_main_model_temp2.pdb #13/A HIS 328 NE2
and /M MG 2 MG: 2.0Å
> select clear
> select #13/A:305@ND1
1 atom, 1 residue, 1 model selected
> select add #13/K:3@OP2
2 atoms, 2 residues, 1 model selected
> distance #13/A:305@ND1 #13/K:3@OP2
Distance between halfcleaved_HNH_center_main_model_temp2.pdb #13/A HIS 305 ND1
and /K DA 3 OP2: 3.2Å
> select #13/K:3@O5'
1 atom, 1 residue, 1 model selected
> select add #13/A:280@NH1
2 atoms, 2 residues, 1 model selected
> distance #13/K:3@O5' #13/A:280@NH1
Distance between halfcleaved_HNH_center_main_model_temp2.pdb #13/K DA 3 O5'
and /A ARG 280 NH1: 2.8Å
> select #13/K:3@OP2
1 atom, 1 residue, 1 model selected
> select add #13/A:280@NH2
2 atoms, 2 residues, 1 model selected
> distance #13/K:3@OP2 #13/A:280@NH2
Distance between halfcleaved_HNH_center_main_model_temp2.pdb #13/K DA 3 OP2
and /A ARG 280 NH2: 2.4Å
> select add #11
8 pseudobonds, 2 models selected
> color sel dim gray
> show #!2 models
> hide #!2 models
> show #!4 models
> unsel
Unknown command: unsel
> select
179387 atoms, 183813 bonds, 57 pseudobonds, 19979 residues, 49 models selected
> select clear
> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/figures/structure/HNH/HNH_cat_0p8.tif" width 1984 height
> 1210 supersample 3
> show #!2 models
> hide #!4 models
> hide #!11 models
> select #2/E:31@O
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select clear
> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/figures/structure/HNH/HNH_cat_1fsj.tif" width 1984 height
> 1210 supersample 3
> lighting soft
> show #!4 models
> hide #!2 models
> lighting full
> lighting simple
> lighting full
> lighting simple
> lighting soft
> lighting simple
> lighting soft
> lighting simple
> lighting soft
> lighting simple
> show #!2 models
> hide #!4 models
> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/figures/structure/HNH/HNH_cat_1fsj.tif" width 1984 height
> 1210 supersample 3
> hide #!2 models
> show #!4 models
> hide #!4 models
> show #!4 models
> volume #4 level 0.09
> volume #4 level 0.1
> volume #4 level 0.95
> volume #4 level 0.095
> volume #4 level 0.09
> volume #4 level 0.08
> volume #4 level 0.09
> select #13/K:6
22 atoms, 24 bonds, 1 residue, 1 model selected
> show #13/L atoms
> select clear
> show #13/L,J atoms
> select clear
> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/figures/chimera_session.cxs"
——— End of log from Mon Mar 24 00:43:04 2025 ———
opened ChimeraX session
> volume #4 level 0.08
> hide #13/J,L atoms
> hide #13/K:6-46 atoms
> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/figures/structure/HNH/HNH_zoom_out.tif" width 1984 height
> 1210 supersample 3
> lighting soft
> lighting simple
> lighting soft
> lighting simple
> lighting full
> lighting simple
> lighting full
> lighting simple
> lighting full
> lighting simple
> lighting soft
> lighting simple
> lighting soft
> lighting simple
> volume #4 level 0.06
> show #13/A:83,85 atoms
> show #13/K:39-40 atoms
> show #13/L:6-7 atoms
> select clear
> show #13/L,J #13/K:7-46 atoms
> color #13/L light gray
> color #13/K dim gray
> color #13/J dark red
> color #13/I rebecca purple
> color #13/B forest green
> color #13/C,D,E,F,G,H khaki
> color #13/A steel blue
> color #13/A:232-350 dark turquoise
> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/figures/structure/PAM/PAM_zoom_out.tif" width 1984 height
> 1210 supersample 3
> color #13/A. byhet
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color #13/A byhetero
> ui tool show "Side View"
> hide #13/K:7-46 #13/L cartoons
> hide #13/K:7-46 #13/L atoms
> show #13/K:39-40 #13/L:6-7 atoms
> ui tool show Distances
> show #!11 models
Exactly two atoms must be selected!
> hide #!4 models
> show #13/K:39-41 #13/L:6-7 atoms
> select #13/A:83@OD1
1 atom, 1 residue, 1 model selected
> select add #13/K:40@N2
2 atoms, 2 residues, 1 model selected
> distance #13/A:83@OD1 #13/K:40@N2
Distance between halfcleaved_HNH_center_main_model_temp2.pdb #13/A ASP 83 OD1
and /K DG 40 N2: 3.013Å
> distance style color black
[Repeated 2 time(s)]
> ui tool show "Color Actions"
> distance style color dimgrey
[Repeated 2 time(s)]
> select #13/A:85@NZ
1 atom, 1 residue, 1 model selected
> select add #13/K:41@O2
2 atoms, 2 residues, 1 model selected
> distance #13/A:85@NZ #13/K:41@O2
Distance between halfcleaved_HNH_center_main_model_temp2.pdb #13/A LYS 85 NZ
and /K DC 41 O2: 3.020Å
> select #13/A:85@NZ
1 atom, 1 residue, 1 model selected
> select add #13/L:6@N2
2 atoms, 2 residues, 1 model selected
> distance #13/A:85@NZ #13/L:6@N2
Distance between halfcleaved_HNH_center_main_model_temp2.pdb #13/A LYS 85 NZ
and /L DG 6 N2: 3.258Å
> select #13/A:83@OD1
1 atom, 1 residue, 1 model selected
> select add #13/A:85@NZ
2 atoms, 2 residues, 1 model selected
> distance #13/A:83@OD1 #13/A:85@NZ
Distance between halfcleaved_HNH_center_main_model_temp2.pdb #13/A ASP 83 OD1
and LYS 85 NZ: 2.939Å
> select add #11
2 atoms, 12 pseudobonds, 2 residues, 3 models selected
> color sel dim gray
> select clear
> select add #13/A:85
9 atoms, 9 bonds, 1 residue, 1 model selected
> select add #13/A:83
17 atoms, 15 bonds, 2 residues, 1 model selected
> color sel steel blue
> color sel byhetero
> color sel dim gray
> select clear
> show #!4 models
> volume #4 level 0.08
> volume #4 level 0.07
> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/figures/structure/PAM/PAM_0p07.tif" width 1984 height
> 1210 supersample 3
> hide #!4 models
> hide #13/K:39 atoms
> show #!4 models
> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/figures/structure/PAM/PAM_0p07.tif" width 1984 height
> 1210 supersample 3
> show #11.1 models
> distance style decimalPlaces 1
[Repeated 2 time(s)]
> hide #11.1 models
> view #13/L
> volume #4 level 0.06
> show #13/k,l cartoons
> show #13/k:7-46 #13/l atoms
> hide #!4 models
> select #13/A:178
12 atoms, 12 bonds, 1 residue, 1 model selected
> show sel atoms
> select #13/A:193
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> show #!4 models
> hide #!11 models
> hide #13/A:83,85 atoms
> select clear
> surface dust #4 size 7.25
> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/figures/structure/PAM/sideview_with_unwinding.tif" width
> 1984 height 1210 supersample 3
> show #13/A:191 atoms
> select #13/A:193@OD1
1 atom, 1 residue, 1 model selected
> select add #13/L:9@N2
2 atoms, 2 residues, 1 model selected
> distance #13/A:193@OD1 #13/L:9@N2
Distance between halfcleaved_HNH_center_main_model_temp2.pdb #13/A ASN 193 OD1
and /L DG 9 N2: 2.6Å
> show #!11 models
> select #13/K:39
19 atoms, 20 bonds, 1 residue, 1 model selected
> hide sel cartoons
> hide #!4 models
> select #13/K:39@OP1
1 atom, 1 residue, 1 model selected
> select add #13/A:191@OG
2 atoms, 2 residues, 1 model selected
> distance #13/K:39@OP1 #13/A:191@OG
Distance between halfcleaved_HNH_center_main_model_temp2.pdb #13/K DC 39 OP1
and /A SER 191 OG: 2.9Å
> show sel cartoons
> show #!4 models
> color sel dim gray
> select clear
> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/figures/structure/PAM/sideview_with_unwinding.tif" width
> 1984 height 1210 supersample 3
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!13 models
> show #!13 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> volume #4 level 0.09
> volume #4 level 0.05
> volume #4 level 0.06
> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/figures/structure/PAM/sideview_with_unwinding.tif" width
> 1984 height 1210 supersample 3
> hide #!4 models
> show #!4 models
> hide #!11 models
> select #13/K:4
4 atoms, 3 bonds, 1 residue, 1 model selected
> select add #13/K:3
25 atoms, 26 bonds, 2 residues, 1 model selected
> select add #13/K:2
45 atoms, 47 bonds, 3 residues, 1 model selected
> select up
886 atoms, 986 bonds, 45 residues, 1 model selected
> select down
45 atoms, 47 bonds, 3 residues, 1 model selected
> hide #!4 models
> select add #13/K:1
54 atoms, 56 bonds, 4 residues, 1 model selected
> hide sel cartoons
> select clear
> select #13/K:3@P
1 atom, 1 residue, 1 model selected
> select up
21 atoms, 23 bonds, 1 residue, 1 model selected
> select up
886 atoms, 986 bonds, 45 residues, 1 model selected
> select down
21 atoms, 23 bonds, 1 residue, 1 model selected
> select down
1 atom, 1 residue, 1 model selected
> select up
21 atoms, 23 bonds, 1 residue, 1 model selected
> select add #13/K:2@O3'
22 atoms, 23 bonds, 2 residues, 1 model selected
> select up
41 atoms, 45 bonds, 2 residues, 1 model selected
> color sel byhetero
> select clear
> select #13/K:6
22 atoms, 24 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> select #13/A:295
6 atoms, 5 bonds, 1 residue, 1 model selected
> select add #13/I:140
12 atoms, 10 bonds, 2 residues, 1 model selected
> show sel atoms
> show #!4 models
> hide #!4 models
> select #13/K:6
22 atoms, 24 bonds, 1 residue, 1 model selected
> select add #13/K:7
42 atoms, 45 bonds, 2 residues, 1 model selected
> hide sel cartoons
> show #!4 models
> volume #4 level 0.09
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
22 atoms, 24 bonds, 1 residue, 1 model selected
> hide #!4 models
> select subtract #13/K:6@O3'
21 atoms, 23 bonds, 1 residue, 1 model selected
> hide sel atoms
> show #!4 models
> hide #!4 models
> select #13/K:7@OP1
1 atom, 1 residue, 1 model selected
> select up
20 atoms, 21 bonds, 1 residue, 1 model selected
> show sel cartoons
> select #13/K:6@O3'
1 atom, 1 residue, 1 model selected
> hide sel atoms
> show #!4 models
> hide #!4 models
> select #13/I:50
9 atoms, 8 bonds, 1 residue, 1 model selected
> select add #13/I:51
18 atoms, 16 bonds, 2 residues, 1 model selected
> show sel atoms
> show #!4 models
> volume #4 level 0.06
> volume #4 level 0.08
> select #13/I:51@CD
1 atom, 1 residue, 1 model selected
> select up
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
11 atoms, 9 bonds, 2 residues, 1 model selected
> select up
18 atoms, 17 bonds, 2 residues, 1 model selected
> hide sel atoms
> select clear
> volume #4 level 0.1
> color #13/i byhetero
> select clear
> select #13/K:7
20 atoms, 21 bonds, 1 residue, 1 model selected
> volume #4 level 0.07
> select clear
> volume #4 level 0.09
> show #!2 models
> hide #!2 models
> hide #!4 models
> select #13/A:295@SG
1 atom, 1 residue, 1 model selected
> select add #13/I:140@SG
2 atoms, 2 residues, 1 model selected
> distance #13/A:295@SG #13/I:140@SG
Distance between halfcleaved_HNH_center_main_model_temp2.pdb #13/A CYS 295 SG
and /I CYS 140 SG: 3.9Å
> show #!11 models
> color sel dim gray
> select clear
> hide #13/A:230-350 atoms
> hide #13/o atoms
> select #13/A:295
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> show #!4 models
> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/figures/structure/HNH/cas8_cas6_cys_pair_0p09.tif" width
> 1984 height 1210 supersample 3
> hide #!4 models
> show #11.1 models
> hide #11.1 models
> show #!2 models
> select #2/E:706@CG
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select #2/E:706@CD
1 atom, 1 residue, 1 model selected
> select up
7 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
[Repeated 1 time(s)]
> select clear
> select #2/E:706@CG
1 atom, 1 residue, 1 model selected
> select up
7 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #2/E:707@CD1
1 atom, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel atoms
[Repeated 1 time(s)]
> select clear
> select #13/I:140@SG
1 atom, 1 residue, 1 model selected
> select add #13/A:295@SG
2 atoms, 2 residues, 1 model selected
> select up
12 atoms, 10 bonds, 2 residues, 1 model selected
> hide sel atoms
> select clear
> show #13/A:305,304,280,328
> select #2/E:718
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #13/A:319
16 atoms, 14 bonds, 2 residues, 2 models selected
> show sel atoms
> show #13/O
> select clear
> hide #!11 models
> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/figures/structure/HNH/HNH_cat_1fsj_2.tif" width 1984
> height 1210 supersample 3
> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/figures/chimera_session.cxs"
——— End of log from Mon Mar 24 13:31:18 2025 ———
opened ChimeraX session
> hide #!2 models
> ui tool show "Side View"
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> hide #!13 models
> close #12
> open "/Users/zxc755/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/Type
> I-F_HNH/Manuscript/halfcleaved_HNH_center_main_model_temp2.pdb"
Chain information for halfcleaved_HNH_center_main_model_temp2.pdb #12
---
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
> hide #12 atoms
> show #12 cartoons
> cartoon style nucleic xsection oval width 1 thickness 1
> color #12/L light gray
> color #12/K dim gray
> color #12/J dark red
> color #12/I rebecca purple
> color #12/B forest green
> color #12/C,D,E,F,G,H khaki
> color #12/A steel blue
> color #12/A:232-350 dark turquoise
> color #12/M red
> color #12/o blue
> select clear
> select #12/K:6
22 atoms, 24 bonds, 1 residue, 1 model selected
> hide sel cartoons
> show sel atoms
> style stick
Changed 179387 atom styles
> select clear
> show #!2 models
> hide #!2 models
> show #!4 models
> select #12/K:7
20 atoms, 21 bonds, 1 residue, 1 model selected
> hide #12/K cartoons
> show #12/k atoms
> select clear
> volume #4 level 0.06
> hide #!4 models
> select #12/A:295
6 atoms, 5 bonds, 1 residue, 1 model selected
> select add #12/I:50
15 atoms, 13 bonds, 2 residues, 1 model selected
> select add #12/I:140
21 atoms, 18 bonds, 3 residues, 1 model selected
> show sel atoms
> show #!4 models
> hide #!4 models
> select #12/A:290
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> show #!4 models
> volume #4 level 0.08
> hide #!4 models
> select #12/A:296
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> select #12/I:51
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> show #!4 models
> volume #4 level 0.07
> volume #4 level 0.09
> volume #4 level 0.05
> surface dust #4 size 7.25
> color #12/K:1-4 red
> show #12/m,o atoms
> select clear
> close #13
> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/figures/chimera_session.cxs"
——— End of log from Tue Mar 25 00:19:58 2025 ———
opened ChimeraX session
> close #12
> hide #!4 models
> open "/Users/zxc755/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/Type
> I-F_HNH/Manuscript/halfcleaved_HNH_center_main_model_temp.pdb"
Chain information for halfcleaved_HNH_center_main_model_temp.pdb #12
---
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
> style stick
Changed 155168 atom styles
> color #12/L light gray
> color #12/K dim gray
> color #12/J dark red
> color #12/I rebecca purple
> color #12/B forest green
> color #12/C,D,E,F,G,H khaki
> color #12/A steel blue
> color #12/A:232-350 dark turquoise
> cartoon style nucleic xsection oval width 1 thickness 1
> show #12 cartoons
> hide #12 atoms
> hide #12/k:1-6 cartoons
> show #12/k:1-6 atoms
> show #12/m,o atoms
> color #12/m red
> color #12/o blue
> select clear
> open "/Users/zxc755/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/Type
> I-F_HNH/Manuscript/maps_models/maybe_better/deepEMhancer/half/halfcleaved_HNH_center_sharp3Å.mrc"
Opened halfcleaved_HNH_center_sharp3Å.mrc as #13, grid size 420,420,420,
pixel 0.725, shown at level 0.00305, step 2, values float32
> volume #13 step 1
> volume #13 level 0.01
> volume #13 level 0.02
> transparency #13.1 50
> color zone #13 near #12 distance 5
> select subtract #11
Nothing selected
> hide #!12 models
> color zone #13 near #12/a,b,c,d,e,f,g,h,i,j,k,l distance 5
> color zone #13 near #12/a,b,c,d,e,f,g,h,i,j,k,l distance 5 near #12/m,o dis
> 1
Repeated keyword argument "near"
> color zone #13 near #12/a,b,c,d,e,f,g,h,i,j,k,l distance 5 #12/m,o dis 1
Expected a keyword
> color zone #13 near #12/a,b,c,d,e,f,g,h,i,j,k,l distance 3
> color zone #13 near #12/a,b,c,d,e,f,g,h,i,j,k,l distance 3.5
> color zone #13 near #12/ dis 3.5
Expected a keyword
> color zone #13 near #12 distance 3.5
> color zone #13 near #12 distance 3
> color zone #13 near #12 distance 1
> color zone #13 near #12 distance 1.5
> color zone #13 near #12 distance 2
> color zone #13 near #12 distance 2.4
> color zone #13 near #12 distance 2.5
> color zone #13 near #12 distance 3
> color zone #13 near #12 distance 4
> color zone #13 near #12 distance 4.5
> color zone #13 near #12 distance 5
> lighting soft
> hide #!13 models
> open "/Users/zxc755/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/Type
> I-F_HNH/Manuscript/maps_models/maybe_better/deepEMhancer/half/halfcleaved_HNH_in_sharp3Å.mrc"
Opened halfcleaved_HNH_in_sharp3Å.mrc as #14, grid size 420,420,420, pixel
0.725, shown at level 0.00277, step 2, values float32
> volume #14 step 1
> volume #14 level 0.02
> hide #!14 models
> show #!14 models
> hide #!14 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 #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
> color #15/L light gray
> color #15/K dim gray
> color #15/J dark red
> color #15/I rebecca purple
> color #15/B forest green
> color #15/C,D,E,F,G,H khaki
> color #15/A steel blue
> color #15/A:232-350 dark turquoise
> hide #15 atoms
> show #!14 models
> color zone #14 near #15 distance 5
> hide #!15 models
> show #!15 models
> hide #!14 models
> show #!14 models
> show cartoons #15
Expected ',' or a keyword
> show #15 cartoons
> hide #!14 models
> combine #15
> delete #15/b,c,d,e,f,g,h,j,k,l
> hide #!16 models
> show #!16 models
> hide #!16 models
> delete #15/b,c,d,e,f,g,h,j,k,l,i
> delete #15/a:1-230
> delete #15/a:1-231
> show #!14 models
> transparency #14.1 50
> fitmap #15 inMap #14
Fit molecule halfcleaved_HNH_inwards_refined.pdb (#15) to map
halfcleaved_HNH_in_sharp3Å.mrc (#14) using 897 atoms
average map value = 0.1033, steps = 48
shifted from previous position = 0.103
rotated from previous position = 0.723 degrees
atoms outside contour = 296, contour level = 0.02
Position of halfcleaved_HNH_inwards_refined.pdb (#15) relative to
halfcleaved_HNH_in_sharp3Å.mrc (#14) coordinates:
Matrix rotation and translation
0.99995867 0.00821061 0.00390412 -2.00149362
-0.00817612 0.99992812 -0.00876986 2.45517496
-0.00397584 0.00873757 0.99995392 -1.09279831
Axis 0.69359957 0.31218363 -0.64920029
Axis point 0.00000000 120.00927253 275.85141597
Rotation angle (degrees) 0.72313237
Shift along axis 0.08767530
> hide #!14 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 #17
---
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/postcleavage_HNH_inwards_3p93Å.mrc"
Opened postcleavage_HNH_inwards_3p93Å.mrc as #18, grid size 420,420,420,
pixel 0.725, shown at level 0.0417, step 2, values float32
> close #18
> open "/Users/zxc755/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/Type
> I-F_HNH/Manuscript/maps_models/maybe_better/deepEMhancer/post/post_HNH_in_sharp_4p5.mrc"
Opened post_HNH_in_sharp_4p5.mrc as #18, grid size 420,420,420, pixel 0.725,
shown at level 0.0257, step 2, values float32
> volume #18 step 1
> hide #!15 models
> show #!15 models
> hide #!17 models
> transparency #18.1 50
> lighting simple
> fitmap #15 inMap #18
Fit molecule halfcleaved_HNH_inwards_refined.pdb (#15) to map
post_HNH_in_sharp_4p5.mrc (#18) using 897 atoms
average map value = 0.1722, steps = 88
shifted from previous position = 5.79
rotated from previous position = 18.5 degrees
atoms outside contour = 305, contour level = 0.025678
Position of halfcleaved_HNH_inwards_refined.pdb (#15) relative to
post_HNH_in_sharp_4p5.mrc (#18) coordinates:
Matrix rotation and translation
0.98515450 -0.14232903 -0.09598467 36.22127193
0.16215106 0.95508370 0.24803662 -52.49007293
0.05637058 -0.25991841 0.96398381 44.34612442
Axis -0.83066353 -0.24914793 0.49791908
Axis point 0.00000000 129.04516803 229.89711725
Rotation angle (degrees) 17.80344657
Shift along axis 5.07088499
> hide #17 atoms
> show #17 cartoons
> show #!17 models
> hide #!17 models
> hide #!15 models
> show #!15 models
> show #!16 models
> hide #!16 models
> hide #!15 models
> show #!16 models
> hide #!16 models
> show #!17 models
> select add #18
2 models selected
> ui tool show "Color Actions"
> color sel navajo white
> lighting simple
> lighting soft
> lighting simple
> color #17/DA light gray
> color #17/EA dim gray
> color #17/FA dark red
> color #17/Ca rebecca purple
> color #17/Ba forest green
> color #17/Da,Db,Dc,Dd,De,Df khaki
> color #17/Aa steel blue
> color #17/Aa:232-350 dark turquoise
> color #17/L light gray
> color #17/K dim gray
> color #17/J dark red
> color #17/I rebecca purple
> color #17/B forest green
> color #17/C,D,E,F,G,H khaki
> color #17/A steel blue
> color #17/A:232-350 dark turquoise
> select subtract #18
Nothing selected
> hide #!18 models
> show #!18 models
> hide #!17 models
> hide #!18 models
> open "/Users/zxc755/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/Type
> I-F_HNH/Manuscript/maps_models/maybe_better/deepEMhancer/post/post_HNH_cent_sharp.mrc"
Opened post_HNH_cent_sharp.mrc as #19, grid size 420,420,420, pixel 0.725,
shown at level 0.00149, step 2, values float32
> 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 #20
---
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
> hide #20 atoms
> show #20 cartoons
> volume #19 step 1
> volume #19 level 0.07
> volume #19 level 0.05
> volume #19 level 0.02
> volume #19 level 0.01
> combine #19
No structures specified
> combine #20
> hide #!20 models
> delete #21/a,b,c,d,e,f,g,h,k,l
> fitmap #21 inMap #19
Fit molecule copy of postcleavage_HNH_center_refined.pdb (#21) to map
post_HNH_cent_sharp.mrc (#19) using 2726 atoms
average map value = 0.1694, steps = 2000
shifted from previous position = 0.186
rotated from previous position = 0.199 degrees
atoms outside contour = 1261, contour level = 0.01
Position of copy of postcleavage_HNH_center_refined.pdb (#21) relative to
post_HNH_cent_sharp.mrc (#19) coordinates:
Matrix rotation and translation
0.99999396 0.00180060 0.00297193 -0.76393106
-0.00180072 0.99999838 0.00003869 0.16921571
-0.00297185 -0.00004404 0.99999558 0.56555929
Axis -0.01190446 0.85519891 -0.51816321
Axis point 165.64366772 0.00000000 257.94336417
Rotation angle (degrees) 0.19910813
Shift along axis -0.13924475
> select #21/J:51
23 atoms, 25 bonds, 1 residue, 1 model selected
> ui mousemode right "rotate selected models"
> view matrix models
> #21,0.99951,0.00060373,-0.031401,4.2416,-0.0016237,0.99947,-0.032468,6.0991,0.031365,0.032503,0.99898,-9.4868
> fitmap #21 inMap #19
Fit molecule copy of postcleavage_HNH_center_refined.pdb (#21) to map
post_HNH_cent_sharp.mrc (#19) using 2726 atoms
average map value = 0.1688, steps = 2000
shifted from previous position = 1.36
rotated from previous position = 2.61 degrees
atoms outside contour = 1266, contour level = 0.01
Position of copy of postcleavage_HNH_center_refined.pdb (#21) relative to
post_HNH_cent_sharp.mrc (#19) coordinates:
Matrix rotation and translation
0.99999350 0.00327561 0.00150351 -0.76518814
-0.00327402 0.99999408 -0.00105700 0.62813683
-0.00150696 0.00105207 0.99999831 -0.07731006
Axis 0.28081232 0.40083125 -0.87205433
Axis point 178.64402650 242.89942515 0.00000000
Rotation angle (degrees) 0.21516256
Shift along axis 0.10432118
> delete #21/i:119-133
> fitmap #21 inMap #19
Fit molecule copy of postcleavage_HNH_center_refined.pdb (#21) to map
post_HNH_cent_sharp.mrc (#19) using 2605 atoms
average map value = 0.1781, steps = 2000
shifted from previous position = 0.132
rotated from previous position = 0.117 degrees
atoms outside contour = 1140, contour level = 0.01
Position of copy of postcleavage_HNH_center_refined.pdb (#21) relative to
post_HNH_cent_sharp.mrc (#19) coordinates:
Matrix rotation and translation
0.99999500 0.00239001 0.00207238 -0.60674616
-0.00239146 0.99999689 0.00070090 0.14244066
-0.00207070 -0.00070585 0.99999761 0.40363617
Axis -0.21704908 0.63924101 -0.73774021
Axis point 79.27931343 260.84792943 -0.00000000
Rotation angle (degrees) 0.18567412
Shift along axis -0.07503103
> show #21/j atoms
> style stick
Changed 229983 atom styles
> select clear
> select #21/J:44
20 atoms, 21 bonds, 1 residue, 1 model selected
> view matrix models
> #21,0.99372,-0.10871,0.026365,13.992,0.10722,0.99284,0.052567,-20.988,-0.031891,-0.04941,0.99827,11.548
> select up
1288 atoms, 1444 bonds, 60 residues, 1 model selected
> fitmap #21 inMap #19
Fit molecule copy of postcleavage_HNH_center_refined.pdb (#21) to map
post_HNH_cent_sharp.mrc (#19) using 2605 atoms
average map value = 0.1752, steps = 2000
shifted from previous position = 4.3
rotated from previous position = 7.23 degrees
atoms outside contour = 1149, contour level = 0.01
Position of copy of postcleavage_HNH_center_refined.pdb (#21) relative to
post_HNH_cent_sharp.mrc (#19) coordinates:
Matrix rotation and translation
0.99998549 0.00368109 0.00393188 -1.30544186
-0.00367497 0.99999203 -0.00156309 0.73010434
-0.00393760 0.00154862 0.99999105 0.48740849
Axis 0.27751762 0.70184056 -0.65605168
Axis point 94.79211019 0.00000000 320.39166369
Rotation angle (degrees) 0.32121992
Shift along axis -0.16963143
> view matrix models
> #21,0.95316,-0.16312,0.2547,-4.7007,0.14,0.98441,0.10651,-33.244,-0.2681,-0.065869,0.96114,54.875
> fitmap #21 inMap #19
Fit molecule copy of postcleavage_HNH_center_refined.pdb (#21) to map
post_HNH_cent_sharp.mrc (#19) using 2605 atoms
average map value = 0.1731, steps = 2000
shifted from previous position = 0.932
rotated from previous position = 18.4 degrees
atoms outside contour = 1177, contour level = 0.01
Position of copy of postcleavage_HNH_center_refined.pdb (#21) relative to
post_HNH_cent_sharp.mrc (#19) coordinates:
Matrix rotation and translation
0.99994904 -0.00778267 -0.00643051 1.98761314
0.00779564 0.99996762 0.00199459 -1.51674316
0.00641478 -0.00204462 0.99997733 -0.91523181
Axis -0.19616124 -0.62382235 0.75654904
Axis point 206.49736911 250.60632995 0.00000000
Rotation angle (degrees) 0.58990690
Shift along axis -0.13613214
> view matrix models
> #21,0.99995,-0.0077827,-0.0064305,3.3447,0.0077956,0.99997,0.0019946,-2.7803,0.0064148,-0.0020446,0.99998,0.39857
> fitmap #21 inMap #19
Fit molecule copy of postcleavage_HNH_center_refined.pdb (#21) to map
post_HNH_cent_sharp.mrc (#19) using 2605 atoms
average map value = 0.1778, steps = 2000
shifted from previous position = 1.77
rotated from previous position = 0.414 degrees
atoms outside contour = 1144, contour level = 0.01
Position of copy of postcleavage_HNH_center_refined.pdb (#21) relative to
post_HNH_cent_sharp.mrc (#19) coordinates:
Matrix rotation and translation
0.99999337 -0.00330202 -0.00153324 0.70289684
0.00330074 0.99999420 -0.00083994 -0.52418630
0.00153600 0.00083487 0.99999847 -0.38974171
Axis 0.22416395 -0.41079927 0.88373892
Axis point 155.63582398 210.62363526 0.00000000
Rotation angle (degrees) 0.21403999
Shift along axis 0.02846957
> delete #21/j:1-41
> fitmap #21 inMap #19
Fit molecule copy of postcleavage_HNH_center_refined.pdb (#21) to map
post_HNH_cent_sharp.mrc (#19) using 1727 atoms
average map value = 0.02377, steps = 68
shifted from previous position = 0.607
rotated from previous position = 0.441 degrees
atoms outside contour = 1066, contour level = 0.01
Position of copy of postcleavage_HNH_center_refined.pdb (#21) relative to
post_HNH_cent_sharp.mrc (#19) coordinates:
Matrix rotation and translation
0.99996474 -0.00055599 -0.00837886 1.69415235
0.00053058 0.99999525 -0.00303455 0.64823116
0.00838051 0.00303000 0.99996029 -1.81624530
Axis 0.33963693 -0.93858608 0.06085174
Axis point 216.66154710 0.00000000 207.10057130
Rotation angle (degrees) 0.51154276
Shift along axis -0.14354572
> view matrix models
> #21,0.95152,0.063441,0.30097,-58.133,0.017073,0.9661,-0.25762,48.854,-0.30711,0.25027,0.91818,-0.5168
> fitmap #21 inMap #19
Fit molecule copy of postcleavage_HNH_center_refined.pdb (#21) to map
post_HNH_cent_sharp.mrc (#19) using 1727 atoms
average map value = 0.01942, steps = 92
shifted from previous position = 1.42
rotated from previous position = 9.42 degrees
atoms outside contour = 1173, contour level = 0.01
Position of copy of postcleavage_HNH_center_refined.pdb (#21) relative to
post_HNH_cent_sharp.mrc (#19) coordinates:
Matrix rotation and translation
0.97435965 -0.00668895 0.22489671 -33.93326133
0.03560741 0.99154562 -0.12477740 17.25587377
-0.22216072 0.12958605 0.96636022 5.49530082
Axis 0.49286534 0.86623732 0.08195521
Axis point 2.77043250 0.00000000 148.29261146
Rotation angle (degrees) 14.95412576
Shift along axis -1.32647815
> view matrix models
> #21,0.90553,-0.2837,0.31547,16.944,0.29673,0.95494,0.0070231,-29.813,-0.30325,0.08725,0.94891,27.343
> fitmap #21 inMap #19
Fit molecule copy of postcleavage_HNH_center_refined.pdb (#21) to map
post_HNH_cent_sharp.mrc (#19) using 1727 atoms
average map value = 0.01933, steps = 104
shifted from previous position = 2.05
rotated from previous position = 9.43 degrees
atoms outside contour = 1170, contour level = 0.01
Position of copy of postcleavage_HNH_center_refined.pdb (#21) relative to
post_HNH_cent_sharp.mrc (#19) coordinates:
Matrix rotation and translation
0.94411256 -0.12450182 0.30520610 -21.00938346
0.14744888 0.98763632 -0.05322902 -8.92619050
-0.29480552 0.09525648 0.95079751 24.92749364
Axis 0.21988344 0.88852194 0.40271582
Axis point 74.52306659 0.00000000 80.67313058
Rotation angle (degrees) 19.73351564
Shift along axis -2.51203568
> view matrix models
> #21,0.94411,-0.1245,0.30521,-17.873,0.14745,0.98764,-0.053229,-5.6643,-0.29481,0.095256,0.9508,23.681
> fitmap #21 inMap #19
Fit molecule copy of postcleavage_HNH_center_refined.pdb (#21) to map
post_HNH_cent_sharp.mrc (#19) using 1727 atoms
average map value = 0.01942, steps = 156
shifted from previous position = 3.04
rotated from previous position = 8.27 degrees
atoms outside contour = 1166, contour level = 0.01
Position of copy of postcleavage_HNH_center_refined.pdb (#21) relative to
post_HNH_cent_sharp.mrc (#19) coordinates:
Matrix rotation and translation
0.97438343 -0.01578899 0.22433822 -31.97489437
0.04417306 0.99153739 -0.12207515 15.64761333
-0.22051229 0.12885771 0.96683505 5.34685589
Axis 0.48795736 0.86504446 0.11660060
Axis point 3.97780903 0.00000000 139.84528015
Rotation angle (degrees) 14.89958612
Shift along axis -1.44305704
> view matrix models
> #21,0.97881,0.079073,-0.18889,14.498,-0.093393,0.99329,-0.068145,23.787,0.18223,0.084342,0.97963,-36.826
> fitmap #21 inMap #19
Fit molecule copy of postcleavage_HNH_center_refined.pdb (#21) to map
post_HNH_cent_sharp.mrc (#19) using 1727 atoms
average map value = 0.02378, steps = 112
shifted from previous position = 4.26
rotated from previous position = 12.1 degrees
atoms outside contour = 1061, contour level = 0.01
Position of copy of postcleavage_HNH_center_refined.pdb (#21) relative to
post_HNH_cent_sharp.mrc (#19) coordinates:
Matrix rotation and translation
0.99995850 -0.00058011 -0.00909169 1.82468704
0.00055786 0.99999684 -0.00244989 0.54145676
0.00909308 0.00244471 0.99995567 -1.79847577
Axis 0.25943577 -0.96387493 0.06031750
Axis point 197.73964432 0.00000000 204.27550886
Rotation angle (degrees) 0.54048814
Shift along axis -0.15698708
> select clear
> select #21/J:50
20 atoms, 21 bonds, 1 residue, 1 model selected
> view matrix models
> #21,0.96924,-0.18193,0.16576,13.795,0.16697,0.98085,0.10023,-33.405,-0.18082,-0.069465,0.98106,39.844
> fitmap #21 inMap #19
Fit molecule copy of postcleavage_HNH_center_refined.pdb (#21) to map
post_HNH_cent_sharp.mrc (#19) using 1727 atoms
average map value = 0.02378, steps = 120
shifted from previous position = 0.698
rotated from previous position = 15.5 degrees
atoms outside contour = 1064, contour level = 0.01
Position of copy of postcleavage_HNH_center_refined.pdb (#21) relative to
post_HNH_cent_sharp.mrc (#19) coordinates:
Matrix rotation and translation
0.99996372 -0.00034050 -0.00851103 1.66866582
0.00031330 0.99999484 -0.00319750 0.69973282
0.00851207 0.00319472 0.99995867 -1.87660250
Axis 0.35130930 -0.93556970 0.03593210
Axis point 220.86482619 0.00000000 200.72582758
Rotation angle (degrees) 0.52126798
Shift along axis -0.13586127
> show #!20 models
> hide #!20 models
> show #!20 models
> view matrix models
> #21,0.94284,-0.16526,0.28937,-7.4067,0.16063,0.98621,0.039865,-23.627,-0.29196,0.0088937,0.95639,41.501
> fitmap #21 inMap #19
Fit molecule copy of postcleavage_HNH_center_refined.pdb (#21) to map
post_HNH_cent_sharp.mrc (#19) using 1727 atoms
average map value = 0.02377, steps = 140
shifted from previous position = 0.641
rotated from previous position = 19.9 degrees
atoms outside contour = 1065, contour level = 0.01
Position of copy of postcleavage_HNH_center_refined.pdb (#21) relative to
post_HNH_cent_sharp.mrc (#19) coordinates:
Matrix rotation and translation
0.99996409 -0.00060556 -0.00845233 1.72034129
0.00057980 0.99999518 -0.00304995 0.64758353
0.00845413 0.00304494 0.99995963 -1.83001040
Axis 0.33840585 -0.93869583 0.06581501
Axis point 216.32111144 0.00000000 208.46719481
Rotation angle (degrees) 0.51597228
Shift along axis -0.14615257
> hide #!20 models
> delete #21/i:107-118
> fitmap #21 inMap #19
Fit molecule copy of postcleavage_HNH_center_refined.pdb (#21) to map
post_HNH_cent_sharp.mrc (#19) using 1617 atoms
average map value = 0.025, steps = 44
shifted from previous position = 0.0515
rotated from previous position = 0.51 degrees
atoms outside contour = 976, contour level = 0.01
Position of copy of postcleavage_HNH_center_refined.pdb (#21) relative to
post_HNH_cent_sharp.mrc (#19) coordinates:
Matrix rotation and translation
0.99991658 -0.00665991 -0.01106673 3.46514203
0.00669212 0.99997347 0.00287541 -1.15618478
0.01104728 -0.00294923 0.99993463 -0.94027532
Axis -0.21995713 -0.83509609 0.50421561
Axis point 74.57354161 0.00000000 307.17000003
Rotation angle (degrees) 0.75864102
Shift along axis -0.27075880
> view matrix models
> #21,0.9761,-0.050009,0.2115,-22.223,0.037779,0.99739,0.061477,-14.46,-0.21402,-0.052017,0.97544,41.647
> fitmap #21 inMap #19
Fit molecule copy of postcleavage_HNH_center_refined.pdb (#21) to map
post_HNH_cent_sharp.mrc (#19) using 1617 atoms
average map value = 0.025, steps = 112
shifted from previous position = 0.714
rotated from previous position = 13.5 degrees
atoms outside contour = 978, contour level = 0.01
Position of copy of postcleavage_HNH_center_refined.pdb (#21) relative to
post_HNH_cent_sharp.mrc (#19) coordinates:
Matrix rotation and translation
0.99991534 -0.00691325 -0.01102344 3.51324748
0.00694686 0.99997133 0.00301354 -1.20471924
0.01100229 -0.00308986 0.99993470 -0.89660439
Axis -0.22833637 -0.82401113 0.51852498
Axis point 70.41448246 0.00000000 312.48223472
Rotation angle (degrees) 0.76577763
Shift along axis -0.27441187
> hide #!21 models
> hide #!19 models
> show #!19 models
> show #!18 models
> hide #!18 models
> show #!17 models
> hide #!17 models
> show #!17 models
> hide #!19 models
> show #!18 models
> hide #!18 models
> hide #!17 models
> show #!16 models
> hide #!16 models
> show #!14 models
> select add #14
20 atoms, 21 bonds, 1 residue, 3 models selected
> transparency sel 0
> select clear
> show #!13 models
> hide #!14 models
> show #!14 models
> hide #!14 models
> show #!14 models
> hide #!14 models
> show #!14 models
> hide #!14 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> show #!13 models
> hide #!4 models
> lighting soft
> show #!14 models
> hide #!13 models
> show #!13 models
> hide #!14 models
> show #!14 models
> hide #!13 models
> show #!13 models
> hide #!14 models
> show #!14 models
> hide #!14 models
> show #!14 models
> hide #!13 models
> show #!13 models
> hide #!14 models
> hide #!13 models
> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/figures/chimera_session.cxs"
——— End of log from Wed Mar 26 12:19:53 2025 ———
opened ChimeraX session
> show #!13 models
> ui tool show "Color Actions"
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> color #13 navajo white
> show #!12 models
> transparency #13.1 50
> lighting simple
> lighting full
> lighting soft
> lighting simple
> lighting soft
> lighting simple
> lighting soft
> lighting simple
> view
> lighting soft
> lighting simple
> hide #12/l,k cartoons
> show #12/k:39-40
> show #12/l:6-7
> show #12/l:6-8
> hide #12/l:6 atoms
> show #12/a:83,85 atoms
> color #12/a:83,85 byhetero
> ui tool show "Side View"
> show #12/l:6-7
> hide #12/l:8 atoms
> hide #12/k:39 atoms
> show #12/k:41 atoms
> hide #!13 models
> show #11 models
> ui tool show Distances
> select #12/A:85@NZ
1 atom, 1 residue, 1 model selected
> select add #12/A:83@OD1
2 atoms, 2 residues, 1 model selected
> distance #12/A:85@NZ #12/A:83@OD1
Distance between halfcleaved_HNH_center_main_model_temp.pdb #12/A LYS 85 NZ
and ASP 83 OD1: 2.939Å
> select #12/A:85@NZ
1 atom, 1 residue, 1 model selected
> select add #12/K:41@O2
2 atoms, 2 residues, 1 model selected
> distance #12/A:85@NZ #12/K:41@O2
Distance between halfcleaved_HNH_center_main_model_temp.pdb #12/A LYS 85 NZ
and /K DC 41 O2: 3.020Å
> select #12/A:85@NZ
1 atom, 1 residue, 1 model selected
> select add #12/L:6@N2
2 atoms, 2 residues, 1 model selected
> distance #12/A:85@NZ #12/L:6@N2
Distance between halfcleaved_HNH_center_main_model_temp.pdb #12/A LYS 85 NZ
and /L DG 6 N2: 3.258Å
> select #12/K:40@N2
1 atom, 1 residue, 1 model selected
> select add #12/A:83@OD1
2 atoms, 2 residues, 1 model selected
> distance #12/K:40@N2 #12/A:83@OD1
Distance between halfcleaved_HNH_center_main_model_temp.pdb #12/K DG 40 N2 and
/A ASP 83 OD1: 3.013Å
> select add #11
2 atoms, 4 pseudobonds, 2 residues, 3 models selected
> color sel dim gray
> select clear
> show #!13 models
> hide #11.1 models
> lighting soft
> lighting full
> lighting simple
> color #12/a byhetero
> surface zone #13 nearAtoms #12/a,k,l
> surface zone #13 nearAtoms #12/a,k,l distance 10
> surface zone #13 nearAtoms #12/a,k,l distance 5
> surface zone #13 nearAtoms #12/a,k,l distance 10
> surface zone #13 nearAtoms #12/a:1-90 #12/k:39-46 #12/l:1-8 distance 10
> surface zone #13 nearAtoms #12/a:1-90 #12/k:39-46 #12/l:1-8 distance 5
> hide #12/b,c cartoons
> hide #12/b,c,d cartoons
> lighting soft
> lighting simple
> lighting full
> lighting simple
> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/figures/structure/PAM/PAM_sharp.tif" width 1984 height
> 1210 supersample 3
> hide #!13 models
> show #!13 models
> hide #!13 models
> show #!13 models
> show #12 cartoons
> show #12/j,k,l atoms
> select #12
24113 atoms, 24865 bonds, 7 pseudobonds, 2801 residues, 3 models selected
> nucleotides sel ladder
> select clear
> hide #12 cartoons
> show #12 cartoons
> surface zone #13 nearAtoms #12 distance 10
> surface dust #13 size 7.25
> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/figures/structure/PAM/PAM_sharp_zoom_out.tif" width 1984
> height 1210 supersample 3
> hide #!13 models
> hide #!12 models
> show #!12 models
> show #!13 models
> hide #12/l,k,j cartoons
> nucleotides #!12 atoms
> style nucleic & #!12 stick
Changed 2368 atom styles
> nucleotides #!12 fill
> style nucleic & #!12 stick
Changed 2368 atom styles
> nucleotides #!12 tube/slab shape ellipsoid
> nucleotides #!12 tube/slab shape box
> nucleotides #!12 slab
> style nucleic & #!12 stick
Changed 2368 atom styles
> nucleotides #!12 fill
> style nucleic & #!12 stick
Changed 2368 atom styles
> nucleotides #!12 atoms
> style nucleic & #!12 stick
Changed 2368 atom styles
> nucleotides #!12 fill
> style nucleic & #!12 stick
Changed 2368 atom styles
> nucleotides #!12 atoms
> style nucleic & #!12 stick
Changed 2368 atom styles
> nucleotides #!12 atoms
> style nucleic & #!12 stick
Changed 2368 atom styles
> nucleotides #!12 fill
> style nucleic & #!12 stick
Changed 2368 atom styles
> nucleotides #!12 atoms
> style nucleic & #!12 stick
Changed 2368 atom styles
> lighting soft
> lighting simple
> hide #12/a:83,85 atoms
> hide #!13 models
> select #12/A:178
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #12/A:193
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #12/A:192
14 atoms, 12 bonds, 2 residues, 1 model selected
> select add #12/A:191
20 atoms, 17 bonds, 3 residues, 1 model selected
> select add #12/A:178
32 atoms, 29 bonds, 4 residues, 1 model selected
> show sel atoms
> show #!13 models
> hide #!13 models
> select #12/A:191@OG
1 atom, 1 residue, 1 model selected
> select add #12/K:39@OP1
2 atoms, 2 residues, 1 model selected
> distance #12/A:191@OG #12/K:39@OP1
Distance between halfcleaved_HNH_center_main_model_temp.pdb #12/A SER 191 OG
and /K DC 39 OP1: 2.884Å
> select #12/A:193@OD1
1 atom, 1 residue, 1 model selected
> select add #12/L:9@N2
2 atoms, 2 residues, 1 model selected
> distance #12/A:193@OD1 #12/L:9@N2
Distance between halfcleaved_HNH_center_main_model_temp.pdb #12/A ASN 193 OD1
and /L DG 9 N2: 2.565Å
> show #!14 models
> hide #!14 models
> show #!13 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> select #12/A:205
9 atoms, 8 bonds, 1 residue, 1 model selected
> show #12/a:205 atoms
> show #!13 models
> hide #12/a:205 atoms
> color zone #13 near #12 distance 10
> color #12/L light gray
> color #12/K dim gray
> color #12/J dark red
> color #12/I rebecca purple
> color #12/B forest green
> color #12/C,D,E,F,G,H khaki
> color #12/A steel blue
> color #12/A:232-350 dark turquoise
> color zone #13 near #12 distance 10
> color #12 dim gray
> volume #!13 style image
> volume #!13 style surface
> transparency #13.1 0
> transparency #13.1 50
> color #12 white
[Repeated 1 time(s)]
> color #12 black
> color #12 gray
> color #12 dim gray
> color #12 light gray
> color #12 dim gray
> color #12 red
> orange
Unknown command: orange
> color #12 orange
> color #12/DA light gray
> color #12/EA dim gray
> color #12/FA dark red
> color #12/Ca rebecca purple
> color #12/Ba forest green
> color #12/Da,Db,Dc,Dd,De,Df khaki
> color #12/Aa steel blue
> color #12/Aa:232-350 dark turquoise
> color zone #13 near #12 distance 10
> color #13 navajo white
> transparency #13.1 50
> color #12/DA light gray
> color #12/EA dim gray
> color #12/FA dark red
> color #12/Ca rebecca purple
> color #12/Ba forest green
> color #12/Da,Db,Dc,Dd,De,Df khaki
> color #12/Aa steel blue
> color #12/Aa:232-350 dark turquoise
> color zone #13 near #12 distance 10
> color #13 navajo white
> transparency #13 50
> color #12/DA light gray
> color #12/EA dim gray
> color #12/FA dark red
> color #12/Ca rebecca purple
> color #12/Ba forest green
> color #12/Da,Db,Dc,Dd,De,Df khaki
> color #12/Aa steel blue
> color #12/Aa:232-350 dark turquoise
> color zone #13 near #12 distance 10
> color #12 dim gray
> transparency #13 50
> color #12/DA light gray
> color #12/EA dim gray
> color #12/FA dark red
> color #12/Ca rebecca purple
> color #12/Ba forest green
> color #12/Da,Db,Dc,Dd,De,Df khaki
> color #12/Aa steel blue
> color #12/Aa:232-350 dark turquoise
> color zone #13 near #12 distance 10
> color #12/L light gray
> color #12/K dim gray
> color #12/J dark red
> color #12/I rebecca purple
> color #12/B forest green
> color #12/C,D,E,F,G,H khaki
> color #12/A steel blue
> color #12/A:232-350 dark turquoise
> color zone #13 near #12 distance 10
> color #12 dim gray
> transparency #13 50
> color #12/L light gray
> color #12/K dim gray
> color #12/J dark red
> color #12/I rebecca purple
> color #12/B forest green
> color #12/C,D,E,F,G,H khaki
> color #12/A steel blue
> color #12/A:232-350 dark turquoise
> color #13 navajo white
> transparency #13 50
> color #12/L light gray
> color #12/K dim gray
> color #12/J dark red
> color #12/I rebecca purple
> color #12/B forest green
> color #12/C,D,E,F,G,H khaki
> color #12/A steel blue
> color #12/A:232-350 dark turquoise
> color zone #13 near #12 distance 10
> color #12 dim gray
> transparency #13 50
> color #12/L light gray
> color #12/K dim gray
> color #12/J dark red
> color #12/I rebecca purple
> color #12/B forest green
> color #12/C,D,E,F,G,H khaki
> color #12/A steel blue
> color #12/A:232-350 dark turquoise
> color #13 navajo white
> transparency #13 50
> color #12/L light gray
> color #12/K dim gray
> color #12/J dark red
> color #12/I rebecca purple
> color #12/B forest green
> color #12/C,D,E,F,G,H khaki
> color #12/A steel blue
> color #12/A:232-350 dark turquoise
> color zone #13 near #12 distance 10
> color #12 dim gray
> transparency #13 50
> color #12 rosy brown
> color #12 orange
> color #12 sienna
> color #12/L light gray
> color #12/K dim gray
> color #12/J dark red
> color #12/I rebecca purple
> color #12/B forest green
> color #12/C,D,E,F,G,H khaki
> color #12/A steel blue
> color #12/A:232-350 dark turquoise
> color zone #13 near #12 distance 10
> color #12 sienna
> transparency #13 50
> color #12/L light gray
> color #12/K dim gray
> color #12/J dark red
> color #12/I rebecca purple
> color #12/B forest green
> color #12/C,D,E,F,G,H khaki
> color #12/A steel blue
> color #12/A:232-350 dark turquoise
> color #13 navajo white
> transparency #13 50
> color #12/L light gray
> color #12/K dim gray
> color #12/J dark red
> color #12/I rebecca purple
> color #12/B forest green
> color #12/C,D,E,F,G,H khaki
> color #12/A steel blue
> color #12/A:232-350 dark turquoise
> color zone #13 near #12 distance 10
> color #12 sienna
> transparency #13 50
> color #12/L light gray
> color #12/K dim gray
> color #12/J dark red
> color #12/I rebecca purple
> color #12/B forest green
> color #12/C,D,E,F,G,H khaki
> color #12/A steel blue
> color #12/A:232-350 dark turquoise
> color #13 navajo white
> transparency #13 50
> select clear
> color #12/L light gray
> color #12/K dim gray
> color #12/J dark red
> color #12/I rebecca purple
> color #12/B forest green
> color #12/C,D,E,F,G,H khaki
> color #12/A steel blue
> color #12/A:232-350 dark turquoise
> color zone #13 near #12 distance 10
> color #12 sienna
> transparency #13 50
> color #12/L light gray
> color #12/K dim gray
> color #12/J dark red
> color #12/I rebecca purple
> color #12/B forest green
> color #12/C,D,E,F,G,H khaki
> color #12/A steel blue
> color #12/A:232-350 dark turquoise
> color zone #13 near #12 distance 10
> color #12 peru
> transparency #13 50
> color #12/L light gray
> color #12/K dim gray
> color #12/J dark red
> color #12/I rebecca purple
> color #12/B forest green
> color #12/C,D,E,F,G,H khaki
> color #12/A steel blue
> color #12/A:232-350 dark turquoise
> color zone #13 near #12 distance 10
> color #12 khaki
> transparency #13 50
> color #12/L light gray
> color #12/K dim gray
> color #12/J dark red
> color #12/I rebecca purple
> color #12/B forest green
> color #12/C,D,E,F,G,H khaki
> color #12/A steel blue
> color #12/A:232-350 dark turquoise
> color zone #13 near #12 distance 10
> color #12 violet
> transparency #13 50
> color #12/L light gray
> color #12/K dim gray
> color #12/J dark red
> color #12/I rebecca purple
> color #12/B forest green
> color #12/C,D,E,F,G,H khaki
> color #12/A steel blue
> color #12/A:232-350 dark turquoise
> color zone #13 near #12 distance 10
> color #12 alice blue
> transparency #13 50
> select #12
24113 atoms, 24865 bonds, 9 pseudobonds, 2801 residues, 3 models selected
> color sel violet
> select subtract #12
Nothing selected
> select add #12
24113 atoms, 24865 bonds, 9 pseudobonds, 2801 residues, 3 models selected
> select subtract #12
Nothing selected
> select add #12
24113 atoms, 24865 bonds, 9 pseudobonds, 2801 residues, 3 models selected
> select subtract #12
Nothing selected
> select add #12
24113 atoms, 24865 bonds, 9 pseudobonds, 2801 residues, 3 models selected
> color sel lemon chiffon
> color sel light coral
> color sel burly wood
> color sel pale green
> color sel gray
> select clear
> color #12/L light gray
> color #12/K dim gray
> color #12/J dark red
> color #12/I rebecca purple
> color #12/B forest green
> color #12/C,D,E,F,G,H khaki
> color #12/A steel blue
> color #12/A:232-350 dark turquoise
> color #12/o blue
> color zone #13 near #12/o distance 1
> surface dust #13 size 7.25
> surface dust #13 size 0
> transparency #13 50
> color zone #13 near #12
> color zone #13 near #12 distance 10
> transparency #13 50
> surface dust #13 size 7.25
> color #12 byhetero
> color #12/L light gray
> color #12/K dim gray
> color #12/J dark red
> color #12/I rebecca purple
> color #12/B forest green
> color #12/C,D,E,F,G,H khaki
> color #12/A steel blue
> color #12/A:232-350 dark turquoise
> color #12/a byhetero
> hide #12/a:192 atoms
> select add #11
6 pseudobonds, 2 models selected
> color sel white
> select clear
> select add #11
6 pseudobonds, 2 models selected
> color sel yellow
> color sel dark orange
> select clear
> select add #11
6 pseudobonds, 2 models selected
> color sel orange red
> select clear
> hide #12/j atoms
> hide #12/c,d,e,f,g,h,i cartoons
> color #12 red
> color #12 blue
> color #12 green
> color #12 cyan
> select clear
> color #12/a byhetero
> select clear
> select add #11
6 pseudobonds, 2 models selected
> color sel dark red
> color sel red
> select clear
> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/figures/structure/PAM/sideview_with_unwinding_shar_colormap.tif"
> width 1984 height 1210 supersample 3
> hide #12 atoms
> show #12/k:39,40 atoms
> show #12/l:7-8 atoms
> select #13
3 models selected
> select clear
> show #12/a:83,85 atoms
> show #12/k:40-41 atoms
> show #12/l:6 atoms
> hide #12/k:39 #12/l:8 atoms
> select clear
> hide #12 cartoons
> show #12/a:32-86 cartoons
> lighting soft
> lighting simple
> lighting full
> lighting simple
> lighting full
> lighting simple
> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/figures/structure/PAM/PAM_sharp_colormap.tif" width 1984
> height 1210 supersample 3
> view
> show #12 cartoons
> select clear
> color #12/L light gray
> color #12/K dim gray
> color #12/J dark red
> color #12/I rebecca purple
> color #12/B forest green
> color #12/C,D,E,F,G,H khaki
> color #12/A steel blue
> color #12/A:232-350 dark turquoise
> hide #!11 models
> hide #!13 models
> lighting soft
> lighting simple
> lighting full
> lighting soft
> lighting simple
> lighting soft
> lighting simple
> lighting soft
> lighting simple
> lighting soft
> lighting simple
> show #!13 models
> lighting soft
> lighting simple
> lighting soft
> lighting simple
> lighting soft
> lighting simple
[Repeated 1 time(s)]
> lighting soft
> lighting simple
> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/figures/structure/PAM/PAM_sharp_zoom_out_colormap.tif"
> width 1984 height 1210 supersample 3
> color #12/m,o turquoise
> color zone #13 near #12 distance 10
> surface dust #13 size 0
> color zone #13 near #12 distance 10
> color #12/o blue
> color zone #13 near #12 distance 1
> color zone #13 near #12 distance 10
> color #12/o blue
> color zone #13 near #12/o distance 1
> color blue zon #13 nea #12/o
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> select #13 & zon 5 #12
Expected a keyword
> zone #13 within 5 of #12
Expected a keyword
> select zone #13 nea #12 dis 5
Missing or invalid "range" argument: Expected a number
> zone #13 nea #12 dis 5
Expected a keyword
> zone #13 nea #12 dis 5
Expected a keyword
> color zone #13 near #12 distance 5
> split map #13
Expected a structures specifier or a keyword
> volume copy #13
Opened halfcleaved_HNH_center_sharp3Å.mrc copy as #22, grid size 420,420,420,
pixel 0.725, shown at step 1, values float32
> show #!13 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> hide #!22 models
> show #!22 models
> color #22 nea #12 dis 5
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color zone #22 near #12 distance 5
> split map #22 nea #12
Expected a structures specifier or a keyword
> color zone #13 near #12 distance 5 split map
Expected a keyword
> split map zon #22 nea #12 dis 5
Expected a structures specifier or a keyword
> ui tool show "Color Zone"
> volume splitbyzone #22
Opened halfcleaved_HNH_center_sharp3Å.mrc copy 0 as #23.1, grid size
420,420,420, pixel 0.725, shown at level 0.02, step 1, values float32
Opened halfcleaved_HNH_center_sharp3Å.mrc copy 1 as #23.2, grid size
420,420,420, pixel 0.725, shown at level 0.02, step 1, values float32
Opened halfcleaved_HNH_center_sharp3Å.mrc copy 2 as #23.3, grid size
420,420,420, pixel 0.725, shown at level 0.02, step 1, values float32
Opened halfcleaved_HNH_center_sharp3Å.mrc copy 3 as #23.4, grid size
420,420,420, pixel 0.725, shown at level 0.02, step 1, values float32
Opened halfcleaved_HNH_center_sharp3Å.mrc copy 4 as #23.5, grid size
420,420,420, pixel 0.725, shown at level 0.02, step 1, values float32
Opened halfcleaved_HNH_center_sharp3Å.mrc copy 5 as #23.6, grid size
420,420,420, pixel 0.725, shown at level 0.02, step 1, values float32
Opened halfcleaved_HNH_center_sharp3Å.mrc copy 6 as #23.7, grid size
420,420,420, pixel 0.725, shown at level 0.02, step 1, values float32
Opened halfcleaved_HNH_center_sharp3Å.mrc copy 7 as #23.8, grid size
420,420,420, pixel 0.725, shown at level 0.02, step 1, values float32
Opened halfcleaved_HNH_center_sharp3Å.mrc copy 8 as #23.9, grid size
420,420,420, pixel 0.725, shown at level 0.02, step 1, values float32
Opened halfcleaved_HNH_center_sharp3Å.mrc copy 9 as #23.10, grid size
420,420,420, pixel 0.725, shown at level 0.02, step 1, values float32
Opened halfcleaved_HNH_center_sharp3Å.mrc copy 10 as #23.11, grid size
420,420,420, pixel 0.725, shown at level 0.02, step 1, values float32
> show #!22 models
> hide #!22 models
> hide #!23 models
> show #!23 models
> hide #!23.1 models
> show #!23.1 models
> hide #!23.1 models
> show #!23.1 models
> hide #!23.2 models
> show #!23.2 models
> hide #!23.2 models
> show #!23.2 models
> hide #!23.2 models
> show #!23.2 models
> hide #!23.1 models
> show #!23.1 models
> hide #!23.1 models
> hide #!23.3 models
> show #!23.3 models
> hide #!12 models
> hide #!23.11 models
> show #!23.11 models
> hide #!23.11 models
> show #!23.11 models
> hide #!23.10 models
> show #!23.10 models
> hide #!23.10 models
> show #!23.10 models
> select add #23.10
2 models selected
> color sel turquoise
> select subtract #23.10
Nothing selected
> hide #!23.9 models
> show #!23.9 models
> hide #!23.9 models
> show #!23.9 models
> hide #!23.9 models
> show #!23.9 models
> hide #!23.8 models
> show #!23.8 models
> hide #!23.8 models
> show #!23.8 models
> show #!23.1 models
> hide #!23.1 models
> show #!23.1 models
> hide #!23 models
> show #!23 models
> hide #!23.1 models
> show #!23.1 models
> hide #!23.1 models
> show #!23.1 models
> hide #!23.1 models
> show #!23.1 models
> hide #!23.1 models
> show #!23.1 models
> hide #!23.1 models
> hide #!23.2 models
> hide #!23.3 models
> hide #!23.4 models
> hide #!23.5 models
> hide #!23.6 models
> hide #!23.9 models
> show #!23.9 models
> hide #!23.8 models
> show #!23.8 models
> hide #!23.8 models
> show #!23.8 models
> show #!23.6 models
> show #!23.5 models
> show #!23.4 models
> show #!23.3 models
> show #!23.2 models
> show #!23.1 models
> show #!22 models
> show #!21 models
> show #!20 models
> show #!19 models
> show #!18 models
> hide #!18 models
> hide #!19 models
> hide #!20 models
> hide #!21 models
> hide #!22 models
> close #22
> hide #!23.1 models
> show #!23.1 models
> hide #!23.1 models
> show #!23.1 models
> close #23
> color zone #13 near #12
> show #!13 models
> color zone #13 near #12 distance 4
> color zone #13 near #12 distance 4.25
> color zone #13 near #12 distance 5
> volume splitbyzone #13
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 10 as #22.11, grid size
420,420,420, pixel 0.725, shown at level 0.02, step 1, values float32
> hide #!22 models
> show #!22 models
> hide #!22.1 models
> show #!22.1 models
> hide #!22.1 models
> view
> hide #!22.2 models
> show #!22.2 models
> hide #!22.2 models
> hide #!22.3 models
> hide #!22.8 models
> hide #!22.10 models
> show #!22.10 models
> hide #!22.10 models
> show #!22.10 models
> select add #22.10
2 models selected
> color sel turquoise
> select subtract #22.10
Nothing selected
> select #22.10
2 models selected
> color sel dark turquoise
> select clear
> show #!22.8 models
> hide #!22.8 models
> show #!22.8 models
> hide #!22.8 models
> show #!22.8 models
> hide #!22.8 models
> show #!22.8 models
> hide #!22.4 models
> show #!22.4 models
> hide #!22.4 models
> show #!22.4 models
> hide #!22.4 models
> show #!22.4 models
> hide #!22.4 models
> show #!22.4 models
> hide #!22.4 models
> show #!22.4 models
> hide #!22.4 models
> show #!22.4 models
> hide #!22.4 models
> show #!22.4 models
> hide #!22.4 models
> show #!22.4 models
> hide #!22.4 models
> show #!22.4 models
> hide #!22.4 models
> show #!22.4 models
> hide #!22.4 models
> show #!22.4 models
> hide #!22.4 models
> show #!22.4 models
> hide #!22.4 models
> show #!22.4 models
> hide #!22.4 models
> show #!22.4 models
> show #!22.3 models
> lighting soft
> lighting simple
> show #!22.2 models
> hide #!22.2 models
> show #!22.2 models
> hide #!22.2 models
> show #!22.2 models
> volume #22.1-11 hide
> volume #22.2 show
> show #!22.3 models
> show #!22.1 models
> hide #!22.1 models
> show #!22.4 models
> show #!22.5 models
> show #!22.6 models
> show #!22.9 models
> show #!22.7 models
> hide #!22.7 models
> show #!22.8 models
> show #!22.7 models
> show #!22.10 models
> show #!22.11 models
> hide #!22.8 models
> show #!22.8 models
> hide #!22.8 models
> show #!22.8 models
> hide #!22.8 models
> show #!22.8 models
> transparency #22 50
> show #!13 models
> hide #!13 models
> show #!12 models
> select #12/K:2
8 atoms, 8 bonds, 1 residue, 1 model selected
> select up
833 atoms, 926 bonds, 43 residues, 1 model selected
> select down
8 atoms, 8 bonds, 1 residue, 1 model selected
> hide #12/k:1-3 atoms
> hide #12/k:1-3 cartoons
> show #12/a:280,304-305,319,328 atoms
> color #12/a byhetero
> hide #!22.10 models
> show #!22.10 models
> hide #!22.10 models
> show #!22.10 models
> hide #!22.10 models
> show #!22.10 models
> hide #!22.10 models
> show #!22.10 models
> color #22.10 #ff2600ff models
> select add #22.10
8 atoms, 8 bonds, 1 residue, 3 models selected
> color sel dark turquoise
> select clear
> select add #22.10
2 models selected
> transparency sel 50
> select clear
> show #12/o,m atoms
> color #12/m red
> select clear
> volume #22 hide
> select #12/A:309
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel cartoons
> show sel atoms
> select #12/A:309@N
1 atom, 1 residue, 1 model selected
> select add #12/O:1@O
2 atoms, 2 residues, 1 model selected
> distance #12/A:309@N #12/O:1@O
Distance between halfcleaved_HNH_center_main_model_temp.pdb #12/A LEU 309 N
and /O HOH 1 O: 3.004Å
> distance #12/A:309@N #12/O:1@O
Distance already exists; modify distance properties with 'distance style'
> show #!11 models
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel atoms
> show sel cartoons
> select #12/O:1@O
1 atom, 1 residue, 1 model selected
> show #12/k:1-3 atoms
> select #12/K:2@O3'
1 atom, 1 residue, 1 model selected
> select add #12/K:2@C3'
2 atoms, 1 residue, 1 model selected
> select add #12/K:2@C2'
3 atoms, 1 residue, 1 model selected
> select add #12/K:2@C1'
4 atoms, 1 residue, 1 model selected
> select add #12/K:2@O4'
5 atoms, 1 residue, 1 model selected
> select add #12/K:2@C4'
6 atoms, 1 residue, 1 model selected
> select add #12/K:2@C5'
7 atoms, 1 residue, 1 model selected
> select add #12/K:2@O5'
8 atoms, 1 residue, 1 model selected
> hide sel atoms
> show sel atoms
> select subtract #12/K:2@O3'
7 atoms, 1 residue, 1 model selected
> select up
8 atoms, 8 bonds, 1 residue, 1 model selected
> select down
7 atoms, 1 residue, 1 model selected
> hide sel atoms
> select #12/K:2@O3'
1 atom, 1 residue, 1 model selected
> color sel dim gray
> select clear
> hide #12.1 models
> select #12/O:1@O
1 atom, 1 residue, 1 model selected
> select add #12/K:3@OP2
2 atoms, 2 residues, 1 model selected
> distance #12/O:1@O #12/K:3@OP2
Distance between halfcleaved_HNH_center_main_model_temp.pdb #12/O HOH 1 O and
/K DA 3 OP2: 2.868Å
> select #12/A:280@NH2
1 atom, 1 residue, 1 model selected
> select add #12/K:3@OP2
2 atoms, 2 residues, 1 model selected
> distance #12/A:280@NH2 #12/K:3@OP2
Distance between halfcleaved_HNH_center_main_model_temp.pdb #12/A ARG 280 NH2
and /K DA 3 OP2: 2.709Å
> select #12/K:3@OP1
1 atom, 1 residue, 1 model selected
> select add #12/M:2@MG
2 atoms, 2 residues, 1 model selected
> distance #12/K:3@OP1 #12/M:2@MG
Distance between halfcleaved_HNH_center_main_model_temp.pdb #12/K DA 3 OP1 and
/M MG 2 MG: 2.496Å
> select #12/A:328@NE2
1 atom, 1 residue, 1 model selected
> select add #12/M:2@MG
2 atoms, 2 residues, 1 model selected
> distance #12/A:328@NE2 #12/M:2@MG
Distance between halfcleaved_HNH_center_main_model_temp.pdb #12/A HIS 328 NE2
and /M MG 2 MG: 1.829Å
> select #12/M:2@MG
1 atom, 1 residue, 1 model selected
> select add #12/A:304@ND1
2 atoms, 2 residues, 1 model selected
> distance #12/M:2@MG #12/A:304@ND1
Distance between halfcleaved_HNH_center_main_model_temp.pdb #12/M MG 2 MG and
/A HIS 304 ND1: 2.331Å
> select #12/A:305@ND1
1 atom, 1 residue, 1 model selected
> select #12/K:3@OP2
1 atom, 1 residue, 1 model selected
Exactly two atoms must be selected!
> select add #12/A:305@ND1
2 atoms, 2 residues, 1 model selected
> distance #12/K:3@OP2 #12/A:305@ND1
Distance between halfcleaved_HNH_center_main_model_temp.pdb #12/K DA 3 OP2 and
/A HIS 305 ND1: 2.858Å
> select clear
> volume #22 show
> color #12/k byhetero
> select clear
> select add #11
13 pseudobonds, 2 models selected
> color sel orange red
> select clear
> hide #12/a cartoons
> show #12/a cartoons
> select #12/K:6
11 atoms, 11 bonds, 1 residue, 1 model selected
> select add #12/K:7
31 atoms, 32 bonds, 2 residues, 1 model selected
> hide sel cartoons
> select clear
> select #22.8
2 models selected
> select clear
> hide #!22.8 models
> show #!22.8 models
> hide #!22.8 models
> show #!22.8 models
> color zone #22.8 near #12/a distance 5
> color #12/a:232-350 dark turquoise
> color zone #22.8 near #12/a distance 5
> transparency
> #22.1.1#22.2.1#22.3.1#22.4.1#22.5.1#22.6.1#22.7.1#22.8.1#22.9.1#22.10.1#22.11.1
> 0
> transparency
> #22.1.1#22.2.1#22.3.1#22.4.1#22.5.1#22.6.1#22.7.1#22.8.1#22.9.1#22.10.1#22.11.1
> 50
> combine #12
> hide #!12 models
> hide #!22 models
> hide #!23 models
> show #!23 models
> select #23/K:2@O3'
1 atom, 1 residue, 1 model selected
> select up
8 atoms, 8 bonds, 1 residue, 1 model selected
> select up
833 atoms, 926 bonds, 43 residues, 1 model selected
> select down
8 atoms, 8 bonds, 1 residue, 1 model selected
> select down
1 atom, 1 residue, 1 model selected
> select clear
> close #23
> show #12 models
> show #12 cartoons
> select #12/K:2
8 atoms, 8 bonds, 1 residue, 1 model selected
> select up
833 atoms, 926 bonds, 43 residues, 1 model selected
> select down
8 atoms, 8 bonds, 1 residue, 1 model selected
> select add #12/K:3
12 atoms, 11 bonds, 2 residues, 1 model selected
> color darkred turqoise
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> color sel darkred turqoise
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> select clear
> select #12/K:2
8 atoms, 8 bonds, 1 residue, 1 model selected
> select add #12/K:3
12 atoms, 11 bonds, 2 residues, 1 model selected
> color sel dark turquoise
> select clear
> select #12/M:2@MG
1 atom, 1 residue, 1 model selected
> color sel darkred turqoise
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> select clear
> select #12/M:2@MG
1 atom, 1 residue, 1 model selected
> select down
1 atom, 1 residue, 1 model selected
> select down
1 atom, 1 residue, 1 model selected
> select down
1 atom, 1 residue, 1 model selected
> color sel dark turquoise
> select clear
> close #22
> color zone #13 near #12 distance 5
> volume splitbyzone #13
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 10 as #22.11, grid size
420,420,420, pixel 0.725, shown at level 0.02, step 1, values float32
Opened halfcleaved_HNH_center_sharp3Å.mrc 11 as #22.12, grid size
420,420,420, pixel 0.725, shown at level 0.02, step 1, values float32
Opened halfcleaved_HNH_center_sharp3Å.mrc 12 as #22.13, grid size
420,420,420, pixel 0.725, shown at level 0.02, step 1, values float32
Opened halfcleaved_HNH_center_sharp3Å.mrc 13 as #22.14, grid size
420,420,420, pixel 0.725, shown at level 0.02, step 1, values float32
> close #22
> color #12/L light gray
> color #12/K dim gray
> color #12/J dark red
> color #12/I rebecca purple
> color #12/B forest green
> color #12/C,D,E,F,G,H khaki
> color #12/A steel blue
> color #12/A:232-350 dark turquoise
> select #12/K:2
8 atoms, 8 bonds, 1 residue, 1 model selected
> select add #12/K:3
12 atoms, 11 bonds, 2 residues, 1 model selected
> select up
833 atoms, 926 bonds, 43 residues, 1 model selected
> select up
24113 atoms, 24865 bonds, 2801 residues, 1 model selected
> select down
833 atoms, 926 bonds, 43 residues, 1 model selected
> select down
12 atoms, 11 bonds, 2 residues, 1 model selected
> select down
12 atoms, 11 bonds, 2 residues, 1 model selected
> select down
12 atoms, 11 bonds, 2 residues, 1 model selected
> select clear
> select add #12/K:3
4 atoms, 3 bonds, 1 residue, 1 model selected
> select add #12/K:2
12 atoms, 11 bonds, 2 residues, 1 model selected
> color sel dark turquoise
[Repeated 1 time(s)]
> select clear
> color zone #13 near #12 distance 5
> hide #!12 models
> show #!13 models
> volume splitbyzone #13
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
> hide #!22.1 models
> show #!22.1 models
> hide #!22.1 models
> show #!13 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> hide #!22.6 models
> show #!22.6 models
> transparency
> #22.2.1#22.3.1#22.4.1#22.5.1#22.6.1#22.7.1#22.8.1#22.9.1#22.10.1 50
> show #12 models
> color #12/a byhetero
> select #12/K:2
8 atoms, 8 bonds, 1 residue, 1 model selected
> hide #12/k:1-6 cartoons
> show #12/k:1-3 atoms
> volume #22 hide
> select subtract #12/K:2@O3'
7 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #12/K:2@O3'
1 atom, 1 residue, 1 model selected
> select up
8 atoms, 8 bonds, 1 residue, 1 model selected
> select up
833 atoms, 926 bonds, 43 residues, 1 model selected
> select down
8 atoms, 8 bonds, 1 residue, 1 model selected
> select #12/K:3@P
1 atom, 1 residue, 1 model selected
> select up
4 atoms, 3 bonds, 1 residue, 1 model selected
> select add #12/K:2@O3'
5 atoms, 3 bonds, 2 residues, 1 model selected
> color sel dim gray
> color sel byhetero
> select clear
> select #12/M:2@MG
1 atom, 1 residue, 1 model selected
> color sel red
> select clear
> volume #22 show
> transparency #22 90
> transparency #22 80
> transparency #22 75
> hide #12/a cartoons
> show #12/a cartoons
> lighting soft
> lighting simple
> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/figures/structure/HNH/HNH_sharp_colormap.tif" width 1729
> height 1210 supersample 3
> view
> view #22
> hide #12 atoms
> transparency #22 10
> transparency #22 25
> transparency #22 40
> transparency #22 50
> transparency #22 60
> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/figures/structure/HNH/HNH_sharp_zoom_out_colormap.tif"
> width 1729 height 1210 supersample 3
> show #12/k:6 atoms
> show #12/k:6-7 atoms
> hide #12/k cartoons
> hide #!22.8 models
> show #!22.8 models
> hide #!22.8 models
> show #!22.8 models
> hide #!22.8 models
> show #!22.8 models
> hide #!22.8 models
> show #!22.8 models
> hide #!22.8 models
> show #!22.8 models
> hide #!22 models
> show #!13 models
> transparency #13.1 0
> transparency #13.1 50
> hide #!13 models
> select #12/I:140
6 atoms, 5 bonds, 1 residue, 1 model selected
> select add #12/A:295
12 atoms, 10 bonds, 2 residues, 1 model selected
> show sel atoms
> color sel byhetero
> select clear
> show #!13 models
> hide #12.1 models
> color #12 cyan
> transparency #13 90
> transparency #13 75
> color #12 dim gray
> color #12 khaki
> select #12
24113 atoms, 24865 bonds, 16 pseudobonds, 2801 residues, 3 models selected
> color sel light salmon
> color sel dark goldenrod
> color sel olive
> color sel green
> color sel olive
> color sel misty rose
> color sel lavender blush
> color sel snow
> color sel dark green
> color sel white
> color sel light yellow
> color sel ghost white
> color sel mint cream
> color sel white smoke
> color sel papaya whip
> color sel moccasin
> color sel navajo white
> select clear
> color #12 byhetero
> select #12/K:6@C5'
1 atom, 1 residue, 1 model selected
> select up
11 atoms, 11 bonds, 1 residue, 1 model selected
> select up
833 atoms, 926 bonds, 43 residues, 1 model selected
> color sel pale goldenrod
> color #12 pale goldenrod
> color #12/a,i byhetero
> select clear
> color #12 ivory
> color #12 orange red
> color #12 chocolate
> select clear
> color #12 goldenrod
> select clear
> color #12/a,i byhetero
> select clear
> hide #!13 models
> show #!13 models
> hide #!13 models
> hide #!12 models
> hide #!11 models
> open "/Users/zxc755/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/Type
> I-F_HNH/Manuscript/halfcleaved_HNH_center_main_model_temp_editing.pdb"
Chain information for halfcleaved_HNH_center_main_model_temp_editing.pdb #23
---
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
> style stick
Changed 253112 atom styles
> close #23
> open "/Users/zxc755/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/Type
> I-F_HNH/Manuscript/halfcleaved_HNH_center_main_model_temp_editing.pdb"
Chain information for halfcleaved_HNH_center_main_model_temp_editing.pdb #23
---
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
> style stick
Changed 253112 atom styles
> color #23/j red
> colse #23
Unknown command: colse #23
> close #23
> open "/Users/zxc755/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/Type
> I-F_HNH/Manuscript/halfcleaved_HNH_center_main_model_temp_editing.pdb"
Chain information for halfcleaved_HNH_center_main_model_temp_editing.pdb #23
---
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
> style stu
Expected a keyword
> style stick
Changed 253111 atom styles
> select #23/J:61@P
1 atom, 1 residue, 1 model selected
> select add #23/J:60@O3'
2 atoms, 2 residues, 1 model selected
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> close #23
> show #!22 models
> hide #!22.1 models
> show #!22.1 models
> hide #!22.1 models
> show #!22.1 models
> hide #!22.1 models
> show #!22.1 models
> hide #!22.1 models
> transparency
> #22.2.1#22.3.1#22.4.1#22.5.1#22.6.1#22.7.1#22.8.1#22.9.1#22.10.1 0
> view
> lighting soft
> hide #!22.2 models
> hide #!22.6 models
> hide #!22.7 models
> hide #!22.8 models
> hide #!22.9 models
> hide #!22.10 models
> show #!22.10 models
> hide #!22.4 models
> hide #!22.5 models
> show #!22.2 models
> hide #!22.3 models
> show #!22.9 models
> hide #!22.9 models
> show #!12 models
> show #12 cartoons
> show #12/j,k,l atoms
> hide #12/j,k,l cartoons
> hide #12 cartoons
> show #!22.9 models
> hide #!22.9 models
> show #!22.7 models
> hide #!22.7 models
> show #!22.7 models
> hide #!22.7 models
> hide #12/k,l atoms
> show #!22.3 models
> show #!22.9 models
> hide #!22.9 models
> show #!22.4 models
> hide #!22.2 models
> hide #!12 models
> show #!22.9 models
> show #!22.8 models
> show #!22.7 models
> hide #!22.9 models
> hide #!22.10 models
> show #!22.10 models
> hide #!22.4 models
> hide #!22.3 models
> hide #!22.7 models
> show #!22.7 models
> show #!22.3 models
> show #!22.4 models
> hide #!22.8 models
> show #!22.9 models
> show #!22.5 models
> hide #!22.3 models
> show #!22.3 models
> hide #!22.3 models
> show #!22.3 models
> hide #!22.3 models
> show #!22.3 models
> hide #!22.3 models
> show #!22.3 models
> hide #!22.3 models
> show #!22.3 models
> hide #!22.3 models
> show #!22.3 models
> hide #!22.3 models
> show #!22.3 models
> hide #!22.3 models
> show #!22.3 models
> show #!21 models
> hide #!21 models
> show #!21 models
> hide #!21 models
> show #!22.6 models
> volume #22 copy
Expected a keyword
> volume copy #22
Opened halfcleaved_HNH_center_sharp3Å.mrc 0 copy as #23, grid size
420,420,420, pixel 0.725, shown at step 1, values float32
Opened halfcleaved_HNH_center_sharp3Å.mrc 1 copy as #24, grid size
420,420,420, pixel 0.725, shown at step 1, values float32
Opened halfcleaved_HNH_center_sharp3Å.mrc 2 copy as #25, grid size
420,420,420, pixel 0.725, shown at step 1, values float32
Opened halfcleaved_HNH_center_sharp3Å.mrc 3 copy as #26, grid size
420,420,420, pixel 0.725, shown at step 1, values float32
Opened halfcleaved_HNH_center_sharp3Å.mrc 4 copy as #27, grid size
420,420,420, pixel 0.725, shown at step 1, values float32
Opened halfcleaved_HNH_center_sharp3Å.mrc 5 copy as #28, grid size
420,420,420, pixel 0.725, shown at step 1, values float32
Opened halfcleaved_HNH_center_sharp3Å.mrc 6 copy as #29, grid size
420,420,420, pixel 0.725, shown at step 1, values float32
Opened halfcleaved_HNH_center_sharp3Å.mrc 7 copy as #30, grid size
420,420,420, pixel 0.725, shown at step 1, values float32
Opened halfcleaved_HNH_center_sharp3Å.mrc 8 copy as #31, grid size
420,420,420, pixel 0.725, shown at step 1, values float32
Opened halfcleaved_HNH_center_sharp3Å.mrc 9 copy as #32, grid size
420,420,420, pixel 0.725, shown at step 1, values float32
> close #23-27-29,30,32
Expected a models specifier or a keyword
> close #23-27,29,30,32
> select add #31
2 models selected
> select add #28
4 models selected
> ui mousemode right "rotate selected models"
Drag select of 28 halfcleaved_HNH_center_sharp3Å.mrc 5 copy , 31
halfcleaved_HNH_center_sharp3Å.mrc 8 copy
> select clear
> select add #28
2 models selected
> select add #31
4 models selected
> view matrix models
> #28,1,0,0,-15.745,0,1,0,17.233,0,0,1,35.558,#31,1,0,0,-15.745,0,1,0,17.233,0,0,1,35.558
> hide #!22 models
> show #!22 models
> hide #!22 models
> show #!22 models
> show #!22.9 models
> show #!22.6 models
Drag select of 28 halfcleaved_HNH_center_sharp3Å.mrc 5 copy
> view matrix models #28,1,0,0,-26.099,0,1,0,28.092,0,0,1,69.137
> undo
> view matrix models #28,1,0,0,-27.45,0,1,0,25.948,0,0,1,59.885
> undo
> view matrix models
> #28,1,0,0,-61.332,0,1,0,40.335,0,0,1,88.812,#31,1,0,0,-61.332,0,1,0,40.335,0,0,1,88.812
> view matrix models
> #28,0.99986,-0.0031587,-0.016157,-58.015,0.0031298,0.99999,-0.0018136,40.189,0.016163,0.0017628,0.99987,86.175,#31,0.99986,-0.0031587,-0.016157,-58.015,0.0031298,0.99999,-0.0018136,40.189,0.016163,0.0017628,0.99987,86.175
> view matrix models
> #28,0.9887,0.14469,-0.039276,-77.926,-0.05202,0.57675,0.81526,-6.0261,0.14062,-0.804,0.57776,271.07,#31,0.9887,0.14469,-0.039276,-77.926,-0.05202,0.57675,0.81526,-6.0261,0.14062,-0.804,0.57776,271.07
> view matrix models
> #28,0.9887,0.14469,-0.039276,-85.135,-0.05202,0.57675,0.81526,15.862,0.14062,-0.804,0.57776,246.68,#31,0.9887,0.14469,-0.039276,-85.135,-0.05202,0.57675,0.81526,15.862,0.14062,-0.804,0.57776,246.68
> view matrix models
> #28,0.9887,0.14469,-0.039276,-81.276,-0.05202,0.57675,0.81526,19.835,0.14062,-0.804,0.57776,247.27,#31,0.9887,0.14469,-0.039276,-81.276,-0.05202,0.57675,0.81526,19.835,0.14062,-0.804,0.57776,247.27
> view matrix models
> #28,0.9887,0.14469,-0.039276,-79.275,-0.05202,0.57675,0.81526,15.652,0.14062,-0.804,0.57776,250.56,#31,0.9887,0.14469,-0.039276,-79.275,-0.05202,0.57675,0.81526,15.652,0.14062,-0.804,0.57776,250.56
> view matrix models
> #28,0.9887,0.14469,-0.039276,-77.942,-0.05202,0.57675,0.81526,16.097,0.14062,-0.804,0.57776,249.3,#31,0.9887,0.14469,-0.039276,-77.942,-0.05202,0.57675,0.81526,16.097,0.14062,-0.804,0.57776,249.3
> hide #!28 models
> hide #!22.6 models
> select clear
> show #!28 models
> volume copy #28,31
Opened halfcleaved_HNH_center_sharp3Å.mrc 5 copy as #23, grid size
420,420,420, pixel 0.725, shown at step 1, values float32
Opened halfcleaved_HNH_center_sharp3Å.mrc 8 copy as #24, grid size
420,420,420, pixel 0.725, shown at step 1, values float32
> select add #24
2 models selected
> select add #23
4 models selected
> hide #!23 models
> view matrix models
> #23,0.9887,0.14469,-0.039276,8.0563,-0.05202,0.57675,0.81526,-113.04,0.14062,-0.804,0.57776,129.77,#24,0.9887,0.14469,-0.039276,8.0563,-0.05202,0.57675,0.81526,-113.04,0.14062,-0.804,0.57776,129.77
> view matrix models
> #23,0.043581,0.44731,-0.89332,249.71,0.41027,0.80728,0.42424,-149.29,0.91092,-0.38499,-0.14834,101.97,#24,0.043581,0.44731,-0.89332,249.71,0.41027,0.80728,0.42424,-149.29,0.91092,-0.38499,-0.14834,101.97
> view matrix models
> #23,0.31764,-0.21312,-0.92395,341.68,-0.32375,0.89148,-0.31693,58.267,0.89123,0.3998,0.21417,-119.07,#24,0.31764,-0.21312,-0.92395,341.68,-0.32375,0.89148,-0.31693,58.267,0.89123,0.3998,0.21417,-119.07
> view matrix models
> #23,0.59224,0.40091,-0.69894,170.96,-0.54032,0.8411,0.024613,71.479,0.59774,0.36308,0.71476,-154.16,#24,0.59224,0.40091,-0.69894,170.96,-0.54032,0.8411,0.024613,71.479,0.59774,0.36308,0.71476,-154.16
> view matrix models
> #23,0.69706,-0.11362,-0.70796,246.89,-0.1613,0.93721,-0.30923,51.937,0.69864,0.32974,0.63496,-158.3,#24,0.69706,-0.11362,-0.70796,246.89,-0.1613,0.93721,-0.30923,51.937,0.69864,0.32974,0.63496,-158.3
> view matrix models
> #23,0.69706,-0.11362,-0.70796,252.59,-0.1613,0.93721,-0.30923,47.072,0.69864,0.32974,0.63496,-159,#24,0.69706,-0.11362,-0.70796,252.59,-0.1613,0.93721,-0.30923,47.072,0.69864,0.32974,0.63496,-159
> view matrix models
> #23,0.69706,-0.11362,-0.70796,252.6,-0.1613,0.93721,-0.30923,49.338,0.69864,0.32974,0.63496,-154.62,#24,0.69706,-0.11362,-0.70796,252.6,-0.1613,0.93721,-0.30923,49.338,0.69864,0.32974,0.63496,-154.62
> show #!31 models
> show #!22.3 models
> hide #!22.3 models
> view matrix models
> #23,0.53219,-0.46563,-0.70708,340.77,-0.13597,0.77732,-0.61423,119.83,0.83563,0.42303,0.35037,-150.59,#24,0.53219,-0.46563,-0.70708,340.77,-0.13597,0.77732,-0.61423,119.83,0.83563,0.42303,0.35037,-150.59
> view matrix models
> #23,0.53219,-0.46563,-0.70708,348.32,-0.13597,0.77732,-0.61423,144.51,0.83563,0.42303,0.35037,-125.55,#24,0.53219,-0.46563,-0.70708,348.32,-0.13597,0.77732,-0.61423,144.51,0.83563,0.42303,0.35037,-125.55
> view matrix models
> #23,0.53219,-0.46563,-0.70708,340.03,-0.13597,0.77732,-0.61423,154.48,0.83563,0.42303,0.35037,-128.41,#24,0.53219,-0.46563,-0.70708,340.03,-0.13597,0.77732,-0.61423,154.48,0.83563,0.42303,0.35037,-128.41
> view
> view matrix models
> #23,0.53219,-0.46563,-0.70708,339.08,-0.13597,0.77732,-0.61423,161.1,0.83563,0.42303,0.35037,-130.68,#24,0.53219,-0.46563,-0.70708,339.08,-0.13597,0.77732,-0.61423,161.1,0.83563,0.42303,0.35037,-130.68
> show #!22.3 models
> view matrix models
> #23,0.53219,-0.46563,-0.70708,343.45,-0.13597,0.77732,-0.61423,159.05,0.83563,0.42303,0.35037,-136.71,#24,0.53219,-0.46563,-0.70708,343.45,-0.13597,0.77732,-0.61423,159.05,0.83563,0.42303,0.35037,-136.71
> view matrix models
> #23,0.53219,-0.46563,-0.70708,341.97,-0.13597,0.77732,-0.61423,158.87,0.83563,0.42303,0.35037,-137.21,#24,0.53219,-0.46563,-0.70708,341.97,-0.13597,0.77732,-0.61423,158.87,0.83563,0.42303,0.35037,-137.21
> view matrix models
> #23,0.53219,-0.46563,-0.70708,341.85,-0.13597,0.77732,-0.61423,158.37,0.83563,0.42303,0.35037,-137,#24,0.53219,-0.46563,-0.70708,341.85,-0.13597,0.77732,-0.61423,158.37,0.83563,0.42303,0.35037,-137
> hide #!22.3 models
> select clear
> show #!23 models
> show #!28 models
> show #!22.6 models
> hide #!28 models
> hide #!23 models
> hide #!22.6 models
> show #!22.3 models
> show #!28 models
> hide #!28 models
> show #!23 models
> show #!22.4 models
> show #!22.6 models
> show #!28 models
> hide #!28 models
> hide #!23 models
> hide #!22.3 models
> hide #!22.4 models
> show #!22.2 models
> show #!28 models
> show #!23 models
> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/figures/chimera_session.cxs"
——— End of log from Thu Mar 27 17:05:34 2025 ———
opened ChimeraX session
> hide #!22.6 models
> hide #!22.2 models
> show #!22.6 models
> hide #!22.6 models
> hide #!23 models
> hide #!28 models
> show #!28 models
> select add #28
2 models selected
> select add #31
4 models selected
> ui mousemode right "rotate selected models"
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> view matrix models
> #28,0.99705,0.030134,-0.070522,-54.036,0.023972,0.75103,0.65984,-13.412,0.072847,-0.65958,0.74809,214.74,#31,0.99705,0.030134,-0.070522,-54.036,0.023972,0.75103,0.65984,-13.412,0.072847,-0.65958,0.74809,214.74
> show #!23 models
> show #!22.6 models
> hide #!28 models
> hide #!23 models
> hide #!22.6 models
> select clear
> open "/Users/zxc755/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/Type
> I-F_HNH/Manuscript/halfcleaved_HNH_center_main_model_temp_editing.pdb"
Chain information for halfcleaved_HNH_center_main_model_temp_editing.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 | 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
> volume #22 hide
> volume #24-25 hide
> volume #31 hide
> style stick
Changed 253111 atom styles
> show #25 cartoons
> hide #25
> show #25 & nucleic
> color #25/L light gray
> color #25/K dim gray
> color #25/J dark red
> color #25/I rebecca purple
> color #25/B forest green
> color #25/C,D,E,F,G,H khaki
> color #25/A steel blue
> color #25/A:232-350 dark turquoise
> hide #25 & nucleic cartoons
> show #25
> hide #25
> show #25 & nucleic
> show #25/j
> open 3i4h
Summary of feedback from opening 3i4h fetched from pdb
---
note | Fetching compressed mmCIF 3i4h from http://files.rcsb.org/download/3i4h.cif
3i4h title:
Crystal structure of Cas6 in Pyrococcus furiosus [more info...]
Chain information for 3i4h #26
---
Chain | Description | UniProt
X | endoribonuclease | Q8U1S4_PYRFU 8-270
> hide #!22 models
> hide #!26 models
> show #!26 models
> hide #!25 models
> show #!25 models
> select #26/X:34
4 atoms, 3 bonds, 1 residue, 1 model selected
> view matrix models #26,1,0,0,11.063,0,1,0,112.94,0,0,1,76.569
Drag select of 48 residues
> view matrix models #26,1,0,0,25.302,0,1,0,250.11,0,0,1,200.98
> view matrix models #26,1,0,0,73.305,0,1,0,249.54,0,0,1,132.47
> view matrix models
> #26,0.6118,0.31311,-0.72641,89.838,-0.77626,0.41421,-0.47524,242.91,0.15208,0.85463,0.49646,158
> view matrix models
> #26,0.20919,0.21723,-0.95344,137.17,-0.96272,0.21674,-0.16184,238.54,0.17149,0.95175,0.25447,203.29
> view matrix models
> #26,-0.18257,0.38275,-0.90563,144.87,-0.7876,0.49443,0.36774,240.71,0.58852,0.78041,0.21118,199.4
> view matrix models
> #26,0.24049,0.042201,-0.96973,126.99,-0.49179,0.86663,-0.084247,255.09,0.83685,0.49716,0.22917,198.15
> view matrix models
> #26,0.24049,0.042201,-0.96973,115.81,-0.49179,0.86663,-0.084247,256.61,0.83685,0.49716,0.22917,201.79
> select #26 & name="tyr"
Expected a keyword
> select ::name="TYR"
15699 atoms, 15721 bonds, 1261 residues, 36 models selected
> select #26::name="tyr"
192 atoms, 193 bonds, 16 residues, 1 model selected
> select #26::name="tyr" #26::name=lys
390 atoms, 373 bonds, 38 residues, 1 model selected
> select #26::name="tyr" #26::name=lys,his
1913 atoms, 1970 bonds, 2 pseudobonds, 232 residues, 2 models selected
> select #26::name="tyr" #26::name=lys
390 atoms, 373 bonds, 38 residues, 1 model selected
> select #26::name=lys
198 atoms, 178 bonds, 22 residues, 1 model selected
> select #26::name=his
80 atoms, 82 bonds, 8 residues, 1 model selected
> view matrix models
> #26,-0.89794,0.08841,0.43115,111.17,0.14503,0.98434,0.10021,254.49,-0.41554,0.15251,-0.8967,209.66
> select #26::name="his,lys"
Nothing selected
> select #26::name=his,lys
1913 atoms, 1970 bonds, 2 pseudobonds, 232 residues, 2 models selected
> select #26::name=his::name=lys
278 atoms, 260 bonds, 30 residues, 1 model selected
> select #26::name=his::name=lys::name=tyr
470 atoms, 455 bonds, 46 residues, 1 model selected
> show sel
> select clear
> mmaker #26 to #25/i
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 I (#25)
with 3i4h, chain X (#26), sequence alignment score = 33.6
RMSD between 6 pruned atom pairs is 1.546 angstroms; (across all 156 pairs:
18.266)
> hide #!26 models
> hide #!25 models
> open "/Users/zxc755/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/Type
> I-F_HNH/Manuscript/halfcleaved_HNH_center_main_model_temp_editing.pdb"
Chain information for halfcleaved_HNH_center_main_model_temp_editing.pdb #27
---
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
> style stick
Changed 279140 atom styles
> hide #27
> show #27 cartoons
> show #27/j,k,l
> hide #27/j,k,l cartoons
> color #27/L light gray
> color #27/K dim gray
> color #27/J dark red
> color #27/I rebecca purple
> color #27/B forest green
> color #27/C,D,E,F,G,H khaki
> color #27/A steel blue
> color #27/A:232-350 dark turquoise
> color #27/O blue
> color #27/M red
> volume #13 show
> color zone #13 near #27 distance 10
> color zone #13 near #27 distance 6
> color zone #13 near #27 distance 4
> color zone #13 near #27 distance 8
> transparency #13 50
> volume #13 hide
> hide #27 models
> close #27
> open "/Users/zxc755/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/Type
> I-F_HNH/Manuscript/halfcleaved_HNH_center_main_model_temp_editing.pdb"
Chain information for halfcleaved_HNH_center_main_model_temp_editing.pdb #27
---
Chain | Description
A | No description available
B | No description available
C E | No description available
D | 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
> style stick
Changed 279111 atom styles
> hide #27
> show #27 cartoons
> show #27 & nucleic
> color #27/L light gray
> color #27/K dim gray
> color #27/J dark red
> color #27/I rebecca purple
> color #27/B forest green
> color #27/C,D,E,F,G,H khaki
> color #27/A steel blue
> color #27/A:232-350 dark turquoise
> color #27/O blue
> color #27/M red
> hide #27& nucleic
> hide #27& nucleic cartoons
> hide #27& nucleic
> show #27 & nucleic
> select clear
> select P
1109 atoms, 1108 residues, 15 models selected
> color sel byhetero
> select clear
> hide #!27 models
> open 3pkm
Summary of feedback from opening 3pkm fetched from pdb
---
note | Fetching compressed mmCIF 3pkm from http://files.rcsb.org/download/3pkm.cif
3pkm title:
Crystal structure of Cas6 with its substrate RNA [more info...]
Chain information for 3pkm #29
---
Chain | Description | UniProt
A X | CRISPR-associated endoribonuclease Cas6 | CAS6_PYRFU 8-270
G | 5'-R(*AP*UP*UP*AP*CP*AP*AP*UP*AP*A)-3' |
R | 5'-R(P*UP*UP*AP*CP*AP*AP*UP*AP*A)-3' |
3pkm mmCIF Assemblies
---
1| author_defined_assembly
2| author_defined_assembly
Drag select of 237 residues, 3 pseudobonds, 27 shapes
> hide sel cartoons
> select #29/A:106
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel cartoons
Drag select of 71 atoms, 71 bonds, 27 shapes
> hide sel
Drag select of 13 atoms
> hide sel
> close #29
> show #27 models
> view
> close #27
> open "/Users/zxc755/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/Type
> I-F_HNH/Manuscript/halfcleaved_HNH_center_main_model_temp_editing.pdb"
Chain information for halfcleaved_HNH_center_main_model_temp_editing.pdb #27
---
Chain | Description
A | No description available
B | No description available
C E | No description available
D | 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
> style sty
Expected a keyword
> style stick
Changed 279111 atom styles
> hide #27
> color #27/L light gray
> color #27/K dim gray
> color #27/J dark red
> color #27/I rebecca purple
> color #27/B forest green
> color #27/C,D,E,F,G,H khaki
> color #27/A steel blue
> color #27/A:232-350 dark turquoise
> color #27/O blue
> color #27/M red
> show #27 cartoons
> show #27/j,k,l,m,o
> hide #27 & nucleic cartoons
> select P
1109 atoms, 1108 residues, 15 models selected
> select #27::P
Nothing selected
> select #27::name=P
Nothing selected
> select #27 & P
112 atoms, 111 residues, 1 model selected
> color sel byhetero
> select clear
> hide #27 models
> open /Users/zxc755/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/Phenix/eLBOW_54/elbow.001.pdb
> view
> close #29
> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/figures/chimera_session.cxs"
——— End of log from Mon Mar 31 18:07:43 2025 ———
opened ChimeraX session
> open /Users/zxc755/Downloads/J620_abinitio_map.mrc
Opened J620_abinitio_map.mrc as #29, grid size 128,128,128, pixel 2.38, shown
at level 0.218, step 1, values float32
> hide #!29 models
> show #!29 models
> view
> lighting soft
> lighting simple
> lighting soft
> ui tool show "Color Actions"
> select add #29
2 models selected
> color sel dark khaki
[Repeated 1 time(s)]
> color sel navajo white
> select clear
> lighting soft
> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/figures/structure/half_abinitio.tif" width 1984 height
> 1210 supersample 3 transparentBackground true
> open /Users/zxc755/Downloads/half_hetref_J623_map.mrc
Opened half_hetref_J623_map.mrc as #30, grid size 128,128,128, pixel 2.38,
shown at level 0.227, step 1, values float32
> select add #30
2 models selected
> color sel navajo white
> hide #!29 models
> select clear
> volume #30 level 0.5
> volume #30 level 0.3
> volume #30 level 0.35
> volume #30 level 0.33
> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/figures/structure/half_hetref.tif" width 1984 height 1210
> supersample 3
> hide #!30 models
Unsupported scale factor (0.000000) detected on Display0
[Repeated 7 time(s)]
> show #!31 models
> hide #!31 models
> show #!29 models
> show #!30 models
> hide #!30 models
> show #!30 models
> hide #!29 models
> show #!13 models
> hide #!30 models
> show #!30 models
> hide #!30 models
> color #12/L light gray
> color #12/K dim gray
> color #12/J dark red
> color #12/I rebecca purple
> color #12/B forest green
> color #12/C,D,E,F,G,H salmon
> color #12/A steel blue
> color #12/A:232-350 dark turquoise
> color #12/O blue
> color #12/M red
> color zone #13 near #12 distance 10
> show #!22.1 models
> hide #!22 models
> hide #!22.1 models
> show #!22.2 models
> hide #!22.2 models
> show #!22.2 models
> hide #!22.2 models
> show #!22.2 models
> hide #!22.2 models
> color #22.2 salmon
> show #!22.2 models
> hide #!22.2 models
> hide #!13 models
> show #!22.2 models
> show #!22.1 models
> hide #!22.2 models
> show #!22.2 models
> hide #!22.1 models
> show #!22.1 models
> hide #!22.2 models
> show #!22.2 models
> hide #!22.1 models
> show #!22.3 models
> hide #!22.2 models
> show #!22.2 models
> surface dust #22.2-9 size 10
> hide #!22.3 models
> show #!22.3 models
> hide #!22.2 models
> show #!22.4 models
> hide #!22.3 models
> show #!22.5 models
> show #!22.3 models
> hide #!22.3 models
> show #!22.2 models
> hide #!22.2 models
> show #!22.3 models
> show #!22.7 models
> hide #!22.7 models
> surface dust #22.5 size 10
> surface dust #22.4 size 10
> surface dust #22.6 size 10
> surface dust #22.7 size 10
> surface dust #22.8 size 10
> surface dust #22.9 size 10
> show #!22.6 models
> hide #!22.3 models
> surface dust #22.6 size 10
> hide #!22.4 models
> hide #!22.5 models
> show #!22.7 models
> hide #!22.6 models
> show #!22.8 models
> show #!22.9 models
> surface dust #22.7 size 10
> surface dust #22.8 size 10
> surface dust #22.9 size 10
> show #!22.10 models
> hide #!22.10 models
> view
> hide #!22.9 models
> hide #!22.8 models
> hide #!22.7 models
> show #!22.6 models
> show #!22.9 models
> hide #!22.9 models
> hide #!22.6 models
> show #!22.5 models
> show #!22.4 models
> hide #!22.5 models
> hide #!22.4 models
> show #!22.3 models
> show #!22.4 models
> show #!22.2 models
> hide #!22.4 models
> hide #!22.3 models
> show #!22.3 models
> show #!22.4 models
> hide #!22.4 models
> show #!22.4 models
> hide #!22.4 models
> show #!22.4 models
> hide #!22.4 models
> show #!22.9 models
> show #!22.8 models
> show #!22.7 models
> show #!22.4 models
> show #!22.5 models
> show #!22.6 models
> show #!22.10 models
> view
[Repeated 1 time(s)]
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!12 models
> volume #22 hide
> show #12
> hide #12
> show #12 cartoons
> show #12 & nucleic
> volume #22 hide mod
Expected a keyword
> volume #22 hide model
Expected a keyword
> hide #22 models
> show #22
> hide #!22.1 models
> hide #22 models
> show #!13 models
> hide #!13 models
> show #22 models
> hide #!22.1 models
> transparency #22 70
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> lighting flat
> show #12/A:83,85
> color #12/A byhetero
> hide #12 & nucleic cartoons
> ui tool show "Side View"
> hide #!22.10 models
> hide #!22.9 models
> hide #!22.6 models
> hide #!22.5 models
> hide #!22.3 models
> show #!22.3 models
> hide #!22.3 models
> show #!22.3 models
> hide #!22.2 models
> hide #12/c,d,e,f,g,h,i cartoons
> show #!22.9 models
> hide #!22.9 models
> hide #12/c,d,e,f,g,h,i,j cartoons
> hide #12/j
> color #12/l wheat
> color #22.7 wheat
> show #!22.2 models
> hide #!22.2 models
> show #!21 models
> hide #!21 models
> show #!11 models
> select add #11
13 pseudobonds, 2 models selected
> color sel black
> color sel slate gray
> color sel gray
> color sel dim gray
> select subtract #11
Nothing selected
> hide #!11 models
> show #!11 models
> show #!22.5 models
> show #!22.2 models
> show #!22.6 models
> show #!22.9 models
> show #!22.10 models
> hide #!12 models
> transparency #22 0
> lighting soft
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> color #22.7 gold
> color #22.7 khaki
> color #22.7 dark khaki
> color #22.7 olive
> color #22.7 dark khaki
> view
> color #22.7 goldenrod
> color #22.7 orange
> color #22.7 dark orange
> color #22.7 dark khaki
> show #!12 models
> transparency #22 70
> graphics silhouettes true
> lighting flat
[Repeated 2 time(s)]
> lighting soft
> lighting flat
> lighting soft
> lighting flat
> lighting shadows true intensity 0.5
> lighting flat
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> transparency #22 80
> transparency #22 99
> transparency #22 90
> transparency #12/l:1-6 50
> select add #11
13 pseudobonds, 2 models selected
> color sel crimson
> color sel brown
> color sel saddle brown
> color sel indian red
> color sel yellow
> color sel gold
[Repeated 1 time(s)]
> color sel orange
> color sel dark orange
> color sel goldenrod
> color sel salmon
> color sel dark khaki
> color sel peru
> color sel dark goldenrod
> select subtract #11
Nothing selected
> view
> hide #!22.2 models
> show #!22.2 models
> hide #!22.2 models
> hide #!22.5 models
> hide #!22.6 models
> hide #!22.7 models
> show #!22.7 models
> hide #!22.8 models
> show #!22.8 models
> hide #!22.9 models
> hide #!22.10 models
> show #!22.10 models
> hide #!22 models
> show #!22 models
> graphics silhouettes false
> graphics silhouettes true
> lighting flat
> volume #22.8 level 0.03
> volume #22.8 level 0.02
> volume #22 level 0.07
> volume #22 level 0.05
> hide #!22 models
> show #!22 models
> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/figures/structure/PAM/PAM_sharp_2.tif" width 1984 height
> 1210 supersample 3
> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/figures/structure/PAM/PAM_sharp_2.tif" width 1984 height
> 1210 supersample 4
> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/figures/structure/PAM/PAM_session.cxs"
[Repeated 1 time(s)]
> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/figures/structure/PAM/PAM_sharp_2.tif" width 1984 height
> 1210 supersample 3
> graphics silhouettes false
> graphics silhouettes true
> hide #12/a:83,85
> volume #22 level 0.02
> show #!22.5 models
> show #!22.9 models
> show #12/j
> hide #12/a,b
> hide #12/a,b cartoons
> hide #!22.5 models
> hide #!22.4 models
> hide #!22.3 models
> hide #!12 models
> open "/Users/zxc755/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/Type
> I-F_HNH/Manuscript/halfcleaved_HNH_center_main_model_temp.pdb"
Chain information for halfcleaved_HNH_center_main_model_temp.pdb #32
---
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
> hide #!32 models
> show #!32 models
> style ato
Expected a keyword
> style stick
Changed 303224 atom styles
> cki #32
Unknown command: cki #32
> close #32
> open "/Users/zxc755/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/Type
> I-F_HNH/Manuscript/halfcleaved_HNH_center_main_model_temp2.pdb"
Chain information for halfcleaved_HNH_center_main_model_temp2.pdb #32
---
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
> style stick
Changed 303277 atom styles
> close #32
> open "/Users/zxc755/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/Type
> I-F_HNH/Manuscript/halfcleaved_HNH_center_main_model_temp_editing.pdb"
Chain information for halfcleaved_HNH_center_main_model_temp_editing.pdb #32
---
Chain | Description
A | No description available
B | No description available
C E | No description available
D | 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
> style stick
Changed 303198 atom styles
> hide #32
> show #32 cartoons
Computing secondary structure
> cartoon style nucleic xsection oval width 1 thickness 1
> color #32/L dark khaki
> 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
> hide #32 & nucleic cartoons
> show #32 & nucleic
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!32 models
> show #!32 models
> hide #!32 models
> show #!32 models
> hide #!32 models
> show #!32 models
> hide #!32 models
> show #!32 models
> hide #!32 models
> show #!32 models
> hide #!32 models
> show #!32 models
> hide #!32 models
> hide #!22.7 models
> show #!22.7 models
> show #!32 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!12 models
> color #22.7 khaki
> color #22.7 dark khaki
> hide #!12 models
> color #32/l khaki
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> hide #!22.7 models
> show #!22.7 models
> hide #!32 models
> show #!12 models
> show #12/m,o
> hide #!22.8 models
> hide #!22.9 models
> hide #!22.7 models
> show #!22.5 models
> show #!22.4 models
> hide #!22.4 models
> show #12/a cartoons
> hide #12/j
> show #!22.4 models
> show #12/a:304,305
> hide #!22 models
> select #12/A:280
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #12/A:319
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #12/A:280
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel
> select clear
> select #12/K:2@C2'
1 atom, 1 residue, 1 model selected
> select add #12/K:2@C1'
2 atoms, 1 residue, 1 model selected
> select add #12/K:2@O4'
3 atoms, 1 residue, 1 model selected
> select add #12/K:2@O5'
4 atoms, 1 residue, 1 model selected
> select add #12/K:2@C5'
5 atoms, 1 residue, 1 model selected
> select add #12/K:2@C4'
6 atoms, 1 residue, 1 model selected
> select add #12/K:2@C3'
7 atoms, 1 residue, 1 model selected
> hide sel
> select clear
> select #12/K:3@P
1 atom, 1 residue, 1 model selected
> select up
4 atoms, 3 bonds, 1 residue, 1 model selected
> select up
833 atoms, 926 bonds, 43 residues, 1 model selected
> select down
4 atoms, 3 bonds, 1 residue, 1 model selected
> select up
833 atoms, 926 bonds, 43 residues, 1 model selected
> select down
4 atoms, 3 bonds, 1 residue, 1 model selected
> select add #12/K:2@O3'
5 atoms, 3 bonds, 2 residues, 1 model selected
> color sel byhetero
> select clear
> select #12/A:328
10 atoms, 10 bonds, 1 residue, 1 model selected
> show sel
> select clear
> show #!22 models
> hide #!22 models
> hide #!12 models
> show #!12 models
> show #!22 models
> hide #!22 models
> hide #!12 models
> show #!22 models
> show #!12 models
> transparency #22 90
> transparency #22 95
> hide #!22 models
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> lighting shadows true intensity 0.5
> graphics silhouettes false
> graphics silhouettes true
> lighting shadows false
> lighting flat
[Repeated 1 time(s)]
> graphics silhouettes false
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting flat
> lighting shadows true intensity 0.5
> lighting flat
> graphics silhouettes false
> show #!22 models
> graphics silhouettes true
> view
> view orient
[Repeated 1 time(s)]
> show #12/a
> volume #22 level 0.05
> volume #22 level 0.09
> volume #22 level 0.02
> hide #12/a
> hide #!12 models
> show #!22.2 models
> show #!22.3 models
> hide #!22.4 models
> hide #!22.5 models
> hide #!22.2 models
> show #!12 models
> hide #12/a cartoons
> show #12/b cartoons
> hide #12/k,l
> show #12/b
> hide #12/b
> hide #12/b cartoons
> hide #!22.3 models
> show #!22.2 models
> show #12/c,d,e,f,g,h
> show #12/c,d,e,f,g,h cartoons
> hide #12/c,d,e,f,g,h
> hide #!22.2 models
> hide #12/c,d,e,f,g,h cartoons
> show #!22.9 models
> show #!22.8 models
> show #!22.7 models
> show #12/j,k,l
> hide #!12 models
> show #!32 models
> hide #!32 models
> show #!12 models
> show #!32 models
> hide #!32 models
> show #!32 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!22.2 models
> show #!22.3 models
> show #!22.4 models
> show #!22.5 models
> show #!22.6 models
> hide #!22 models
> hide #!32 models
> show #!32 models
> show #32/m,o
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> select #32/l
247 atoms, 280 bonds, 1 pseudobond, 12 residues, 2 models selected
> color sel khaki
> color sel burly wood
> color sel rosy brown
> color sel midnight blue
> color sel purple
> color sel rebecca purple
> color sel cornflower blue
> color sel dodger blue
> color sel peru
> color sel dark goldenrod
> color sel dark orange
> color sel orange
> color sel dark orange
> color sel orange
> color sel dark orange
> select clear
> show #!22.1 models
> select add #22.7
2 models selected
> select subtract #22.7
Nothing selected
> select add #22.7
2 models selected
> color sel dark orange
> select clear
> hide #!22.1 models
> hide #!22 models
> show #!22 models
> hide #!22 models
> show #!13 models
> hide #!13 models
> hide #!11 models
> show #!13 models
> graphics silhouettes false
> lighting simple
> lighting soft
> color zone #13 near #32 distance 10
> hide #!13 models
> show #!22.1 models
> hide #!22 models
> select #32/K:40@N1
1 atom, 1 residue, 1 model selected
> select up
3 atoms, 1 bond, 2 residues, 1 model selected
> select up
41 atoms, 44 bonds, 2 residues, 1 model selected
> color sel indigo
> color sel peru
> color sel maroon
> color sel hot pink
> show #!22 models
> view
> select clear
> hide #32/c,d,e,f,g,h,j, car
> hide #32/c,d,e,f,g,h,j cartoons
> hide #!22 models
> show #!22 models
> hide #!22.1 models
> hide #!22.2 models
> hide #!22.6 models
> hide #!22.7 models
> show #!22.7 models
> hide #!22.8 models
> show #!22.8 models
> hide #!22.9 models
> hide #!22.10 models
> show #!22.10 models
> hide #32/m,o
> show #32/a:83,85
> color #32/a byhetero
> show #!11 models
> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/figures/chimera_session.cxs"
——— End of log from Wed Apr 23 13:09:57 2025 ———
opened ChimeraX session
> lighting flat
> graphics silhouettes false
> graphics silhouettes true
> hide #!11 models
> show #!11 models
> ui tool show Distances
> hide #!22 models
> select #32/A:85@NZ
1 atom, 1 residue, 1 model selected
> select add #32/L:6@N2
2 atoms, 2 residues, 1 model selected
> distance #32/A:85@NZ #32/L:6@N2
Distance between halfcleaved_HNH_center_main_model_temp_editing.pdb #32/A LYS
85 NZ and /L DG 6 N2: 3.258Å
> distance style radius 0.04
[Repeated 2 time(s)]
> distance style radius 0.03
[Repeated 2 time(s)]
> distance style radius 0.02
[Repeated 2 time(s)]
> distance style radius 0.01
[Repeated 2 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)]
> distance style decimalPlaces 2
[Repeated 2 time(s)]
> distance style decimalPlaces 1
[Repeated 2 time(s)]
> select #32/A:85@NZ
1 atom, 1 residue, 1 model selected
> select add #32/K:41@O2
2 atoms, 2 residues, 1 model selected
> distance #32/A:85@NZ #32/K:41@O2
Distance between halfcleaved_HNH_center_main_model_temp_editing.pdb #32/A LYS
85 NZ and /K DC 41 O2: 3.0Å
> select #32/A:83@OD1
1 atom, 1 residue, 1 model selected
> select add #32/A:85@NZ
2 atoms, 2 residues, 1 model selected
> distance #32/A:83@OD1 #32/A:85@NZ
Distance between halfcleaved_HNH_center_main_model_temp_editing.pdb #32/A ASP
83 OD1 and LYS 85 NZ: 2.9Å
> select #32/K:40@N2
1 atom, 1 residue, 1 model selected
> select #32/A:83@OD1
1 atom, 1 residue, 1 model selected
> select add #32/K:40@N2
2 atoms, 2 residues, 1 model selected
> distance #32/A:83@OD1 #32/K:40@N2
Distance between halfcleaved_HNH_center_main_model_temp_editing.pdb #32/A ASP
83 OD1 and /K DG 40 N2: 3.0Å
> distance style dashes 4
[Repeated 2 time(s)]
> distance style dashes 5
[Repeated 2 time(s)]
> distance style radius 0.04
[Repeated 2 time(s)]
> distance style radius 0.05
[Repeated 2 time(s)]
> distance style radius 0.04
[Repeated 2 time(s)]
> distance style radius 0.05
[Repeated 2 time(s)]
> select clear
> select add #11
17 pseudobonds, 2 models selected
> color sel peru
> color sel light salmon
> color sel olive
> color sel teal
> select clear
> close sel
> delete sel
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> close #32
> open "/Users/zxc755/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/Type
> I-F_HNH/Manuscript/halfcleaved_HNH_center_main_model_temp_editing.pdb"
Chain information for halfcleaved_HNH_center_main_model_temp_editing.pdb #32
---
Chain | Description
A | No description available
B | No description available
C E | No description available
D | 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
> style stick
Changed 303202 atom styles
> 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
> color #32/k:40 hot pink
> hide #32
> show #32/k,l
> show #32/a,b cartoons
Computing secondary structure
> color #32/a byhetero
> show #32/a:83-85
> select #32/A:83@OD1
1 atom, 1 residue, 1 model selected
> select add #32/K:40@N2
2 atoms, 2 residues, 1 model selected
> distance #32/A:83@OD1 #32/K:40@N2
Distance between halfcleaved_HNH_center_main_model_temp_editing.pdb #32/A ASP
83 OD1 and /K DG 40 N2: 3.0Å
> select #32/A:85@NZ
1 atom, 1 residue, 1 model selected
> select add #32/A:83@OD1
2 atoms, 2 residues, 1 model selected
> distance #32/A:85@NZ #32/A:83@OD1
Distance between halfcleaved_HNH_center_main_model_temp_editing.pdb #32/A LYS
85 NZ and ASP 83 OD1: 2.7Å
> select #32/A:85@NZ
1 atom, 1 residue, 1 model selected
> select add #32/L:6@N2
2 atoms, 2 residues, 1 model selected
> distance #32/A:85@NZ #32/L:6@N2
Distance between halfcleaved_HNH_center_main_model_temp_editing.pdb #32/A LYS
85 NZ and /L DG 6 N2: 3.1Å
> select #32/K:41@O2
1 atom, 1 residue, 1 model selected
> select add #32/A:85@NZ
2 atoms, 2 residues, 1 model selected
> distance #32/K:41@O2 #32/A:85@NZ
Distance between halfcleaved_HNH_center_main_model_temp_editing.pdb #32/K DC
41 O2 and /A LYS 85 NZ: 2.9Å
> select add #11
2 atoms, 17 pseudobonds, 2 residues, 3 models selected
> color sel dark khaki
> color sel teal
> select clear
> select #32/A:85
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel steel blue
> color sel byhetero
> select clear
> select #32/K:41@O2
1 atom, 1 residue, 1 model selected
> color sel dim gray
> select clear
> select #32/L:7@C2
1 atom, 1 residue, 1 model selected
> select up
19 atoms, 20 bonds, 1 residue, 1 model selected
> color sel hot pink
> select clear
> show #!22 models
> hide #!22 models
> distance style radius 0.04
[Repeated 2 time(s)]
> distance style radius 0.05
[Repeated 2 time(s)]
> show #11.1 models
> hide #11.1 models
> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/figures/structure/PAM/PAM_nomap.tif" width 1984 height
> 1210 supersample 3
> show #!22 models
> hide #!22 models
> graphics silhouettes false
> graphics silhouettes true
> lighting flat
> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/figures/structure/PAM/PAM_session.cxs"
> close #1-10
> close #14-21
> close #23-31
> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/figures/structure/PAM/PAM_session.cxs"
> show #32 cartoons
> hide #32/a
> cartoon style nucleic xsection oval width 1 thickness 1
> show #!22 models
> show #!22.2 models
> show #!22.6 models
> show #!22.9 models
> show #32/j
> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/figures/structure/PAM/PAM_zoomout.tif" width 1984 height
> 1210 supersample 3
> hide #32/j,k,l cartoons
> select clear
> hide #!22 models
> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/figures/structure/PAM/PAM_zoomout_nomap.tif" width 1984
> height 1210 supersample 3
> show #!22 models
> hide #!22 models
> show #!22 models
> hide #!22 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 #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/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 #2
---
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
> hide #1-2
> hide #32/k:1-6
> show #1-2 cartoons
Computing secondary structure
[Repeated 1 time(s)]
> color #1,2/L dark orange
> color #1,2/K dim gray
> color #1,2/J dark red
> color #1,2/I rebecca purple
> color #1,2/B forest green
> color #1,2/C,D,E,F,G,H salmon
> color #1,2/A steel blue
> color #1,2/A:232-350 dark turquoise
> color #1,2/O blue
> color #1,2/M red
> cartoon style nucleic xsection oval width 1 thickness 1
> hide #1-2 & nucleic cartoons
> color #32/k dim gray
> color #32/l dark orange
> select clear
> mmaker #1/a:150-200 to #32/a:150-200
Computing secondary structure
[Repeated 1 time(s)] 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 halfcleaved_HNH_inwards_refined.pdb, chain A (#1), sequence alignment
score = 253.2
RMSD between 51 pruned atom pairs is 0.259 angstroms; (across all 51 pairs:
0.259)
> mmaker #2/a:150-200 to #32/a:150-200
Computing secondary structure
[Repeated 1 time(s)] 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 halfcleaved_HNH_outwards_refined.pdb, chain A (#2), sequence alignment
score = 241.2
RMSD between 51 pruned atom pairs is 0.283 angstroms; (across all 51 pairs:
0.283)
> combine #1
> combine #2
> combine #32
> morph #2 #32 #1 #5 #4
Computed 201 frame morph #6
> coordset #6 1,201
> hide #!3 models
> hide #!6 models
> show #!6 models
> show #6 & nucleic cartoons
> cartoon style nucleic xsection oval width 1 thickness 1
> nucleotides #!6 ladder
> show #6 & nucleic
> hide #!6 models
> close #1-5
> 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 #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/NTS_cleaved/halfcleaved_HNH_inwards_refined.pdb"
Chain information for halfcleaved_HNH_inwards_refined.pdb #2
---
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_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 #3
---
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
> combine #32
> hide #1-4
> show #1-4 cartoons
Computing secondary structure
[Repeated 2 time(s)]
> color #1-4/L dark orange
> color #1-4/K dim gray
> color #1-4/J dark red
> color #1-4/I rebecca purple
> color #1-4/B forest green
> color #1-4/C,D,E,F,G,H salmon
> color #1-4/A steel blue
> color #1-4/A:232-350 dark turquoise
> color #1-4/O blue
> color #1-4/M red
> hide #!4 models
> hide #!3 models
> hide #!2 models
> hide #!1 models
> morph #1 #3 #4 #32 #2
Computed 201 frame morph #5
> coordset #5 1,201
> close #5
> morph #1 #32 #2 #4 #3
Computed 201 frame morph #5
> coordset #5 1,201
> hide #5/k:1-6
> hide #5/k:1-6 cartoons
> show #5 & nucleic
> style stick
Changed 192721 atom styles
> nucleotides #!5 ladder
> cartoon style nucleic xsection oval width 1 thickness 1
> lighting flat
> graphics silhouettes false
> graphics silhouettes true
> movie record
> movie encode /Users/zxc755/Desktop/movie1.mp4 framerate 25.0
Movie saved to /Users/zxc755/Desktop/movie1.mp4
> hide #!5 models
> show #!32 models
> show #!22 models
> show #32/k
> hide #!22 models
> select #32/K:2@O5'
1 atom, 1 residue, 1 model selected
> select add #32/K:2@C4'
2 atoms, 1 residue, 1 model selected
> select add #32/K:2@O4'
3 atoms, 1 residue, 1 model selected
> select add #32/K:2@C1'
4 atoms, 1 residue, 1 model selected
> select add #32/K:2@C2'
5 atoms, 1 residue, 1 model selected
> select add #32/K:2@C3'
6 atoms, 1 residue, 1 model selected
> hide sel
> select #32/K:2@C5'
1 atom, 1 residue, 1 model selected
> hide sel
> show #32/m,o
> select clear
> show #32/a:280,305,304
> select #32/K:3@P
1 atom, 1 residue, 1 model selected
> select add #32/K:2@O3'
2 atoms, 2 residues, 1 model selected
> select add #32/K:3@OP1
3 atoms, 2 residues, 1 model selected
> select add #32/K:3@OP2
4 atoms, 2 residues, 1 model selected
> select add #32/K:3@O5'
5 atoms, 2 residues, 1 model selected
> color sel byhetero
> select clear
> hide #32.1 models
> select #32/A:328
10 atoms, 10 bonds, 1 residue, 1 model selected
> show sel
> select clear
> select #32/A:304@ND1
1 atom, 1 residue, 1 model selected
> select add #32/M:2@MG
2 atoms, 2 residues, 1 model selected
> distance #32/A:304@ND1 #32/M:2@MG
Distance between halfcleaved_HNH_center_main_model_temp_editing.pdb #32/A HIS
304 ND1 and /M MG 2 MG: 2.3Å
> select #32/A:328@NE2
1 atom, 1 residue, 1 model selected
> select add #32/M:2@MG
2 atoms, 2 residues, 1 model selected
> distance #32/A:328@NE2 #32/M:2@MG
Distance between halfcleaved_HNH_center_main_model_temp_editing.pdb #32/A HIS
328 NE2 and /M MG 2 MG: 1.8Å
> hide #11.1 models
> select #32/O:1@O
1 atom, 1 residue, 1 model selected
> select add #32/K:3@OP2
2 atoms, 2 residues, 1 model selected
> distance #32/O:1@O #32/K:3@OP2
Distance between halfcleaved_HNH_center_main_model_temp_editing.pdb #32/O HOH
1 O and /K DA 3 OP2: 2.9Å
> select #32/A:280@NH2
1 atom, 1 residue, 1 model selected
> select add #32/K:3@OP2
2 atoms, 2 residues, 1 model selected
> distance #32/A:280@NH2 #32/K:3@OP2
Distance between halfcleaved_HNH_center_main_model_temp_editing.pdb #32/A ARG
280 NH2 and /K DA 3 OP2: 2.7Å
> select #32/A:308
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #32/A:309
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel
> hide sel cartoons
> select #32/A:309@N
1 atom, 1 residue, 1 model selected
> select add #32/O:1@O
2 atoms, 2 residues, 1 model selected
> distance #32/A:309@N #32/O:1@O
Distance between halfcleaved_HNH_center_main_model_temp_editing.pdb #32/A LEU
309 N and /O HOH 1 O: 3.0Å
> select #32/A:309@CA
1 atom, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel cartoons
> hide sel
> select #32/M:2@MG
1 atom, 1 residue, 1 model selected
> select add #32/K:3@OP1
2 atoms, 2 residues, 1 model selected
> distance #32/M:2@MG #32/K:3@OP1
Distance between halfcleaved_HNH_center_main_model_temp_editing.pdb #32/M MG 2
MG and /K DA 3 OP1: 2.5Å
> color #11 teal
> select clear
> select #32/A:305@ND1
1 atom, 1 residue, 1 model selected
> select add #32/K:3@OP2
2 atoms, 2 residues, 1 model selected
> distance sel
Distance between halfcleaved_HNH_center_main_model_temp_editing.pdb #32/A HIS
305 ND1 and /K DA 3 OP2: 2.9Å
> color #11 teal
> distance style radius 0.04
[Repeated 2 time(s)]
> distance style radius 0.05
[Repeated 2 time(s)]
> distance style dashes 4
[Repeated 2 time(s)]
> distance style dashes 5
[Repeated 2 time(s)]
> distance style dashes 4
[Repeated 2 time(s)]
> distance style dashes 3
[Repeated 2 time(s)]
> distance style dashes 2
[Repeated 2 time(s)]
> distance style dashes 1
[Repeated 2 time(s)]
> distance style dashes 2
[Repeated 2 time(s)]
> distance style dashes 3
[Repeated 2 time(s)]
> distance style dashes 4
[Repeated 2 time(s)]
> distance style dashes 5
[Repeated 2 time(s)]
> distance style dashes 6
[Repeated 2 time(s)]
> distance style dashes 7
[Repeated 2 time(s)]
> distance style dashes 8
[Repeated 2 time(s)]
> distance style dashes 7
[Repeated 2 time(s)]
> distance style dashes 8
[Repeated 2 time(s)]
> distance style dashes 7
[Repeated 2 time(s)]
> distance style dashes 6
[Repeated 2 time(s)]
> distance style dashes 5
[Repeated 2 time(s)]
> select clear
> show #!22 models
> hide #!22 models
> show #!22 models
> hide #!22 models
> show #!22 models
> hide #!22 models
> show #!22 models
> hide #!22 models
> show #!22 models
> hide #!22 models
> show #!22 models
> hide #!22 models
> show #!22 models
> hide #!22 models
> show #!22 models
> hide #!22 models
> show #32/a:319
> show #!22 models
> hide #!22 models
> select #32/A:320
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #32/A:320
8 atoms, 7 bonds, 1 residue, 1 model selected
> select clear
> ~distance #12/A:85@NZ #12/A:83@OD1
> ~distance #12/K:3@OP2 #12/A:305@ND1
> ~distance #12/M:2@MG #12/A:304@ND1
> ~distance #12/K:40@N2 #12/A:83@OD1
> ~distance #12/A:85@NZ #12/K:41@O2
> ~distance #12/A:193@OD1 #12/L:9@N2
> ~distance #12/A:280@NH2 #12/K:3@OP2
> ~distance #12/A:85@NZ #12/L:6@N2
> ~distance #12/A:191@OG #12/K:39@OP1
> ~distance #12/A:328@NE2 #12/M:2@MG
> ~distance #12/A:309@N #12/O:1@O
> ~distance #12/K:3@OP1 #12/M:2@MG
> ~distance #12/O:1@O #12/K:3@OP2
> select #32/A:305@ND1
1 atom, 1 residue, 1 model selected
> select add #32/K:3@OP2
2 atoms, 2 residues, 1 model selected
> select ~sel & ##selected
24089 atoms, 24845 bonds, 12 pseudobonds, 2799 residues, 3 models selected
> select clear
> select #32/A:305@ND1
1 atom, 1 residue, 1 model selected
> select add #32/K:3@OP2
2 atoms, 2 residues, 1 model selected
> ~distance sel
> select #32/K:3@O5'
1 atom, 1 residue, 1 model selected
> select add #32/A:305@ND1
2 atoms, 2 residues, 1 model selected
> distance sel
Distance between halfcleaved_HNH_center_main_model_temp_editing.pdb #32/K DA 3
O5' and /A HIS 305 ND1: 2.9Å
> distance style radius 0.04
[Repeated 2 time(s)]
> distance style radius 0.05
[Repeated 2 time(s)]
> color #11 teal
> select clear
> hide #32 cartoons
> hide #32/j
> show #32/a cartoons
> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/figures/structure/HNH/HNH_cat_nomap.tif" width 1984
> height 1210 supersample 3
> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/figures/structure/HNH/HNH_cat_session.cxs"
> show #32 cartoons
> hide #32/k:1-6 cartoons
> select #32/J:48
23 atoms, 25 bonds, 1 residue, 1 model selected
> show #32/j
> show #32/k:6 cartoons
> select clear
> hide #!11 models
> hide #32/a
> hide #32/m,o
> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/figures/structure/HNH/HNH_cat_zoomout_nomap.tif" width
> 1984 height 1210 supersample 3
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!13 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> show #!13 models
> surface dust #13 size 10
> hide #!32 models
> lighting soft
> lighting full
> lighting soft
> lighting simple
> lighting soft
> view
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting soft
> lighting flat
> lighting soft
> set bgColor gray
> set bgColor white
> view #13
> show #!32 models
> hide #!13 models
> hide #!32 models
> show #!12 models
> color #12/L dark orange
> color #12/K dim gray
> color #12/J dark red
> color #12/I rebecca purple
> color #12/B forest green
> color #12/C,D,E,F,G,H salmon
> color #12/A steel blue
> color #12/A:232-350 dark turquoise
> color #12/O dark turquoise
> color #12/M dark turquoise
> color #12/k:1-3 dark turquoise
> hide #!12 models
> show #!13 models
> color zone #13 near #12 distance 10
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> volume #13 level 0.05
> volume #13 change image level 0.0001303,0 level 0.002946,0.8 level 1.983,1
> volume #13 level 0.09
> volume #13 level 0.06
> volume #13 level 0.05
> volume #13 level 0.03
> turn x 90
[Repeated 3 time(s)]
> hide #!13 models
> show #!32 models
> hide #!32 models
> show #!22 models
> lighting soft
> graphics silhouettes true
> graphics silhouettes false
> lighting soft
> lighting full
> lighting soft
> lighting simple
> lighting soft
> show #!32 models
> graphics silhouettes true
> lighting flat
> hide #!32 models
> hide #!22 models
> show #!22 models
> hide #!22 models
> show #!22 models
> hide #!22 models
> show #!32 models
> hide #!32 models
> show #!32 models
> cd "/Users/zxc755/Library/CloudStorage/OneDrive-UniversityofCopenhagen/Type
> I-F_HNH/Manuscript"
Current working directory is: /Users/zxc755/Library/CloudStorage/OneDrive-
UniversityofCopenhagen/Type I-F_HNH/Manuscript
> save "/Users/zxc755/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/Type I-F_HNH/Manuscript/chimerax_session.cxs"
——— End of log from Fri Apr 25 19:29:02 2025 ———
opened ChimeraX session
> hide #!32 models
> show #!32 models
> graphics silhouettes false
> graphics silhouettes true
> hide #!32 models
> show #!1 models
> show #!2 models
> show #!3 models
> hide #!3 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> show #!32 models
> hide #1,2,32 cartoons
> hide #1,2,32
> show #1,2,32/a
> show #1,2,32/a cartoons
> hide #1,2,32
> show #!22 models
> hide #!22 models
> show #!22 models
> hide #!22 models
> open "/Users/zxc755/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/Type
> I-F_HNH/Manuscript/IFhnh_Manuscript/maps_and_models/NTS_cleaved/halfcleaved_HNH_center_fullTS_sharp.mrc"
Opened halfcleaved_HNH_center_fullTS_sharp.mrc as #7, grid size 420,420,420,
pixel 0.725, shown at level 0.00325, step 2, values float32
> open "/Users/zxc755/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/Type
> I-F_HNH/Manuscript/IFhnh_Manuscript/maps_and_models/NTS_cleaved/halfcleaved_HNH_center_main_map_sharp.mrc"
Opened halfcleaved_HNH_center_main_map_sharp.mrc as #8, grid size 420,420,420,
pixel 0.725, shown at level 0.00305, step 2, values float32
> 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 #9, grid size 420,420,420, pixel 0.725,
shown at level 0.00277, step 2, values float32
> 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 #10, grid size 420,420,420, pixel
0.725, shown at level 0.0029, step 2, values float32
> close #7,8
> hide #!2 models
> hide #!1 models
> color zone #9 near #2 distance 10
> color zone #10 near #1 distance 10
> ui tool show "Color Zone"
> volume splitbyzone #9
Opened halfcleaved_HNH_in_sharp.mrc 0 as #7.1, grid size 420,420,420, pixel
0.725, shown at level 0.00277, 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 0.00277, 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 0.00277, 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 0.00277, 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 0.00277, 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 0.00277, 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 0.00277, 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 0.00277, 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 0.00277, step 1, values float32
> volume splitbyzone #10
Opened halfcleaved_HNH_out_sharp.mrc 0 as #8.1, grid size 420,420,420, pixel
0.725, shown at level 0.0029, 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 0.0029, 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 0.0029, 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 0.0029, 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 0.0029, 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 0.0029, 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 0.0029, 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 0.0029, 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 0.0029, step 1, values float32
> hide #!7.1 models
> show #!7.1 models
> hide #!7.1 models
> hide #!7.4 models
> hide #!7.5 models
> hide #!7.6 models
> hide #!7.7 models
> hide #!7.8 models
> hide #!7.9 models
> hide #!8.1 models
> hide #!8.4 models
> hide #!8.5 models
> hide #!8.6 models
> hide #!8.7 models
> hide #!8.8 models
> hide #!8.9 models
> hide #!8 models
> show #!2 models
> transparency #7,8 90
> volume dus #7,8 siz 10
Expected a density maps specifier or a keyword
> surface dust #7.2 size 7.25
> surface dust #7.3 size 7.25
> surface dust #8 size 10
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> hide #!7 models
> show #!7 models
> volume #7.2 level 0.002
> volume #7 level 0.002
> volume #8 level 0.002
> hide #!2 models
> hide #!7 models
> show #!8 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!32 models
> show #!7 models
> show #!2 models
> hide #!1 models
> hide #!8 models
> surface dust #7 size 10
> show #!1 models
> hide #!2 models
> show #!8 models
> hide #!7 models
> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/figures/structure/subunits_with_map/Cas8_out.tif" width
> 1984 height 1210 supersample 3 transparentBackground true
> show #!2 models
> hide #!1 models
> show #!7 models
> hide #!8 models
> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/figures/structure/subunits_with_map/Cas8_in.tif" width
> 1984 height 1210 supersample 3
> hide #!2 models
> hide #!7 models
> show #!22 models
> show #!32 models
> hide #!22.2 models
> hide #!22.3 models
> hide #!22.6 models
> hide #!22.7 models
> hide #!22.8 models
> hide #!22.9 models
> hide #!22.10 models
> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/figures/structure/subunits_with_map/Cas8_cent.tif" width
> 1984 height 1210 supersample 3
> hide #!32 models
> hide #!22.5 models
> show #!22.5 models
> hide #!22 models
> show #!7 models
> show #!8 models
> hide #!7 models
> show #!7 models
> hide #!8 models
> show #!7.4 models
> show #!7.5 models
> show #!7.6 models
> show #!7.7 models
> show #!7.8 models
> show #!7.9 models
> hide #!7.9 models
> show #!7.9 models
> hide #!7.4 models
> hide #!7.5 models
> hide #!7.6 models
> hide #!7.7 models
> hide #!7.8 models
> hide #!7.9 models
> show #!2 models
> show #!1 models
> show #!8 models
> hide #!7 models
> hide #!2 models
> hide #!1 models
> hide #!8 models
> show #!22 models
> show #!32 models
> hide #!32 models
> hide #!22 models
> show #!7 models
> show #!8 models
> hide #!7 models
> show #!1 models
> hide #!1 models
> show #!1 models
> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/figures/structure/subunits_with_map/Cas8_out_2.tif" width
> 1984 height 1210 supersample 3
> hide #!8 models
> show #!7 models
> show #!2 models
> hide #!1 models
> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/figures/structure/subunits_with_map/Cas8_in_2.tif" width
> 1984 height 1210 supersample 3
> hide #!2 models
> hide #!7 models
> show #!22 models
> show #!32 models
> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/figures/structure/subunits_with_map/Cas8_cent_2.tif"
> width 1984 height 1210 supersample 3
> hide #!32 models
> hide #!22 models
> show #!22 models
> show #!32 models
> hide #!32 models
> hide #!22 models
> show #!1 models
> show #!2 models
> hide #!2 models
> hide #!1 models
> open "/Users/zxc755/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/Type
> I-F_HNH/Manuscript/IFhnh_Manuscript/maps_and_models/apo/apo_HNH_center_refined.pdb"
Chain information for apo_HNH_center_refined.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
> 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 #15
---
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_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 #16
---
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_cent_sharp.mrc"
Opened apo_HNH_cent_sharp.mrc as #17, grid size 420,420,420, pixel 0.725,
shown at level 0.00199, step 2, values float32
> 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 #18, grid size 420,420,420, pixel 0.725, shown
at level 0.00173, step 2, values float32
> 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 #19, grid size 420,420,420, pixel 0.725, shown
at level 0.00214, step 2, values float32
> hide #!19 models
> hide #!18 models
> hide #!17 models
> color ##14/L dark orange;col ##14/K dim gray;col ##14/J dark red;col ##14/I
> rebecca purple;col ##14/B forest green;col ##14/C,D,E,F,G,H salmon;col
> ##14/A steel blue;col ##14/A:232-350 dark turquoise; col ##14/O blue; col
> ##14/M red
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color #14/L dark orange
> color #14/K dim gray
> color #14/J dark red
> color #14/I rebecca purple
> color #14/B forest green
> color #14/C,D,E,F,G,H salmon
> color #14/A steel blue
> color #14/A:232-350 dark turquoise
> color #14/O blue
> color #14/M red
> color #15/L dark orange
> color #15/K dim gray
> color #15/J dark red
> color #15/I rebecca purple
> color #15/B forest green
> color #15/C,D,E,F,G,H salmon
> color #15/A steel blue
> color #15/A:232-350 dark turquoise
> color #15/O blue
> color #15/M red
> color #16/L dark orange
> color #16/K dim gray
> color #16/J dark red
> color #16/I rebecca purple
> color #16/B forest green
> color #16/C,D,E,F,G,H salmon
> color #16/A steel blue
> color #16/A:232-350 dark turquoise
> color #16/O blue
> color #16/M red
> color zone #17 near #14 distance 10
> color zone #18 near #15 distance 10
> color zone #19 near #16 distance 10
> hide #!16 models
> show #!16 models
> hide #!16 models
> hide #!15 models
> hide #!14 models
> show #!17 models
> show #!18 models
> show #!19 models
> hide #!19 models
> hide #!18 models
> hide #!17 models
> 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 #20
---
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/postcleavage_HNH_inwards_refined.pdb"
Chain information for postcleavage_HNH_inwards_refined.pdb #21
---
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/postcleavage_HNH_outwards.pdb"
Chain information for postcleavage_HNH_outwards.pdb #23
---
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_cent_sharp.mrc"
Opened post_HNH_cent_sharp.mrc as #24, grid size 420,420,420, pixel 0.725,
shown at level 0.00328, step 2, values float32
> 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 #25, grid size 420,420,420, pixel 0.725, shown
at level 0.0257, step 2, values float32
> 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 #26, grid size 420,420,420, pixel 0.725,
shown at level 0.00342, step 2, values float32
> hide #!20 models
> hide #!21 models
> hide #!23 models
> color #20/L dark orange
> color #20/K dim gray
> color #20/J dark red
> color #20/I rebecca purple
> color #20/B forest green
> color #20/C,D,E,F,G,H salmon
> color #20/A steel blue
> color #20/A:232-350 dark turquoise
> color #20/O blue
> color #20/M red
> color #21/L dark orange
> color #21/K dim gray
> color #21/J dark red
> color #21/I rebecca purple
> color #21/B forest green
> color #21/C,D,E,F,G,H salmon
> color #21/A steel blue
> color #21/A:232-350 dark turquoise
> color #21/O blue
> color #21/M red
> color #23/L dark orange
> color #23/K dim gray
> color #23/J dark red
> color #23/I rebecca purple
> color #23/B forest green
> color #23/C,D,E,F,G,H salmon
> color #23/A steel blue
> color #23/A:232-350 dark turquoise
> color #23/O blue
> color #23/M red
> color zone #24 near #20 distance 10
> color zone #25 near #21 distance 10
> color zone #26 near #23 distance 10
> hide #!26 models
> hide #!25 models
> hide #!24 models
> show #!17 models
> hide #!17 models
> volume splitbyzone #17
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_cent_sharp.mrc 6 as #27.7, grid size 420,420,420, pixel 0.725,
shown at level 0.00199, step 1, values float32
> hide #!27.1 models
> hide #!27.4 models
> hide #!27.5 models
> hide #!27.6 models
> hide #!27.7 models
> volume splitbyzone #18
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_in_sharp.mrc 6 as #28.7, grid size 420,420,420, pixel 0.725,
shown at level 0.00173, step 1, values float32
> hide #!28.1 models
> hide #!28.4 models
> hide #!28.5 models
> hide #!28.6 models
> hide #!28.7 models
> volume splitbyzone #19
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 apo_HNH_out_sharp.mrc 6 as #29.7, grid size 420,420,420, pixel 0.725,
shown at level 0.00214, step 1, values float32
> hide #!29.1 models
> hide #!29.4 models
> show #!29.4 models
> hide #!29.4 models
> hide #!29.5 models
> hide #!29.6 models
> hide #!29.7 models
> hide #!27 models
> hide #!28 models
> hide #!29 models
> volume splitbyzone #24
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_cent_sharp.mrc 8 as #30.9, grid size 420,420,420, pixel 0.725,
shown at level 0.00328, step 1, values float32
> volume splitbyzone #25
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 0.0257, 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_in_sharp.mrc 8 as #31.9, grid size 420,420,420, pixel 0.725,
shown at level 0.0257, step 1, values float32
> volume splitbyzone #26
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
Opened post_HNH_out_sharp.mrc 8 as #33.9, grid size 420,420,420, pixel 0.725,
shown at level 0.00342, step 1, values float32
> hide #!30.1 models
> hide #!30.4 models
> hide #!30.5 models
> hide #!30.6 models
> hide #!30.7 models
> hide #!30.8 models
> hide #!30.9 models
> hide #!31.1 models
> hide #!31.4 models
> hide #!31.5 models
> hide #!31.6 models
> hide #!31.7 models
> hide #!31.8 models
> hide #!31.9 models
> hide #!33.1 models
> hide #!33.4 models
> hide #!33.5 models
> hide #!33.6 models
> hide #!33.7 models
> hide #!33.8 models
> hide #!33.9 models
> show #!32 models
> hide #!32 models
> show #!22 models
> hide #!22 models
> show #!29 models
> show #!28 models
> show #!27 models
> transparency 90
> surface dust siz 10
Missing or invalid "surfaces" argument: invalid surfaces specifier
> surface dust #27-31 #33 size 10
> hide #!33 models
> hide #!31 models
> hide #!30 models
> hide #!29 models
> hide #!28 models
Must specify one map, got 10
> fitmap #27.2 inMap #22.4
Fit map apo_HNH_cent_sharp.mrc 1 in map halfcleaved_HNH_center_sharp3Å.mrc 3
using 53530 points
correlation = 0, correlation about mean = 0, overlap = 0
steps = 24, shift = 0, angle = 0 degrees
Position of apo_HNH_cent_sharp.mrc 1 (#27.2) relative to
halfcleaved_HNH_center_sharp3Å.mrc 3 (#22.4) coordinates:
Matrix rotation and translation
1.00000000 0.00000000 0.00000000 0.00000000
0.00000000 1.00000000 0.00000000 0.00000000
0.00000000 0.00000000 1.00000000 0.00000000
Axis 0.00000000 0.00000000 1.00000000
Axis point 0.00000000 0.00000000 0.00000000
Rotation angle (degrees) 0.00000000
Shift along axis 0.00000000
> hide #!27.2 models
> show #!27.2 models
> hide #!27.2 models
> show #!27.2 models
> show #!22 models
> hide #!22.4 models
> show #!22.4 models
> hide #!22.4 models
> show #!22.4 models
> hide #!22.4 models
> show #!22.4 models
> hide #!27.2 models
> show #!27.2 models
> fitmap #27.2 inMap #22.4
Fit map apo_HNH_cent_sharp.mrc 1 in map halfcleaved_HNH_center_sharp3Å.mrc 3
using 53530 points
correlation = 0, correlation about mean = 0, overlap = 0
steps = 24, shift = 0, angle = 0 degrees
Position of apo_HNH_cent_sharp.mrc 1 (#27.2) relative to
halfcleaved_HNH_center_sharp3Å.mrc 3 (#22.4) coordinates:
Matrix rotation and translation
1.00000000 0.00000000 0.00000000 0.00000000
0.00000000 1.00000000 0.00000000 0.00000000
0.00000000 0.00000000 1.00000000 0.00000000
Axis 0.00000000 0.00000000 1.00000000
Axis point 0.00000000 0.00000000 0.00000000
Rotation angle (degrees) 0.00000000
Shift along axis 0.00000000
> select #27.2
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #27.2,-0.90481,-0.32416,-0.27613,332.21,0.31284,-0.94596,0.085389,229.16,-0.28888,-0.0091226,0.95732,44.701
> view matrix models
> #27.2,-0.97923,-0.19279,0.06285,325.19,0.18122,-0.97109,-0.15536,293.34,0.090985,-0.14075,0.98586,0.54729
> undo
[Repeated 2 time(s)]
> close #27-31
> close #33
> color #14-16/a steel blue
> show #!14 models
> hide #!14 models
> show #!14 models
> show #!15 models
> hide #!15 models
> hide #!14 models
> show #!14 models
> hide #!14 models
> show #!14 models
> hide #!14 models
> color #20,21,23/a steel blue
> color zone #17 near #14 distance 10
> color zone #18 near #15 distance 10
> color zone #19 near #16 distance 10
> color #24 nea #20 dis 10
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color zone #24 near #20 distance 10
> color zone #25 near #21 distance 10
> color zone #26 near #23 distance 10
> volume splitbyzone #17
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
> volume splitbyzone #18
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
> volume splitbyzone #19
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
> volume splitbyzone #24
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
> volume splitbyzone #25
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 0.0257, 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
> volume splitbyzone #26
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
> hide #!33 models
> hide #!33.1 models
> hide #!33.3 models
> show #!33 models
> hide #!33.4 models
> hide #!33.5 models
> hide #!33.6 models
> hide #!33.7 models
> hide #!33.8 models
> hide #!31.8 models
> hide #!31.7 models
> hide #!31.6 models
> hide #!31.5 models
> hide #!31.4 models
> hide #!31.3 models
> hide #!31.1 models
> hide #!30.8 models
> hide #!30.7 models
> hide #!30.6 models
> hide #!30.5 models
> hide #!30.4 models
> hide #!30.3 models
> hide #!30.1 models
> hide #!29.6 models
> hide #!29.5 models
> hide #!29.4 models
> hide #!29.3 models
> hide #!29.1 models
> hide #!28.6 models
> hide #!28.5 models
> hide #!28.4 models
> hide #!28.3 models
> hide #!28.1 models
> hide #!27.6 models
> hide #!27.5 models
> hide #!27.4 models
> hide #!27.3 models
> hide #!27.1 models
> hide #!22 models
> transparency #27-31,33 90
> show #!22 models
> hide #!28 models
> hide #!29 models
> hide #!30 models
> hide #!31 models
> hide #!33 models
> fitmap #27.2 inMap #22.4
Fit map apo_HNH_cent_sharp.mrc 1 in map halfcleaved_HNH_center_sharp3Å.mrc 3
using 82885 points
correlation = 0, correlation about mean = 0, overlap = 0
steps = 24, shift = 0, angle = 0 degrees
Position of apo_HNH_cent_sharp.mrc 1 (#27.2) relative to
halfcleaved_HNH_center_sharp3Å.mrc 3 (#22.4) coordinates:
Matrix rotation and translation
1.00000000 0.00000000 0.00000000 0.00000000
0.00000000 1.00000000 0.00000000 0.00000000
0.00000000 0.00000000 1.00000000 0.00000000
Axis 0.00000000 0.00000000 1.00000000
Axis point 0.00000000 0.00000000 0.00000000
Rotation angle (degrees) 0.00000000
Shift along axis 0.00000000
> select #27.2
2 models selected
> select add #27
13 models selected
> view matrix models
> #27,-0.9851,0.028378,0.1696,261.6,0.012815,-0.97143,0.23698,244.5,0.17148,0.23562,0.9566,-52.331
Drag select of 27.2 apo_HNH_cent_sharp.mrc 1
> view matrix models
> #27.2,1,4.8572e-17,6.1062e-16,-14.27,8.32e-32,1,4.1633e-16,-23.71,3.8858e-16,1.6653e-16,1,-1.3138
> view matrix models
> #27.2,1,4.8572e-17,6.1062e-16,10.218,8.32e-32,1,4.1633e-16,-19.262,3.8858e-16,1.6653e-16,1,-23.993
> color #27.2 red
> view matrix models
> #27.2,1,0.0011286,0.00024256,-17.671,-0.0011282,1,-0.001653,-23.156,-0.00024442,0.0016527,1,0.99344
> view matrix models
> #27.2,0.98647,0.15904,0.039716,-44.71,-0.15822,0.86043,0.48439,-45.115,0.042865,-0.48412,0.87395,80.037
> surface dust #27-31,33 size 10
> hide #!27 models
> select add #27
13 models selected
> select subtract #27
Nothing selected
> hide #!22 models
> show #!22 models
> show #!30 models
> select add #30
17 models selected
> color #30.2 green
> view matrix models
> #30,0.99278,0.11969,0.0075487,-17.819,-0.11662,0.97821,-0.17177,45.003,-0.027942,0.16965,0.98511,-26.609
> select subtract #30
Nothing selected
> hide #!30 models
> hide #!22 models
> show #!2 models
> hide #!2 models
> show #!7 models
> show #!28 models
> color #28.2 red
> color #29.2 red
> color #31.2 green
> color #33.2 green
> select add #28
13 models selected
> view matrix models
> #28,-0.93864,-0.18774,0.28933,282.81,0.11817,-0.96316,-0.24158,292.86,0.32402,-0.19257,0.92624,-7.1144
> view matrix models
> #28,-0.93864,-0.18774,0.28933,281.83,0.11817,-0.96316,-0.24158,308.33,0.32402,-0.19257,0.92624,-20.3
> view matrix models
> #28,-0.94765,-0.24867,0.20033,309.6,0.18207,-0.93615,-0.30078,306.85,0.26233,-0.24856,0.93242,-0.83323
> view matrix models
> #28,-0.95707,-0.19669,0.2129,302.83,0.13597,-0.95335,-0.26952,311.55,0.25597,-0.229,0.93917,-4.0077
> view matrix models
> #28,-0.95956,-0.22645,0.1672,313.45,0.18549,-0.95546,-0.22952,299.35,0.21173,-0.18923,0.95883,-5.8084
> view matrix models
> #28,-0.95956,-0.22645,0.1672,313,0.18549,-0.95546,-0.22952,299.82,0.21173,-0.18923,0.95883,-5.8642
> view matrix models
> #28,-0.94956,-0.28011,0.14095,322.64,0.23523,-0.93354,-0.2705,294.86,0.20736,-0.2237,0.95235,0.5275
> select subtract #28
Nothing selected
> hide #!28 models
> show #!31 models
> select add #31
17 models selected
> view matrix models
> #31,0.95745,0.28853,-0.0061963,-39.992,-0.2858,0.94498,-0.15916,77.745,-0.040066,0.15415,0.98723,-22.047
> view matrix models
> #31,0.98495,0.16362,0.055651,-31.707,-0.14812,0.9651,-0.21598,59.788,-0.089048,0.20449,0.97481,-20.953
> view matrix models
> #31,0.98502,0.15503,0.075475,-31.759,-0.13914,0.9732,-0.18309,50.935,-0.10184,0.16984,0.98019,-13.582
> view matrix models
> #31,0.98251,0.17881,0.052001,-31.724,-0.16394,0.96301,-0.21385,60.765,-0.088316,0.20159,0.97548,-20.561
> view matrix models
> #31,0.98782,0.1293,0.086525,-28.788,-0.10934,0.97261,-0.20513,49.258,-0.11068,0.19317,0.9749,-15.438
> select subtract #31
Nothing selected
> hide #!31 models
> hide #!7 models
> show #!8 models
> show #!29 models
> select add #29
13 models selected
> view matrix models
> #29,-0.96301,-0.11026,0.24587,268.61,0.020435,-0.93971,-0.34137,320.74,0.26869,-0.32372,0.9072,1.2682
> view matrix models
> #29,-0.92586,-0.36935,0.079794,337.56,0.33423,-0.89898,-0.28307,279.15,0.17629,-0.23541,0.95577,1.8338
> view matrix models
> #29,-0.9501,-0.28304,0.13113,324.32,0.24497,-0.93725,-0.24809,292.2,0.19312,-0.20359,0.95982,-2.6028
> view matrix models
> #29,-0.94885,-0.296,0.10988,328.51,0.25817,-0.9277,-0.26968,291.73,0.18176,-0.22752,0.95666,1.6234
> view matrix models
> #29,-0.95084,-0.25098,0.18144,313.28,0.21054,-0.95351,-0.21564,295.36,0.22712,-0.16684,0.95947,-11.512
> view matrix models
> #29,-0.94437,-0.26912,0.18906,314.35,0.22158,-0.94541,-0.23894,296.14,0.24304,-0.18376,0.95245,-10.94
> hide #!29 models
> select subtract #29
Nothing selected
> show #!33 models
> select add #33
17 models selected
> view matrix models
> #33,0.95382,0.29041,-0.076702,-29.712,-0.30037,0.92263,-0.24193,98.778,0.0005105,0.25379,0.96726,-42.939
> view matrix models
> #33,0.96865,0.24664,-0.029782,-31.412,-0.24842,0.96286,-0.10577,62.659,0.0025886,0.10985,0.99394,-24.767
> view matrix models
> #33,0.9728,0.17623,-0.15036,-2.5415,-0.20302,0.96116,-0.18696,65.208,0.11158,0.2124,0.97079,-60.099
> view matrix models
> #33,0.98074,0.15825,0.11447,-37.799,-0.13348,0.97094,-0.19866,54.576,-0.14258,0.17955,0.97336,-11.971
> view matrix models
> #33,0.98222,0.15787,0.10163,-34.87,-0.13329,0.96753,-0.21473,54.252,-0.13223,0.19737,0.97137,-14.291
> view matrix models
> #33,0.98222,0.15787,0.10163,-35.019,-0.13329,0.96753,-0.21473,54.238,-0.13223,0.19737,0.97137,-13.879
> fitmap #33.2 inMap #8.4
Fit map post_HNH_out_sharp.mrc 1 in map halfcleaved_HNH_out_sharp.mrc 3 using
87660 points
correlation = 0.2302, correlation about mean = 0.1069, overlap = 657.4
steps = 364, shift = 12.6, angle = 27.8 degrees
Position of post_HNH_out_sharp.mrc 1 (#33.2) relative to
halfcleaved_HNH_out_sharp.mrc 3 (#8.4) coordinates:
Matrix rotation and translation
0.88487665 -0.11856540 -0.45048370 86.96048472
0.12698700 0.99183644 -0.01160897 -10.81407486
0.44818257 -0.04693306 0.89270917 -57.31875206
Axis -0.03789003 -0.96394524 0.26338929
Axis point 159.50208814 0.00000000 151.60629729
Rotation angle (degrees) 27.78400581
Shift along axis -7.96790445
> fitmap #33.2 inMap #8.2
Fit map post_HNH_out_sharp.mrc 1 in map halfcleaved_HNH_out_sharp.mrc 1 using
87660 points
correlation = 0.7507, correlation about mean = 0.6577, overlap = 3498
steps = 300, shift = 13.1, angle = 25.8 degrees
Position of post_HNH_out_sharp.mrc 1 (#33.2) relative to
halfcleaved_HNH_out_sharp.mrc 1 (#8.2) coordinates:
Matrix rotation and translation
0.99883251 0.02105205 -0.04347916 3.28381267
-0.01860045 0.99825524 0.05604021 -3.01589348
0.04458306 -0.05516605 0.99748136 2.36658331
Axis -0.75501980 -0.59788649 -0.26921525
Axis point 0.00000000 33.34610426 68.86626768
Rotation angle (degrees) 4.22334809
Shift along axis -1.31330194
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!33 models
> show #!29 models
> fitmap #29.2 inMap #8.2
Fit map apo_HNH_out_sharp.mrc 1 in map halfcleaved_HNH_out_sharp.mrc 1 using
83162 points
correlation = 0.6154, correlation about mean = 0.4909, overlap = 1988
steps = 108, shift = 0.371, angle = 3.89 degrees
Position of apo_HNH_out_sharp.mrc 1 (#29.2) relative to
halfcleaved_HNH_out_sharp.mrc 1 (#8.2) coordinates:
Matrix rotation and translation
0.99774720 -0.00616969 0.06680170 -7.75363432
0.00547813 0.99992955 0.01053061 -2.15873626
-0.06686197 -0.01014094 0.99771070 11.37852778
Axis -0.15227290 0.98460707 0.08580135
Axis point 165.97569556 0.00000000 121.59503582
Rotation angle (degrees) 3.89203832
Shift along axis 0.03145444
> select subtract #33
Nothing selected
> hide #!29 models
> hide #!8 models
> show #!7 models
> show #!28 models
> fitmap #28.2 inMap #7.2
Fit map apo_HNH_in_sharp.mrc 1 in map halfcleaved_HNH_in_sharp.mrc 1 using
78989 points
correlation = 0.6568, correlation about mean = 0.5566, overlap = 1483
steps = 100, shift = 1.93, angle = 2.75 degrees
Position of apo_HNH_in_sharp.mrc 1 (#28.2) relative to
halfcleaved_HNH_in_sharp.mrc 1 (#7.2) coordinates:
Matrix rotation and translation
0.99894275 -0.01608144 0.04306693 -3.27929226
0.01666443 0.99977384 -0.01321212 -2.52037376
-0.04284472 0.01391584 0.99898482 4.13599960
Axis 0.28299722 0.89622541 0.34160298
Axis point 109.08725783 0.00000000 67.16502763
Rotation angle (degrees) 2.74722295
Shift along axis -1.77398382
> hide #!28 models
> show #!31 models
> fitmap #31.2 inMap #7.2
Fit map post_HNH_in_sharp.mrc 1 in map halfcleaved_HNH_in_sharp.mrc 1 using
83790 points
correlation = 0.5948, correlation about mean = 0.441, overlap = 2814
steps = 152, shift = 1.12, angle = 4.52 degrees
Position of post_HNH_in_sharp.mrc 1 (#31.2) relative to
halfcleaved_HNH_in_sharp.mrc 1 (#7.2) coordinates:
Matrix rotation and translation
0.99726035 0.04676217 -0.05731570 1.19747961
-0.04518981 0.99857380 0.02842974 4.02672915
0.05856339 -0.02576177 0.99795123 -4.59092844
Axis -0.34397877 -0.73553868 -0.58366211
Axis point 85.75257186 0.00000000 12.62773521
Rotation angle (degrees) 4.51795970
Shift along axis -0.69417165
> hide #!31 models
> show #!22 models
> hide #!22.4 models
> show #!22.4 models
> hide #!22.4 models
> show #!22.4 models
> hide #!7 models
> show #!30 models
> fitmap #30.2 inMap #22.4
Fit map post_HNH_cent_sharp.mrc 1 in map halfcleaved_HNH_center_sharp3Å.mrc 3
using 86342 points
correlation = 0.7861, correlation about mean = 0.6973, overlap = 3404
steps = 84, shift = 0.298, angle = 2.98 degrees
Position of post_HNH_cent_sharp.mrc 1 (#30.2) relative to
halfcleaved_HNH_center_sharp3Å.mrc 3 (#22.4) coordinates:
Matrix rotation and translation
0.99880892 0.03024374 0.03828920 -9.33094617
-0.03093378 0.99936719 0.01755928 3.13913491
-0.03773391 -0.01872279 0.99911241 9.35512683
Axis -0.34850229 0.73022926 -0.58763201
Axis point 242.75204382 0.00000000 250.82225024
Rotation angle (degrees) 2.98383902
Shift along axis 0.04677237
> hide #!30 models
> show #!27 models
> fitmap #27.2 inMap #22.4
Fit map apo_HNH_cent_sharp.mrc 1 in map halfcleaved_HNH_center_sharp3Å.mrc 3
using 82885 points
correlation = 0.608, correlation about mean = 0.4719, overlap = 1708
steps = 124, shift = 1.2, angle = 3.81 degrees
Position of apo_HNH_cent_sharp.mrc 1 (#27.2) relative to
halfcleaved_HNH_center_sharp3Å.mrc 3 (#22.4) coordinates:
Matrix rotation and translation
0.97832698 0.19020262 0.08184916 -54.13025495
-0.20662179 0.87084737 0.44601826 -34.04774174
0.01355572 -0.45326352 0.89127348 78.28203288
Axis -0.91268658 0.06931143 -0.40273953
Axis point 0.00000000 156.71923356 124.12929737
Rotation angle (degrees) 29.51532960
Shift along axis 15.51679105
> show #!14 models
> style stick
Changed 332211 atom styles
> hide #14
> show #14/a cartoons
Computing secondary structure
> color #14/a red
> fitmap #14/a inMap #27.2
Fit molecule apo_HNH_center_refined.pdb (#14) to map apo_HNH_cent_sharp.mrc 1
(#27.2) using 2728 atoms
average map value = 0.0141, steps = 2000
shifted from previous position = 21.7
rotated from previous position = 19 degrees
atoms outside contour = 2485, contour level = 0.0019908
Position of apo_HNH_center_refined.pdb (#14) relative to
apo_HNH_cent_sharp.mrc 1 (#27.2) coordinates:
Matrix rotation and translation
0.87515076 -0.42346707 0.23406577 55.94220375
0.48348878 0.74666401 -0.45687137 70.79007602
0.01870149 0.51299950 0.85818516 -55.77887122
Axis 0.72097898 0.16009669 0.67420944
Axis point 0.00000000 146.26043027 68.91682292
Rotation angle (degrees) 42.26858727
Shift along axis 14.05976817
> select #14/A:169
8 atoms, 7 bonds, 1 residue, 1 model selected
> view matrix models
> #14,-0.60187,-0.59648,-0.531,396.65,0.776,-0.27978,-0.56529,167.42,0.18862,-0.75229,0.63126,115.81
> fitmap #14/a inMap #27.2
Fit molecule apo_HNH_center_refined.pdb (#14) to map apo_HNH_cent_sharp.mrc 1
(#27.2) using 2728 atoms
average map value = 0.04066, steps = 124
shifted from previous position = 2.25
rotated from previous position = 10.1 degrees
atoms outside contour = 1852, contour level = 0.0019908
Position of apo_HNH_center_refined.pdb (#14) relative to
apo_HNH_cent_sharp.mrc 1 (#27.2) coordinates:
Matrix rotation and translation
-0.82083116 -0.46116689 -0.33698869 392.52408221
0.45571980 -0.17311548 -0.87312688 269.72015669
0.34431924 -0.87026214 0.35226145 171.58912907
Axis 0.00250785 -0.59643049 0.80266081
Axis point 145.87352872 275.32026651 0.00000000
Rotation angle (degrees) 145.16922813
Shift along axis -22.15706392
> view matrix models
> #14,-0.91976,-0.13361,0.36905,259.57,0.12723,-0.991,-0.041693,295.14,0.3713,0.0086066,0.92847,-56.6
> view matrix models
> #14,-0.94601,-0.32105,-0.044503,348.25,0.30157,-0.82153,-0.48389,302.66,0.1188,-0.47119,0.874,58.735
> fitmap #14/a inMap #27.2
Fit molecule apo_HNH_center_refined.pdb (#14) to map apo_HNH_cent_sharp.mrc 1
(#27.2) using 2728 atoms
average map value = 0.1677, steps = 128
shifted from previous position = 5.27
rotated from previous position = 18.3 degrees
atoms outside contour = 544, contour level = 0.0019908
Position of apo_HNH_center_refined.pdb (#14) relative to
apo_HNH_cent_sharp.mrc 1 (#27.2) coordinates:
Matrix rotation and translation
-0.98941113 -0.04220312 0.13886890 304.43360331
-0.05300114 -0.78565708 -0.61638777 392.25034981
0.13511682 -0.61722111 0.77510102 112.81565364
Axis -0.07270707 0.32735899 -0.94209860
Axis point 148.46002111 215.26270714 0.00000000
Rotation angle (degrees) 179.67164584
Shift along axis -0.01126639
> select clear
> hide #!14 models
> show #!14 models
> hide #!14 models
> hide #!27 models
> show #!30 models
> show #!20 models
> hide #20
> show #20/a
> color #20/a green
> hide #20
> show #20/a cartoons
Computing secondary structure
> fitmap #20/a inMap #30.2
Fit molecule postcleavage_HNH_center_refined.pdb (#20) to map
post_HNH_cent_sharp.mrc 1 (#30.2) using 2728 atoms
average map value = 0.2822, steps = 108
shifted from previous position = 5.73
rotated from previous position = 12.7 degrees
atoms outside contour = 221, contour level = 0.0032808
Position of postcleavage_HNH_center_refined.pdb (#20) relative to
post_HNH_cent_sharp.mrc 1 (#30.2) coordinates:
Matrix rotation and translation
0.99338756 0.11381514 0.01507534 -17.65419683
-0.10945975 0.97851549 -0.17471692 44.27616892
-0.03463688 0.17191148 0.98450329 -25.68733743
Axis 0.83464546 0.11970190 -0.53762293
Axis point 0.00000000 156.57774257 231.16518944
Rotation angle (degrees) 11.98467665
Shift along axis 4.37504802
> show #!32 models
> show #!14 models
> show #!17 models
> hide #!17 models
> show #!27 models
> hide #!20 models
> hide #!22 models
> hide #!27 models
> hide #!30 models
> hide #!32 models
> hide #!14 models
> show #!15 models
> hide #15-6
> hide #15
> hide #15,16
> show #15,16/a cartoons
Computing secondary structure
[Repeated 1 time(s)]
> color #15,16/a red
> show #!28 models
> select #15/A:341
14 atoms, 15 bonds, 1 residue, 1 model selected
> view matrix models
> #15,-0.93405,-0.34831,-0.078927,345.57,0.30616,-0.66712,-0.67913,293.42,0.1839,-0.65851,0.72976,90.717
> fitmap #15/a nea #28.2
Expected a keyword
> fitmap #15/a inMap #28.2
Fit molecule apo_HNH_inwards_refined.pdb (#15) to map apo_HNH_in_sharp.mrc 1
(#28.2) using 2728 atoms
average map value = 0.02958, steps = 260
shifted from previous position = 11.6
rotated from previous position = 23.4 degrees
atoms outside contour = 2054, contour level = 0.0017272
Position of apo_HNH_inwards_refined.pdb (#15) relative to apo_HNH_in_sharp.mrc
1 (#28.2) coordinates:
Matrix rotation and translation
-0.79630665 -0.43561221 -0.41968766 386.18629814
0.58540743 -0.38030007 -0.71600978 230.23651908
0.15229535 -0.81585162 0.55784610 144.52477351
Axis -0.08500291 -0.48697238 0.86927120
Axis point 158.93131778 227.39289934 0.00000000
Rotation angle (degrees) 144.03543017
Shift along axis -19.31456020
> view matrix models
> #15,-0.94602,-0.14843,-0.28813,357.26,0.24355,-0.9121,-0.32979,304.65,-0.21385,-0.38217,0.89901,84.308
> fitmap #15/a inMap #28.2
Fit molecule apo_HNH_inwards_refined.pdb (#15) to map apo_HNH_in_sharp.mrc 1
(#28.2) using 2728 atoms
average map value = 0.1223, steps = 184
shifted from previous position = 7.42
rotated from previous position = 24 degrees
atoms outside contour = 707, contour level = 0.0017272
Position of apo_HNH_inwards_refined.pdb (#15) relative to apo_HNH_in_sharp.mrc
1 (#28.2) coordinates:
Matrix rotation and translation
-0.96127242 -0.26981301 0.05618076 335.20428011
0.25014099 -0.93972629 -0.23311799 292.00968965
0.11569280 -0.21003679 0.97082425 10.38879106
Axis 0.04406009 -0.11360351 0.99254871
Axis point 147.82603778 169.13090853 0.00000000
Rotation angle (degrees) 164.81546446
Shift along axis -8.09281367
> select clear
> hide #!15 models
> hide #!28 models
> show #!31 models
> show #!15 models
> hide #!15 models
> show #!21 models
> show #!20 models
> hide #!20 models
> show #!23 models
> hide #!23 models
> hide #21,23
> show #21,23/a cartoons
Computing secondary structure
[Repeated 1 time(s)]
> color #21,23/a green
> fitmap #21/a inMap #31.2
Fit molecule postcleavage_HNH_inwards_refined.pdb (#21) to map
post_HNH_in_sharp.mrc 1 (#31.2) using 2703 atoms
average map value = 0.2685, steps = 112
shifted from previous position = 5.5
rotated from previous position = 13.7 degrees
atoms outside contour = 520, contour level = 0.025678
Position of postcleavage_HNH_inwards_refined.pdb (#21) relative to
post_HNH_in_sharp.mrc 1 (#31.2) coordinates:
Matrix rotation and translation
0.98616651 0.13380918 0.09783004 -31.07144516
-0.11332146 0.97498229 -0.19122706 47.65695927
-0.12097049 0.17749548 0.97665833 -11.51991642
Axis 0.74507872 0.44213088 -0.49937760
Axis point 0.00000000 84.76781023 229.63504986
Rotation angle (degrees) 14.32599614
Shift along axis 3.67272934
> hide #!31 models
> show #!33 models
> show #!23 models
> hide #!21 models
> fitmap #23/a inMap #33.2
Fit molecule postcleavage_HNH_outwards.pdb (#23) to map post_HNH_out_sharp.mrc
1 (#33.2) using 2728 atoms
average map value = 0.2713, steps = 180
shifted from previous position = 7.21
rotated from previous position = 13.7 degrees
atoms outside contour = 230, contour level = 0.003418
Position of postcleavage_HNH_outwards.pdb (#23) relative to
post_HNH_out_sharp.mrc 1 (#33.2) coordinates:
Matrix rotation and translation
0.98012633 0.16191619 0.11461028 -37.06976884
-0.13594647 0.96898777 -0.20635229 53.55638420
-0.14446774 0.18667045 0.97174236 -10.17466150
Axis 0.70553647 0.46508503 -0.53470946
Axis point 0.00000000 78.56032267 238.27779114
Rotation angle (degrees) 16.17234589
Shift along axis 4.19468674
> show #!20 models
> hide #!23 models
> hide #!33 models
> show #!30 models
> show #!33 models
> hide #!33 models
> show #!33 models
> hide #!33 models
> show #!33 models
> hide #!33 models
> hide #!30 models
> show #!21 models
> hide #!21 models
> show #!21 models
> show #!23 models
> hide #!23 models
> hide #!21 models
> show #!14 models
> show #!32 models
> hide #!32 models
> hide #!20 models
> hide #!14 models
> show #!15 models
> show #!21 models
> show #!2 models
> hide #!2 models
> hide #!15 models
> hide #!21 models
> show #!16 models
> show #!23 models
> show #!1 models
> show #!29 models
> select #16/A:287
5 atoms, 4 bonds, 1 residue, 1 model selected
> view matrix models
> #16,0.62757,-0.044878,-0.77726,162.91,0.38861,0.88314,0.26278,-73.948,0.67464,-0.46696,0.57167,26.566
> view matrix models
> #16,-0.40419,-0.68046,-0.61123,393.44,0.90481,-0.39532,-0.15824,86.915,-0.13395,-0.617,0.77548,143.78
> view matrix models
> #16,-0.39826,-0.68007,-0.61555,393.45,0.90771,-0.38883,-0.1577,112.35,-0.1321,-0.62154,0.77216,126.84
> fitmap #23/a inMap #29.2
Fit molecule postcleavage_HNH_outwards.pdb (#23) to map apo_HNH_out_sharp.mrc
1 (#29.2) using 2728 atoms
average map value = 0.1546, steps = 40
shifted from previous position = 0.0804
rotated from previous position = 0.183 degrees
atoms outside contour = 645, contour level = 0.0021375
Position of postcleavage_HNH_outwards.pdb (#23) relative to
apo_HNH_out_sharp.mrc 1 (#29.2) coordinates:
Matrix rotation and translation
0.98502518 0.17240574 0.00128825 -22.90899269
-0.16981904 0.97148276 -0.16547731 53.93769403
-0.02978076 0.16278055 0.98621276 -24.79677780
Axis 0.69074579 0.06537784 -0.72013610
Axis point 285.26360326 179.92837540 0.00000000
Rotation angle (degrees) 13.74559352
Shift along axis 5.55909429
> view matrix models
> #16,-0.89523,-0.41361,-0.16578,367.07,0.41729,-0.64769,-0.63747,283.05,0.15628,-0.63986,0.75243,90.762
> fitmap #23/a inMap #29.2
Fit molecule postcleavage_HNH_outwards.pdb (#23) to map apo_HNH_out_sharp.mrc
1 (#29.2) using 2728 atoms
average map value = 0.1546, steps = 40
shifted from previous position = 0.0116
rotated from previous position = 0.0128 degrees
atoms outside contour = 644, contour level = 0.0021375
Position of postcleavage_HNH_outwards.pdb (#23) relative to
apo_HNH_out_sharp.mrc 1 (#29.2) coordinates:
Matrix rotation and translation
0.98500387 0.17252839 0.00115057 -22.91842576
-0.16996614 0.97147812 -0.16535350 53.95165575
-0.02964593 0.16267828 0.98623369 -24.80251774
Axis 0.69024031 0.06480160 -0.72067265
Axis point 285.13190470 179.83196787 0.00000000
Rotation angle (degrees) 13.74619735
Shift along axis 5.55142851
> hide #!29 models
> show #!29 models
> view matrix models
> #16,-0.88458,-0.38657,-0.26093,381.82,0.46041,-0.81307,-0.35627,265.27,-0.074434,-0.43529,0.89721,76.738
> fitmap #23/a inMap #29.2
Fit molecule postcleavage_HNH_outwards.pdb (#23) to map apo_HNH_out_sharp.mrc
1 (#29.2) using 2728 atoms
average map value = 0.1546, steps = 28
shifted from previous position = 0.0105
rotated from previous position = 0.016 degrees
atoms outside contour = 645, contour level = 0.0021375
Position of postcleavage_HNH_outwards.pdb (#23) relative to
apo_HNH_out_sharp.mrc 1 (#29.2) coordinates:
Matrix rotation and translation
0.98502926 0.17238229 0.00130491 -22.90911466
-0.16979162 0.97147864 -0.16552961 53.94066736
-0.02980207 0.16282995 0.98620396 -24.80004337
Axis 0.69090730 0.06545276 -0.71997434
Axis point 285.31689662 179.95179673 0.00000000
Rotation angle (degrees) 13.74665869
Shift along axis 5.55788562
> fitmap #16/A inMap #29.2
Fit molecule apo_HNH_outwards_refined.pdb (#16) to map apo_HNH_out_sharp.mrc 1
(#29.2) using 2684 atoms
average map value = 0.1709, steps = 164
shifted from previous position = 5.87
rotated from previous position = 25 degrees
atoms outside contour = 433, contour level = 0.0021375
Position of apo_HNH_outwards_refined.pdb (#16) relative to
apo_HNH_out_sharp.mrc 1 (#29.2) coordinates:
Matrix rotation and translation
-0.96402236 -0.25980162 0.05624954 334.31569824
0.23888339 -0.93953169 -0.24538732 293.59018493
0.11660025 -0.22312178 0.96779185 12.48674161
Axis 0.04428161 -0.12002525 0.99178278
Axis point 148.03200436 169.10595691 0.00000000
Rotation angle (degrees) 165.43913121
Shift along axis -8.05006265
Must specify one map, got 0
> fitmap #23/a inMap #33.2
Fit molecule postcleavage_HNH_outwards.pdb (#23) to map post_HNH_out_sharp.mrc
1 (#33.2) using 2728 atoms
average map value = 0.2714, steps = 60
shifted from previous position = 0.085
rotated from previous position = 0.177 degrees
atoms outside contour = 229, contour level = 0.003418
Position of postcleavage_HNH_outwards.pdb (#23) relative to
post_HNH_out_sharp.mrc 1 (#33.2) coordinates:
Matrix rotation and translation
0.98009236 0.16199252 0.11479281 -37.09053836
-0.13597963 0.96897219 -0.20640359 53.56869743
-0.14466688 0.18668509 0.97170992 -10.14527457
Axis 0.70529698 0.46553397 -0.53463472
Axis point 0.00000000 78.41673669 238.26776560
Rotation angle (degrees) 16.18077713
Shift along axis 4.20221993
> show #!33 models
> show #!8 models
> select clear
> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/figures/structure/cas8_movement/cas8_out_overlap_maps.tif"
> width 1984 height 1210 supersample 3
> hide #!33 models
> hide #!29 models
> hide #!8 models
> color #1/a steel blue
> color #8.3 steel blue
> show #!8 models
> hide #!8.3 models
> show #!8.3 models
> hide #!8 models
> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/figures/structure/cas8_movement/cas8_out_overlap.tif"
> width 1984 height 1210 supersample 3
> show #!8 models
> show #!29 models
> show #!33 models
> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/figures/structure/cas8_movement/cas8_out_overlap_maps.tif"
> width 1984 height 1210 supersample 3
> hide #!33 models
> hide #!29 models
> hide #!23 models
> hide #!16 models
> hide #!8 models
> hide #!1 models
> show #!32 models
> color #32/a steel blue
> show #!22 models
> color #22.4 steel blue
> color #22.5 steel blue
> show #!30 models
> show #!29 models
> hide #!29 models
> show #!27 models
> show #!14 models
> show #!15 models
> hide #!15 models
> show #!20 models
> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/figures/structure/cas8_movement/cas8_cent_overlap_maps.tif"
> width 1984 height 1210 supersample 3
> hide #!30 models
> hide #!27 models
> hide #!22 models
> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/figures/structure/cas8_movement/cas8_cent_overlap.tif"
> width 1984 height 1210 supersample 3
> hide #!32 models
> hide #!20 models
> hide #!14 models
> show #!2 models
> color #2/a steel blue
> show #!16 models
> hide #!16 models
> show #!15 models
> show #!21 models
> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/figures/structure/cas8_movement/cas8_in_overlap.tif"
> width 1984 height 1210 supersample 3
> show #!31 models
> show #!28 models
> volume step 1
> volume #31.2 level 0.03
> volume #31.2 level 0.07
> show #!7 models
> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/figures/structure/cas8_movement/cas8_in_overlap_maps.tif"
> width 1984 height 1210 supersample 3
> hide #!2 models
> hide #!7 models
> hide #!31 models
> hide #!28 models
> hide #!21 models
> hide #!15 models
> show #!14 models
> show #!32 models
> show #!20 models
> show #!30 models
> show #!27 models
> show #!22 models
> hide #!22 models
> show #!22 models
> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/figures/structure/cas8_movement/cas8_cent_overlap_maps.tif"
> width 1984 height 1210 supersample 3
> hide #!20 models
> hide #!22 models
> hide #!27 models
> hide #!30 models
> hide #!32 models
> hide #!14 models
> show #!16 models
> show #!1 models
> show #!23 models
> show #!29 models
> show #!33 models
> show #!8 models
> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/figures/structure/cas8_movement/cas8_out_overlap_maps.tif"
> width 1984 height 1210 supersample 3
> hide #!8 models
> hide #!16 models
> hide #!23 models
> hide #!29 models
> hide #!33 models
> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/chimerax_session.cxs"
> show #!32 models
> hide #!1 models
> show #!22 models
> transparency #22 100
> transparency #22 90
> hide #!22 models
> hide #!32 models
> show #!2 models
> show #!7 models
> color #7.3 steel blue
> show #!15 models
> show #!31 models
> show #!28 models
> show #!21 models
> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/figures/structure/cas8_movement/cas8_in_overlap.tif"
> width 1984 height 1210 supersample 3
> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/figures/structure/cas8_movement/cas8_in_overlap_maps.tif"
> width 1984 height 1210 supersample 3
> hide #!31 models
> hide #!28 models
> hide #!7 models
> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/figures/structure/cas8_movement/cas8_in_overlap.tif"
> width 1984 height 1210 supersample 3
> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/chimerax_session.cxs"
——— End of log from Thu May 1 15:38:06 2025 ———
opened ChimeraX session
> hide #!2 models
> hide #!15 models
> hide #!21 models
> show #!32 models
> select #32/a:283
9 atoms, 8 bonds, 1 residue, 1 model selected
> select ::name="ASN"
15560 atoms, 13797 bonds, 1945 residues, 14 models selected
> select clear
> show #!16 models
> hide #!16 models
> show #!14 models
> show #!16 models
> hide #!16 models
> show #!16 models
> hide #!16 models
> show #!20 models
> color #14/a salmon
> ui tool show "Color Actions"
> color #20/a orchid
> color #20/a aquamarine
> color #20/a sea green
> color #20/a pale green
> color #15/a salmon
> color #16/a salmon
> color #21/a pale green
> color #23/a pale green
> color #30.2 #31.2 #33.2 pale green
> color #27.2 #28.2 #29.2 salmon
> show #!27 models
> show #!30 models
> hide #!30 models
> show #!30 models
> hide #!30 models
> show #!30 models
> hide #!30 models
> show #!30 models
> color #27.2 #28.2 #29.2 #14-16/a salmon
> color #30.2 #31.2 #33.2 #20-21/a #23/a pale green
> show #!22 models
> color #27.2 #28.2 #29.2 #14-16/a hot pink
> color #30.2 #31.2 #33.2 #20-21/a #23/a forest green
> hide #!27 models
> show #!27 models
> hide #!27 models
> show #!27 models
> hide #!27 models
> show #!27 models
> hide #!27 models
> show #!27 models
> hide #!27 models
> show #!27 models
> color #27.2 #28.2 #29.2 #14-16/a plum
> color #30.2 #31.2 #33.2 #20-21/a #23/a dark sea green
> color #27.2 #28.2 #29.2 #14-16/a vermilion
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color #27.2 #28.2 #29.2 #14-16/a dark orange
> color #30.2 #31.2 #33.2 #20-21/a #23/a bluish green
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color #27.2 #28.2 #29.2 #14-16/a warm beige
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color #27.2 #28.2 #29.2 #14-16/a beige
> color #30.2 #31.2 #33.2 #20-21/a #23/a sof gra
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color #30.2 #31.2 #33.2 #20-21/a #23/a dim gray
> color #30.2 #31.2 #33.2 #20-21/a #23/a light gray
> color #30.2 #31.2 #33.2 #20-21/a #23/a gray
> color #27.2 #28.2 #29.2 #14-16/a plum
> transparency 70
> transparency 100
> transparency 80
> color #27.2 #28.2 #29.2 #14-16/a dark gray
> color #30.2 #31.2 #33.2 #20-21/a #23/a medium sea green
> color #27.2 #28.2 #29.2 #14-16/a plum
> color #30.2 #31.2 #33.2 #20-21/a #23/a pale green
> color #30.2 #31.2 #33.2 #20-21/a #23/a dark gray
> color #27.2 #28.2 #29.2 #14-16/a orange
> color #30.2 #31.2 #33.2 #20-21/a #23/a teal
> color #30.2 #31.2 #33.2 #20-21/a #23/a cyan
> color #30.2 #31.2 #33.2 #20-21/a #23/a turquoise
> color #27.2 #28.2 #29.2 #14-16/a chocolate
> color #27.2 #28.2 #29.2 #14-16/a coral
> color #30.2 #31.2 #33.2 #20-21/a #23/a olive
> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/figures/structure/cas8_movement/cas8_cent_overlap_maps2.tif"
> width 1984 height 1210 supersample 3
> hide #!14 models
> hide #!20 models
> hide #!22 models
> hide #!27 models
> hide #!30 models
> hide #!32 models
> show #!15 models
> show #!2 models
> show #!21 models
> show #!7 models
> show #!28 models
> show #!31 models
> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/figures/structure/cas8_movement/cas8_in_overlap_maps2.tif"
> width 1984 height 1210 supersample 3
> hide #!31 models
> hide #!28 models
> hide #!21 models
> hide #!15 models
> hide #!7 models
> hide #!2 models
> show #!1 models
> show #!8 models
> show #!16 models
> show #!26 models
> hide #!26 models
> show #!29 models
> show #!33 models
> show #!23 models
> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/figures/structure/cas8_movement/cas8_out_overlap_maps2.tif"
> width 1984 height 1210 supersample 3
> hide #!8 models
> hide #!16 models
> hide #!23 models
> hide #!29 models
> hide #!33 models
> hide #!1 models
> show #!22 models
> show #!22.3 models
> show #!22.2 models
> show #!22.6 models
> show #!22.7 models
> show #!22.8 models
> show #!22.9 models
> transparency 100
> show #!22.1 models
> hide #!22.1 models
> hide #!22.2 models
> hide #!22.3 models
> hide #!22.4 models
> hide #!22.5 models
> hide #!22.6 models
> hide #!22.7 models
> hide #!22.8 models
> hide #!22.9 models
> show #!22.4 models
> show #!22.5 models
> hide #!22.5 models
> show #!22.5 models
> hide #!22.5 models
> show #!22.5 models
> show #!22.3 models
> hide #!22.5 models
> hide #!22.4 models
> show #!22.9 models
> hide #!22.9 models
> show #!22.9 models
> hide #!22.9 models
> show #!22.2 models
> hide #!22.2 models
> show #!22.2 models
> hide #!22.2 models
> show #!22.2 models
> transparency 80
> show #!22.4 models
> hide #!22.4 models
> show #!22.4 models
> hide #!22.3 models
> hide #!22.4 models
> show #!22.3 models
> hide #!22.3 models
> hide #!22.2 models
> show #!22.6 models
> show #!22.9 models
> hide #!22.9 models
> show #!22.9 models
> show #!22.7 models
> show #!22.8 models
> hide #!22.9 models
> show #!22.2 models
> show #!22.5 models
> show #!22.4 models
> show #!22.3 models
> show #!22.9 models
> transparency #22.2 100
> transparency #22 100
> show #!32 models
> show #32 cartoons
> hide #32 cartoons
> hide #!22.9 models
> hide #!22.8 models
> hide #!22.7 models
> hide #!22.6 models
> hide #!22.3 models
> hide #!22.2 models
> show #!22.2 models
> show #!22.3 models
> hide #!22.3 models
> hide #!22.2 models
> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/figures/structure/subunits_with_map/silhouette_cas8.tif"
> width 1984 height 1210 supersample 3 transparentBackground true
> hide #!22.5 models
> hide #!22.4 models
> show #!22.3 models
> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/figures/structure/subunits_with_map/silhouette_cas5.tif"
> width 1984 height 1210 supersample 3
> hide #!22.3 models
> show #!22.6 models
> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/figures/structure/subunits_with_map/silhouette_cas6.tif"
> width 1984 height 1210 supersample 3 transparentBackground true
> hide #!22.6 models
> show #!22.3 models
> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/figures/structure/subunits_with_map/silhouette_cas5.tif"
> width 1984 height 1210 supersample 3 transparentBackground true
> hide #!22.3 models
> show #!22.2 models
> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/figures/structure/subunits_with_map/silhouette_cas7_6x.tif"
> width 1984 height 1210 supersample 3 transparentBackground true
> hide #!22.2 models
> show #!22.7 models
> show #!22.8 models
> show #!22.9 models
> hide #!22.8 models
> hide #!22.7 models
> show #!22.7 models
> hide #!22.7 models
> show #!22.2 models
> show #32/c cartoons
> color #32/c green
> color zone #22.2 near #32 distance 10
> volume splitbyzone #22.2
Opened halfcleaved_HNH_center_sharp3Å.mrc 1 0 as #34.1, grid size
420,420,420, pixel 0.725, shown at level 0.02, step 1, values float32
Opened halfcleaved_HNH_center_sharp3Å.mrc 1 1 as #34.2, grid size
420,420,420, pixel 0.725, shown at level 0.02, 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 0.02, 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 0.02, 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 0.02, 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 0.02, 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 0.02, 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 0.02, 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 0.02, 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 0.02, 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 0.02, 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 0.02, 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 0.02, step 1, values float32
> hide #!22 models
> hide #!34.1 models
> hide #!34.2 models
> hide #!34.4 models
> show #!34.4 models
> hide #!34.4 models
> hide #!34.5 models
> hide #!34.6 models
> hide #!34.8 models
> hide #!34.7 models
> hide #!34.9 models
> hide #!34.10 models
> hide #!34.11 models
> hide #!34.12 models
> hide #!34.13 models
> transparency 100
> surface dust siz 10
Missing or invalid "surfaces" argument: invalid surfaces specifier
> dus siz 10
Unknown command: dus siz 10
> surface dust #34.3 size 7.25
> hide #!32 models
> show #!22 models
> show #!22.8 models
> hide #!22.9 models
> hide #!22.8 models
> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/figures/structure/subunits_with_map/silhouette_cas7.tif"
> width 1984 height 1210 supersample 3 transparentBackground true
> show #!22.2 models
> show #!22.3 models
> show #!22.4 models
> show #!22.5 models
> show #!22.6 models
> show #!22.9 models
> hide #!22.9 models
> show #!22.9 models
> hide #!22.9 models
> show #!22.9 models
> hide #!22.9 models
> show #!22.8 models
> show #!22.7 models
> hide #!22.7 models
> hide #!22.8 models
> hide #!22.6 models
> hide #!22.5 models
> hide #!22.4 models
> hide #!22.3 models
> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/figures/structure/subunits_with_map/silhouette_cas7_6x_2.tif"
> width 1984 height 1210 supersample 3 transparentBackground true
> show #!22.4 models
> show #!22.5 models
> show #!22.3 models
> show #!22.6 models
> transparency 0
> lighting soft
> lighting simple
> lighting soft
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> show #!22.7 models
> show #!22.8 models
> show #!22.9 models
> show (#22.2-9#34.3#!22,34 & sidechain) target ab
> ui tool show "Side View"
> turn x 90
[Repeated 3 time(s)]
> view
> turn x -90
> turn x 90
> show #!17 models
> hide #!17 models
> show #!18 models
> hide #!18 models
> show #!26 models
> hide #!26 models
> show #!26 models
> hide #!26 models
> show #!26 models
> hide #!26 models
> lighting soft
> lighting simple
> lighting soft
> lighting simple
> lighting soft
> view
> turn x 90
[Repeated 3 time(s)]
> turn x -90
> turn x 90
> turn x -90
> turn x 90
> turn x -90
> turn x 90
> turn x -90
> turn x 90
> turn x -90
[Repeated 1 time(s)]
> turn x 90
[Repeated 1 time(s)]
> turn x -90
> hide #!34.3 models
> hide #!34 models
> hide #!22 models
> show #!22 models
> show #!1 models
> show #!2 models
> hide #!22 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!1 models
> show #!32 models
> hide #32/b cartoons
> hide #32/c cartoons
> show #32/a cartoons
> hide #!32 models
> show #!32 models
> hide #!32 models
> show #!32 models
> hide #!32 models
> show #!32 models
> hide #!32 models
> show #!32 models
> hide #!32 models
> show #!22 models
> hide #!22 models
> show #!22 models
> hide #!22 models
> show #!22 models
> hide #!22 models
> hide #!2 models
> show #!32 models
> show #!1 models
> hide #!32 models
> show #!32 models
> hide #!1 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!32 models
> show #!32 models
> hide #!32 models
> show #!32 models
> hide #!32 models
> show #!32 models
> hide #!32 models
> show #!32 models
> hide #!32 models
> show #!32 models
> hide #!32 models
> show #!32 models
> hide #!2 models
> show #!1 models
> hide #!32 models
> show #!2 models
> hide #!2 models
> show #!32 models
> hide #!32 models
> show #!32 models
> hide #!32 models
> show #!32 models
> hide #!32 models
> show #!32 models
> hide #!32 models
> show #!32 models
> hide #!32 models
> show #!32 models
> hide #!32 models
> show #!32 models
> hide #!32 models
> show #!32 models
> select ~sel & ##selected
Nothing selected
> show #32/a cartoons
> hide #1/a cartoons
> show #1/a cartoons
> hide #32/a cartoons
> show #32/a cartoons
> hide #1/a cartoons
> show #1/a cartoons
> hide #32/a cartoons
> show #32/a cartoons
> hide #1/a cartoons
> show #1/a cartoons
> hide #32/a cartoons
> show #32/a cartoons
> hide #1/a cartoons
> show #1/a cartoons
> hide #32/a cartoons
> show #32/a cartoons
> hide #1/a cartoons
> show #1/a cartoons
> hide #32/a cartoons
> show #32/a cartoons
> hide #1/a cartoons
> show #1/a cartoons
> hide #32/a cartoons
> show #32/a cartoons
> hide #1/a cartoons
> show #1/a cartoons
> hide #32/a cartoons
> show #32/a cartoons
> hide #1/a cartoons
> show #1/a cartoons
> hide #32/a cartoons
> show #32/a cartoons
> hide #1/a cartoons
> show #1/a cartoons
> hide #32/a cartoons
> show #32/a cartoons
> hide #1/a cartoons
> show #1/a cartoons
> hide #32/a cartoons
> show #32/a cartoons
> hide #1/a cartoons
> show #1/a cartoons
> hide #32/a cartoons
> show #32/a cartoons
> hide #1/a cartoons
> show #1/a cartoons
> hide #32/a cartoons
> show #32/a cartoons
> hide #1/a cartoons
> show #1/a cartoons
> hide #32/a cartoons
> show #32/a cartoons
> hide #1/a cartoons
> show #1/a cartoons
> hide #32/a cartoons
> show #32/a cartoons
> hide #!1 models
> show #!33 models
> hide #!33 models
> hide #!32 models
> show #!25 models
> view
> surface dust siz 10
Missing or invalid "surfaces" argument: invalid surfaces specifier
> surface dust #25 size 10
> volume level 0.05
> volume level 0.06
> hide #!25 models
> show #!24 models
> hide #!24 models
> show #!26 models
> lighting simple
> lighting soft
> lighting simple
> lighting soft
> graphics silhouettes true
> graphics silhouettes false
> transparency 0
> hide #!26 models
> show #!22 models
> volume #22 show
> hide #!22.2 models
> show #!22.2 models
> hide #!22.3 models
> show #!22.3 models
> hide #!22.4 models
> show #!22.4 models
> hide #!22.5 models
> show #!22.5 models
> hide #!22.6 models
> show #!22.6 models
> hide #!22.7 models
> show #!22.7 models
> hide #!22.8 models
> show #!22.8 models
> hide #!22.9 models
> show #!22.9 models
> hide #!22.2 models
> show #!22.2 models
> hide #!22.2 models
> show #!22.2 models
> hide #!22.2 models
> show #!22.2 models
> lighting soft
> lighting simple
> lighting soft
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> transparency 0
> volume level 0.05
> hide #!22.1 models
> transparency 90
> transparency 10
> transparency 1
> transparency 0
> lighting simple
> lighting shadows true
> lighting shadows false
> graphics silhouettes true
> graphics silhouettes false
> lighting full
> lighting simple
> hide #!22.2 models
> hide #!22.3 models
> hide #!22.4 models
> hide #!22.5 models
> hide #!22.6 models
> hide #!22.10 models
> show #!22.10 models
> hide #!22.10 models
> show #!32 models
> hide #32 cartoons
> show #32/j,k,l
> hide #32/k:1-3
> transparency 90
> lighting flat
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> volume #22 level 0.03
> volume #22 level 0.02
> volume #22 level 0.01
> volume #22 level 0.005
> volume #22 level 0.001
> volume #22 level 0.0001
> volume #22 level 0.02
> hide #32
> hide #!22.9 models
> hide #!22.8 models
> hide #!22.7 models
> show #!22.6 models
> hide #!22.6 models
> show #!22.5 models
> show #!22.4 models
> show #32/a
> hide #32
> hide #!22.5 models
> hide #!22.4 models
> show #!22.3 models
> show #32/b
> hide #!22.3 models
> show #!22.2 models
> hide #32
> show #32/c
> color #32/c salmon
> show #32/c-h
> hide #32
> hide #!22.2 models
> show #!22.6 models
> hide #!22.6 models
> show #!22.6 models
> show #32/i
> hide #!22.6 models
> show #!22.6 models
> show #32/d,b
> show #32/j:41-60
> show #32/j:41-65
> hide #32
> hide #!22.6 models
> show #!22.2 models
> show #!22.3 models
> show #!22.4 models
> show #!22.5 models
> show #!22.6 models
> show #!22.7 models
> show #!22.8 models
> show #!22.9 models
> show #!22.10 models
> hide #!22.10 models
> hide #!22 models
> hide #!32 models
> show #!32 models
> show #32 cartoons
> hide #32/k:1-3 cartoons
> show #32/a:304
> show #32/a:305
> show #32/m,o
> graphics silhouettes false
> graphics silhouettes true
> select ~sel & ##selected
Nothing selected
> show #32/a:328,319
> show #32/a:328,319,280
> show #32/k
> select #32/A:281
9 atoms, 8 bonds, 1 residue, 1 model selected
> select clear
> show #!11 models
> show #32/a:83-85
> show #32/l
> color #32/k:40 #32/l:6 hot pink
> color #32/k:40 #32/l:7 hot pink
> color #32/l:7 orange
> color #32/l:6 orange
> color #32/l:7 hot pink
> hide #32 & nucleic cartoons
> show #32/j
> show #!22 models
> show #!22.10 models
> hide #!22 models
> hide #!32 models
> show #!8 models
> show #!8.4 models
> show #!8.5 models
> show #!8.6 models
> show #!8.7 models
> show #!8.8 models
> show #!8.9 models
> hide #!8.9 models
> show #!8.9 models
> show #!1 models
> show #1 cartoons
> hide #!8 models
> select #1/I:140
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel
> show #1/a:295
> show #!8 models
> show #1/a:319,304,305,328,280
> color #1/a:319,304,305,328,280 byhetero
> show #!2 models
> hide #!1 models
> hide #!8 models
> show #!7 models
> color #2/a:319,304,305,328,280 byhetero
> show #2/a:319,304,305,328,280
> show #2/a:295
> volume #7 level 0.02
> show #!7.4 models
> show #!7.5 models
> show #!7.6 models
> show #!7.7 models
> show #!7.8 models
> show #!7.9 models
> show #!7.1 models
> hide #!7.1 models
> volume #7 level 0.01
> volume #7 level 0.02
> hide #!7 models
> show #!9 models
> volume #9 level 0.02
> volume #9 level 0.01
> volume #9 level 0.002
> show #2 cartoons
> surface dust siz 5
Missing or invalid "surfaces" argument: invalid surfaces specifier
> surface dust #9 size 5
> hide #!2 models
> show #!2 models
> hide #!9 models
Drag select of 3 atoms, 57 residues, 2 bonds
> show sel
> hide #!2 models
> show #!1 models
Drag select of 2 atoms, 16 residues
> show sel
> hide #!1 models
> show #!12 models
> hide #!12 models
> show #!2 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!9 models
> hide #!9 models
> show #!7 models
> hide #!7 models
> show #!7 models
> show #2/i
> color #2/i,a byhetero
> hide #!2 models
> show #!1 models
> show #!10 models
> hide #!10 models
> show #!8 models
> hide #!7 models
> hide sel
> select clear
> show #1-2/j
> hide #1-2 & nucleic cartoons
> select clear
> show #!2 models
> hide #!1 models
> show #!7 models
> hide #!8 models
> hide #1-2
> show #1-2 cartoons
> show #!1 models
> show #!3 models
> hide #!7 models
> show #!8 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> hide #!2 models
> hide #!8 models
> hide #!1 models
> show #!19 models
> hide #!19 models
> show #!10 models
> hide #!10 models
> show #!32 models
> select #32/A:193
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #32/A:192
14 atoms, 12 bonds, 2 residues, 1 model selected
> show sel
> select clear
> hide #32/k 1-33
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide #32/k:1-33
> select #32/K:34@P
1 atom, 1 residue, 1 model selected
> select add #32/K:34@OP1
2 atoms, 1 residue, 1 model selected
> select add #32/K:34@OP2
3 atoms, 1 residue, 1 model selected
> select add #32/K:34@O5'
4 atoms, 1 residue, 1 model selected
> select add #32/K:34@C5'
5 atoms, 1 residue, 1 model selected
> hide sel
> select #32/a:220-243
196 atoms, 197 bonds, 24 residues, 1 model selected
> show #32/k
> select clear
> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/chimerax_session.cxs"
——— End of log from Mon May 12 14:04:47 2025 ———
opened ChimeraX session
> hide #!11 models
> hide #!32 models
> show #!16 models
> hide #16 cartoons
> show #16/j
> show #!29 models
> hide #!29 models
> show #!29 models
> show #!28 models
> hide #!28 models
> show #!19 models
> hide #!19 models
> show #!19 models
> hide #!19 models
> show #!19 models
> hide #!19 models
> show #!19 models
> hide #!19 models
> select #29.2
2 models selected
> hide #!29.2 models
> show #!29.2 models
> hide #!29.2 models
> show #!29.6 models
> volume #29 level 0.02
> hide #!29.6 models
> show #!27 models
> hide #!27 models
> show #!26 models
> hide #!26 models
> show #!19 models
> hide #!16 models
> hide #!19 models
> show #!29.6 models
> show #!16 models
> show #!15 models
> hide #!15 models
> show #!14 models
> show #!15 models
> hide #!15 models
> hide #!14 models
> combine #16
> hide #!16 models
> hide #!35 models
> show #!35 models
> fitmap #35/j inMap #29.6
Fit molecule copy of apo_HNH_outwards_refined.pdb (#35) to map
apo_HNH_out_sharp.mrc 5 (#29.6) using 1288 atoms
average map value = 0.3487, steps = 184
shifted from previous position = 2.25
rotated from previous position = 3.92 degrees
atoms outside contour = 340, contour level = 0.02
Position of copy of apo_HNH_outwards_refined.pdb (#35) relative to
apo_HNH_out_sharp.mrc 5 (#29.6) coordinates:
Matrix rotation and translation
-0.94445333 -0.26862857 0.18933201 314.24147225
0.22085794 -0.94540525 -0.23964699 296.35999000
0.24337151 -0.18451992 0.95221989 -10.86743333
Axis 0.11124727 -0.10905253 0.98779127
Axis point 138.91057616 167.65489171 0.00000000
Rotation angle (degrees) 165.65451579
Shift along axis -8.09505614
> volume #29 level 0.002
> volume #29 level 0.0002
> volume #29 level 0.002
> hide #!35 models
> hide #!29 models
> show #!30 models
> hide #!30.2 models
> show #!30.8 models
> show #!30.7 models
> show #!30.6 models
> hide #!30.6 models
> show #!30.5 models
> show #!1 models
> show #!3 models
> hide #!3 models
> hide #1 cartoons
> show #1/j-l
> hide #!1 models
> show #!20 models
> hide #20 cartoons
> show #20/j-l
> fitmap #20/j inMap #30.8
Fit molecule postcleavage_HNH_center_refined.pdb (#20) to map
post_HNH_cent_sharp.mrc 7 (#30.8) using 1288 atoms
average map value = 0.3259, steps = 228
shifted from previous position = 2.32
rotated from previous position = 3 degrees
atoms outside contour = 457, contour level = 0.05
Position of postcleavage_HNH_center_refined.pdb (#20) relative to
post_HNH_cent_sharp.mrc 7 (#30.8) coordinates:
Matrix rotation and translation
0.99292341 0.11846591 0.00830222 -17.69757193
-0.11532901 0.97858172 -0.17051988 44.51738269
-0.02832520 0.16835570 0.98531926 -26.31185417
Axis 0.81987504 0.08861632 -0.56564306
Axis point 0.00000000 162.56775146 238.40498938
Rotation angle (degrees) 11.92686357
Shift along axis 4.31828685
> volume #30 level 0.002
> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/figures/structure/subunits_with_map/nucleotides_post.tif"
> width 1984 height 1210 supersample 3
> hide #!30 models
> hide #!20 models
> show #!35 models
> show #!19 models
> hide #!19 models
> show #!29 models
> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/figures/structure/subunits_with_map/nucleotides_apo.tif"
> width 1984 height 1210 supersample 3
> hide #!29 models
> hide #!35 models
> show #!30 models
> show #!20 models
> select #20/l:1
17 atoms, 19 bonds, 1 residue, 1 model selected
> select clear
> hide #!30 models
> show #20 cartoons
> cartoon style nucleic xsection oval width 1 thickness 1
> color #20/L dark orange
> color #20/K dim gray
> color #20/J dark red
> color #20/I rebecca purple
> color #20/B forest green
> color #20/C,D,E,F,G,H salmon
> color #20/A steel blue
> color #20/A:232-350 dark turquoise
> color #20/O blue
> color #20/M red
> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/figures/structure/post_full_cartoon.tif" width 1984
> height 1210 supersample 3
> hide #!20 models
> show #!16 models
> show #16 cartoons
> color #16/L dark orange
> color #16/K dim gray
> color #16/J dark red
> color #16/I rebecca purple
> color #16/B forest green
> color #16/C,D,E,F,G,H salmon
> color #16/A steel blue
> color #16/A:232-350 dark turquoise
> color #16/O blue
> color #16/M red
> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/figures/structure/apo_full_cartoon.tif" width 1984 height
> 1210 supersample 3
> hide #!16 models
> show #!32 models
> 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
> show #32/m,o
> show #32 cartoons
> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/figures/structure/half_full_cartoon.tif" width 1984
> height 1210 supersample 3
> hide #!32 models
> show #!13 models
> hide #!13 models
> show #!13 models
> lighting simple
> graphics silhouettes false
> ui tool show "Surface Color"
> color sample #13.1 map #13 palette #ff0000:#ffffff:#0000ff
Map values for surface "surface": minimum 0.04997, mean 0.05, maximum 0.05003
> 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 #36, grid size
420,420,420, pixel 0.725, shown at level 0.0319, step 2, values float32
> hide #!13 models
> hide #!36 models
> open "/Users/zxc755/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/Type
> I-F_HNH/Manuscript/maps_models/fsc_and_halfmaps/halfcleaved_HNH_center/J635_005_volume_map_half_A.mrc"
Opened J635_005_volume_map_half_A.mrc as #37, grid size 420,420,420, pixel
0.725, shown at level 0.138, step 2, values float32
> color sample #13.1 map #37 palette
> 0.04997,#ff0000:0.05,#ffffff:0.05003,#0000ff
Map values for surface "surface": minimum -0.3311, mean 0.05689, maximum
0.4275
> show #!13 models
> hide #!37 models
> key red-white-blue :0.05 :0.05 :0.05 showTool true
> ui mousemode right "color key"
> color sample #13.1 map #37 palette 2,#ff0000:2.5,#ffffff:3,#0000ff
Map values for surface "surface": minimum -0.3311, mean 0.05689, maximum
0.4275
> color sample #13.1 map #37 palette 2.1,#ff0000:2.3,#ffffff:2.8,#0000ff
Map values for surface "surface": minimum -0.3311, mean 0.05689, maximum
0.4275
> show #!37 models
> hide #!37 models
> show #!37 models
> hide #!37 models
> hide #38 models
> show #38 models
> hide #!13 models
> show #!36 models
> color sample #36.1 map #37 palette 2.1,#ff0000:2.3,#ffffff:2.8,#0000ff
Map values for surface "surface": minimum -0.3316, mean 0.02939, maximum
0.3335
> key red-white-blue :2.1 :2.3 :2.8 showTool true
> key red-white-blue :2.1 :2.5 :3.0 showTool true
[Repeated 1 time(s)]
> color sample #36.1 map #37 palette 2.1,#ff0000:2.5,#ffffff:3,#0000ff
Map values for surface "surface": minimum -0.3316, mean 0.02939, maximum
0.3335
> color single #36.1
> color sample #36.1 map #37 palette 2.1,#ff0000:2.5,#ffffff:3,#0000ff
Map values for surface "surface": minimum -0.3316, mean 0.02939, maximum
0.3335
> color single #36.1
> color sample #36.1 map #37 palette 2.5,#ff0000:3,#ffffff:3.5,#0000ff
Map values for surface "surface": minimum -0.3316, mean 0.02939, maximum
0.3335
> color sample #36.1 map #37 palette 3,#ff0000:3,#ffffff:3.5,#0000ff
Map values for surface "surface": minimum -0.3316, mean 0.02939, maximum
0.3335
> color sample #36.1 map #37 palette 3,#ff0000:3.5,#ffffff:3.5,#0000ff
Map values for surface "surface": minimum -0.3316, mean 0.02939, maximum
0.3335
> color sample #36.1 map #37 palette 3,#ff0000:3.5,#ffffff:4,#0000ff
Map values for surface "surface": minimum -0.3316, mean 0.02939, maximum
0.3335
> key red-white-blue :3.0 :3.5 :4.0 showTool true
> color sample #36.1 map #37 palette 3,#ff0000:3.5,#ffffff:4,#0000ff
Map values for surface "surface": minimum -0.3316, mean 0.02939, maximum
0.3335
> color sample #36.1 map #37 palette 3,#ff0000:3.5,#ffffff:4,#0000ff
Map values for surface "surface": minimum -0.3316, mean 0.02939, maximum
0.3335
> color sample #36.1 map #37 palette 2,#ff0000:3.5,#ffffff:4,#0000ff
Map values for surface "surface": minimum -0.3316, mean 0.02939, maximum
0.3335
> color single #36.1
> key red-white-blue :2.0 :3.5 :4.0 showTool true
> color sample #36.1 map #37 palette 2,#0433ff:2.5,#ffffff:3,#ff2600
Map values for surface "surface": minimum -0.3316, mean 0.02939, maximum
0.3335
> hide #38 models
> hide #!36 models
> ui mousemode right translate
Unsupported scale factor (0.000000) detected on Display0
[Repeated 9 time(s)]
> show #!32 models
> show #!22 models
> color #32/a byhetero
> hide #!32 models
> show #!13 models
> show #!32 models
> hide #!22 models
> hide #!13 models
> volume zone #13 nearAtoms #32/a:304,305,328,319,280 #32/k:2-3 #32/o range 2
> newMap true
Opened halfcleaved_HNH_center_sharp3Å.mrc zone as #39, grid size 420,420,420,
pixel 0.725, shown at step 1, values float32
Unknown or unsupported skia image format
> transparency #39 90
> close #39
> volume zone #13 nearAtoms #32/a:304,305,328,319,280 #32/k:2-3 #32/o range
> 1.5 newMap true
Opened halfcleaved_HNH_center_sharp3Å.mrc zone as #39, grid size 420,420,420,
pixel 0.725, shown at step 1, values float32
> transparency #39 90
> hide #32/k cartoons
> volume zone #13 nearAtoms #32/o range 2 newMap true
Opened halfcleaved_HNH_center_sharp3Å.mrc zone as #40, grid size 420,420,420,
pixel 0.725, shown at step 1, values float32
> volume #40 level 0.02
> close #40
> volume zone #13 nearAtoms #32/o range 0.5 newMap true
Opened halfcleaved_HNH_center_sharp3Å.mrc zone as #40, grid size 420,420,420,
pixel 0.725, shown at step 1, values float32
> volume #40 level 0.02
> close #40
> volume zone #13 nearAtoms #32/o range 1 newMap true
Opened halfcleaved_HNH_center_sharp3Å.mrc zone as #40, grid size 420,420,420,
pixel 0.725, shown at step 1, values float32
> volume #40 level 0.02
> transparency #40 90
> color #40 blue
> color #39 turquoise
> lighting flat
> graphics silhouettes false
> graphics silhouettes true
> color #32/k:3 byhetero
> hide #!39 models
> show #!39 models
> hide #!39 models
> show #!39 models
> hide #!39 models
> show #!39 models
> hide #!39 models
> show #!39 models
> hide #!39 models
> show #!39 models
> close #39
> hide #!40 models
> show #!40 models
> select #32/A:280@CG
1 atom, 1 residue, 1 model selected
> select add #32/A:305@ND1
2 atoms, 2 residues, 1 model selected
> select add #32/A:319@CG
3 atoms, 3 residues, 1 model selected
> select add #32/A:304@ND1
4 atoms, 4 residues, 1 model selected
> select add #32/M:2@MG
5 atoms, 1 bond, 5 residues, 1 model selected
> select add #32/K:2@O5'
6 atoms, 1 bond, 6 residues, 1 model selected
> select add #32/K:3@P
7 atoms, 1 bond, 7 residues, 1 model selected
> select up
9 atoms, 1 bond, 8 residues, 1 model selected
> select up
62 atoms, 60 bonds, 8 residues, 1 model selected
> volume zone nea sel range 1.5 newmap tru
Missing or invalid "volumes" argument: invalid density maps specifier
> volume zone #13 nearAtoms sel range 1.5 newMap true
Opened halfcleaved_HNH_center_sharp3Å.mrc zone as #39, grid size 420,420,420,
pixel 0.725, shown at step 1, values float32
> select clear
> transparency #39 90
> volume #39 level 0.03
> volume #39 level 0.02
> volume #39 level 0.002
> surface dust #40 size 7.25
> surface dust #39 size 7.25
> surface dust siz 0
Missing or invalid "surfaces" argument: invalid surfaces specifier
> surface dust #39-40 size 0
> volume #39 level 0.09
> show #!11 models
> volume #39 level 0.04054
> hide #!39 models
> hide #!40 models
> select #32/A:280,304,305,319,328
49 atoms, 48 bonds, 5 residues, 1 model selected
> select #32/A:280,304,305,319,328 #32/k:1-3
61 atoms, 60 bonds, 2 pseudobonds, 7 residues, 2 models selected
> volume zone #13 nearAtoms sel range 1.5 newMap true
Opened halfcleaved_HNH_center_sharp3Å.mrc zone as #41, grid size 420,420,420,
pixel 0.725, shown at step 1, values float32
> close #41
> show #!39 models
> show #!40 models
> volume #39 level 0.04
> volume #39 level 0.05
> volume #49 level .03
No volumes specified
> volume #39 level .03
> volume #39 level .04
> volume #40 level .04
> volume #40 level .03
> volume #40 level .025
> volume #40 level .021
> volume #40 level .02
> volume #40 level .01
> volume #40 level .02
> select clear
> 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
> save "/Users/zxc755/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/Type
> I-F_HNH/Manuscript/figures/structure/HNH/cat_pocket_with_nucleotide.tif"
> width 1938 height 1210 supersample 3
> save cat_pocket_with_nucleotide_test.tif supersample 3
> save "/Users/zxc755/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/Type
> I-F_HNH/Manuscript/figures/structure/HNH/HNH_cat_session.cxs" includeMaps
> true
> close #1-10,12,14-31,33-38
> save HNH_cat_session.cxs includeMaps true
——— End of log from Wed May 14 12:43:12 2025 ———
opened ChimeraX session
> hide #!39 models
> select add /M:2@MG
1 atom, 1 residue, 1 model selected
> select add /A:304@ND1
2 atoms, 2 residues, 1 model selected
> select add /A:304@CE1
3 atoms, 2 residues, 1 model selected
> select add /A:304@NE2
4 atoms, 2 residues, 1 model selected
> select add /A:304@CD2
5 atoms, 2 residues, 1 model selected
> select add /A:304@CG
6 atoms, 2 residues, 1 model selected
> select add /A:304@CB
7 atoms, 2 residues, 1 model selected
> select add /A:328@CD2
8 atoms, 3 residues, 1 model selected
> select add /A:328@NE2
9 atoms, 3 residues, 1 model selected
> select add /A:328@CE1
10 atoms, 3 residues, 1 model selected
> select add /A:328@ND1
11 atoms, 3 residues, 1 model selected
> select add /A:328@CG
12 atoms, 3 residues, 1 model selected
> select add /A:328@CB
13 atoms, 3 residues, 1 model selected
> select add /A:319@ND2
14 atoms, 4 residues, 1 model selected
> select add /A:319@OD1
15 atoms, 4 residues, 1 model selected
> select add /A:319@CB
16 atoms, 4 residues, 1 model selected
> select add /A:305@CB
17 atoms, 5 residues, 1 model selected
> select add /A:305@CG
18 atoms, 5 residues, 1 model selected
> select add /A:305@CD2
19 atoms, 5 residues, 1 model selected
> select add /A:305@NE2
20 atoms, 5 residues, 1 model selected
> select add /A:305@CE1
21 atoms, 5 residues, 1 model selected
> select add /A:305@ND1
22 atoms, 5 residues, 1 model selected
> select add /K:3@OP2
23 atoms, 6 residues, 1 model selected
> select add /K:3@P
24 atoms, 6 residues, 1 model selected
> select add /K:3@O5'
25 atoms, 6 residues, 1 model selected
> select add /K:3@OP1
26 atoms, 6 residues, 1 model selected
> select subtract /K:3@P
25 atoms, 6 residues, 1 model selected
> select add /K:3@P
26 atoms, 6 residues, 1 model selected
> select add /K:2@O3'
27 atoms, 7 residues, 1 model selected
> select add /K:2@C3'
28 atoms, 7 residues, 1 model selected
> select add /K:2@C4'
29 atoms, 7 residues, 1 model selected
> select add /K:2@C5'
30 atoms, 7 residues, 1 model selected
> select add /K:2@O5'
31 atoms, 7 residues, 1 model selected
> select add /K:2@O4'
32 atoms, 7 residues, 1 model selected
> select add /K:2@C2'
33 atoms, 7 residues, 1 model selected
> select add /K:2@C1'
34 atoms, 7 residues, 1 model selected
> select add /A:280@NH2
35 atoms, 8 residues, 1 model selected
> select add /A:280@NH1
36 atoms, 8 residues, 1 model selected
> select add /A:280@CZ
37 atoms, 8 residues, 1 model selected
> select add /A:280@NE
38 atoms, 8 residues, 1 model selected
> select add /A:280@CD
39 atoms, 8 residues, 1 model selected
> volume zone #13 nearAtoms sel range 1.5 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 add /A:280@CG
40 atoms, 8 residues, 1 model selected
> select add /A:280@CB
41 atoms, 8 residues, 1 model selected
> close #1
> volume zone #13 nearAtoms sel range 1.5 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 clear
> volume #1 level 0.02
> show (#1,40#!11,32 & sidechain) target ab
> ui tool show "Side View"
> hide #32
> show #32/a:280,304,305,319
> show #32/a:280,304,305,319,328 #32/o,m
> show #32/a:280,304,305,319,328 #32/o,m #32/k:1-3
> hide #32 cartoons
> show #32/a cartoons
> cd /Users/zxc755/Library/CloudStorage/OneDrive-UniversityofCopenhagen/Type
> I-F_HNH/Manuscript/figures/structure/HNH
Expected name of a folder to open/read; a name of 'browse' will bring up a
file browser or a keyword
> cd /Users/zxc755/Library/CloudStorage/OneDrive-UniversityofCopenhagen/Type
> I-F_HNH/Manuscript/figures/structure/HNH/
Expected name of a folder to open/read; a name of 'browse' will bring up a
file browser or a keyword
> cd "/Users/zxc755/OneDrive - University of Copenhagen/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
> 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
> save cat_pocket_with_nucleotide_2.tif supersample 3
> 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 #2
---
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 #3, grid size 420,420,420, pixel
0.725, shown at level 0.0029, step 2, values float32
> hide #!1 models
> hide #!2 models
> hide #!3 models
> hide #!32 models
> hide #!40 models
> show #!3 models
> show #!2 models
> style stick
Changed 48201 atom styles
> hide #2
> show #2 cartoons
Computing secondary structure
> transparency #3 90
> color #2/L dark orange
> color #2/K dim gray
> color #2/J dark red
> color #2/I rebecca purple
> color #2/B forest green
> color #2/C,D,E,F,G,H salmon
> color #2/A steel blue
> color #2/A:232-350 dark turquoise
> color #2/O blue
> color #2/M red
> show #2/a:319,280,304,305
> color #2/a byhetero
> volume #3 level 0.005
> volume #3 level 0.05
> volume #3 level 0.09
> show #2/a:328
> hide #2 cartoons
> show #2/a cartoons
> hide #!3 models
> hide #!2 models
> show #!32 models
> select #32/A:332
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel
> select #32/A:333
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel
> show #!13 models
> volume #13 level 0.02
> hide #!11 models
> hide #!13 models
> hide #!32 models
> 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 #!5 models
> style stick
Changed 71932 atom styles
> hide #4
> show #4/a cartoons
Computing secondary structure
> show #4/m
> color #4/L dark orange
> color #4/K dim gray
> color #4/J dark red
> color #4/I rebecca purple
> color #4/B forest green
> color #4/C,D,E,F,G,H salmon
> color #4/A steel blue
> color #4/A:232-350 dark turquoise
> color #4/O blue
> color #4/M red
> color #4/a byhetero
> show #4/a:280,319,304,305
> show #4/a:280,319,304,305,328
> select #4/a280,319,304,305,328 #4/m
1 atom, 1 residue, 1 model selected
> select #4/a:280,319,304,305,328 #4/m
50 atoms, 48 bonds, 6 residues, 1 model selected
> volume zone #5 nearAtoms sel range 1.5 newMap true
Opened post_HNH_cent_sharp.mrc zone as #6, grid size 420,420,420, pixel 0.725,
shown at step 1, values float32
> transparency #6 90
> volume #6 level 0.02
> hide #!6 models
> show #!5 models
> hide #!5 models
> show #!6 models
> volume #6 level 0.09
> 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
> hide #!6 models
> transparency #7 90
> hide #!7 models
> show #!6 models
> volume #6 level 0.12
> volume #6 level 0.1
> volume #6 level 0.08
> volume #6 level 0.06
> select clear
> show #!32 models
> hide #!32 models
> combine #4
> hide #!4 models
> hide #!6 models
> show #!32 models
> mmaker #8/a:220-350 to #32/a:220-350
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 (#8), sequence
alignment score = 600
RMSD between 122 pruned atom pairs is 0.599 angstroms; (across all 123 pairs:
0.646)
> color #8/a salmon
> hide #!32 models
> hide #!8 models
> show #!6 models
> show #!4 models
> show #!5 models
> hide #!5 models
> hide #!6 models
> select add #4/A:328@NE2
1 atom, 1 residue, 1 model selected
> select add #4/A:304@ND1
2 atoms, 2 residues, 1 model selected
> select add #4/A:280@CZ
3 atoms, 3 residues, 1 model selected
> select add #4/A:305@CE1
4 atoms, 4 residues, 1 model selected
> select add #4/A:319@CG
5 atoms, 5 residues, 1 model selected
> select add #4/A:332
12 atoms, 6 bonds, 6 residues, 1 model selected
> select up
56 atoms, 54 bonds, 6 residues, 1 model selected
> volume zone #5 nearAtoms sel range 1.5 newMap true
Opened post_HNH_cent_sharp.mrc zone as #9, grid size 420,420,420, pixel 0.725,
shown at step 1, values float32
> close #9
> select add #4/M:1@MG
57 atoms, 54 bonds, 7 residues, 1 model selected
> select up
407 atoms, 415 bonds, 50 residues, 1 model selected
> select down
57 atoms, 54 bonds, 7 residues, 1 model selected
> volume zone #5 nearAtoms sel range 1.5 newMap true
Opened post_HNH_cent_sharp.mrc zone as #9, grid size 420,420,420, pixel 0.725,
shown at step 1, values float32
> transparency #9 90
> volume #9 level 0.06
> select clear
> hide #!9 models
> select #4/A:332
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel
> select clear
> show #!9 models
> 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
> color #9 #ffcc99ff models
> color #9 #ffd479ff models
> color #9 white
> transparency #9 90
> ui tool show "Color Actions"
> color #9 lavender
> color #9 violet
> color #9 navy
> color #9 navajowhite
> color #9 blanchedalmond
> save cat_pocket_empty.tif supersample 3
> hide #!9 models
> show #!8 models
> hide #!4 models
> show #!32 models
> color #8 salmon
> select #32/K:2@C3'
1 atom, 1 residue, 1 model selected
> select add #32/K:2@C4'
2 atoms, 1 residue, 1 model selected
> select #32/K:2@C4'
1 atom, 1 residue, 1 model selected
> select add #32/K:2@C3'
2 atoms, 1 residue, 1 model selected
> select add #32/K:2@C5'
3 atoms, 1 residue, 1 model selected
> select add #32/K:2@O5'
4 atoms, 1 residue, 1 model selected
> select add #32/K:2@O4'
5 atoms, 1 residue, 1 model selected
> select add #32/K:2@C1'
6 atoms, 1 residue, 1 model selected
> select add #32/K:2@C2'
7 atoms, 1 residue, 1 model selected
> hide sel
> select #32/K:2@O3'
1 atom, 1 residue, 1 model selected
> color sel byhetero
> select clear
> select #32/O:1@O
1 atom, 1 residue, 1 model selected
> hide sel
> hide #!8 models
> show #!8 models
> select #8/A:332
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel
> select clear
> select add #8/A:332@CG2
1 atom, 1 residue, 1 model selected
> select up
3 atoms, 1 bond, 2 residues, 2 models selected
> select up
14 atoms, 12 bonds, 2 residues, 2 models selected
> hide sel
> select clear
> combine #8
> hide #!8 models
> mmaker #10/a to #32/a
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 copy of postcleavage_HNH_center_refined.pdb, chain A (#10),
sequence alignment score = 1678.6
RMSD between 328 pruned atom pairs is 0.795 angstroms; (across all 340 pairs:
0.913)
> mmaker #10/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 copy of postcleavage_HNH_center_refined.pdb, chain A (#10),
sequence alignment score = 542.1
RMSD between 110 pruned atom pairs is 0.556 angstroms; (across all 111 pairs:
0.605)
> save cat_half_post_superimpose.tif supersample 3
> hide #!10 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> close #10
> show #!4 models
> hide #!4 models
> hide #!32 models
> show #!4 models
> close #4
> 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 #10, grid size 420,420,420, pixel 0.725,
shown at level 0.00328, step 2, values float32
> color #4/L dark orange
> color #4/K dim gray
> color #4/J dark red
> color #4/I rebecca purple
> color #4/B forest green
> color #4/C,D,E,F,G,H salmon
> color #4/A steel blue
> color #4/A:232-350 dark turquoise
> color #4/O blue
> color #4/M red
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!10 models
> hide #!4 models
> show #!4 models
> style stick
Changed 95663 atom styles
> hide #4
> show #4/a cartoons
Computing secondary structure
> show #4/a:319,280,304,305 #4/m
> show #4/a:319,280,304,305,328 #4/m
> color #4/a byhetero
> combine #4
> hide #!4 models
> mmaker #12/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 (#12), sequence
alignment score = 542.1
RMSD between 110 pruned atom pairs is 0.556 angstroms; (across all 111 pairs:
0.605)
> color #12 salmon
> show #!32 models
> select #32/A:333@CG
1 atom, 1 residue, 1 model selected
> select up
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel
> save cat_half_post_superimpose_2.tif supersample 3
> hide #!32 models
> hide #!12 models
> show #!12 models
> show #!4 models
> hide #!12 models
> show #!8 models
> hide #!8 models
> show #!6 models
> hide #!6 models
> show #!7 models
> hide #!7 models
> show #!5 models
> hide #!5 models
> show #!6 models
> show #!9 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> ui tool show Distances
> show #!11 models
> select #4/A:304@ND1
1 atom, 1 residue, 1 model selected
> select add #4/M:1@MG
2 atoms, 2 residues, 1 model selected
> distance #4/A:304@ND1 #4/M:1@MG
Distance between postcleavage_HNH_center_refined.pdb #4/A HIS 304 ND1 and /M
MG 1 MG: 3.141Å
> distance style dashes 5
[Repeated 2 time(s)]
> distance style radius 0.09
[Repeated 2 time(s)]
> distance style radius 0.08
[Repeated 2 time(s)]
> distance style radius 0.07
[Repeated 2 time(s)]
> distance style radius 0.06
[Repeated 2 time(s)]
> distance style radius 0.05
[Repeated 2 time(s)]
> color #11 teal
> select clear
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!9 models
> save cat_pocket_empty_2.tif supersample 3
> graphics silhouettes false
> graphics silhouettes true
> lighting simple
> lighting soft
> lighting flat
> lighting shadows true intensity 0.5
> lighting full
> graphics silhouettes false
> lighting full
> lighting shadows false
> lighting shadows true
> lighting shadows false
> graphics silhouettes true
> graphics silhouettes false
> lighting flat
> graphics silhouettes false
> graphics silhouettes true
> hide #!4 models
> hide #!9 models
> show #!32 models
> show #32/a:232
> show #!10 models
> hide #!10 models
> show #11.1 models
> hide #11.1 models
> hide #!32 models
> show #!32 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!8 models
> combine #32
> hide #!32 models
> hide #!14 models
> show #!14 models
> morph#8 #14
Unknown command: morph#8 #14
> morph #8 #14
Computed 51 frame morph #15
> coordset #15 1,51
> show #!32 models
> hide #!32 models
> close #15
> show #!12 models
> hide #!12 models
> show #!14 models
> hide #!14 models
> show #!14 models
> close #14
> open "/Users/zxc755/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/Type
> I-F_HNH/Manuscript/maps_models/postcleavage_HNH_center_with_TS_for_morph.pdb"
Summary of feedback from opening /Users/zxc755/Library/CloudStorage/OneDrive-
UniversityofCopenhagen/Type
I-F_HNH/Manuscript/maps_models/postcleavage_HNH_center_with_TS_for_morph.pdb
---
warning | Ignored bad PDB record found on line 59
SSBOND 1 CYS Aa 295 CYS Ca 140
Chain information for postcleavage_HNH_center_with_TS_for_morph.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
K | No description available
L | No description available
> color #14/L dark orange
> color #14/K dim gray
> color #14/J dark red
> color #14/I rebecca purple
> color #14/B forest green
> color #14/C,D,E,F,G,H salmon
> color #14/A steel blue
> color #14/A:232-350 dark turquoise
> color #14/O blue
> color #14/M red
> style stick
Changed 142917 atom styles
> hide #14
> show #14/a cartoons
Computing secondary structure
> show #14/k:1-3
> show #!32 models
> mmaker #14/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 postcleavage_HNH_center_with_TS_for_morph.pdb, chain A (#14), sequence
alignment score = 542.1
RMSD between 110 pruned atom pairs is 0.556 angstroms; (across all 111 pairs:
0.605)
> show #14/a:280,304,305,317,328
> show #14/a:280,304,305,319,328
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel
> select clear
> morph #14 #32
Computed 51 frame morph #15
> coordset #15 1,51
> show #15/k:1-3
> show #15/k
> open "/Users/zxc755/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/Type
> I-F_HNH/Manuscript/maps_models/halfcleaved_HNH_center_main_model_for_cat_morph.pdb"
Chain information for halfcleaved_HNH_center_main_model_for_cat_morph.pdb #16
---
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
k | No description available
> style stick
Changed 190521 atom styles
> hide #16
> close #15
> show #16/a cartoons
> hide #!16 models
> show #!16 models
> show #16/a
> view
> hide #!16 models
> show #!16 models
> show #!14 models
> hide #!14 models
> hide #!16 models
> show #!16 models
> close #16
> open "/Users/zxc755/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/Type
> I-F_HNH/Manuscript/maps_models/halfcleaved_HNH_center_main_model_for_cat_morph.pdb"
Chain information for halfcleaved_HNH_center_main_model_for_cat_morph.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
k | No description available
> style stick
Changed 167030 atom styles
> hide #16
> hide #15
> show #15/a cartoons
> hide #!15 models
> show #!15 models
> show #15
> show #15/A cartoons
Computing secondary structure
> hide #15
> show #15/Kk
> show #15
> select #15/k:2@C4'
1 atom, 1 residue, 1 model selected
> select up
8 atoms, 8 bonds, 1 residue, 1 model selected
> select up
12 atoms, 12 bonds, 2 residues, 1 model selected
> hide #15
> show sel
> select clear
> color #15/L dark orange
> color #15/K dim gray
> color #15/J dark red
> color #15/I rebecca purple
> color #15/B forest green
> color #15/C,D,E,F,G,H salmon
> color #15/A steel blue
> color #15/A:232-350 dark turquoise
> color #15/O blue
> color #15/M red
> show #!14 models
> hide #!14 models
> show #!14 models
> select #15/k:2@O5'
1 atom, 1 residue, 1 model selected
> select add #15/k:2@C5'
2 atoms, 1 residue, 1 model selected
> delete sel
> morph #14 #15
models have different number of chains, 12 (Morph -
postcleavage_HNH_center_with_TS_for_morph.pdb #/A,Morph -
postcleavage_HNH_center_with_TS_for_morph.pdb #/B,Morph -
postcleavage_HNH_center_with_TS_for_morph.pdb #/C,Morph -
postcleavage_HNH_center_with_TS_for_morph.pdb #/D,Morph -
postcleavage_HNH_center_with_TS_for_morph.pdb #/E,Morph -
postcleavage_HNH_center_with_TS_for_morph.pdb #/F,Morph -
postcleavage_HNH_center_with_TS_for_morph.pdb #/G,Morph -
postcleavage_HNH_center_with_TS_for_morph.pdb #/H,Morph -
postcleavage_HNH_center_with_TS_for_morph.pdb #/I,Morph -
postcleavage_HNH_center_with_TS_for_morph.pdb #/J,Morph -
postcleavage_HNH_center_with_TS_for_morph.pdb #/K,Morph -
postcleavage_HNH_center_with_TS_for_morph.pdb #/L) and 13
(halfcleaved_HNH_center_main_model_for_cat_morph.pdb
#15/A,halfcleaved_HNH_center_main_model_for_cat_morph.pdb
#15/B,halfcleaved_HNH_center_main_model_for_cat_morph.pdb
#15/C,halfcleaved_HNH_center_main_model_for_cat_morph.pdb
#15/D,halfcleaved_HNH_center_main_model_for_cat_morph.pdb
#15/E,halfcleaved_HNH_center_main_model_for_cat_morph.pdb
#15/F,halfcleaved_HNH_center_main_model_for_cat_morph.pdb
#15/G,halfcleaved_HNH_center_main_model_for_cat_morph.pdb
#15/H,halfcleaved_HNH_center_main_model_for_cat_morph.pdb
#15/I,halfcleaved_HNH_center_main_model_for_cat_morph.pdb
#15/J,halfcleaved_HNH_center_main_model_for_cat_morph.pdb
#15/K,halfcleaved_HNH_center_main_model_for_cat_morph.pdb
#15/L,halfcleaved_HNH_center_main_model_for_cat_morph.pdb #15/k)
> morph #14/A,Kk #15/A,Kk
models have different number of chains, 12 (Morph -
postcleavage_HNH_center_with_TS_for_morph.pdb #/A,Morph -
postcleavage_HNH_center_with_TS_for_morph.pdb #/B,Morph -
postcleavage_HNH_center_with_TS_for_morph.pdb #/C,Morph -
postcleavage_HNH_center_with_TS_for_morph.pdb #/D,Morph -
postcleavage_HNH_center_with_TS_for_morph.pdb #/E,Morph -
postcleavage_HNH_center_with_TS_for_morph.pdb #/F,Morph -
postcleavage_HNH_center_with_TS_for_morph.pdb #/G,Morph -
postcleavage_HNH_center_with_TS_for_morph.pdb #/H,Morph -
postcleavage_HNH_center_with_TS_for_morph.pdb #/I,Morph -
postcleavage_HNH_center_with_TS_for_morph.pdb #/J,Morph -
postcleavage_HNH_center_with_TS_for_morph.pdb #/K,Morph -
postcleavage_HNH_center_with_TS_for_morph.pdb #/L) and 13
(halfcleaved_HNH_center_main_model_for_cat_morph.pdb
#15/A,halfcleaved_HNH_center_main_model_for_cat_morph.pdb
#15/B,halfcleaved_HNH_center_main_model_for_cat_morph.pdb
#15/C,halfcleaved_HNH_center_main_model_for_cat_morph.pdb
#15/D,halfcleaved_HNH_center_main_model_for_cat_morph.pdb
#15/E,halfcleaved_HNH_center_main_model_for_cat_morph.pdb
#15/F,halfcleaved_HNH_center_main_model_for_cat_morph.pdb
#15/G,halfcleaved_HNH_center_main_model_for_cat_morph.pdb
#15/H,halfcleaved_HNH_center_main_model_for_cat_morph.pdb
#15/I,halfcleaved_HNH_center_main_model_for_cat_morph.pdb
#15/J,halfcleaved_HNH_center_main_model_for_cat_morph.pdb
#15/K,halfcleaved_HNH_center_main_model_for_cat_morph.pdb
#15/L,halfcleaved_HNH_center_main_model_for_cat_morph.pdb #15/k)
> close #14
> open "/Users/zxc755/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/Type
> I-F_HNH/Manuscript/maps_models/postcleavage_HNH_center_with_TS_for_morph.pdb"
Summary of feedback from opening /Users/zxc755/Library/CloudStorage/OneDrive-
UniversityofCopenhagen/Type
I-F_HNH/Manuscript/maps_models/postcleavage_HNH_center_with_TS_for_morph.pdb
---
warning | Ignored bad PDB record found on line 59
SSBOND 1 CYS Aa 295 CYS Ca 140
Chain information for postcleavage_HNH_center_with_TS_for_morph.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
K | No description available
L | No description available
> hide #!14 models
> color #14/L dark orange
> color #14/K dim gray
> color #14/J dark red
> color #14/I rebecca purple
> color #14/B forest green
> color #14/C,D,E,F,G,H salmon
> color #14/A steel blue
> color #14/A:232-350 dark turquoise
> color #14/O blue
> color #14/M red
> show #!14 models
> hide #!14 models
> style #14 stick
Changed 23523 atom styles
> hide #14
> show #14/A cartoons
Computing secondary structure
> show #!14 models
> hide #!14 models
> show #!14 models
> mmaker #14/A:232-350 to #15/A:232-250
Computing secondary structure
[Repeated 1 time(s)] 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_for_cat_morph.pdb, chain A (#15)
with postcleavage_HNH_center_with_TS_for_morph.pdb, chain A (#14), sequence
alignment score = 94.9
RMSD between 19 pruned atom pairs is 0.653 angstroms; (across all 19 pairs:
0.653)
> show #14,15/A:280
> show #14,15/A:280,319,304,305,329
> show #14,15/A:280,319,304,305,328
> hide #14-15/A:329
> show #14/Kk:1-3
> morph #14 #15
models have different number of chains, 12 (Morph -
postcleavage_HNH_center_with_TS_for_morph.pdb #/A,Morph -
postcleavage_HNH_center_with_TS_for_morph.pdb #/B,Morph -
postcleavage_HNH_center_with_TS_for_morph.pdb #/C,Morph -
postcleavage_HNH_center_with_TS_for_morph.pdb #/D,Morph -
postcleavage_HNH_center_with_TS_for_morph.pdb #/E,Morph -
postcleavage_HNH_center_with_TS_for_morph.pdb #/F,Morph -
postcleavage_HNH_center_with_TS_for_morph.pdb #/G,Morph -
postcleavage_HNH_center_with_TS_for_morph.pdb #/H,Morph -
postcleavage_HNH_center_with_TS_for_morph.pdb #/I,Morph -
postcleavage_HNH_center_with_TS_for_morph.pdb #/J,Morph -
postcleavage_HNH_center_with_TS_for_morph.pdb #/K,Morph -
postcleavage_HNH_center_with_TS_for_morph.pdb #/L) and 13
(halfcleaved_HNH_center_main_model_for_cat_morph.pdb
#15/A,halfcleaved_HNH_center_main_model_for_cat_morph.pdb
#15/B,halfcleaved_HNH_center_main_model_for_cat_morph.pdb
#15/C,halfcleaved_HNH_center_main_model_for_cat_morph.pdb
#15/D,halfcleaved_HNH_center_main_model_for_cat_morph.pdb
#15/E,halfcleaved_HNH_center_main_model_for_cat_morph.pdb
#15/F,halfcleaved_HNH_center_main_model_for_cat_morph.pdb
#15/G,halfcleaved_HNH_center_main_model_for_cat_morph.pdb
#15/H,halfcleaved_HNH_center_main_model_for_cat_morph.pdb
#15/I,halfcleaved_HNH_center_main_model_for_cat_morph.pdb
#15/J,halfcleaved_HNH_center_main_model_for_cat_morph.pdb
#15/K,halfcleaved_HNH_center_main_model_for_cat_morph.pdb
#15/L,halfcleaved_HNH_center_main_model_for_cat_morph.pdb #15/k)
> close #15
> open "/Users/zxc755/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/Type
> I-F_HNH/Manuscript/maps_models/halfcleaved_HNH_center_main_model_for_cat_morph.pdb"
Chain information for halfcleaved_HNH_center_main_model_for_cat_morph.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
k | No description available
> close #15
> hide #!14 models
> show #!32 models
> hide #!32 models
> show #!14 models
> hide #!14 models
> show #!32 models
> hide #32
> show #32/b cartoons
> hide #32/b cartoons
> show #32/k,l
> show #32/a:83,85
> color #32/k:40 #32/l:7 hot pink
> select add #32/A:85@CE
1 atom, 1 residue, 1 model selected
> select up
3 atoms, 1 bond, 2 residues, 1 model selected
> select up
17 atoms, 15 bonds, 2 residues, 1 model selected
> volume zone #13 nearAtoms rang 1 new tru
Invalid "nearAtoms" argument: invalid atoms specifier
> volume zone #13 nearAtoms sel range 1 newMap true
Opened halfcleaved_HNH_center_sharp3Å.mrc zone as #15, grid size 420,420,420,
pixel 0.725, shown at step 1, values float32
> transparency #15 90
> hide #32/a:200-350 cartoons
> hide #32/k:1-38
> hide #32/l:9-12
> select #32/L:7@N3
1 atom, 1 residue, 1 model selected
> select add #32/K:40@O6
2 atoms, 2 residues, 1 model selected
> select up
41 atoms, 44 bonds, 2 residues, 1 model selected
> volume zone #13 nearAtoms sel range 1 newMap true
Opened halfcleaved_HNH_center_sharp3Å.mrc zone as #16, grid size 420,420,420,
pixel 0.725, shown at step 1, values float32
> select up
4 atoms, 2 bonds, 2 residues, 1 model selected
> select up
41 atoms, 44 bonds, 2 residues, 1 model selected
> volume zone #13 nearAtoms sel range 1 newMap true
Opened halfcleaved_HNH_center_sharp3Å.mrc zone as #17, grid size 420,420,420,
pixel 0.725, shown at step 1, values float32
> transparency 16-17 90
Missing or invalid "percent" argument: Expected a number
> transparency #16-17 90
> hide #11.1 models
> hide #32/a:1-20
> hide #32/a:1-20 cartoons
> hide #32/a:87-200 cartoons
Drag select of 163 atoms, 183 bonds
> select up
169 atoms, 185 bonds, 10 residues, 1 model selected
> select up
202 atoms, 225 bonds, 10 residues, 1 model selected
Drag select of 133 atoms, 152 bonds
> select up
142 atoms, 154 bonds, 8 residues, 1 model selected
> select up
161 atoms, 179 bonds, 8 residues, 1 model selected
> hide sel
> select #15
2 models selected
> color sel steel blue
> select #16
2 models selected
> color sel hot pink
> select clear
> select #17
2 models selected
> color zone sel near #32
> transparency sel 90
> select clear
> select #32/L:5@C4'
1 atom, 1 residue, 1 model selected
> select add #32/K:42@C4
2 atoms, 2 residues, 1 model selected
> select up
41 atoms, 44 bonds, 2 residues, 1 model selected
> hide sel
Drag select of 8 residues
> 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:46
21 atoms, 18 bonds, 3 residues, 1 model selected
> select add #32/A:49
28 atoms, 25 bonds, 4 residues, 1 model selected
> show sel
> select clear
> show #32/b:95
> select #32/K:39@C4
1 atom, 1 residue, 1 model selected
> select up
3 atoms, 1 bond, 2 residues, 1 model selected
> select up
41 atoms, 44 bonds, 2 residues, 1 model selected
> hide sel
> volume zone #13 nearAtoms #32 range 1 newMap true
Opened halfcleaved_HNH_center_sharp3Å.mrc zone as #18, grid size 420,420,420,
pixel 0.725, shown at step 1, values float32
> color zone #18 near #32 distance 10
> volume #18 level 0.01
> hide #!32 models
> hide #!17 models
> hide #!16 models
> hide #!15 models
> show #!15 models
> show #!16 models
> show #!17 models
> show #!32 models
> volume #18 level 0.0001
> lighting soft
> lighting flat
> close #18
> select #32/A:47@CG
1 atom, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel
> show #32/b:90-100 cartoons
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
10 atoms, 10 bonds, 1 residue, 1 model selected
> color byhetero
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select add #32/A:49@CD
3 atoms, 1 bond, 2 residues, 1 model selected
> select up
13 atoms, 13 bonds, 2 residues, 1 model selected
> hide sel
> show #32/a:32
> show #32/a:42
> select clear
[Repeated 1 time(s)]
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel
> select clear
> show #32/a:82
> show #32/K:42
> hide #!16 models
> show #!16 models
> hide #!16 models
> show #!16 models
> hide #!15 models
> show #!15 models
> hide #!17 models
> show #!17 models
> hide #!17 models
> select add #32/K:41@P
1 atom, 1 residue, 1 model selected
> select up
3 atoms, 1 bond, 2 residues, 1 model selected
> select #32/K:41@C1'
1 atom, 1 residue, 1 model selected
> select up
3 atoms, 1 bond, 2 residues, 1 model selected
> select up
41 atoms, 44 bonds, 2 residues, 1 model selected
> select add #32/K:42@P
42 atoms, 44 bonds, 3 residues, 1 model selected
> select add #32/K:42@OP1
43 atoms, 44 bonds, 3 residues, 1 model selected
> select add #32/K:42@OP2
44 atoms, 44 bonds, 3 residues, 1 model selected
> select add #32/K:42@O5'
45 atoms, 44 bonds, 3 residues, 1 model selected
> select up
61 atoms, 66 bonds, 3 residues, 1 model selected
> select down
45 atoms, 44 bonds, 3 residues, 1 model selected
> volume zone #13 nearAtoms sel range 1 newMap true
Opened halfcleaved_HNH_center_sharp3Å.mrc zone as #18, grid size 420,420,420,
pixel 0.725, shown at step 1, values float32
> hide #!18 models
> show #!17 models
> hide #!17 models
> show #!18 models
> hide #!18 models
> show #!17 models
> show #!18 models
> hide #!17 models
> transparency #18 90
> hide #!18 models
> select #32/K:42@C4
1 atom, 1 residue, 1 model selected
> select up
20 atoms, 21 bonds, 1 residue, 1 model selected
> select subtract #32/K:42@OP2
19 atoms, 20 bonds, 1 residue, 1 model selected
> select subtract #32/K:42@OP1
18 atoms, 19 bonds, 1 residue, 1 model selected
> select subtract #32/K:42@P
17 atoms, 18 bonds, 1 residue, 1 model selected
> select subtract #32/K:42@O5'
16 atoms, 17 bonds, 1 residue, 1 model selected
> hide sel
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
22 atoms, 24 bonds, 1 residue, 1 model selected
> color sel orange
> color sel dark orange
> select #32/K:41@C4
1 atom, 1 residue, 1 model selected
> select up
19 atoms, 20 bonds, 1 residue, 1 model selected
> select add #32/K:42@P
20 atoms, 20 bonds, 2 residues, 1 model selected
> select up
39 atoms, 42 bonds, 2 residues, 1 model selected
> color sel dim gray
> hide #!16 models
> select add #32/K:40@C6
1 atom, 1 bond, 1 residue, 1 model selected
> select up
3 atoms, 1 bond, 2 residues, 1 model selected
> select up
41 atoms, 44 bonds, 2 residues, 1 model selected
> color sel hot pink
> select clear
> show #!16 models
> show #!18 models
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select down
1 bond, 1 model selected
> select #32/B:95@CB
1 atom, 1 residue, 1 model selected
> select add #32/B:95@CG
2 atoms, 1 residue, 1 model selected
> select add #32/B:95@ND1
3 atoms, 1 residue, 1 model selected
> select add #32/B:95@CE1
4 atoms, 1 residue, 1 model selected
> select add #32/B:95@NE2
5 atoms, 1 residue, 1 model selected
> select add #32/B:95@CD2
6 atoms, 1 residue, 1 model selected
> volume zone #13 nearAtoms sel range 1 newMap true
Opened halfcleaved_HNH_center_sharp3Å.mrc zone as #19, grid size 420,420,420,
pixel 0.725, shown at step 1, values float32
> color zone #19 near #32
> hide #!19 models
> show #!19 models
> select ~sel & ##selected
24085 atoms, 24839 bonds, 13 pseudobonds, 2799 residues, 3 models selected
> color #19 forest green
> transparency #19 90
> select clear
> select add #32/A:82@OD1
1 atom, 1 residue, 1 model selected
> select add #32/A:82@ND2
2 atoms, 1 residue, 1 model selected
> select add #32/A:82@CG
3 atoms, 1 residue, 1 model selected
> select add #32/A:82@CB
4 atoms, 1 residue, 1 model selected
> select add #32/A:42@NZ
5 atoms, 2 residues, 1 model selected
> select add #32/A:42@CE
6 atoms, 2 residues, 1 model selected
> select add #32/A:42@CD
7 atoms, 2 residues, 1 model selected
> select add #32/A:42@CG
8 atoms, 2 residues, 1 model selected
> select add #32/A:42@CB
9 atoms, 2 residues, 1 model selected
> select add #32/A:46@OG1
10 atoms, 3 residues, 1 model selected
> select add #32/A:46@CB
11 atoms, 3 residues, 1 model selected
> select add #32/A:46@CG2
12 atoms, 3 residues, 1 model selected
> hide #!15 models
> select add #32/A:85@NZ
13 atoms, 4 residues, 1 model selected
> select add #32/A:85@CE
14 atoms, 4 residues, 1 model selected
> select add #32/A:85@CD
15 atoms, 4 residues, 1 model selected
> select add #32/A:85@CG
16 atoms, 4 residues, 1 model selected
> select add #32/A:85@CB
17 atoms, 4 residues, 1 model selected
> select add #32/A:83@CB
18 atoms, 5 residues, 1 model selected
> select add #32/A:83@CG
19 atoms, 5 residues, 1 model selected
> select add #32/A:83@OD2
20 atoms, 5 residues, 1 model selected
> select add #32/A:83@OD1
21 atoms, 5 residues, 1 model selected
> volume zone #13 nearAtoms sel range 1 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
> color #20 steel blue
> transparency #20 90
> select #18
2 models selected
> color zone sel near #32
> color #32/:l dar ora
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color #32/:L dark ora
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color #32/:L ora
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> hide #!18 models
> select #32/L:6@OP2
1 atom, 1 residue, 1 model selected
> select up
22 atoms, 24 bonds, 1 residue, 1 model selected
> color sel orange
> color sel dark orange
> color #32/L dark orange
> color #32/L:7 hot pink
> show #!18 models
> select #18
2 models selected
> color zone sel near #32
> transparency sel 90
> select clear
> ui tool show Distances
> hide #!16 models
> show #!16 models
> hide #!16 models
> hide #!18 models
> hide #!19 models
> hide #!20 models
> show #!17 models
> hide #!17 models
> select #32/A:82@ND2
1 atom, 1 residue, 1 model selected
> select add #32/K:42@OP1
2 atoms, 2 residues, 1 model selected
> distance #32/A:82@ND2 #32/K:42@OP1
Distance between halfcleaved_HNH_center_main_model_temp_editing.pdb #32/A ASN
82 ND2 and /K DT 42 OP1: 2.690Å
> distance style radius 0.04
[Repeated 2 time(s)]
> distance style radius 0.05
[Repeated 2 time(s)]
> select #32/A:42@NZ
1 atom, 1 residue, 1 model selected
> select add #32/K:41@OP1
2 atoms, 2 residues, 1 model selected
> distance #32/A:42@NZ #32/K:41@OP1
Distance between halfcleaved_HNH_center_main_model_temp_editing.pdb #32/A LYS
42 NZ and /K DC 41 OP1: 2.885Å
> select #32/A:46@OG1
1 atom, 1 residue, 1 model selected
> select add #32/K:40@OP1
2 atoms, 2 residues, 1 model selected
> distance #32/A:46@OG1 #32/K:40@OP1
Distance between halfcleaved_HNH_center_main_model_temp_editing.pdb #32/A THR
46 OG1 and /K DG 40 OP1: 2.817Å
> select #32/B:95@ND1
1 atom, 1 residue, 1 model selected
> select add #32/K:40@OP1
2 atoms, 2 residues, 1 model selected
> distance #32/B:95@ND1 #32/K:40@OP1
Distance between halfcleaved_HNH_center_main_model_temp_editing.pdb #32/B HIS
95 ND1 and /K DG 40 OP1: 2.646Å
> 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 #!1 models
> show #!3 models
> show #!4 models
> show #!2 models
> show #!5 models
> show #!6 models
> hide #!6 models
> hide #!5 models
> hide #!4 models
> hide #!3 models
> hide #!2 models
> show #!3 models
> show #!4 models
> graphics silhouettes true
> graphics silhouettes width 1
> lighting multiShadow 600
> ui tool show Toolbar
> volume zone #2 nearAtoms #1/A range 2 newMap true
Opened post_HNH_in_sharp.mrc zone as #8, grid size 420,420,420, pixel 0.725,
shown at step 1, values float32
> volume zone #2 nearAtoms #2/A range 2 newMap true
no atoms specified for zone
> volume zone #2 nearAtoms #3/A range 2 newMap true
Opened post_HNH_in_sharp.mrc zone as #10, grid size 420,420,420, pixel 0.725,
shown at step 1, values float32
> volume morph #8,10
Opened morph as #30, grid size 420,420,420, pixel 0.725, shown at step 1,
values float32
> hide #!1 models
> close session
> open /Users/gmontoya/Downloads/cas8_movment.cxs format session
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
opened ChimeraX session
> show #!22 models
> show #!25 models
> show #!14 models
> graphics silhouettes true
> graphics silhouettes width 1
> lighting multiShadow 600
> hide #!25 models
> hide #!22 models
> show #!22 models
> show #!25 models
> hide #!25 models
> hide #!22 models
> show #!4 models
> ui tool show Matchmaker
> matchmaker #14/A to #4/A pairing ss
Parameters
---
Chain pairing | ss
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 postcleavage_HNH_center.pdb, chain A (#4) with apo_HNH_center.pdb,
chain A (#14), sequence alignment score = 1511.2
RMSD between 184 pruned atom pairs is 1.025 angstroms; (across all 340 pairs:
3.799)
> show #!25 models
> matchmaker #25/A to #4/A pairing ss
Parameters
---
Chain pairing | ss
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 postcleavage_HNH_center.pdb, chain A (#4) with
apo_HNH_outwards_refined.pdb, chain A (#25), sequence alignment score = 1630.9
RMSD between 194 pruned atom pairs is 1.023 angstroms; (across all 336 pairs:
10.486)
> hide #!14 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> dssp
> hide #!4 models
> show #!4 models
> hide #!25 models
> show #!25 models
> close session
> open /Users/gmontoya/Downloads/cas8_movment.cxs format session
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
opened ChimeraX session
> show #!1 models
> show #!3 models
> show #!4 models
> graphics silhouettes true
> graphics silhouettes width 1
> lighting multiShadow 600
> hide #!3 models
> hide #!1 models
> show #!1 models
> show #!3 models
> dssp
> hide #!3 models
> hide #!1 models
> show #!3 models
> show #!1 models
> morph #3:A,4:A,1:A frames 40
Require at least 2 structures for morph
> morph #3,4 frames 40
Computed 41 frame morph #8
> coordset #8 1,41
> morph #3/A,4/A frames 40
Require at least 2 structures for morph
> morph #3,4,1 frames 40
Computed 81 frame morph #10
> coordset #10 1,81
> hide #!1 models
> close #8
> select #10/A:1-215
1702 atoms, 1736 bonds, 213 residues, 1 model selected
> hide sel cartoons
> select #10/A:1-215
1702 atoms, 1736 bonds, 213 residues, 1 model selected
> show sel cartoons
> select #10/A:1-210
1662 atoms, 1695 bonds, 208 residues, 1 model selected
> hide sel cartoons
> hide #!10 models
> show #!3 models
> show #!4 models
> show #!1 models
> move 30 #1
Missing or invalid "axis" argument: Expected 3 floats or "x", or "y", or "z"
or two atoms
> move x 30 #1
Expected an integer >= 1 or a keyword
> move x 30 models #1
> move x 30 models #13
> move x 30 models #3
> move x -30 models #3
> close session
> open /Users/gmontoya/Downloads/cas8_movment.cxs format session
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
opened ChimeraX session
> show #!22 models
> show #!25 models
> show #!14 models
> graphics silhouettes true
> graphics silhouettes width 1
> lighting multiShadow 600
> hide #!25 models
> hide #!22 models
> show #!25 models
> hide #!25 models
> show #!4 models
> matchmaker #4 to #14 chain A
Expected a keyword
> 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)
> hide #!4 models
> show #!4 models
> show #!5 models
> show #!9 models
> matrixcopy #4 to #5
Unknown command: matrixcopy #4 to #5
> copy #4 to #5 transform true
Unknown command: copy #4 to #5 transform true
> hide #!9 models
> show #!9 models
> fitmap #4 to #9 move true
Expected a keyword
> fitmap #4 inMap #9 moveWholeMolecules true
Fit molecule postcleavage_HNH_center.pdb (#4) to map apo_HNH_cent_sharp.mrc
(#9) using 23513 atoms
average map value = 0.2887, steps = 96
shifted from previous position = 1.39
rotated from previous position = 1.86 degrees
atoms outside contour = 2792, contour level = 0.0019908
Position of postcleavage_HNH_center.pdb (#4) relative to
apo_HNH_cent_sharp.mrc (#9) coordinates:
Matrix rotation and translation
-0.99666193 0.08128198 -0.00763119 294.01909484
-0.08106989 -0.99639770 -0.02488551 320.13744438
-0.00962645 -0.02418378 0.99966118 6.22053499
Axis 0.00432191 0.01228865 -0.99991515
Axis point 153.53195307 154.12916032 0.00000000
Rotation angle (degrees) 175.34344235
Shift along axis -1.01522796
> close session
> open /Users/gmontoya/Downloads/cas8_movment.cxs format session
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
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
> hide #!15 models
> hide #!14 models
> hide #!7 models
> hide #!4 models
> hide #!3 models
> hide #!1 models
> hide #!22 models
> hide #!25 models
> select #32/J-L
2375 atoms, 2659 bonds, 1 pseudobond, 115 residues, 2 models selected
> show sel cartoons
> close session
> open /Users/gmontoya/Documents/Anders/map_continuousTS.cxs format session
Opened halfcleaved_HNH_center_fullTS_sharp.mrc as #2, grid size 420,420,420,
pixel 0.725, shown at level 0.05, step 1, values float32
Opened halfcleaved_HNH_center_fullTS_sharp.mrc zone as #3, grid size
420,420,420, pixel 0.725, shown at level 0.05, step 1, values float32
Opened halfcleaved_HNH_center_fullTS_sharp.mrc zone as #4, grid size
420,420,420, pixel 0.725, shown at level 0.041, step 1, values float32
Opened halfcleaved_HNH_center_fullTS_sharp.mrc zone as #5, grid size
420,420,420, pixel 0.725, shown at level 0.0211, step 1, values float32
opened ChimeraX session
> show #!1 models
> hide #!4 models
> hide #!5 models
> select #1/A,K
3661 atoms, 3827 bonds, 386 residues, 1 model selected
> save /Users/gmontoya/Downloads/fullTS.pdb selectedOnly true
> close session
> open /Users/gmontoya/Downloads/cas8_movment2.cxs format session
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
opened ChimeraX session
> open /Users/gmontoya/Downloads/fullTS.pdb
Summary of feedback from opening /Users/gmontoya/Downloads/fullTS.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 PRO D 64 GLU D 70 1 7
Start residue of secondary structure not found: HELIX 2 2 TYR D 112 GLU D 128
1 17
Start residue of secondary structure not found: HELIX 3 3 LEU D 132 ALA D 143
1 12
Start residue of secondary structure not found: HELIX 4 4 SER D 174 SER D 176
1 3
Start residue of secondary structure not found: HELIX 5 5 ALA D 187 ALA D 201
1 15
140 messages similar to the above omitted
Chain information for fullTS.pdb #8
---
Chain | Description
A | No description available
K | No description available
> matchmaker #8/A to #14/A
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 apo_HNH_center.pdb, chain A (#14) with fullTS.pdb, chain A (#8),
sequence alignment score = 1528.6
RMSD between 181 pruned atom pairs is 1.066 angstroms; (across all 340 pairs:
4.131)
> select add #8
3661 atoms, 3827 bonds, 386 residues, 1 model selected
> hide #!1 models
> hide #!3 models
> hide #!4 models
> hide #!7 models
> hide #!14 models
> hide #!15 models
> hide #!22 models
> hide #!25 models
> hide #!32 models
> color bychain
> select clear
> select #1/K
484 atoms, 538 bonds, 24 residues, 1 model selected
> nucleotides #8 ladder
> select #1/K
484 atoms, 538 bonds, 24 residues, 1 model selected
> hide #8 cartoons
> hide #8 atoms
> show #8 atoms
> undo
> show #8 cartoons
> show #8 atoms
> hide #8 atoms
> select #1/K
484 atoms, 538 bonds, 24 residues, 1 model selected
> show #8 atoms
> nucleotides #8 stubs
> select #1/K
484 atoms, 538 bonds, 24 residues, 1 model selected
> hide #8 cartoons
> select #8/K
933 atoms, 1041 bonds, 46 residues, 1 model selected
> nucleotides sel stubs
> nucleotides sel tube/slab shape muffler
> hide sel atoms
> undo
> select #8/K
933 atoms, 1041 bonds, 46 residues, 1 model selected
> hide sel cartoons
> hide sel atoms
> select #8/K
933 atoms, 1041 bonds, 46 residues, 1 model selected
> show sel cartoons
> select #8/A
2728 atoms, 2786 bonds, 340 residues, 1 model selected
> hide sel atoms
> show sel cartoons
> select clear
> show #!22 models
> show #!14 models
> show #!25 models
> hide #!25 models
> hide #!22 models
> hide #8 models
> show #8 models
> hide #8 models
> show #8 models
> hide #8 models
> show #8 models
> close session
> open /Users/gmontoya/Downloads/cas8_movment2.cxs format session
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
opened ChimeraX session
> open /Users/gmontoya/Downloads/fullTS.pdb
Summary of feedback from opening /Users/gmontoya/Downloads/fullTS.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 PRO D 64 GLU D 70 1 7
Start residue of secondary structure not found: HELIX 2 2 TYR D 112 GLU D 128
1 17
Start residue of secondary structure not found: HELIX 3 3 LEU D 132 ALA D 143
1 12
Start residue of secondary structure not found: HELIX 4 4 SER D 174 SER D 176
1 3
Start residue of secondary structure not found: HELIX 5 5 ALA D 187 ALA D 201
1 15
140 messages similar to the above omitted
Chain information for fullTS.pdb #8
---
Chain | Description
A | No description available
K | No description available
> select add #8
3661 atoms, 3827 bonds, 386 residues, 1 model selected
> color byattribute chain
No known/registered numeric attribute chain
> color bychain
> undo
> select subtract #8
Nothing selected
> select #8 color bychain
Expected a keyword
> select #8 color sel bychain
Expected a keyword
> select #8
3661 atoms, 3827 bonds, 386 residues, 1 model selected
> colorsel bychain
Unknown command: colorsel bychain
> color sel bychain
> select clear
> matchmaker #8/A to #14/A
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 apo_HNH_center.pdb, chain A (#14) with fullTS.pdb, chain A (#8),
sequence alignment score = 1528.6
RMSD between 181 pruned atom pairs is 1.066 angstroms; (across all 340 pairs:
4.131)
> select #8/K
933 atoms, 1041 bonds, 46 residues, 1 model selected
> show sel cartoons
> hide sel cartoons
> show sel cartoons
> nucleotides sel stubs
> nucleotides sel ladder
> select clear
> hide #!32 models
> hide #!25 models
> hide #!22 models
> hide #!15 models
> hide #!7 models
> hide #!4 models
> hide #!3 models
> hide #!1 models
> select #14/A:1-215
1702 atoms, 1736 bonds, 213 residues, 1 model selected
> hide sel cartoons
> select #22/A:1-215
1702 atoms, 1736 bonds, 213 residues, 1 model selected
> hide sel cartoons
> select #25/A:1-215
1683 atoms, 1717 bonds, 211 residues, 1 model selected
> hide sel cartoons
> select #7/A:1-215
1702 atoms, 1736 bonds, 213 residues, 1 model selected
> hide sel cartoons
> select #32/A:1-215
1702 atoms, 1736 bonds, 1 pseudobond, 213 residues, 2 models selected
> hide sel cartoons
> select #15/A:1-215
1702 atoms, 1736 bonds, 213 residues, 1 model selected
> hide sel cartoons
> select #1/A:1-215
1702 atoms, 1736 bonds, 213 residues, 1 model selected
> hide sel cartoons
> select #3/A:1-215
1702 atoms, 1736 bonds, 213 residues, 1 model selected
> hide sel cartoons
> select #4/A:1-215
1702 atoms, 1736 bonds, 213 residues, 1 model selected
> hide sel cartoons
> select #8/A:1-215
1702 atoms, 1736 bonds, 213 residues, 1 model selected
> hide sel cartoons
> select #8/K
933 atoms, 1041 bonds, 46 residues, 1 model selected
> cartoon style tube
Expected an atoms specifier or a keyword
> cartoon sel style tube
Expected a keyword
> cartoon sel style tube
Expected a keyword
> cartoon style sel modeHelix tube sides 20
> select #8/K
933 atoms, 1041 bonds, 46 residues, 1 model selected
> nucleotides sel ladder
> nucleotides sel stubs
> hide sel atoms
> select #8/K
933 atoms, 1041 bonds, 46 residues, 1 model selected
> cartoon style width 1.5 thickness 0.3
> cartoon style width 1 thickness 0.3
> cartoon #8/K width 1 thick 0.3
Expected a keyword
> hide sel atoms
> select add #8
3661 atoms, 3827 bonds, 386 residues, 1 model selected
> select subtract #8
Nothing selected
> select add #8
3661 atoms, 3827 bonds, 386 residues, 1 model selected
> select clear
> select #8/K
933 atoms, 1041 bonds, 46 residues, 1 model selected
> cartoon sel style nucleic oval
Expected a keyword
> cartoon style sel oval
Expected a keyword
> cartoon sel width 1
Expected a keyword
> alias nucrib cartoon style nucleic xsect oval width 1.6 thick 1.6
> cartoon style sel modeHelix tube sides 20
> nucleotides sel stubs
> nucleotides sel ladder
> nucleotides sel tube/slab shape box
> show sel atoms
> nucleotides sel atoms
> style nucleic & sel stick
Changed 933 atom styles
> nucleotides sel fill
> style nucleic & sel stick
Changed 933 atom styles
> nucleotides sel slab
> style nucleic & sel stick
Changed 933 atom styles
> nucleotides sel tube/slab shape box
> nucleotides sel tube/slab shape ellipsoid
> nucleotides sel tube/slab shape muffler
> nucleotides sel ladder
> nucleotides sel stubs
> select clear
> show #!1 models
> hide #!1 models
> hide #!14 models
> select #8/K
933 atoms, 1041 bonds, 46 residues, 1 model selected
> cartoon tube
Expected an atoms specifier or a keyword
> cartoon sel tube
Expected a keyword
> hide sel atoms
> show sel cartoons
> hide sel cartoons
> show sel cartoons
> cartoon sel tube
Expected a keyword
> cartoon byattribute worm
No known/registered numeric attribute worm
> cartoon byattribute sel
No known/registered numeric attribute sel
> cartoon byattribute #8/K
No known/registered numeric attribute #8/K
> cartoon style width 1.5 thickness 0.3
> cartoon sel style width 1.0 thick 0.3
Expected a keyword
> cartoon style #8/k width 1.0 thickness 0.3
> cartoon style #8/k width 0.5 thickness 0.3
> select #8/K:10-46
750 atoms, 836 bonds, 37 residues, 1 model selected
> hide sel cartoons
> lighting soft
> ui tool show "Side View"
> show #!14 models
> hide #!14 models
> show #!14 models
> hide #!14 models
> show #!14 models
> show #!22 models
> color #22 #ff2600ff
> color #22 #ff9300ff
> show #!25 models
> hide #!25 models
> hide #!22 models
> show #!32 models
> hide #!14 models
> hide #!32 models
> show #!14 models
> show #!22 models
> show #!25 models
> hide #!22 models
> hide #!14 models
> hide #8 models
> hide #!25 models
> show #!14 models
> show #8 models
> select #8/K
933 atoms, 1041 bonds, 46 residues, 1 model selected
> color sel dark gray
> select clear
> select #8/K
933 atoms, 1041 bonds, 46 residues, 1 model selected
> color sel black
> select clear
> hide #8 models
> select #14/A:1-215
1702 atoms, 1736 bonds, 213 residues, 1 model selected
> hide sel cartoons
> color #14/cyan
> select #14/A:1-215
1702 atoms, 1736 bonds, 213 residues, 1 model selected
> hide sel cartoons
> color #14/ cyan
> select #14/A:1-215
1702 atoms, 1736 bonds, 213 residues, 1 model selected
> hide sel cartoons
> color #14/A cyan
> show #!1 models
> show #!4 models
> show #!3 models
> show #!22 models
> show #!25 models
> show #!7 models
> show #!32 models
> show #!15 models
> select #1/A:1-215
1702 atoms, 1736 bonds, 213 residues, 1 model selected
> hide sel cartoons
> color #1/A lavender
> select #4/A:1-215
1702 atoms, 1736 bonds, 213 residues, 1 model selected
> hide sel cartoons
> color #4/A cyan
> select #3/A:1-215
1702 atoms, 1736 bonds, 213 residues, 1 model selected
> hide sel cartoons
> color #3/A tangerine
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> select #22/A:1-215
1702 atoms, 1736 bonds, 213 residues, 1 model selected
> hide sel cartoons
> color #22/A lavender
> select #14/A:1-215
1702 atoms, 1736 bonds, 213 residues, 1 model selected
> hide sel cartoons
> color #14/A cyan
> select #25/A:1-215
1683 atoms, 1717 bonds, 211 residues, 1 model selected
> hide sel cartoons
> color #25/A Tangerine
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> select #7/A:1-215
1702 atoms, 1736 bonds, 213 residues, 1 model selected
> hide sel cartoons
> color #7/A lavender
> select #32/A:1-215
1702 atoms, 1736 bonds, 1 pseudobond, 213 residues, 2 models selected
> hide sel cartoons
> color #32/A cyan
> select #15/A:1-215
1702 atoms, 1736 bonds, 213 residues, 1 model selected
> hide sel cartoons
> color #15/A Tangerine
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color #15/A Tangerine
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> hide #!7 models
> hide #!14 models
> hide #!15 models
> hide #!22 models
> hide #!25 models
> hide #!32 models
> select add #15
24110 atoms, 24866 bonds, 2 pseudobonds, 2797 residues, 2 models selected
> select subtract #15
Nothing selected
> select #3/A:1-215
1702 atoms, 1736 bonds, 213 residues, 1 model selected
> hide sel cartoons
> select 3/A:215-400
Expected an objects specifier or a keyword
> color #3/A tangerine
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color #3/A tangerine
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color #3/A tangerine
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> hide #!4 models
> hide #!1 models
> select 3/A:215-400
Expected an objects specifier or a keyword
> color #3/A tangerine
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color sel tangerine
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> select #3/A:1-215
1702 atoms, 1736 bonds, 213 residues, 1 model selected
> hide sel cartoons
> select 3/A:215-400
Expected an objects specifier or a keyword
> color sel tangerine
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> select #3/A216-400
Nothing selected
> select #3/A:216-400
1026 atoms, 1049 bonds, 127 residues, 1 model selected
> color sel tangerine
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color sel gray
> select 3/A:215-400
Expected an objects specifier or a keyword
> color sel tangerine
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> select 3/A:215-400,
Expected an objects specifier or a keyword
> color sel tangerine
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> select #3/A:216-400
1026 atoms, 1049 bonds, 127 residues, 1 model selected
> color sel tangerine
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color sel tangerine
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> select 3/A:215-400
Expected an objects specifier or a keyword
> color sel red
> select 3/A:215-400
Expected an objects specifier or a keyword
> color sel Tangerine
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color sel orange
> ui tool show "Color Actions"
> show #!1 models
> show #!4 models
> show #!7 models
> show #!15 models
> show #!14 models
> show #!22 models
> show #!25 models
> show #!32 models
> select #1/A:1-215
1702 atoms, 1736 bonds, 213 residues, 1 model selected
> hide sel cartoons
> color #1/A plum
> select #4/A:1-215
1702 atoms, 1736 bonds, 213 residues, 1 model selected
> hide sel cartoons
> color #4/A sky blue
> select #3/A:1-215
1702 atoms, 1736 bonds, 213 residues, 1 model selected
> hide sel cartoons
> color #3/A orange
> select #22/A:1-215
1702 atoms, 1736 bonds, 213 residues, 1 model selected
> hide sel cartoons
> color #22/A plum
> select #14/A:1-215
1702 atoms, 1736 bonds, 213 residues, 1 model selected
> hide sel cartoons
> color #14/A sky blue
> select #25/A:1-215
1683 atoms, 1717 bonds, 211 residues, 1 model selected
> hide sel cartoons
> color #25/A orange
> select #7/A:1-215
1702 atoms, 1736 bonds, 213 residues, 1 model selected
> hide sel cartoons
> color #7/A plum
> select #32/A:1-215
1702 atoms, 1736 bonds, 1 pseudobond, 213 residues, 2 models selected
> hide sel cartoons
> color #32/A sky blue
> select #15/A:1-215
1702 atoms, 1736 bonds, 213 residues, 1 model selected
> hide sel cartoons
> color #15/A orange
> show #8 models
> hide #!1 models
> hide #!3 models
> hide #!4 models
> hide #!7 models
> hide #!15 models
> hide #!32 models
> hide #8 models
> show #8 models
> hide #8 models
> show #8 models
> hide #!22 models
> hide #!25 models
> select #8/A
2728 atoms, 2786 bonds, 340 residues, 1 model selected
> color sel sky blue
> select clear
> select #8/A
2728 atoms, 2786 bonds, 340 residues, 1 model selected
> color sel lime
> select clear
> select #8/A
2728 atoms, 2786 bonds, 340 residues, 1 model selected
> color sel chartreuse
> select clear
> lighting soft
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> graphics silhouettes false
> graphics silhouettes true
> lighting soft
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting soft
> show #!4 models
> hide #!4 models
> show #!4 models
> show #!32 models
> hide #!32 models
> hide #!4 models
> show #!25 models
> show #!22 models
> show #!2 models
> hide #!2 models
> show #!1 models
> show #!3 models
> show #!4 models
> show #!32 models
> show #!15 models
> hide #!32 models
> hide #!25 models
> hide #!22 models
> hide #!15 models
> hide #!4 models
> hide #!3 models
> hide #!1 models
> save /Users/gmontoya/Downloads/fig4.2_apo.png width 3000 height 2589
> supersample 4 transparentBackground true
> undo
> hide #!14 models
> hide #!3 models
> hide #!1 models
> show #!22 models
> hide #8 models
> save /Users/gmontoya/Downloads/fig4.1_apo.png width 3000 height 2589
> supersample 4 transparentBackground true
> hide #!22 models
> show #!24 models
> hide #!24 models
> show #!25 models
> save /Users/gmontoya/Downloads/fig4.3_apo.png width 3000 height 2589
> supersample 4 transparentBackground true
> hide #!25 models
> show #!7 models
> save /Users/gmontoya/Downloads/fig4.4_ntscle.png width 3000 height 2589
> supersample 4 transparentBackground true
> hide #!7 models
> show #!32 models
> show #8 models
> save /Users/gmontoya/Downloads/fig4.5_ntscle.png width 3000 height 2589
> supersample 4 transparentBackground true
> hide #8 models
> show #!15 models
> hide #!32 models
> save /Users/gmontoya/Downloads/fig4.6_ntscle.png width 3000 height 2589
> supersample 4 transparentBackground true
> hide #!15 models
> show #!1 models
> save /Users/gmontoya/Downloads/fig4.7_post.png width 3000 height 2589
> supersample 4 transparentBackground true
> hide #!1 models
> show #!4 models
> show #8 models
> save /Users/gmontoya/Downloads/fig4.8_post.png width 3000 height 2589
> supersample 4 transparentBackground true
> hide #!4 models
> show #!3 models
> hide #8 models
> save /Users/gmontoya/Downloads/fig4.9_post.png width 3000 height 2589
> supersample 4 transparentBackground true
> show #!1 models
> hide #!1 models
> ui tool show "Show Sequence Viewer"
> sequence chain #1/A
Alignment identifier is 1/A
> ui tool show "Show Sequence Viewer"
> sequence chain #1/B
Alignment identifier is 1/B
> ui tool show "Show Sequence Viewer"
> sequence chain #1/C
Alignment identifier is 1/C
> ui tool show "Show Sequence Viewer"
> sequence chain #1/D
Alignment identifier is 1/D
> ui tool show "Show Sequence Viewer"
> sequence chain #1/E
Alignment identifier is 1/E
===== Log before crash end =====
Log:
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_movment2.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 15:04:16 2025UCSF 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 format session
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
> show #8 models
> show #9/M atoms
> show #9/N atoms
> hide #!9 models
> show #!9 models
> hide #8 models
> show #8 models
> hide #8 models
> hide #!9 models
> open "/Users/zxc755/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/Type
> I-F_HNH/Manuscript/halfcleaved_HNH_center_main_model_temp2.pdb"
Chain information for halfcleaved_HNH_center_main_model_temp2.pdb #10
---
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
> hide #10 atoms
> show #10 cartoons
> cartoon style nucleic xsection oval width 1.6 thickness 1.6
> color #10/L light gray
> color #10/K dim gray
> color #10/J dark red
> color #10/I rebecca purple
> color #10/B forest green
> color #10/C,D,E,F,G,H khaki
> color #10/A steel blue
> color #10/A:232-350 dark turquoise
> show #10/K atoms
> style stick
Changed 131055 atom styles
> show #10 & nucleic atoms
> select #10
24166 atoms, 24925 bonds, 3 pseudobonds, 2803 residues, 2 models selected
> nucleotides sel ladder
> select clear
> show #!4 models
> volume #4 level 0.06
> show #10/M,N,O atoms
> select clear
> select #10/K:4
4 atoms, 3 bonds, 1 residue, 1 model selected
> select add #10/K:3
25 atoms, 26 bonds, 2 residues, 1 model selected
> select add #10/K:2
45 atoms, 47 bonds, 3 residues, 1 model selected
> select add #10/K:1
54 atoms, 56 bonds, 4 residues, 1 model selected
> hide sel cartoons
> nucleotides sel atoms
> style nucleic & sel stick
Changed 54 atom styles
> select clear
> color zone #4 near #10 distance 10
> transparency 50
> volume #4 level 0.05
> cartoon style nucleic xsection oval width 1 thickness 1
> color #10/L light gray
> color #10/K dim gray
> color #10/J dark red
> color #10/I rebecca purple
> color #10/B forest green
> color #10/C,D,E,F,G,H khaki
> color #10/A steel blue
> color #10/A:232-350 dark turquoise
> color zone #4 near #10 distance 10
> hide #!10 models
> hide #!4 models
> show #!10 models
> select #10/M:1@MG
1 atom, 1 residue, 1 model selected
> color sel red
> select #10/O:1@O
1 atom, 1 residue, 1 model selected
> color sel blue
> select clear
> color zone #4 near #10 distance 10
> show #!4 models
> hide #!10 models
> color zone #4 near #10 distance 5
> volume #4 level 0.09
> lighting soft
> lighting full
> lighting soft
> color zone #4 near #10 distance 4
> color zone #4 near #10 distance 3
> volume #4 level 0.07
> surface zone #4 nearAtoms #10 distance 2.5
> surface zone #4 nearAtoms #10 distance 3
> select add #4
2 models selected
> ui tool show "Color Actions"
> color sel navajo white
> set bgColor white
> lighting simple
> transparency sel 50
> show #!10 models
> volume #4 level 0.05
> volume #4 level 0.09
> volume #4 level 0.08
> color #10 byhetero
> select clear
> select #10/K:1@N9
1 atom, 1 residue, 1 model selected
> select up
9 atoms, 9 bonds, 1 residue, 1 model selected
> select add #10/K:2@OP2
10 atoms, 9 bonds, 2 residues, 1 model selected
> select up
29 atoms, 31 bonds, 2 residues, 1 model selected
> select down
10 atoms, 9 bonds, 2 residues, 1 model selected
> select add #10/K:2@OP1
11 atoms, 12 bonds, 2 residues, 1 model selected
> select add #10/K:2@O2
12 atoms, 17 bonds, 2 residues, 1 model selected
> select add #10/K:2@O4
13 atoms, 20 bonds, 2 residues, 1 model selected
> select add #10/K:2@C5
14 atoms, 21 bonds, 2 residues, 1 model selected
> select add #10/K:2@C7
15 atoms, 24 bonds, 2 residues, 1 model selected
> select add #10/K:3@N6
16 atoms, 25 bonds, 3 residues, 1 model selected
> select up
28 atoms, 27 bonds, 3 residues, 1 model selected
> select up
50 atoms, 55 bonds, 3 residues, 1 model selected
> hide #!4 models
> select subtract #10/K:3@OP1
49 atoms, 53 bonds, 3 residues, 1 model selected
> select subtract #10/K:3@P
48 atoms, 51 bonds, 3 residues, 1 model selected
> select subtract #10/K:3@OP2
47 atoms, 51 bonds, 3 residues, 1 model selected
> select add #10/K:4@P
48 atoms, 51 bonds, 4 residues, 1 model selected
> select add #10/K:4@OP1
49 atoms, 52 bonds, 4 residues, 1 model selected
> select add #10/K:4@OP2
50 atoms, 54 bonds, 4 residues, 1 model selected
> select subtract #10/K:2@O3'
49 atoms, 53 bonds, 4 residues, 1 model selected
> select subtract #10/K:2@C4'
48 atoms, 50 bonds, 4 residues, 1 model selected
> select subtract #10/K:2@O4'
47 atoms, 48 bonds, 4 residues, 1 model selected
> select subtract #10/K:2@C3'
46 atoms, 48 bonds, 4 residues, 1 model selected
> select subtract #10/K:2@C2'
45 atoms, 47 bonds, 4 residues, 1 model selected
> select subtract #10/K:2@C1'
44 atoms, 46 bonds, 4 residues, 1 model selected
> select subtract #10/K:2@C5'
43 atoms, 46 bonds, 4 residues, 1 model selected
> hide sel atoms
> show #10/K:3 atoms
> hide sel atoms
> select #10/K:3@C5'
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select #10/K:3@C4'
1 atom, 1 residue, 1 model selected
> select add #10/K:3@O3'
2 atoms, 1 residue, 1 model selected
> select add #10/K:3@C2'
3 atoms, 1 residue, 1 model selected
> select add #10/K:3@O4'
4 atoms, 1 residue, 1 model selected
> hide sel atoms
> select #10/K:3@C3'
1 atom, 1 residue, 1 model selected
> select add #10/K:3@C1'
2 atoms, 1 residue, 1 model selected
> select add #10/K:3@C8
3 atoms, 1 residue, 1 model selected
> select up
21 atoms, 23 bonds, 1 residue, 1 model selected
> select down
3 atoms, 1 residue, 1 model selected
> select add #10/K:3@N3
4 atoms, 1 residue, 1 model selected
> select add #10/K:3@C4
5 atoms, 1 residue, 1 model selected
> select add #10/K:3@C5
6 atoms, 1 residue, 1 model selected
> select add #10/K:3@N7
7 atoms, 1 residue, 1 model selected
> select add #10/K:3@C6
8 atoms, 1 residue, 1 model selected
> select add #10/K:3@N6
9 atoms, 1 residue, 1 model selected
> select add #10/K:3@N1
10 atoms, 1 residue, 1 model selected
> select add #10/K:3@C2
11 atoms, 1 residue, 1 model selected
> hide sel atoms
> select #10/K:3@N9
1 atom, 1 residue, 1 model selected
> hide sel atoms
> show #!4 models
> select #10/K:2@C5'
1 atom, 1 residue, 1 model selected
> hide sel atoms
> volume #4 level 0.07
> show #10/A:305,304,280,328
> volume #4 level 0.09
> select #10/K:4@O5'
1 atom, 1 residue, 1 model selected
> hide sel atoms
> color #10/M red
> color #10/O blue
> color #10/O dark blue
> color #10/O blue
> volume #4 level 0.07
> show #10/K:2 atoms
> volume #4 level 0.06
> show #10/K:1-2 atoms
> show #!5 models
> hide #!5 models
> show #!2 models
> hide #!2 models
> hide #!4 models
> hide #!10 models
> show #!10 models
> select #10/K:1@O5'
1 atom, 1 residue, 1 model selected
> select add #10/K:1@C5'
2 atoms, 1 residue, 1 model selected
> select add #10/K:1@C4'
3 atoms, 1 residue, 1 model selected
> select add #10/K:1@O4'
4 atoms, 1 residue, 1 model selected
> select add #10/K:1@C1'
5 atoms, 1 residue, 1 model selected
> select add #10/K:1@N9
6 atoms, 1 residue, 1 model selected
> select add #10/K:1@C2'
7 atoms, 1 residue, 1 model selected
> select add #10/K:1@C3'
8 atoms, 1 residue, 1 model selected
> select add #10/K:1@O3'
9 atoms, 1 residue, 1 model selected
> select add #10/K:2@P
10 atoms, 2 residues, 1 model selected
> select add #10/K:2@OP2
11 atoms, 2 residues, 1 model selected
> select add #10/K:2@OP1
12 atoms, 2 residues, 1 model selected
> select add #10/K:2@O5'
13 atoms, 2 residues, 1 model selected
> select add #10/K:2@C5'
14 atoms, 2 residues, 1 model selected
> hide sel atoms
> show #!4 models
> hide #!4 models
> ui tool show Distances
> select #10/O:1@O
1 atom, 1 residue, 1 model selected
> select #10/K:3@OP2
1 atom, 1 residue, 1 model selected
> select add #10/O:1@O
2 atoms, 2 residues, 1 model selected
> distance #10/K:3@OP2 #10/O:1@O
Distance between halfcleaved_HNH_center_main_model_temp2.pdb #10/K DA 3 OP2
and /O HOH 1 O: 2.479Å
> select #10/A:304@ND1
1 atom, 1 residue, 1 model selected
> select add #10/M:1@MG
2 atoms, 2 residues, 1 model selected
> distance #10/A:304@ND1 #10/M:1@MG
Distance between halfcleaved_HNH_center_main_model_temp2.pdb #10/A HIS 304 ND1
and /M MG 1 MG: 2.377Å
> select #10/A:328@NE2
1 atom, 1 residue, 1 model selected
> select add #10/M:1@MG
2 atoms, 2 residues, 1 model selected
> distance #10/A:328@NE2 #10/M:1@MG
Distance between halfcleaved_HNH_center_main_model_temp2.pdb #10/A HIS 328 NE2
and /M MG 1 MG: 2.352Å
> select #10/M:1@MG
1 atom, 1 residue, 1 model selected
> select add #10/K:3@OP1
2 atoms, 2 residues, 1 model selected
> distance #10/M:1@MG #10/K:3@OP1
Distance between halfcleaved_HNH_center_main_model_temp2.pdb #10/M MG 1 MG and
/K DA 3 OP1: 3.166Å
> select #10/A:280@NH2
1 atom, 1 residue, 1 model selected
> select add #10/K:3@OP2
2 atoms, 2 residues, 1 model selected
> distance #10/A:280@NH2 #10/K:3@OP2
Distance between halfcleaved_HNH_center_main_model_temp2.pdb #10/A ARG 280 NH2
and /K DA 3 OP2: 2.389Å
> select #10/A:280@NH1
1 atom, 1 residue, 1 model selected
> select add #10/K:3@O5'
2 atoms, 2 residues, 1 model selected
> distance #10/A:280@NH1 #10/K:3@O5'
Distance between halfcleaved_HNH_center_main_model_temp2.pdb #10/A ARG 280 NH1
and /K DA 3 O5': 2.765Å
> select #10/A:238
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #10/A:319
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> select #10/A:305@ND1
1 atom, 1 residue, 1 model selected
> select add #10/K:3@OP2
2 atoms, 2 residues, 1 model selected
> distance #10/A:305@ND1 #10/K:3@OP2
Distance between halfcleaved_HNH_center_main_model_temp2.pdb #10/A HIS 305 ND1
and /K DA 3 OP2: 3.592Å
> select #10/A:309
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel cartoons
> show sel atoms
> select #10/A:309@N
1 atom, 1 residue, 1 model selected
> select add #10/O:1@O
2 atoms, 2 residues, 1 model selected
> distance #10/A:309@N #10/O:1@O
Distance between halfcleaved_HNH_center_main_model_temp2.pdb #10/A LEU 309 N
and /O HOH 1 O: 3.104Å
> select #10/A:309@N
1 atom, 1 residue, 1 model selected
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel atoms
> show sel cartoons
> select clear
> view
> select #10/A:305@ND1
1 atom, 1 residue, 1 model selected
> select add #10/K:3@OP1
2 atoms, 2 residues, 1 model selected
> distance #10/A:305@ND1 #10/K:3@OP1
Distance between halfcleaved_HNH_center_main_model_temp2.pdb #10/A HIS 305 ND1
and /K DA 3 OP1: 3.734Å
> delete sel
> ~distance #10/A:305@ND1 #10/K:3@OP1
> open "/Users/zxc755/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/Type
> I-F_HNH/Manuscript/halfcleaved_HNH_center_main_model_temp2.pdb"
Chain information for halfcleaved_HNH_center_main_model_temp2.pdb #12
---
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
> style stick
Changed 155221 atom styles
> hide #12 atoms
> color #12/L light gray
> color #12/K dim gray
> color #12/J dark red
> color #12/I rebecca purple
> color #12/B forest green
> color #12/C,D,E,F,G,H khaki
> color #12/A steel blue
> color #12/A:232-350 dark turquoise
> hide #!11 models
> show #!11 models
> close #11
> show #12 cartoons
> cartoon style nucleic xsection oval width 1 thickness 1
> show #12/K:2-3 atoms
> hide #12/K:1-3 cartoons
> select clear
> select #12/K:2@OP1
1 atom, 1 residue, 1 model selected
> select add #12/K:2@OP2
2 atoms, 1 residue, 1 model selected
> select add #12/K:2@P
3 atoms, 1 residue, 1 model selected
> select add #12/K:2@C5'
4 atoms, 1 residue, 1 model selected
> select add #12/K:3@C5'
5 atoms, 2 residues, 1 model selected
> select add #12/K:3@C4'
6 atoms, 2 residues, 1 model selected
> select add #12/K:3@C3'
7 atoms, 2 residues, 1 model selected
> select add #12/K:4
11 atoms, 3 bonds, 3 residues, 1 model selected
> select add #12/K:3@O4'
12 atoms, 3 bonds, 3 residues, 1 model selected
> select add #12/K:3@C2'
13 atoms, 3 bonds, 3 residues, 1 model selected
> select add #12/K:3@C1'
14 atoms, 3 bonds, 3 residues, 1 model selected
> select add #12/K:3@N9
15 atoms, 3 bonds, 3 residues, 1 model selected
> select add #12/K:3@C8
16 atoms, 3 bonds, 3 residues, 1 model selected
> select add #12/K:3@C4
17 atoms, 3 bonds, 3 residues, 1 model selected
> select add #12/K:3@C5
18 atoms, 3 bonds, 3 residues, 1 model selected
> select add #12/K:3@N7
19 atoms, 3 bonds, 3 residues, 1 model selected
> select add #12/K:3@C6
20 atoms, 3 bonds, 3 residues, 1 model selected
> select add #12/K:3@N6
21 atoms, 3 bonds, 3 residues, 1 model selected
> select add #12/K:3@N1
22 atoms, 3 bonds, 3 residues, 1 model selected
> select add #12/K:3@C2
23 atoms, 3 bonds, 3 residues, 1 model selected
> select add #12/K:3@N3
24 atoms, 3 bonds, 3 residues, 1 model selected
> hide sel atoms
> hide sel cartoons
> select #12/K:3@O3'
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select clear
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> select #12/K:2@O5'
1 atom, 1 residue, 1 model selected
> hide sel atoms
> show #12/M,O atoms
> select #12/O:1@O
1 atom, 1 residue, 1 model selected
> color sel blue
> select #12/M:1@MG
1 atom, 1 residue, 1 model selected
> color sel red
> select clear
> show #12/A:304-305,328,280
> select #12/A:319
8 atoms, 7 bonds, 1 residue, 1 model selected
> select ~sel & ##selected
24158 atoms, 24918 bonds, 3 pseudobonds, 2802 residues, 2 models selected
> show #12/A:304-305,328,280,319
> color #12 byhetero
> select #12/O:1@O
1 atom, 1 residue, 1 model selected
> select add #12/M:1@MG
2 atoms, 2 residues, 1 model selected
> select #12/M:1@MG
1 atom, 1 residue, 1 model selected
> select #12/O:1@O
1 atom, 1 residue, 1 model selected
> color sel blue
> select #12/M:1@MG
1 atom, 1 residue, 1 model selected
> color sel red
> select clear
> select #12/A:305@ND1
1 atom, 1 residue, 1 model selected
> select add #12/K:3@OP2
2 atoms, 2 residues, 1 model selected
> distance #12/A:305@ND1 #12/K:3@OP2
Distance between halfcleaved_HNH_center_main_model_temp2.pdb #12/A HIS 305 ND1
and /K DA 3 OP2: 3.159Å
> select #12/A:280@NH2
1 atom, 1 residue, 1 model selected
> select add #12/K:3@OP2
2 atoms, 2 residues, 1 model selected
> distance #12/A:280@NH2 #12/K:3@OP2
Distance between halfcleaved_HNH_center_main_model_temp2.pdb #12/A ARG 280 NH2
and /K DA 3 OP2: 2.389Å
> select #12/A:280@NH1
1 atom, 1 residue, 1 model selected
> select add #12/K:3@O5'
2 atoms, 2 residues, 1 model selected
> distance #12/A:280@NH1 #12/K:3@O5'
Distance between halfcleaved_HNH_center_main_model_temp2.pdb #12/A ARG 280 NH1
and /K DA 3 O5': 2.765Å
> view
> select #12/K:3@OP1
1 atom, 1 residue, 1 model selected
> select add #12/M:1@MG
2 atoms, 2 residues, 1 model selected
> distance #12/K:3@OP1 #12/M:1@MG
Distance between halfcleaved_HNH_center_main_model_temp2.pdb #12/K DA 3 OP1
and /M MG 1 MG: 3.166Å
> select #12/M:1@MG
1 atom, 1 residue, 1 model selected
> select add #12/A:304@ND1
2 atoms, 2 residues, 1 model selected
> distance #12/M:1@MG #12/A:304@ND1
Distance between halfcleaved_HNH_center_main_model_temp2.pdb #12/M MG 1 MG and
/A HIS 304 ND1: 2.377Å
> select #12/A:328@NE2
1 atom, 1 residue, 1 model selected
> select add #12/M:1@MG
2 atoms, 2 residues, 1 model selected
> distance #12/A:328@NE2 #12/M:1@MG
Distance between halfcleaved_HNH_center_main_model_temp2.pdb #12/A HIS 328 NE2
and /M MG 1 MG: 2.352Å
> select clear
> color sel maroon
> color sel teal
> color sel cornflower blue
> color sel dark salmon
> color sel dark khaki
> color sel peru
> select #12/O:1@O
1 atom, 1 residue, 1 model selected
> select add #12/K:3@OP2
2 atoms, 2 residues, 1 model selected
> color sel indigo
> color sel red
> select #12/O:1@O
1 atom, 1 residue, 1 model selected
> color sel blue
> select #12/K:3@OP2
1 atom, 1 residue, 1 model selected
> select add #12/O:1@O
2 atoms, 2 residues, 1 model selected
> distance #12/K:3@OP2 #12/O:1@O
Distance between halfcleaved_HNH_center_main_model_temp2.pdb #12/K DA 3 OP2
and /O HOH 1 O: 2.479Å
> color sel indigo
> select clear
> color sel dark blue
[Repeated 1 time(s)]
> select clear
> select #12/A:309
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #12/O:1@O
9 atoms, 7 bonds, 2 residues, 1 model selected
Exactly two atoms must be selected!
> select clear
> select #12/A LEU 309 N
Expected a keyword
> select #12/A:309
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel cartoons
> select #12/A:309@N
1 atom, 1 residue, 1 model selected
> select add #12/O:1@O
2 atoms, 2 residues, 1 model selected
> distance #12/A:309@N #12/O:1@O
Distance between halfcleaved_HNH_center_main_model_temp2.pdb #12/A LEU 309 N
and /O HOH 1 O: 3.104Å
> distance style decimalPlaces 2
[Repeated 2 time(s)]
> distance style decimalPlaces 1
[Repeated 2 time(s)]
> select subtract #12/O:1@O
1 atom, 1 residue, 1 model selected
> select ~sel & ##selected
24165 atoms, 24925 bonds, 11 pseudobonds, 2803 residues, 3 models selected
> hide #12/A:309 atoms
> show #12/A:309 cartoons
> select clear
> show #!4 models
> volume #4 level 0.07
> volume #4 level 0.08
> select #12/K:2@N3
1 atom, 1 residue, 1 model selected
> select up
20 atoms, 21 bonds, 1 residue, 1 model selected
> select up
886 atoms, 986 bonds, 45 residues, 1 model selected
> select down
20 atoms, 21 bonds, 1 residue, 1 model selected
> hide sel atoms
> surface dust #4 size 7.25
[Repeated 1 time(s)]
> surface dust #4 1
Expected a keyword
> surface dust #4 size 1
> show (sel-residues & sidechain) target ab
> hide sel atoms
> select clear
> select #12/K:3@O5'
1 atom, 1 residue, 1 model selected
> select up
21 atoms, 23 bonds, 1 residue, 1 model selected
> show #12/K:2 atoms
> select #12/K:2@C2
1 atom, 1 residue, 1 model selected
> select up
20 atoms, 21 bonds, 1 residue, 1 model selected
> hide #!4 models
> select subtract #12/K:2@O3'
19 atoms, 20 bonds, 1 residue, 1 model selected
> hide sel atoms
> show #!4 models
> volume #4 level 0.06
> volume #4 level 0.08
> volume #4 level 0.09
> volume #4 level 0.08
> view matrix models
> #12,0.95038,0.072866,-0.30245,40.949,-0.29386,-0.10887,-0.94963,361.72,-0.10212,0.99138,-0.082056,19.143
> show #!10 models
> hide #!10 models
> mmaker #12 to #10
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_temp2.pdb, chain A (#10) with
halfcleaved_HNH_center_main_model_temp2.pdb, chain A (#12), sequence alignment
score = 1753
RMSD between 340 pruned atom pairs is 0.001 angstroms; (across all 340 pairs:
0.001)
> ui tool show "Side View"
> hide #11.1 models
> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/figures/structure/HNH/HNH_cat_0p8.tif" width 1984 height
> 1210 supersample 3 transparentBackground true
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!4 models
> select #2/E:804@O1
1 atom, 1 residue, 1 model selected
> select up
5 atoms, 4 bonds, 1 residue, 1 model selected
> select add #2/E:731@CG
6 atoms, 4 bonds, 2 residues, 1 model selected
> select up
15 atoms, 14 bonds, 2 residues, 1 model selected
> select up
17 atoms, 15 bonds, 3 residues, 1 model selected
> select up
19 atoms, 16 bonds, 4 residues, 1 model selected
> select add #12/A:319@OD1
20 atoms, 16 bonds, 5 residues, 2 models selected
> select up
39 atoms, 35 bonds, 5 residues, 2 models selected
> select add #2/E:31@O
40 atoms, 35 bonds, 6 residues, 2 models selected
> select add #2/E:298@O
41 atoms, 35 bonds, 7 residues, 2 models selected
> select subtract #2/E:298@O
40 atoms, 35 bonds, 6 residues, 2 models selected
> hide #2.1 models
> show #2.1 models
> hide #2.1 models
> show #2.1 models
> hide #2.1 models
> show #2.1 models
> hide #2.1 models
> show #2.1 models
> hide #2.1 models
> show #2.1 models
> hide #2.1 models
> select add #12
24198 atoms, 24953 bonds, 11 pseudobonds, 2808 residues, 4 models selected
> select subtract #12
32 atoms, 28 bonds, 5 residues, 1 model selected
> hide sel atoms
> select #2/E:701@CB
1 atom, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #12/A:319@OD1
1 atom, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #2/E:298@O
1 atom, 1 residue, 1 model selected
> hide sel atoms
> color sel dark blue
> select clear
> show #!4 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/figures/structure/HNH/HNH_cat_0p8.tif" width 1984 height
> 1210 supersample 3
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> hide #!12 models
> hide #!4 models
> show #!2 models
> select #2/E:904@ZN
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select clear
> hide #!2 models
> show #!12 models
> select #12/M:1@MG
1 atom, 1 residue, 1 model selected
> color sel silver
> color sel metallic
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color sel dark gray
> color sel dim gray
> select clear
> color sel red
> select #12/M:1@MG
1 atom, 1 residue, 1 model selected
> color sel red
> color sel dim gray
> select clear
> show #!2 models
> hide #!2 models
> show #!4 models
> color sel red
> color #12/M red
> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/figures/structure/HNH/HNH_cat_0p8.tif" width 1984 height
> 1210 supersample 3
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!4 models
> color sel tan
> color sel dim gray
[Repeated 1 time(s)]
> show #!4 models
> select clear
> hide #!2 models
> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/figures/structure/HNH/HNH_cat_0p8.tif" width 1984 height
> 1210 supersample 3
> hide #!4 models
> show #!2 models
> hide #!11 models
> color #2 yellow
> sle #2/E
Unknown command: sle #2/E
> select #2/E
1109 atoms, 1075 bonds, 4 pseudobonds, 190 residues, 2 models selected
> select clear
> ui tool show "Show Sequence Viewer"
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> hide #!2 models
> open "/Users/zxc755/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/Type
> I-F_HNH/Manuscript/halfcleaved_HNH_center_main_model_temp2.pdb"
Chain information for halfcleaved_HNH_center_main_model_temp2.pdb #13
---
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
> hide #13 atoms
> show #13 cartoons
> cartoon style nucleic xsection oval width 1 thickness 1
> color #13/DA light gray
> color #13/EA dim gray
> color #13/FA dark red
> color #13/Ca rebecca purple
> color #13/Ba forest green
> color #13/Da,Db,Dc,Dd,De,Df khaki
> color #13/Aa steel blue
> color #13/Aa:232-350 dark turquoise
> hide #!12 models
> show #!12 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> show #!13 models
> color #13/L light gray
> color #13/K dim gray
> color #13/J dark red
> color #13/I rebecca purple
> color #13/B forest green
> color #13/C,D,E,F,G,H khaki
> color #13/A steel blue
> color #13/A:232-350 dark turquoise
> color #13 byhetero
> hide #!12 models
> color #13/M red
> show #13/K:2 atoms
> style stick
Changed 179387 atom styles
> select #13/K:3
21 atoms, 23 bonds, 1 residue, 1 model selected
> select add #13/K:4
25 atoms, 26 bonds, 2 residues, 1 model selected
> select add #13/K:2
45 atoms, 47 bonds, 3 residues, 1 model selected
> hide sel cartoons
> show #13/K:3 atoms
> select subtract #13/K:3@O5'
44 atoms, 45 bonds, 3 residues, 1 model selected
> select subtract #13/K:3@OP2
43 atoms, 44 bonds, 3 residues, 1 model selected
> select subtract #13/K:3@OP1
42 atoms, 43 bonds, 3 residues, 1 model selected
> select subtract #13/K:2@O3'
41 atoms, 42 bonds, 3 residues, 1 model selected
> select subtract #13/K:2@C3'
40 atoms, 40 bonds, 3 residues, 1 model selected
> select add #13/K:2@C3'
41 atoms, 40 bonds, 3 residues, 1 model selected
> select subtract #13/K:2@C3'
40 atoms, 40 bonds, 3 residues, 1 model selected
> select add #13/K:2@C3'
41 atoms, 40 bonds, 3 residues, 1 model selected
> hide sel atoms
> select #13/K:2@O3'
1 atom, 1 residue, 1 model selected
> select up
20 atoms, 21 bonds, 1 residue, 1 model selected
> select up
886 atoms, 986 bonds, 45 residues, 1 model selected
> show sel atoms
> select #13/K:4@O5'
1 atom, 1 residue, 1 model selected
> select add #13/K:4@OP1
2 atoms, 1 residue, 1 model selected
> select add #13/K:3@O3'
3 atoms, 2 residues, 1 model selected
> select up
25 atoms, 27 bonds, 2 residues, 1 model selected
> select subtract #13/K:3@O5'
24 atoms, 25 bonds, 2 residues, 1 model selected
> select subtract #13/K:3@P
23 atoms, 23 bonds, 2 residues, 1 model selected
> select subtract #13/K:3@OP1
22 atoms, 23 bonds, 2 residues, 1 model selected
> select subtract #13/K:3@OP2
21 atoms, 23 bonds, 2 residues, 1 model selected
> hide sel atoms
> select up
23 atoms, 24 bonds, 3 residues, 1 model selected
> select up
45 atoms, 49 bonds, 3 residues, 1 model selected
> select down
23 atoms, 24 bonds, 3 residues, 1 model selected
> select #13/K:2@N1
1 atom, 1 residue, 1 model selected
> select up
20 atoms, 21 bonds, 1 residue, 1 model selected
> select subtract #13/K:2@O3'
19 atoms, 20 bonds, 1 residue, 1 model selected
> hide sel atoms
> show #13/A:304-305,328,280
> show #13/M,O
> select #13/O:1@O
1 atom, 1 residue, 1 model selected
> color sel blue
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!4 models
> show #!12 models
> hide #!12 models
> select #13/K:1
9 atoms, 9 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select #13/K:1@O5'
1 atom, 1 residue, 1 model selected
> select add #13/K:1@C5'
2 atoms, 1 residue, 1 model selected
> hide sel atoms
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> select Mg
6 atoms, 6 residues, 6 models selected
> select Zn
5 atoms, 5 residues, 2 models selected
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> select add #2
4547 atoms, 4317 bonds, 16 pseudobonds, 856 residues, 3 models selected
> select subtract #2
1 atom, 1 residue, 1 model selected
> hide #!4 models
> select add #5
6 atoms, 4 bonds, 1 pseudobond, 2 residues, 2 models selected
> select subtract #5
Nothing selected
> select add #5
6 atoms, 4 bonds, 1 pseudobond, 2 residues, 2 models selected
> select subtract #5
Nothing selected
> hide #!5 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> select Zn
5 atoms, 5 residues, 2 models selected
> select add #5
10 atoms, 4 bonds, 1 pseudobond, 6 residues, 3 models selected
> select subtract #5
4 atoms, 4 residues, 1 model selected
> show sel atoms
> show #!2 models
> select water
Expected an objects specifier or a keyword
> ui tool show "Check Waters"
> hbonds #13/O interModel false reveal true restrict any name "water H-bonds"
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: halfcleaved_HNH_center_main_model_temp2.pdb #13/K DG 1 N9
2 hydrogen bonds found
> show #4 models
> select #13/O
1 atom, 1 residue, 1 model selected
> display #13/O :<4
> view #13/O @<4
> select add #13/K:3@N7
2 atoms, 2 residues, 1 model selected
> select up
22 atoms, 23 bonds, 2 residues, 1 model selected
> hide #!2 models
> hide #!4 models
> select subtract #13/K:3@O5'
21 atoms, 21 bonds, 2 residues, 1 model selected
> select subtract #13/K:3@OP2
20 atoms, 20 bonds, 2 residues, 1 model selected
> select subtract #13/K:3@OP1
19 atoms, 19 bonds, 2 residues, 1 model selected
> hide sel atoms
> select #13/K:3@O5'
1 atom, 1 residue, 1 model selected
> select up
21 atoms, 23 bonds, 1 residue, 1 model selected
> show sel atoms
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
21 atoms, 23 bonds, 1 residue, 1 model selected
> select subtract #13/K:3@P
20 atoms, 20 bonds, 1 residue, 1 model selected
> select subtract #13/K:3@OP1
19 atoms, 20 bonds, 1 residue, 1 model selected
> select subtract #13/K:3@OP2
18 atoms, 20 bonds, 1 residue, 1 model selected
> select subtract #13/K:3@O5'
17 atoms, 19 bonds, 1 residue, 1 model selected
> hide sel atoms
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
20 atoms, 21 bonds, 1 residue, 1 model selected
> select subtract #13/K:2@O3'
19 atoms, 20 bonds, 1 residue, 1 model selected
> hide sel atoms
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
9 atoms, 9 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #13/A:308@CD
1 atom, 1 residue, 1 model selected
> select up
7 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel atoms
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> hide sel cartoons
> select #13/A:309@N
1 atom, 1 residue, 1 model selected
> show #13/O atoms
> show #!11 models
> hide #!11 models
> close #11
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel atoms
> show sel cartoons
> hide sel
> select #13/O:1@O
1 atom, 1 residue, 1 model selected
> select add #13/K:3@OP2
2 atoms, 2 residues, 1 model selected
> distance #13/O:1@O #13/K:3@OP2
Distance between halfcleaved_HNH_center_main_model_temp2.pdb #13/O HOH 1 O and
/K DA 3 OP2: 2.5Å
> select #13/A:309
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel atoms
> hide sel cartoons
> show sel atoms
> select #13/A:309@N
1 atom, 1 residue, 1 model selected
> select add #13/O:1@O
2 atoms, 2 residues, 1 model selected
> distance #13/A:309@N #13/O:1@O
Distance between halfcleaved_HNH_center_main_model_temp2.pdb #13/A LEU 309 N
and /O HOH 1 O: 3.1Å
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel atoms
> show sel cartoons
> hide #11.1 models
> select #13/M:2@MG
1 atom, 1 residue, 1 model selected
> select add #13/K:2@O3'
2 atoms, 2 residues, 1 model selected
> distance #13/M:2@MG #13/K:2@O3'
Distance between halfcleaved_HNH_center_main_model_temp2.pdb #13/M MG 2 MG and
/K DT 2 O3': 2.9Å
> select #13/A:304@ND1
1 atom, 1 residue, 1 model selected
> select add #13/M:2@MG
2 atoms, 2 residues, 1 model selected
> distance #13/A:304@ND1 #13/M:2@MG
Distance between halfcleaved_HNH_center_main_model_temp2.pdb #13/A HIS 304 ND1
and /M MG 2 MG: 2.6Å
> select #13/A:328@NE2
1 atom, 1 residue, 1 model selected
> select add #13/M:2@MG
2 atoms, 2 residues, 1 model selected
> distance #13/A:328@NE2 #13/M:2@MG
Distance between halfcleaved_HNH_center_main_model_temp2.pdb #13/A HIS 328 NE2
and /M MG 2 MG: 2.0Å
> select clear
> select #13/A:305@ND1
1 atom, 1 residue, 1 model selected
> select add #13/K:3@OP2
2 atoms, 2 residues, 1 model selected
> distance #13/A:305@ND1 #13/K:3@OP2
Distance between halfcleaved_HNH_center_main_model_temp2.pdb #13/A HIS 305 ND1
and /K DA 3 OP2: 3.2Å
> select #13/K:3@O5'
1 atom, 1 residue, 1 model selected
> select add #13/A:280@NH1
2 atoms, 2 residues, 1 model selected
> distance #13/K:3@O5' #13/A:280@NH1
Distance between halfcleaved_HNH_center_main_model_temp2.pdb #13/K DA 3 O5'
and /A ARG 280 NH1: 2.8Å
> select #13/K:3@OP2
1 atom, 1 residue, 1 model selected
> select add #13/A:280@NH2
2 atoms, 2 residues, 1 model selected
> distance #13/K:3@OP2 #13/A:280@NH2
Distance between halfcleaved_HNH_center_main_model_temp2.pdb #13/K DA 3 OP2
and /A ARG 280 NH2: 2.4Å
> select add #11
8 pseudobonds, 2 models selected
> color sel dim gray
> show #!2 models
> hide #!2 models
> show #!4 models
> unsel
Unknown command: unsel
> select
179387 atoms, 183813 bonds, 57 pseudobonds, 19979 residues, 49 models selected
> select clear
> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/figures/structure/HNH/HNH_cat_0p8.tif" width 1984 height
> 1210 supersample 3
> show #!2 models
> hide #!4 models
> hide #!11 models
> select #2/E:31@O
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select clear
> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/figures/structure/HNH/HNH_cat_1fsj.tif" width 1984 height
> 1210 supersample 3
> lighting soft
> show #!4 models
> hide #!2 models
> lighting full
> lighting simple
> lighting full
> lighting simple
> lighting soft
> lighting simple
> lighting soft
> lighting simple
> lighting soft
> lighting simple
> show #!2 models
> hide #!4 models
> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/figures/structure/HNH/HNH_cat_1fsj.tif" width 1984 height
> 1210 supersample 3
> hide #!2 models
> show #!4 models
> hide #!4 models
> show #!4 models
> volume #4 level 0.09
> volume #4 level 0.1
> volume #4 level 0.95
> volume #4 level 0.095
> volume #4 level 0.09
> volume #4 level 0.08
> volume #4 level 0.09
> select #13/K:6
22 atoms, 24 bonds, 1 residue, 1 model selected
> show #13/L atoms
> select clear
> show #13/L,J atoms
> select clear
> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/figures/chimera_session.cxs"
——— End of log from Mon Mar 24 00:43:04 2025 ———
opened ChimeraX session
> volume #4 level 0.08
> hide #13/J,L atoms
> hide #13/K:6-46 atoms
> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/figures/structure/HNH/HNH_zoom_out.tif" width 1984 height
> 1210 supersample 3
> lighting soft
> lighting simple
> lighting soft
> lighting simple
> lighting full
> lighting simple
> lighting full
> lighting simple
> lighting full
> lighting simple
> lighting soft
> lighting simple
> lighting soft
> lighting simple
> volume #4 level 0.06
> show #13/A:83,85 atoms
> show #13/K:39-40 atoms
> show #13/L:6-7 atoms
> select clear
> show #13/L,J #13/K:7-46 atoms
> color #13/L light gray
> color #13/K dim gray
> color #13/J dark red
> color #13/I rebecca purple
> color #13/B forest green
> color #13/C,D,E,F,G,H khaki
> color #13/A steel blue
> color #13/A:232-350 dark turquoise
> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/figures/structure/PAM/PAM_zoom_out.tif" width 1984 height
> 1210 supersample 3
> color #13/A. byhet
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color #13/A byhetero
> ui tool show "Side View"
> hide #13/K:7-46 #13/L cartoons
> hide #13/K:7-46 #13/L atoms
> show #13/K:39-40 #13/L:6-7 atoms
> ui tool show Distances
> show #!11 models
Exactly two atoms must be selected!
> hide #!4 models
> show #13/K:39-41 #13/L:6-7 atoms
> select #13/A:83@OD1
1 atom, 1 residue, 1 model selected
> select add #13/K:40@N2
2 atoms, 2 residues, 1 model selected
> distance #13/A:83@OD1 #13/K:40@N2
Distance between halfcleaved_HNH_center_main_model_temp2.pdb #13/A ASP 83 OD1
and /K DG 40 N2: 3.013Å
> distance style color black
[Repeated 2 time(s)]
> ui tool show "Color Actions"
> distance style color dimgrey
[Repeated 2 time(s)]
> select #13/A:85@NZ
1 atom, 1 residue, 1 model selected
> select add #13/K:41@O2
2 atoms, 2 residues, 1 model selected
> distance #13/A:85@NZ #13/K:41@O2
Distance between halfcleaved_HNH_center_main_model_temp2.pdb #13/A LYS 85 NZ
and /K DC 41 O2: 3.020Å
> select #13/A:85@NZ
1 atom, 1 residue, 1 model selected
> select add #13/L:6@N2
2 atoms, 2 residues, 1 model selected
> distance #13/A:85@NZ #13/L:6@N2
Distance between halfcleaved_HNH_center_main_model_temp2.pdb #13/A LYS 85 NZ
and /L DG 6 N2: 3.258Å
> select #13/A:83@OD1
1 atom, 1 residue, 1 model selected
> select add #13/A:85@NZ
2 atoms, 2 residues, 1 model selected
> distance #13/A:83@OD1 #13/A:85@NZ
Distance between halfcleaved_HNH_center_main_model_temp2.pdb #13/A ASP 83 OD1
and LYS 85 NZ: 2.939Å
> select add #11
2 atoms, 12 pseudobonds, 2 residues, 3 models selected
> color sel dim gray
> select clear
> select add #13/A:85
9 atoms, 9 bonds, 1 residue, 1 model selected
> select add #13/A:83
17 atoms, 15 bonds, 2 residues, 1 model selected
> color sel steel blue
> color sel byhetero
> color sel dim gray
> select clear
> show #!4 models
> volume #4 level 0.08
> volume #4 level 0.07
> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/figures/structure/PAM/PAM_0p07.tif" width 1984 height
> 1210 supersample 3
> hide #!4 models
> hide #13/K:39 atoms
> show #!4 models
> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/figures/structure/PAM/PAM_0p07.tif" width 1984 height
> 1210 supersample 3
> show #11.1 models
> distance style decimalPlaces 1
[Repeated 2 time(s)]
> hide #11.1 models
> view #13/L
> volume #4 level 0.06
> show #13/k,l cartoons
> show #13/k:7-46 #13/l atoms
> hide #!4 models
> select #13/A:178
12 atoms, 12 bonds, 1 residue, 1 model selected
> show sel atoms
> select #13/A:193
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> show #!4 models
> hide #!11 models
> hide #13/A:83,85 atoms
> select clear
> surface dust #4 size 7.25
> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/figures/structure/PAM/sideview_with_unwinding.tif" width
> 1984 height 1210 supersample 3
> show #13/A:191 atoms
> select #13/A:193@OD1
1 atom, 1 residue, 1 model selected
> select add #13/L:9@N2
2 atoms, 2 residues, 1 model selected
> distance #13/A:193@OD1 #13/L:9@N2
Distance between halfcleaved_HNH_center_main_model_temp2.pdb #13/A ASN 193 OD1
and /L DG 9 N2: 2.6Å
> show #!11 models
> select #13/K:39
19 atoms, 20 bonds, 1 residue, 1 model selected
> hide sel cartoons
> hide #!4 models
> select #13/K:39@OP1
1 atom, 1 residue, 1 model selected
> select add #13/A:191@OG
2 atoms, 2 residues, 1 model selected
> distance #13/K:39@OP1 #13/A:191@OG
Distance between halfcleaved_HNH_center_main_model_temp2.pdb #13/K DC 39 OP1
and /A SER 191 OG: 2.9Å
> show sel cartoons
> show #!4 models
> color sel dim gray
> select clear
> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/figures/structure/PAM/sideview_with_unwinding.tif" width
> 1984 height 1210 supersample 3
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!13 models
> show #!13 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> volume #4 level 0.09
> volume #4 level 0.05
> volume #4 level 0.06
> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/figures/structure/PAM/sideview_with_unwinding.tif" width
> 1984 height 1210 supersample 3
> hide #!4 models
> show #!4 models
> hide #!11 models
> select #13/K:4
4 atoms, 3 bonds, 1 residue, 1 model selected
> select add #13/K:3
25 atoms, 26 bonds, 2 residues, 1 model selected
> select add #13/K:2
45 atoms, 47 bonds, 3 residues, 1 model selected
> select up
886 atoms, 986 bonds, 45 residues, 1 model selected
> select down
45 atoms, 47 bonds, 3 residues, 1 model selected
> hide #!4 models
> select add #13/K:1
54 atoms, 56 bonds, 4 residues, 1 model selected
> hide sel cartoons
> select clear
> select #13/K:3@P
1 atom, 1 residue, 1 model selected
> select up
21 atoms, 23 bonds, 1 residue, 1 model selected
> select up
886 atoms, 986 bonds, 45 residues, 1 model selected
> select down
21 atoms, 23 bonds, 1 residue, 1 model selected
> select down
1 atom, 1 residue, 1 model selected
> select up
21 atoms, 23 bonds, 1 residue, 1 model selected
> select add #13/K:2@O3'
22 atoms, 23 bonds, 2 residues, 1 model selected
> select up
41 atoms, 45 bonds, 2 residues, 1 model selected
> color sel byhetero
> select clear
> select #13/K:6
22 atoms, 24 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> select #13/A:295
6 atoms, 5 bonds, 1 residue, 1 model selected
> select add #13/I:140
12 atoms, 10 bonds, 2 residues, 1 model selected
> show sel atoms
> show #!4 models
> hide #!4 models
> select #13/K:6
22 atoms, 24 bonds, 1 residue, 1 model selected
> select add #13/K:7
42 atoms, 45 bonds, 2 residues, 1 model selected
> hide sel cartoons
> show #!4 models
> volume #4 level 0.09
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
22 atoms, 24 bonds, 1 residue, 1 model selected
> hide #!4 models
> select subtract #13/K:6@O3'
21 atoms, 23 bonds, 1 residue, 1 model selected
> hide sel atoms
> show #!4 models
> hide #!4 models
> select #13/K:7@OP1
1 atom, 1 residue, 1 model selected
> select up
20 atoms, 21 bonds, 1 residue, 1 model selected
> show sel cartoons
> select #13/K:6@O3'
1 atom, 1 residue, 1 model selected
> hide sel atoms
> show #!4 models
> hide #!4 models
> select #13/I:50
9 atoms, 8 bonds, 1 residue, 1 model selected
> select add #13/I:51
18 atoms, 16 bonds, 2 residues, 1 model selected
> show sel atoms
> show #!4 models
> volume #4 level 0.06
> volume #4 level 0.08
> select #13/I:51@CD
1 atom, 1 residue, 1 model selected
> select up
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
11 atoms, 9 bonds, 2 residues, 1 model selected
> select up
18 atoms, 17 bonds, 2 residues, 1 model selected
> hide sel atoms
> select clear
> volume #4 level 0.1
> color #13/i byhetero
> select clear
> select #13/K:7
20 atoms, 21 bonds, 1 residue, 1 model selected
> volume #4 level 0.07
> select clear
> volume #4 level 0.09
> show #!2 models
> hide #!2 models
> hide #!4 models
> select #13/A:295@SG
1 atom, 1 residue, 1 model selected
> select add #13/I:140@SG
2 atoms, 2 residues, 1 model selected
> distance #13/A:295@SG #13/I:140@SG
Distance between halfcleaved_HNH_center_main_model_temp2.pdb #13/A CYS 295 SG
and /I CYS 140 SG: 3.9Å
> show #!11 models
> color sel dim gray
> select clear
> hide #13/A:230-350 atoms
> hide #13/o atoms
> select #13/A:295
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> show #!4 models
> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/figures/structure/HNH/cas8_cas6_cys_pair_0p09.tif" width
> 1984 height 1210 supersample 3
> hide #!4 models
> show #11.1 models
> hide #11.1 models
> show #!2 models
> select #2/E:706@CG
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select #2/E:706@CD
1 atom, 1 residue, 1 model selected
> select up
7 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
[Repeated 1 time(s)]
> select clear
> select #2/E:706@CG
1 atom, 1 residue, 1 model selected
> select up
7 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #2/E:707@CD1
1 atom, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel atoms
[Repeated 1 time(s)]
> select clear
> select #13/I:140@SG
1 atom, 1 residue, 1 model selected
> select add #13/A:295@SG
2 atoms, 2 residues, 1 model selected
> select up
12 atoms, 10 bonds, 2 residues, 1 model selected
> hide sel atoms
> select clear
> show #13/A:305,304,280,328
> select #2/E:718
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #13/A:319
16 atoms, 14 bonds, 2 residues, 2 models selected
> show sel atoms
> show #13/O
> select clear
> hide #!11 models
> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/figures/structure/HNH/HNH_cat_1fsj_2.tif" width 1984
> height 1210 supersample 3
> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/figures/chimera_session.cxs"
——— End of log from Mon Mar 24 13:31:18 2025 ———
opened ChimeraX session
> hide #!2 models
> ui tool show "Side View"
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> hide #!13 models
> close #12
> open "/Users/zxc755/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/Type
> I-F_HNH/Manuscript/halfcleaved_HNH_center_main_model_temp2.pdb"
Chain information for halfcleaved_HNH_center_main_model_temp2.pdb #12
---
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
> hide #12 atoms
> show #12 cartoons
> cartoon style nucleic xsection oval width 1 thickness 1
> color #12/L light gray
> color #12/K dim gray
> color #12/J dark red
> color #12/I rebecca purple
> color #12/B forest green
> color #12/C,D,E,F,G,H khaki
> color #12/A steel blue
> color #12/A:232-350 dark turquoise
> color #12/M red
> color #12/o blue
> select clear
> select #12/K:6
22 atoms, 24 bonds, 1 residue, 1 model selected
> hide sel cartoons
> show sel atoms
> style stick
Changed 179387 atom styles
> select clear
> show #!2 models
> hide #!2 models
> show #!4 models
> select #12/K:7
20 atoms, 21 bonds, 1 residue, 1 model selected
> hide #12/K cartoons
> show #12/k atoms
> select clear
> volume #4 level 0.06
> hide #!4 models
> select #12/A:295
6 atoms, 5 bonds, 1 residue, 1 model selected
> select add #12/I:50
15 atoms, 13 bonds, 2 residues, 1 model selected
> select add #12/I:140
21 atoms, 18 bonds, 3 residues, 1 model selected
> show sel atoms
> show #!4 models
> hide #!4 models
> select #12/A:290
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> show #!4 models
> volume #4 level 0.08
> hide #!4 models
> select #12/A:296
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> select #12/I:51
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> show #!4 models
> volume #4 level 0.07
> volume #4 level 0.09
> volume #4 level 0.05
> surface dust #4 size 7.25
> color #12/K:1-4 red
> show #12/m,o atoms
> select clear
> close #13
> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/figures/chimera_session.cxs"
——— End of log from Tue Mar 25 00:19:58 2025 ———
opened ChimeraX session
> close #12
> hide #!4 models
> open "/Users/zxc755/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/Type
> I-F_HNH/Manuscript/halfcleaved_HNH_center_main_model_temp.pdb"
Chain information for halfcleaved_HNH_center_main_model_temp.pdb #12
---
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
> style stick
Changed 155168 atom styles
> color #12/L light gray
> color #12/K dim gray
> color #12/J dark red
> color #12/I rebecca purple
> color #12/B forest green
> color #12/C,D,E,F,G,H khaki
> color #12/A steel blue
> color #12/A:232-350 dark turquoise
> cartoon style nucleic xsection oval width 1 thickness 1
> show #12 cartoons
> hide #12 atoms
> hide #12/k:1-6 cartoons
> show #12/k:1-6 atoms
> show #12/m,o atoms
> color #12/m red
> color #12/o blue
> select clear
> open "/Users/zxc755/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/Type
> I-F_HNH/Manuscript/maps_models/maybe_better/deepEMhancer/half/halfcleaved_HNH_center_sharp3Å.mrc"
Opened halfcleaved_HNH_center_sharp3Å.mrc as #13, grid size 420,420,420,
pixel 0.725, shown at level 0.00305, step 2, values float32
> volume #13 step 1
> volume #13 level 0.01
> volume #13 level 0.02
> transparency #13.1 50
> color zone #13 near #12 distance 5
> select subtract #11
Nothing selected
> hide #!12 models
> color zone #13 near #12/a,b,c,d,e,f,g,h,i,j,k,l distance 5
> color zone #13 near #12/a,b,c,d,e,f,g,h,i,j,k,l distance 5 near #12/m,o dis
> 1
Repeated keyword argument "near"
> color zone #13 near #12/a,b,c,d,e,f,g,h,i,j,k,l distance 5 #12/m,o dis 1
Expected a keyword
> color zone #13 near #12/a,b,c,d,e,f,g,h,i,j,k,l distance 3
> color zone #13 near #12/a,b,c,d,e,f,g,h,i,j,k,l distance 3.5
> color zone #13 near #12/ dis 3.5
Expected a keyword
> color zone #13 near #12 distance 3.5
> color zone #13 near #12 distance 3
> color zone #13 near #12 distance 1
> color zone #13 near #12 distance 1.5
> color zone #13 near #12 distance 2
> color zone #13 near #12 distance 2.4
> color zone #13 near #12 distance 2.5
> color zone #13 near #12 distance 3
> color zone #13 near #12 distance 4
> color zone #13 near #12 distance 4.5
> color zone #13 near #12 distance 5
> lighting soft
> hide #!13 models
> open "/Users/zxc755/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/Type
> I-F_HNH/Manuscript/maps_models/maybe_better/deepEMhancer/half/halfcleaved_HNH_in_sharp3Å.mrc"
Opened halfcleaved_HNH_in_sharp3Å.mrc as #14, grid size 420,420,420, pixel
0.725, shown at level 0.00277, step 2, values float32
> volume #14 step 1
> volume #14 level 0.02
> hide #!14 models
> show #!14 models
> hide #!14 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 #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
> color #15/L light gray
> color #15/K dim gray
> color #15/J dark red
> color #15/I rebecca purple
> color #15/B forest green
> color #15/C,D,E,F,G,H khaki
> color #15/A steel blue
> color #15/A:232-350 dark turquoise
> hide #15 atoms
> show #!14 models
> color zone #14 near #15 distance 5
> hide #!15 models
> show #!15 models
> hide #!14 models
> show #!14 models
> show cartoons #15
Expected ',' or a keyword
> show #15 cartoons
> hide #!14 models
> combine #15
> delete #15/b,c,d,e,f,g,h,j,k,l
> hide #!16 models
> show #!16 models
> hide #!16 models
> delete #15/b,c,d,e,f,g,h,j,k,l,i
> delete #15/a:1-230
> delete #15/a:1-231
> show #!14 models
> transparency #14.1 50
> fitmap #15 inMap #14
Fit molecule halfcleaved_HNH_inwards_refined.pdb (#15) to map
halfcleaved_HNH_in_sharp3Å.mrc (#14) using 897 atoms
average map value = 0.1033, steps = 48
shifted from previous position = 0.103
rotated from previous position = 0.723 degrees
atoms outside contour = 296, contour level = 0.02
Position of halfcleaved_HNH_inwards_refined.pdb (#15) relative to
halfcleaved_HNH_in_sharp3Å.mrc (#14) coordinates:
Matrix rotation and translation
0.99995867 0.00821061 0.00390412 -2.00149362
-0.00817612 0.99992812 -0.00876986 2.45517496
-0.00397584 0.00873757 0.99995392 -1.09279831
Axis 0.69359957 0.31218363 -0.64920029
Axis point 0.00000000 120.00927253 275.85141597
Rotation angle (degrees) 0.72313237
Shift along axis 0.08767530
> hide #!14 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 #17
---
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/postcleavage_HNH_inwards_3p93Å.mrc"
Opened postcleavage_HNH_inwards_3p93Å.mrc as #18, grid size 420,420,420,
pixel 0.725, shown at level 0.0417, step 2, values float32
> close #18
> open "/Users/zxc755/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/Type
> I-F_HNH/Manuscript/maps_models/maybe_better/deepEMhancer/post/post_HNH_in_sharp_4p5.mrc"
Opened post_HNH_in_sharp_4p5.mrc as #18, grid size 420,420,420, pixel 0.725,
shown at level 0.0257, step 2, values float32
> volume #18 step 1
> hide #!15 models
> show #!15 models
> hide #!17 models
> transparency #18.1 50
> lighting simple
> fitmap #15 inMap #18
Fit molecule halfcleaved_HNH_inwards_refined.pdb (#15) to map
post_HNH_in_sharp_4p5.mrc (#18) using 897 atoms
average map value = 0.1722, steps = 88
shifted from previous position = 5.79
rotated from previous position = 18.5 degrees
atoms outside contour = 305, contour level = 0.025678
Position of halfcleaved_HNH_inwards_refined.pdb (#15) relative to
post_HNH_in_sharp_4p5.mrc (#18) coordinates:
Matrix rotation and translation
0.98515450 -0.14232903 -0.09598467 36.22127193
0.16215106 0.95508370 0.24803662 -52.49007293
0.05637058 -0.25991841 0.96398381 44.34612442
Axis -0.83066353 -0.24914793 0.49791908
Axis point 0.00000000 129.04516803 229.89711725
Rotation angle (degrees) 17.80344657
Shift along axis 5.07088499
> hide #17 atoms
> show #17 cartoons
> show #!17 models
> hide #!17 models
> hide #!15 models
> show #!15 models
> show #!16 models
> hide #!16 models
> hide #!15 models
> show #!16 models
> hide #!16 models
> show #!17 models
> select add #18
2 models selected
> ui tool show "Color Actions"
> color sel navajo white
> lighting simple
> lighting soft
> lighting simple
> color #17/DA light gray
> color #17/EA dim gray
> color #17/FA dark red
> color #17/Ca rebecca purple
> color #17/Ba forest green
> color #17/Da,Db,Dc,Dd,De,Df khaki
> color #17/Aa steel blue
> color #17/Aa:232-350 dark turquoise
> color #17/L light gray
> color #17/K dim gray
> color #17/J dark red
> color #17/I rebecca purple
> color #17/B forest green
> color #17/C,D,E,F,G,H khaki
> color #17/A steel blue
> color #17/A:232-350 dark turquoise
> select subtract #18
Nothing selected
> hide #!18 models
> show #!18 models
> hide #!17 models
> hide #!18 models
> open "/Users/zxc755/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/Type
> I-F_HNH/Manuscript/maps_models/maybe_better/deepEMhancer/post/post_HNH_cent_sharp.mrc"
Opened post_HNH_cent_sharp.mrc as #19, grid size 420,420,420, pixel 0.725,
shown at level 0.00149, step 2, values float32
> 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 #20
---
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
> hide #20 atoms
> show #20 cartoons
> volume #19 step 1
> volume #19 level 0.07
> volume #19 level 0.05
> volume #19 level 0.02
> volume #19 level 0.01
> combine #19
No structures specified
> combine #20
> hide #!20 models
> delete #21/a,b,c,d,e,f,g,h,k,l
> fitmap #21 inMap #19
Fit molecule copy of postcleavage_HNH_center_refined.pdb (#21) to map
post_HNH_cent_sharp.mrc (#19) using 2726 atoms
average map value = 0.1694, steps = 2000
shifted from previous position = 0.186
rotated from previous position = 0.199 degrees
atoms outside contour = 1261, contour level = 0.01
Position of copy of postcleavage_HNH_center_refined.pdb (#21) relative to
post_HNH_cent_sharp.mrc (#19) coordinates:
Matrix rotation and translation
0.99999396 0.00180060 0.00297193 -0.76393106
-0.00180072 0.99999838 0.00003869 0.16921571
-0.00297185 -0.00004404 0.99999558 0.56555929
Axis -0.01190446 0.85519891 -0.51816321
Axis point 165.64366772 0.00000000 257.94336417
Rotation angle (degrees) 0.19910813
Shift along axis -0.13924475
> select #21/J:51
23 atoms, 25 bonds, 1 residue, 1 model selected
> ui mousemode right "rotate selected models"
> view matrix models
> #21,0.99951,0.00060373,-0.031401,4.2416,-0.0016237,0.99947,-0.032468,6.0991,0.031365,0.032503,0.99898,-9.4868
> fitmap #21 inMap #19
Fit molecule copy of postcleavage_HNH_center_refined.pdb (#21) to map
post_HNH_cent_sharp.mrc (#19) using 2726 atoms
average map value = 0.1688, steps = 2000
shifted from previous position = 1.36
rotated from previous position = 2.61 degrees
atoms outside contour = 1266, contour level = 0.01
Position of copy of postcleavage_HNH_center_refined.pdb (#21) relative to
post_HNH_cent_sharp.mrc (#19) coordinates:
Matrix rotation and translation
0.99999350 0.00327561 0.00150351 -0.76518814
-0.00327402 0.99999408 -0.00105700 0.62813683
-0.00150696 0.00105207 0.99999831 -0.07731006
Axis 0.28081232 0.40083125 -0.87205433
Axis point 178.64402650 242.89942515 0.00000000
Rotation angle (degrees) 0.21516256
Shift along axis 0.10432118
> delete #21/i:119-133
> fitmap #21 inMap #19
Fit molecule copy of postcleavage_HNH_center_refined.pdb (#21) to map
post_HNH_cent_sharp.mrc (#19) using 2605 atoms
average map value = 0.1781, steps = 2000
shifted from previous position = 0.132
rotated from previous position = 0.117 degrees
atoms outside contour = 1140, contour level = 0.01
Position of copy of postcleavage_HNH_center_refined.pdb (#21) relative to
post_HNH_cent_sharp.mrc (#19) coordinates:
Matrix rotation and translation
0.99999500 0.00239001 0.00207238 -0.60674616
-0.00239146 0.99999689 0.00070090 0.14244066
-0.00207070 -0.00070585 0.99999761 0.40363617
Axis -0.21704908 0.63924101 -0.73774021
Axis point 79.27931343 260.84792943 -0.00000000
Rotation angle (degrees) 0.18567412
Shift along axis -0.07503103
> show #21/j atoms
> style stick
Changed 229983 atom styles
> select clear
> select #21/J:44
20 atoms, 21 bonds, 1 residue, 1 model selected
> view matrix models
> #21,0.99372,-0.10871,0.026365,13.992,0.10722,0.99284,0.052567,-20.988,-0.031891,-0.04941,0.99827,11.548
> select up
1288 atoms, 1444 bonds, 60 residues, 1 model selected
> fitmap #21 inMap #19
Fit molecule copy of postcleavage_HNH_center_refined.pdb (#21) to map
post_HNH_cent_sharp.mrc (#19) using 2605 atoms
average map value = 0.1752, steps = 2000
shifted from previous position = 4.3
rotated from previous position = 7.23 degrees
atoms outside contour = 1149, contour level = 0.01
Position of copy of postcleavage_HNH_center_refined.pdb (#21) relative to
post_HNH_cent_sharp.mrc (#19) coordinates:
Matrix rotation and translation
0.99998549 0.00368109 0.00393188 -1.30544186
-0.00367497 0.99999203 -0.00156309 0.73010434
-0.00393760 0.00154862 0.99999105 0.48740849
Axis 0.27751762 0.70184056 -0.65605168
Axis point 94.79211019 0.00000000 320.39166369
Rotation angle (degrees) 0.32121992
Shift along axis -0.16963143
> view matrix models
> #21,0.95316,-0.16312,0.2547,-4.7007,0.14,0.98441,0.10651,-33.244,-0.2681,-0.065869,0.96114,54.875
> fitmap #21 inMap #19
Fit molecule copy of postcleavage_HNH_center_refined.pdb (#21) to map
post_HNH_cent_sharp.mrc (#19) using 2605 atoms
average map value = 0.1731, steps = 2000
shifted from previous position = 0.932
rotated from previous position = 18.4 degrees
atoms outside contour = 1177, contour level = 0.01
Position of copy of postcleavage_HNH_center_refined.pdb (#21) relative to
post_HNH_cent_sharp.mrc (#19) coordinates:
Matrix rotation and translation
0.99994904 -0.00778267 -0.00643051 1.98761314
0.00779564 0.99996762 0.00199459 -1.51674316
0.00641478 -0.00204462 0.99997733 -0.91523181
Axis -0.19616124 -0.62382235 0.75654904
Axis point 206.49736911 250.60632995 0.00000000
Rotation angle (degrees) 0.58990690
Shift along axis -0.13613214
> view matrix models
> #21,0.99995,-0.0077827,-0.0064305,3.3447,0.0077956,0.99997,0.0019946,-2.7803,0.0064148,-0.0020446,0.99998,0.39857
> fitmap #21 inMap #19
Fit molecule copy of postcleavage_HNH_center_refined.pdb (#21) to map
post_HNH_cent_sharp.mrc (#19) using 2605 atoms
average map value = 0.1778, steps = 2000
shifted from previous position = 1.77
rotated from previous position = 0.414 degrees
atoms outside contour = 1144, contour level = 0.01
Position of copy of postcleavage_HNH_center_refined.pdb (#21) relative to
post_HNH_cent_sharp.mrc (#19) coordinates:
Matrix rotation and translation
0.99999337 -0.00330202 -0.00153324 0.70289684
0.00330074 0.99999420 -0.00083994 -0.52418630
0.00153600 0.00083487 0.99999847 -0.38974171
Axis 0.22416395 -0.41079927 0.88373892
Axis point 155.63582398 210.62363526 0.00000000
Rotation angle (degrees) 0.21403999
Shift along axis 0.02846957
> delete #21/j:1-41
> fitmap #21 inMap #19
Fit molecule copy of postcleavage_HNH_center_refined.pdb (#21) to map
post_HNH_cent_sharp.mrc (#19) using 1727 atoms
average map value = 0.02377, steps = 68
shifted from previous position = 0.607
rotated from previous position = 0.441 degrees
atoms outside contour = 1066, contour level = 0.01
Position of copy of postcleavage_HNH_center_refined.pdb (#21) relative to
post_HNH_cent_sharp.mrc (#19) coordinates:
Matrix rotation and translation
0.99996474 -0.00055599 -0.00837886 1.69415235
0.00053058 0.99999525 -0.00303455 0.64823116
0.00838051 0.00303000 0.99996029 -1.81624530
Axis 0.33963693 -0.93858608 0.06085174
Axis point 216.66154710 0.00000000 207.10057130
Rotation angle (degrees) 0.51154276
Shift along axis -0.14354572
> view matrix models
> #21,0.95152,0.063441,0.30097,-58.133,0.017073,0.9661,-0.25762,48.854,-0.30711,0.25027,0.91818,-0.5168
> fitmap #21 inMap #19
Fit molecule copy of postcleavage_HNH_center_refined.pdb (#21) to map
post_HNH_cent_sharp.mrc (#19) using 1727 atoms
average map value = 0.01942, steps = 92
shifted from previous position = 1.42
rotated from previous position = 9.42 degrees
atoms outside contour = 1173, contour level = 0.01
Position of copy of postcleavage_HNH_center_refined.pdb (#21) relative to
post_HNH_cent_sharp.mrc (#19) coordinates:
Matrix rotation and translation
0.97435965 -0.00668895 0.22489671 -33.93326133
0.03560741 0.99154562 -0.12477740 17.25587377
-0.22216072 0.12958605 0.96636022 5.49530082
Axis 0.49286534 0.86623732 0.08195521
Axis point 2.77043250 0.00000000 148.29261146
Rotation angle (degrees) 14.95412576
Shift along axis -1.32647815
> view matrix models
> #21,0.90553,-0.2837,0.31547,16.944,0.29673,0.95494,0.0070231,-29.813,-0.30325,0.08725,0.94891,27.343
> fitmap #21 inMap #19
Fit molecule copy of postcleavage_HNH_center_refined.pdb (#21) to map
post_HNH_cent_sharp.mrc (#19) using 1727 atoms
average map value = 0.01933, steps = 104
shifted from previous position = 2.05
rotated from previous position = 9.43 degrees
atoms outside contour = 1170, contour level = 0.01
Position of copy of postcleavage_HNH_center_refined.pdb (#21) relative to
post_HNH_cent_sharp.mrc (#19) coordinates:
Matrix rotation and translation
0.94411256 -0.12450182 0.30520610 -21.00938346
0.14744888 0.98763632 -0.05322902 -8.92619050
-0.29480552 0.09525648 0.95079751 24.92749364
Axis 0.21988344 0.88852194 0.40271582
Axis point 74.52306659 0.00000000 80.67313058
Rotation angle (degrees) 19.73351564
Shift along axis -2.51203568
> view matrix models
> #21,0.94411,-0.1245,0.30521,-17.873,0.14745,0.98764,-0.053229,-5.6643,-0.29481,0.095256,0.9508,23.681
> fitmap #21 inMap #19
Fit molecule copy of postcleavage_HNH_center_refined.pdb (#21) to map
post_HNH_cent_sharp.mrc (#19) using 1727 atoms
average map value = 0.01942, steps = 156
shifted from previous position = 3.04
rotated from previous position = 8.27 degrees
atoms outside contour = 1166, contour level = 0.01
Position of copy of postcleavage_HNH_center_refined.pdb (#21) relative to
post_HNH_cent_sharp.mrc (#19) coordinates:
Matrix rotation and translation
0.97438343 -0.01578899 0.22433822 -31.97489437
0.04417306 0.99153739 -0.12207515 15.64761333
-0.22051229 0.12885771 0.96683505 5.34685589
Axis 0.48795736 0.86504446 0.11660060
Axis point 3.97780903 0.00000000 139.84528015
Rotation angle (degrees) 14.89958612
Shift along axis -1.44305704
> view matrix models
> #21,0.97881,0.079073,-0.18889,14.498,-0.093393,0.99329,-0.068145,23.787,0.18223,0.084342,0.97963,-36.826
> fitmap #21 inMap #19
Fit molecule copy of postcleavage_HNH_center_refined.pdb (#21) to map
post_HNH_cent_sharp.mrc (#19) using 1727 atoms
average map value = 0.02378, steps = 112
shifted from previous position = 4.26
rotated from previous position = 12.1 degrees
atoms outside contour = 1061, contour level = 0.01
Position of copy of postcleavage_HNH_center_refined.pdb (#21) relative to
post_HNH_cent_sharp.mrc (#19) coordinates:
Matrix rotation and translation
0.99995850 -0.00058011 -0.00909169 1.82468704
0.00055786 0.99999684 -0.00244989 0.54145676
0.00909308 0.00244471 0.99995567 -1.79847577
Axis 0.25943577 -0.96387493 0.06031750
Axis point 197.73964432 0.00000000 204.27550886
Rotation angle (degrees) 0.54048814
Shift along axis -0.15698708
> select clear
> select #21/J:50
20 atoms, 21 bonds, 1 residue, 1 model selected
> view matrix models
> #21,0.96924,-0.18193,0.16576,13.795,0.16697,0.98085,0.10023,-33.405,-0.18082,-0.069465,0.98106,39.844
> fitmap #21 inMap #19
Fit molecule copy of postcleavage_HNH_center_refined.pdb (#21) to map
post_HNH_cent_sharp.mrc (#19) using 1727 atoms
average map value = 0.02378, steps = 120
shifted from previous position = 0.698
rotated from previous position = 15.5 degrees
atoms outside contour = 1064, contour level = 0.01
Position of copy of postcleavage_HNH_center_refined.pdb (#21) relative to
post_HNH_cent_sharp.mrc (#19) coordinates:
Matrix rotation and translation
0.99996372 -0.00034050 -0.00851103 1.66866582
0.00031330 0.99999484 -0.00319750 0.69973282
0.00851207 0.00319472 0.99995867 -1.87660250
Axis 0.35130930 -0.93556970 0.03593210
Axis point 220.86482619 0.00000000 200.72582758
Rotation angle (degrees) 0.52126798
Shift along axis -0.13586127
> show #!20 models
> hide #!20 models
> show #!20 models
> view matrix models
> #21,0.94284,-0.16526,0.28937,-7.4067,0.16063,0.98621,0.039865,-23.627,-0.29196,0.0088937,0.95639,41.501
> fitmap #21 inMap #19
Fit molecule copy of postcleavage_HNH_center_refined.pdb (#21) to map
post_HNH_cent_sharp.mrc (#19) using 1727 atoms
average map value = 0.02377, steps = 140
shifted from previous position = 0.641
rotated from previous position = 19.9 degrees
atoms outside contour = 1065, contour level = 0.01
Position of copy of postcleavage_HNH_center_refined.pdb (#21) relative to
post_HNH_cent_sharp.mrc (#19) coordinates:
Matrix rotation and translation
0.99996409 -0.00060556 -0.00845233 1.72034129
0.00057980 0.99999518 -0.00304995 0.64758353
0.00845413 0.00304494 0.99995963 -1.83001040
Axis 0.33840585 -0.93869583 0.06581501
Axis point 216.32111144 0.00000000 208.46719481
Rotation angle (degrees) 0.51597228
Shift along axis -0.14615257
> hide #!20 models
> delete #21/i:107-118
> fitmap #21 inMap #19
Fit molecule copy of postcleavage_HNH_center_refined.pdb (#21) to map
post_HNH_cent_sharp.mrc (#19) using 1617 atoms
average map value = 0.025, steps = 44
shifted from previous position = 0.0515
rotated from previous position = 0.51 degrees
atoms outside contour = 976, contour level = 0.01
Position of copy of postcleavage_HNH_center_refined.pdb (#21) relative to
post_HNH_cent_sharp.mrc (#19) coordinates:
Matrix rotation and translation
0.99991658 -0.00665991 -0.01106673 3.46514203
0.00669212 0.99997347 0.00287541 -1.15618478
0.01104728 -0.00294923 0.99993463 -0.94027532
Axis -0.21995713 -0.83509609 0.50421561
Axis point 74.57354161 0.00000000 307.17000003
Rotation angle (degrees) 0.75864102
Shift along axis -0.27075880
> view matrix models
> #21,0.9761,-0.050009,0.2115,-22.223,0.037779,0.99739,0.061477,-14.46,-0.21402,-0.052017,0.97544,41.647
> fitmap #21 inMap #19
Fit molecule copy of postcleavage_HNH_center_refined.pdb (#21) to map
post_HNH_cent_sharp.mrc (#19) using 1617 atoms
average map value = 0.025, steps = 112
shifted from previous position = 0.714
rotated from previous position = 13.5 degrees
atoms outside contour = 978, contour level = 0.01
Position of copy of postcleavage_HNH_center_refined.pdb (#21) relative to
post_HNH_cent_sharp.mrc (#19) coordinates:
Matrix rotation and translation
0.99991534 -0.00691325 -0.01102344 3.51324748
0.00694686 0.99997133 0.00301354 -1.20471924
0.01100229 -0.00308986 0.99993470 -0.89660439
Axis -0.22833637 -0.82401113 0.51852498
Axis point 70.41448246 0.00000000 312.48223472
Rotation angle (degrees) 0.76577763
Shift along axis -0.27441187
> hide #!21 models
> hide #!19 models
> show #!19 models
> show #!18 models
> hide #!18 models
> show #!17 models
> hide #!17 models
> show #!17 models
> hide #!19 models
> show #!18 models
> hide #!18 models
> hide #!17 models
> show #!16 models
> hide #!16 models
> show #!14 models
> select add #14
20 atoms, 21 bonds, 1 residue, 3 models selected
> transparency sel 0
> select clear
> show #!13 models
> hide #!14 models
> show #!14 models
> hide #!14 models
> show #!14 models
> hide #!14 models
> show #!14 models
> hide #!14 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> show #!13 models
> hide #!4 models
> lighting soft
> show #!14 models
> hide #!13 models
> show #!13 models
> hide #!14 models
> show #!14 models
> hide #!13 models
> show #!13 models
> hide #!14 models
> show #!14 models
> hide #!14 models
> show #!14 models
> hide #!13 models
> show #!13 models
> hide #!14 models
> hide #!13 models
> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/figures/chimera_session.cxs"
——— End of log from Wed Mar 26 12:19:53 2025 ———
opened ChimeraX session
> show #!13 models
> ui tool show "Color Actions"
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> color #13 navajo white
> show #!12 models
> transparency #13.1 50
> lighting simple
> lighting full
> lighting soft
> lighting simple
> lighting soft
> lighting simple
> lighting soft
> lighting simple
> view
> lighting soft
> lighting simple
> hide #12/l,k cartoons
> show #12/k:39-40
> show #12/l:6-7
> show #12/l:6-8
> hide #12/l:6 atoms
> show #12/a:83,85 atoms
> color #12/a:83,85 byhetero
> ui tool show "Side View"
> show #12/l:6-7
> hide #12/l:8 atoms
> hide #12/k:39 atoms
> show #12/k:41 atoms
> hide #!13 models
> show #11 models
> ui tool show Distances
> select #12/A:85@NZ
1 atom, 1 residue, 1 model selected
> select add #12/A:83@OD1
2 atoms, 2 residues, 1 model selected
> distance #12/A:85@NZ #12/A:83@OD1
Distance between halfcleaved_HNH_center_main_model_temp.pdb #12/A LYS 85 NZ
and ASP 83 OD1: 2.939Å
> select #12/A:85@NZ
1 atom, 1 residue, 1 model selected
> select add #12/K:41@O2
2 atoms, 2 residues, 1 model selected
> distance #12/A:85@NZ #12/K:41@O2
Distance between halfcleaved_HNH_center_main_model_temp.pdb #12/A LYS 85 NZ
and /K DC 41 O2: 3.020Å
> select #12/A:85@NZ
1 atom, 1 residue, 1 model selected
> select add #12/L:6@N2
2 atoms, 2 residues, 1 model selected
> distance #12/A:85@NZ #12/L:6@N2
Distance between halfcleaved_HNH_center_main_model_temp.pdb #12/A LYS 85 NZ
and /L DG 6 N2: 3.258Å
> select #12/K:40@N2
1 atom, 1 residue, 1 model selected
> select add #12/A:83@OD1
2 atoms, 2 residues, 1 model selected
> distance #12/K:40@N2 #12/A:83@OD1
Distance between halfcleaved_HNH_center_main_model_temp.pdb #12/K DG 40 N2 and
/A ASP 83 OD1: 3.013Å
> select add #11
2 atoms, 4 pseudobonds, 2 residues, 3 models selected
> color sel dim gray
> select clear
> show #!13 models
> hide #11.1 models
> lighting soft
> lighting full
> lighting simple
> color #12/a byhetero
> surface zone #13 nearAtoms #12/a,k,l
> surface zone #13 nearAtoms #12/a,k,l distance 10
> surface zone #13 nearAtoms #12/a,k,l distance 5
> surface zone #13 nearAtoms #12/a,k,l distance 10
> surface zone #13 nearAtoms #12/a:1-90 #12/k:39-46 #12/l:1-8 distance 10
> surface zone #13 nearAtoms #12/a:1-90 #12/k:39-46 #12/l:1-8 distance 5
> hide #12/b,c cartoons
> hide #12/b,c,d cartoons
> lighting soft
> lighting simple
> lighting full
> lighting simple
> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/figures/structure/PAM/PAM_sharp.tif" width 1984 height
> 1210 supersample 3
> hide #!13 models
> show #!13 models
> hide #!13 models
> show #!13 models
> show #12 cartoons
> show #12/j,k,l atoms
> select #12
24113 atoms, 24865 bonds, 7 pseudobonds, 2801 residues, 3 models selected
> nucleotides sel ladder
> select clear
> hide #12 cartoons
> show #12 cartoons
> surface zone #13 nearAtoms #12 distance 10
> surface dust #13 size 7.25
> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/figures/structure/PAM/PAM_sharp_zoom_out.tif" width 1984
> height 1210 supersample 3
> hide #!13 models
> hide #!12 models
> show #!12 models
> show #!13 models
> hide #12/l,k,j cartoons
> nucleotides #!12 atoms
> style nucleic & #!12 stick
Changed 2368 atom styles
> nucleotides #!12 fill
> style nucleic & #!12 stick
Changed 2368 atom styles
> nucleotides #!12 tube/slab shape ellipsoid
> nucleotides #!12 tube/slab shape box
> nucleotides #!12 slab
> style nucleic & #!12 stick
Changed 2368 atom styles
> nucleotides #!12 fill
> style nucleic & #!12 stick
Changed 2368 atom styles
> nucleotides #!12 atoms
> style nucleic & #!12 stick
Changed 2368 atom styles
> nucleotides #!12 fill
> style nucleic & #!12 stick
Changed 2368 atom styles
> nucleotides #!12 atoms
> style nucleic & #!12 stick
Changed 2368 atom styles
> nucleotides #!12 atoms
> style nucleic & #!12 stick
Changed 2368 atom styles
> nucleotides #!12 fill
> style nucleic & #!12 stick
Changed 2368 atom styles
> nucleotides #!12 atoms
> style nucleic & #!12 stick
Changed 2368 atom styles
> lighting soft
> lighting simple
> hide #12/a:83,85 atoms
> hide #!13 models
> select #12/A:178
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #12/A:193
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #12/A:192
14 atoms, 12 bonds, 2 residues, 1 model selected
> select add #12/A:191
20 atoms, 17 bonds, 3 residues, 1 model selected
> select add #12/A:178
32 atoms, 29 bonds, 4 residues, 1 model selected
> show sel atoms
> show #!13 models
> hide #!13 models
> select #12/A:191@OG
1 atom, 1 residue, 1 model selected
> select add #12/K:39@OP1
2 atoms, 2 residues, 1 model selected
> distance #12/A:191@OG #12/K:39@OP1
Distance between halfcleaved_HNH_center_main_model_temp.pdb #12/A SER 191 OG
and /K DC 39 OP1: 2.884Å
> select #12/A:193@OD1
1 atom, 1 residue, 1 model selected
> select add #12/L:9@N2
2 atoms, 2 residues, 1 model selected
> distance #12/A:193@OD1 #12/L:9@N2
Distance between halfcleaved_HNH_center_main_model_temp.pdb #12/A ASN 193 OD1
and /L DG 9 N2: 2.565Å
> show #!14 models
> hide #!14 models
> show #!13 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> select #12/A:205
9 atoms, 8 bonds, 1 residue, 1 model selected
> show #12/a:205 atoms
> show #!13 models
> hide #12/a:205 atoms
> color zone #13 near #12 distance 10
> color #12/L light gray
> color #12/K dim gray
> color #12/J dark red
> color #12/I rebecca purple
> color #12/B forest green
> color #12/C,D,E,F,G,H khaki
> color #12/A steel blue
> color #12/A:232-350 dark turquoise
> color zone #13 near #12 distance 10
> color #12 dim gray
> volume #!13 style image
> volume #!13 style surface
> transparency #13.1 0
> transparency #13.1 50
> color #12 white
[Repeated 1 time(s)]
> color #12 black
> color #12 gray
> color #12 dim gray
> color #12 light gray
> color #12 dim gray
> color #12 red
> orange
Unknown command: orange
> color #12 orange
> color #12/DA light gray
> color #12/EA dim gray
> color #12/FA dark red
> color #12/Ca rebecca purple
> color #12/Ba forest green
> color #12/Da,Db,Dc,Dd,De,Df khaki
> color #12/Aa steel blue
> color #12/Aa:232-350 dark turquoise
> color zone #13 near #12 distance 10
> color #13 navajo white
> transparency #13.1 50
> color #12/DA light gray
> color #12/EA dim gray
> color #12/FA dark red
> color #12/Ca rebecca purple
> color #12/Ba forest green
> color #12/Da,Db,Dc,Dd,De,Df khaki
> color #12/Aa steel blue
> color #12/Aa:232-350 dark turquoise
> color zone #13 near #12 distance 10
> color #13 navajo white
> transparency #13 50
> color #12/DA light gray
> color #12/EA dim gray
> color #12/FA dark red
> color #12/Ca rebecca purple
> color #12/Ba forest green
> color #12/Da,Db,Dc,Dd,De,Df khaki
> color #12/Aa steel blue
> color #12/Aa:232-350 dark turquoise
> color zone #13 near #12 distance 10
> color #12 dim gray
> transparency #13 50
> color #12/DA light gray
> color #12/EA dim gray
> color #12/FA dark red
> color #12/Ca rebecca purple
> color #12/Ba forest green
> color #12/Da,Db,Dc,Dd,De,Df khaki
> color #12/Aa steel blue
> color #12/Aa:232-350 dark turquoise
> color zone #13 near #12 distance 10
> color #12/L light gray
> color #12/K dim gray
> color #12/J dark red
> color #12/I rebecca purple
> color #12/B forest green
> color #12/C,D,E,F,G,H khaki
> color #12/A steel blue
> color #12/A:232-350 dark turquoise
> color zone #13 near #12 distance 10
> color #12 dim gray
> transparency #13 50
> color #12/L light gray
> color #12/K dim gray
> color #12/J dark red
> color #12/I rebecca purple
> color #12/B forest green
> color #12/C,D,E,F,G,H khaki
> color #12/A steel blue
> color #12/A:232-350 dark turquoise
> color #13 navajo white
> transparency #13 50
> color #12/L light gray
> color #12/K dim gray
> color #12/J dark red
> color #12/I rebecca purple
> color #12/B forest green
> color #12/C,D,E,F,G,H khaki
> color #12/A steel blue
> color #12/A:232-350 dark turquoise
> color zone #13 near #12 distance 10
> color #12 dim gray
> transparency #13 50
> color #12/L light gray
> color #12/K dim gray
> color #12/J dark red
> color #12/I rebecca purple
> color #12/B forest green
> color #12/C,D,E,F,G,H khaki
> color #12/A steel blue
> color #12/A:232-350 dark turquoise
> color #13 navajo white
> transparency #13 50
> color #12/L light gray
> color #12/K dim gray
> color #12/J dark red
> color #12/I rebecca purple
> color #12/B forest green
> color #12/C,D,E,F,G,H khaki
> color #12/A steel blue
> color #12/A:232-350 dark turquoise
> color zone #13 near #12 distance 10
> color #12 dim gray
> transparency #13 50
> color #12 rosy brown
> color #12 orange
> color #12 sienna
> color #12/L light gray
> color #12/K dim gray
> color #12/J dark red
> color #12/I rebecca purple
> color #12/B forest green
> color #12/C,D,E,F,G,H khaki
> color #12/A steel blue
> color #12/A:232-350 dark turquoise
> color zone #13 near #12 distance 10
> color #12 sienna
> transparency #13 50
> color #12/L light gray
> color #12/K dim gray
> color #12/J dark red
> color #12/I rebecca purple
> color #12/B forest green
> color #12/C,D,E,F,G,H khaki
> color #12/A steel blue
> color #12/A:232-350 dark turquoise
> color #13 navajo white
> transparency #13 50
> color #12/L light gray
> color #12/K dim gray
> color #12/J dark red
> color #12/I rebecca purple
> color #12/B forest green
> color #12/C,D,E,F,G,H khaki
> color #12/A steel blue
> color #12/A:232-350 dark turquoise
> color zone #13 near #12 distance 10
> color #12 sienna
> transparency #13 50
> color #12/L light gray
> color #12/K dim gray
> color #12/J dark red
> color #12/I rebecca purple
> color #12/B forest green
> color #12/C,D,E,F,G,H khaki
> color #12/A steel blue
> color #12/A:232-350 dark turquoise
> color #13 navajo white
> transparency #13 50
> select clear
> color #12/L light gray
> color #12/K dim gray
> color #12/J dark red
> color #12/I rebecca purple
> color #12/B forest green
> color #12/C,D,E,F,G,H khaki
> color #12/A steel blue
> color #12/A:232-350 dark turquoise
> color zone #13 near #12 distance 10
> color #12 sienna
> transparency #13 50
> color #12/L light gray
> color #12/K dim gray
> color #12/J dark red
> color #12/I rebecca purple
> color #12/B forest green
> color #12/C,D,E,F,G,H khaki
> color #12/A steel blue
> color #12/A:232-350 dark turquoise
> color zone #13 near #12 distance 10
> color #12 peru
> transparency #13 50
> color #12/L light gray
> color #12/K dim gray
> color #12/J dark red
> color #12/I rebecca purple
> color #12/B forest green
> color #12/C,D,E,F,G,H khaki
> color #12/A steel blue
> color #12/A:232-350 dark turquoise
> color zone #13 near #12 distance 10
> color #12 khaki
> transparency #13 50
> color #12/L light gray
> color #12/K dim gray
> color #12/J dark red
> color #12/I rebecca purple
> color #12/B forest green
> color #12/C,D,E,F,G,H khaki
> color #12/A steel blue
> color #12/A:232-350 dark turquoise
> color zone #13 near #12 distance 10
> color #12 violet
> transparency #13 50
> color #12/L light gray
> color #12/K dim gray
> color #12/J dark red
> color #12/I rebecca purple
> color #12/B forest green
> color #12/C,D,E,F,G,H khaki
> color #12/A steel blue
> color #12/A:232-350 dark turquoise
> color zone #13 near #12 distance 10
> color #12 alice blue
> transparency #13 50
> select #12
24113 atoms, 24865 bonds, 9 pseudobonds, 2801 residues, 3 models selected
> color sel violet
> select subtract #12
Nothing selected
> select add #12
24113 atoms, 24865 bonds, 9 pseudobonds, 2801 residues, 3 models selected
> select subtract #12
Nothing selected
> select add #12
24113 atoms, 24865 bonds, 9 pseudobonds, 2801 residues, 3 models selected
> select subtract #12
Nothing selected
> select add #12
24113 atoms, 24865 bonds, 9 pseudobonds, 2801 residues, 3 models selected
> color sel lemon chiffon
> color sel light coral
> color sel burly wood
> color sel pale green
> color sel gray
> select clear
> color #12/L light gray
> color #12/K dim gray
> color #12/J dark red
> color #12/I rebecca purple
> color #12/B forest green
> color #12/C,D,E,F,G,H khaki
> color #12/A steel blue
> color #12/A:232-350 dark turquoise
> color #12/o blue
> color zone #13 near #12/o distance 1
> surface dust #13 size 7.25
> surface dust #13 size 0
> transparency #13 50
> color zone #13 near #12
> color zone #13 near #12 distance 10
> transparency #13 50
> surface dust #13 size 7.25
> color #12 byhetero
> color #12/L light gray
> color #12/K dim gray
> color #12/J dark red
> color #12/I rebecca purple
> color #12/B forest green
> color #12/C,D,E,F,G,H khaki
> color #12/A steel blue
> color #12/A:232-350 dark turquoise
> color #12/a byhetero
> hide #12/a:192 atoms
> select add #11
6 pseudobonds, 2 models selected
> color sel white
> select clear
> select add #11
6 pseudobonds, 2 models selected
> color sel yellow
> color sel dark orange
> select clear
> select add #11
6 pseudobonds, 2 models selected
> color sel orange red
> select clear
> hide #12/j atoms
> hide #12/c,d,e,f,g,h,i cartoons
> color #12 red
> color #12 blue
> color #12 green
> color #12 cyan
> select clear
> color #12/a byhetero
> select clear
> select add #11
6 pseudobonds, 2 models selected
> color sel dark red
> color sel red
> select clear
> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/figures/structure/PAM/sideview_with_unwinding_shar_colormap.tif"
> width 1984 height 1210 supersample 3
> hide #12 atoms
> show #12/k:39,40 atoms
> show #12/l:7-8 atoms
> select #13
3 models selected
> select clear
> show #12/a:83,85 atoms
> show #12/k:40-41 atoms
> show #12/l:6 atoms
> hide #12/k:39 #12/l:8 atoms
> select clear
> hide #12 cartoons
> show #12/a:32-86 cartoons
> lighting soft
> lighting simple
> lighting full
> lighting simple
> lighting full
> lighting simple
> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/figures/structure/PAM/PAM_sharp_colormap.tif" width 1984
> height 1210 supersample 3
> view
> show #12 cartoons
> select clear
> color #12/L light gray
> color #12/K dim gray
> color #12/J dark red
> color #12/I rebecca purple
> color #12/B forest green
> color #12/C,D,E,F,G,H khaki
> color #12/A steel blue
> color #12/A:232-350 dark turquoise
> hide #!11 models
> hide #!13 models
> lighting soft
> lighting simple
> lighting full
> lighting soft
> lighting simple
> lighting soft
> lighting simple
> lighting soft
> lighting simple
> lighting soft
> lighting simple
> show #!13 models
> lighting soft
> lighting simple
> lighting soft
> lighting simple
> lighting soft
> lighting simple
[Repeated 1 time(s)]
> lighting soft
> lighting simple
> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/figures/structure/PAM/PAM_sharp_zoom_out_colormap.tif"
> width 1984 height 1210 supersample 3
> color #12/m,o turquoise
> color zone #13 near #12 distance 10
> surface dust #13 size 0
> color zone #13 near #12 distance 10
> color #12/o blue
> color zone #13 near #12 distance 1
> color zone #13 near #12 distance 10
> color #12/o blue
> color zone #13 near #12/o distance 1
> color blue zon #13 nea #12/o
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> select #13 & zon 5 #12
Expected a keyword
> zone #13 within 5 of #12
Expected a keyword
> select zone #13 nea #12 dis 5
Missing or invalid "range" argument: Expected a number
> zone #13 nea #12 dis 5
Expected a keyword
> zone #13 nea #12 dis 5
Expected a keyword
> color zone #13 near #12 distance 5
> split map #13
Expected a structures specifier or a keyword
> volume copy #13
Opened halfcleaved_HNH_center_sharp3Å.mrc copy as #22, grid size 420,420,420,
pixel 0.725, shown at step 1, values float32
> show #!13 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> hide #!22 models
> show #!22 models
> color #22 nea #12 dis 5
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color zone #22 near #12 distance 5
> split map #22 nea #12
Expected a structures specifier or a keyword
> color zone #13 near #12 distance 5 split map
Expected a keyword
> split map zon #22 nea #12 dis 5
Expected a structures specifier or a keyword
> ui tool show "Color Zone"
> volume splitbyzone #22
Opened halfcleaved_HNH_center_sharp3Å.mrc copy 0 as #23.1, grid size
420,420,420, pixel 0.725, shown at level 0.02, step 1, values float32
Opened halfcleaved_HNH_center_sharp3Å.mrc copy 1 as #23.2, grid size
420,420,420, pixel 0.725, shown at level 0.02, step 1, values float32
Opened halfcleaved_HNH_center_sharp3Å.mrc copy 2 as #23.3, grid size
420,420,420, pixel 0.725, shown at level 0.02, step 1, values float32
Opened halfcleaved_HNH_center_sharp3Å.mrc copy 3 as #23.4, grid size
420,420,420, pixel 0.725, shown at level 0.02, step 1, values float32
Opened halfcleaved_HNH_center_sharp3Å.mrc copy 4 as #23.5, grid size
420,420,420, pixel 0.725, shown at level 0.02, step 1, values float32
Opened halfcleaved_HNH_center_sharp3Å.mrc copy 5 as #23.6, grid size
420,420,420, pixel 0.725, shown at level 0.02, step 1, values float32
Opened halfcleaved_HNH_center_sharp3Å.mrc copy 6 as #23.7, grid size
420,420,420, pixel 0.725, shown at level 0.02, step 1, values float32
Opened halfcleaved_HNH_center_sharp3Å.mrc copy 7 as #23.8, grid size
420,420,420, pixel 0.725, shown at level 0.02, step 1, values float32
Opened halfcleaved_HNH_center_sharp3Å.mrc copy 8 as #23.9, grid size
420,420,420, pixel 0.725, shown at level 0.02, step 1, values float32
Opened halfcleaved_HNH_center_sharp3Å.mrc copy 9 as #23.10, grid size
420,420,420, pixel 0.725, shown at level 0.02, step 1, values float32
Opened halfcleaved_HNH_center_sharp3Å.mrc copy 10 as #23.11, grid size
420,420,420, pixel 0.725, shown at level 0.02, step 1, values float32
> show #!22 models
> hide #!22 models
> hide #!23 models
> show #!23 models
> hide #!23.1 models
> show #!23.1 models
> hide #!23.1 models
> show #!23.1 models
> hide #!23.2 models
> show #!23.2 models
> hide #!23.2 models
> show #!23.2 models
> hide #!23.2 models
> show #!23.2 models
> hide #!23.1 models
> show #!23.1 models
> hide #!23.1 models
> hide #!23.3 models
> show #!23.3 models
> hide #!12 models
> hide #!23.11 models
> show #!23.11 models
> hide #!23.11 models
> show #!23.11 models
> hide #!23.10 models
> show #!23.10 models
> hide #!23.10 models
> show #!23.10 models
> select add #23.10
2 models selected
> color sel turquoise
> select subtract #23.10
Nothing selected
> hide #!23.9 models
> show #!23.9 models
> hide #!23.9 models
> show #!23.9 models
> hide #!23.9 models
> show #!23.9 models
> hide #!23.8 models
> show #!23.8 models
> hide #!23.8 models
> show #!23.8 models
> show #!23.1 models
> hide #!23.1 models
> show #!23.1 models
> hide #!23 models
> show #!23 models
> hide #!23.1 models
> show #!23.1 models
> hide #!23.1 models
> show #!23.1 models
> hide #!23.1 models
> show #!23.1 models
> hide #!23.1 models
> show #!23.1 models
> hide #!23.1 models
> hide #!23.2 models
> hide #!23.3 models
> hide #!23.4 models
> hide #!23.5 models
> hide #!23.6 models
> hide #!23.9 models
> show #!23.9 models
> hide #!23.8 models
> show #!23.8 models
> hide #!23.8 models
> show #!23.8 models
> show #!23.6 models
> show #!23.5 models
> show #!23.4 models
> show #!23.3 models
> show #!23.2 models
> show #!23.1 models
> show #!22 models
> show #!21 models
> show #!20 models
> show #!19 models
> show #!18 models
> hide #!18 models
> hide #!19 models
> hide #!20 models
> hide #!21 models
> hide #!22 models
> close #22
> hide #!23.1 models
> show #!23.1 models
> hide #!23.1 models
> show #!23.1 models
> close #23
> color zone #13 near #12
> show #!13 models
> color zone #13 near #12 distance 4
> color zone #13 near #12 distance 4.25
> color zone #13 near #12 distance 5
> volume splitbyzone #13
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 10 as #22.11, grid size
420,420,420, pixel 0.725, shown at level 0.02, step 1, values float32
> hide #!22 models
> show #!22 models
> hide #!22.1 models
> show #!22.1 models
> hide #!22.1 models
> view
> hide #!22.2 models
> show #!22.2 models
> hide #!22.2 models
> hide #!22.3 models
> hide #!22.8 models
> hide #!22.10 models
> show #!22.10 models
> hide #!22.10 models
> show #!22.10 models
> select add #22.10
2 models selected
> color sel turquoise
> select subtract #22.10
Nothing selected
> select #22.10
2 models selected
> color sel dark turquoise
> select clear
> show #!22.8 models
> hide #!22.8 models
> show #!22.8 models
> hide #!22.8 models
> show #!22.8 models
> hide #!22.8 models
> show #!22.8 models
> hide #!22.4 models
> show #!22.4 models
> hide #!22.4 models
> show #!22.4 models
> hide #!22.4 models
> show #!22.4 models
> hide #!22.4 models
> show #!22.4 models
> hide #!22.4 models
> show #!22.4 models
> hide #!22.4 models
> show #!22.4 models
> hide #!22.4 models
> show #!22.4 models
> hide #!22.4 models
> show #!22.4 models
> hide #!22.4 models
> show #!22.4 models
> hide #!22.4 models
> show #!22.4 models
> hide #!22.4 models
> show #!22.4 models
> hide #!22.4 models
> show #!22.4 models
> hide #!22.4 models
> show #!22.4 models
> hide #!22.4 models
> show #!22.4 models
> show #!22.3 models
> lighting soft
> lighting simple
> show #!22.2 models
> hide #!22.2 models
> show #!22.2 models
> hide #!22.2 models
> show #!22.2 models
> volume #22.1-11 hide
> volume #22.2 show
> show #!22.3 models
> show #!22.1 models
> hide #!22.1 models
> show #!22.4 models
> show #!22.5 models
> show #!22.6 models
> show #!22.9 models
> show #!22.7 models
> hide #!22.7 models
> show #!22.8 models
> show #!22.7 models
> show #!22.10 models
> show #!22.11 models
> hide #!22.8 models
> show #!22.8 models
> hide #!22.8 models
> show #!22.8 models
> hide #!22.8 models
> show #!22.8 models
> transparency #22 50
> show #!13 models
> hide #!13 models
> show #!12 models
> select #12/K:2
8 atoms, 8 bonds, 1 residue, 1 model selected
> select up
833 atoms, 926 bonds, 43 residues, 1 model selected
> select down
8 atoms, 8 bonds, 1 residue, 1 model selected
> hide #12/k:1-3 atoms
> hide #12/k:1-3 cartoons
> show #12/a:280,304-305,319,328 atoms
> color #12/a byhetero
> hide #!22.10 models
> show #!22.10 models
> hide #!22.10 models
> show #!22.10 models
> hide #!22.10 models
> show #!22.10 models
> hide #!22.10 models
> show #!22.10 models
> color #22.10 #ff2600ff models
> select add #22.10
8 atoms, 8 bonds, 1 residue, 3 models selected
> color sel dark turquoise
> select clear
> select add #22.10
2 models selected
> transparency sel 50
> select clear
> show #12/o,m atoms
> color #12/m red
> select clear
> volume #22 hide
> select #12/A:309
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel cartoons
> show sel atoms
> select #12/A:309@N
1 atom, 1 residue, 1 model selected
> select add #12/O:1@O
2 atoms, 2 residues, 1 model selected
> distance #12/A:309@N #12/O:1@O
Distance between halfcleaved_HNH_center_main_model_temp.pdb #12/A LEU 309 N
and /O HOH 1 O: 3.004Å
> distance #12/A:309@N #12/O:1@O
Distance already exists; modify distance properties with 'distance style'
> show #!11 models
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel atoms
> show sel cartoons
> select #12/O:1@O
1 atom, 1 residue, 1 model selected
> show #12/k:1-3 atoms
> select #12/K:2@O3'
1 atom, 1 residue, 1 model selected
> select add #12/K:2@C3'
2 atoms, 1 residue, 1 model selected
> select add #12/K:2@C2'
3 atoms, 1 residue, 1 model selected
> select add #12/K:2@C1'
4 atoms, 1 residue, 1 model selected
> select add #12/K:2@O4'
5 atoms, 1 residue, 1 model selected
> select add #12/K:2@C4'
6 atoms, 1 residue, 1 model selected
> select add #12/K:2@C5'
7 atoms, 1 residue, 1 model selected
> select add #12/K:2@O5'
8 atoms, 1 residue, 1 model selected
> hide sel atoms
> show sel atoms
> select subtract #12/K:2@O3'
7 atoms, 1 residue, 1 model selected
> select up
8 atoms, 8 bonds, 1 residue, 1 model selected
> select down
7 atoms, 1 residue, 1 model selected
> hide sel atoms
> select #12/K:2@O3'
1 atom, 1 residue, 1 model selected
> color sel dim gray
> select clear
> hide #12.1 models
> select #12/O:1@O
1 atom, 1 residue, 1 model selected
> select add #12/K:3@OP2
2 atoms, 2 residues, 1 model selected
> distance #12/O:1@O #12/K:3@OP2
Distance between halfcleaved_HNH_center_main_model_temp.pdb #12/O HOH 1 O and
/K DA 3 OP2: 2.868Å
> select #12/A:280@NH2
1 atom, 1 residue, 1 model selected
> select add #12/K:3@OP2
2 atoms, 2 residues, 1 model selected
> distance #12/A:280@NH2 #12/K:3@OP2
Distance between halfcleaved_HNH_center_main_model_temp.pdb #12/A ARG 280 NH2
and /K DA 3 OP2: 2.709Å
> select #12/K:3@OP1
1 atom, 1 residue, 1 model selected
> select add #12/M:2@MG
2 atoms, 2 residues, 1 model selected
> distance #12/K:3@OP1 #12/M:2@MG
Distance between halfcleaved_HNH_center_main_model_temp.pdb #12/K DA 3 OP1 and
/M MG 2 MG: 2.496Å
> select #12/A:328@NE2
1 atom, 1 residue, 1 model selected
> select add #12/M:2@MG
2 atoms, 2 residues, 1 model selected
> distance #12/A:328@NE2 #12/M:2@MG
Distance between halfcleaved_HNH_center_main_model_temp.pdb #12/A HIS 328 NE2
and /M MG 2 MG: 1.829Å
> select #12/M:2@MG
1 atom, 1 residue, 1 model selected
> select add #12/A:304@ND1
2 atoms, 2 residues, 1 model selected
> distance #12/M:2@MG #12/A:304@ND1
Distance between halfcleaved_HNH_center_main_model_temp.pdb #12/M MG 2 MG and
/A HIS 304 ND1: 2.331Å
> select #12/A:305@ND1
1 atom, 1 residue, 1 model selected
> select #12/K:3@OP2
1 atom, 1 residue, 1 model selected
Exactly two atoms must be selected!
> select add #12/A:305@ND1
2 atoms, 2 residues, 1 model selected
> distance #12/K:3@OP2 #12/A:305@ND1
Distance between halfcleaved_HNH_center_main_model_temp.pdb #12/K DA 3 OP2 and
/A HIS 305 ND1: 2.858Å
> select clear
> volume #22 show
> color #12/k byhetero
> select clear
> select add #11
13 pseudobonds, 2 models selected
> color sel orange red
> select clear
> hide #12/a cartoons
> show #12/a cartoons
> select #12/K:6
11 atoms, 11 bonds, 1 residue, 1 model selected
> select add #12/K:7
31 atoms, 32 bonds, 2 residues, 1 model selected
> hide sel cartoons
> select clear
> select #22.8
2 models selected
> select clear
> hide #!22.8 models
> show #!22.8 models
> hide #!22.8 models
> show #!22.8 models
> color zone #22.8 near #12/a distance 5
> color #12/a:232-350 dark turquoise
> color zone #22.8 near #12/a distance 5
> transparency
> #22.1.1#22.2.1#22.3.1#22.4.1#22.5.1#22.6.1#22.7.1#22.8.1#22.9.1#22.10.1#22.11.1
> 0
> transparency
> #22.1.1#22.2.1#22.3.1#22.4.1#22.5.1#22.6.1#22.7.1#22.8.1#22.9.1#22.10.1#22.11.1
> 50
> combine #12
> hide #!12 models
> hide #!22 models
> hide #!23 models
> show #!23 models
> select #23/K:2@O3'
1 atom, 1 residue, 1 model selected
> select up
8 atoms, 8 bonds, 1 residue, 1 model selected
> select up
833 atoms, 926 bonds, 43 residues, 1 model selected
> select down
8 atoms, 8 bonds, 1 residue, 1 model selected
> select down
1 atom, 1 residue, 1 model selected
> select clear
> close #23
> show #12 models
> show #12 cartoons
> select #12/K:2
8 atoms, 8 bonds, 1 residue, 1 model selected
> select up
833 atoms, 926 bonds, 43 residues, 1 model selected
> select down
8 atoms, 8 bonds, 1 residue, 1 model selected
> select add #12/K:3
12 atoms, 11 bonds, 2 residues, 1 model selected
> color darkred turqoise
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> color sel darkred turqoise
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> select clear
> select #12/K:2
8 atoms, 8 bonds, 1 residue, 1 model selected
> select add #12/K:3
12 atoms, 11 bonds, 2 residues, 1 model selected
> color sel dark turquoise
> select clear
> select #12/M:2@MG
1 atom, 1 residue, 1 model selected
> color sel darkred turqoise
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> select clear
> select #12/M:2@MG
1 atom, 1 residue, 1 model selected
> select down
1 atom, 1 residue, 1 model selected
> select down
1 atom, 1 residue, 1 model selected
> select down
1 atom, 1 residue, 1 model selected
> color sel dark turquoise
> select clear
> close #22
> color zone #13 near #12 distance 5
> volume splitbyzone #13
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 10 as #22.11, grid size
420,420,420, pixel 0.725, shown at level 0.02, step 1, values float32
Opened halfcleaved_HNH_center_sharp3Å.mrc 11 as #22.12, grid size
420,420,420, pixel 0.725, shown at level 0.02, step 1, values float32
Opened halfcleaved_HNH_center_sharp3Å.mrc 12 as #22.13, grid size
420,420,420, pixel 0.725, shown at level 0.02, step 1, values float32
Opened halfcleaved_HNH_center_sharp3Å.mrc 13 as #22.14, grid size
420,420,420, pixel 0.725, shown at level 0.02, step 1, values float32
> close #22
> color #12/L light gray
> color #12/K dim gray
> color #12/J dark red
> color #12/I rebecca purple
> color #12/B forest green
> color #12/C,D,E,F,G,H khaki
> color #12/A steel blue
> color #12/A:232-350 dark turquoise
> select #12/K:2
8 atoms, 8 bonds, 1 residue, 1 model selected
> select add #12/K:3
12 atoms, 11 bonds, 2 residues, 1 model selected
> select up
833 atoms, 926 bonds, 43 residues, 1 model selected
> select up
24113 atoms, 24865 bonds, 2801 residues, 1 model selected
> select down
833 atoms, 926 bonds, 43 residues, 1 model selected
> select down
12 atoms, 11 bonds, 2 residues, 1 model selected
> select down
12 atoms, 11 bonds, 2 residues, 1 model selected
> select down
12 atoms, 11 bonds, 2 residues, 1 model selected
> select clear
> select add #12/K:3
4 atoms, 3 bonds, 1 residue, 1 model selected
> select add #12/K:2
12 atoms, 11 bonds, 2 residues, 1 model selected
> color sel dark turquoise
[Repeated 1 time(s)]
> select clear
> color zone #13 near #12 distance 5
> hide #!12 models
> show #!13 models
> volume splitbyzone #13
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
> hide #!22.1 models
> show #!22.1 models
> hide #!22.1 models
> show #!13 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> hide #!22.6 models
> show #!22.6 models
> transparency
> #22.2.1#22.3.1#22.4.1#22.5.1#22.6.1#22.7.1#22.8.1#22.9.1#22.10.1 50
> show #12 models
> color #12/a byhetero
> select #12/K:2
8 atoms, 8 bonds, 1 residue, 1 model selected
> hide #12/k:1-6 cartoons
> show #12/k:1-3 atoms
> volume #22 hide
> select subtract #12/K:2@O3'
7 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #12/K:2@O3'
1 atom, 1 residue, 1 model selected
> select up
8 atoms, 8 bonds, 1 residue, 1 model selected
> select up
833 atoms, 926 bonds, 43 residues, 1 model selected
> select down
8 atoms, 8 bonds, 1 residue, 1 model selected
> select #12/K:3@P
1 atom, 1 residue, 1 model selected
> select up
4 atoms, 3 bonds, 1 residue, 1 model selected
> select add #12/K:2@O3'
5 atoms, 3 bonds, 2 residues, 1 model selected
> color sel dim gray
> color sel byhetero
> select clear
> select #12/M:2@MG
1 atom, 1 residue, 1 model selected
> color sel red
> select clear
> volume #22 show
> transparency #22 90
> transparency #22 80
> transparency #22 75
> hide #12/a cartoons
> show #12/a cartoons
> lighting soft
> lighting simple
> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/figures/structure/HNH/HNH_sharp_colormap.tif" width 1729
> height 1210 supersample 3
> view
> view #22
> hide #12 atoms
> transparency #22 10
> transparency #22 25
> transparency #22 40
> transparency #22 50
> transparency #22 60
> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/figures/structure/HNH/HNH_sharp_zoom_out_colormap.tif"
> width 1729 height 1210 supersample 3
> show #12/k:6 atoms
> show #12/k:6-7 atoms
> hide #12/k cartoons
> hide #!22.8 models
> show #!22.8 models
> hide #!22.8 models
> show #!22.8 models
> hide #!22.8 models
> show #!22.8 models
> hide #!22.8 models
> show #!22.8 models
> hide #!22.8 models
> show #!22.8 models
> hide #!22 models
> show #!13 models
> transparency #13.1 0
> transparency #13.1 50
> hide #!13 models
> select #12/I:140
6 atoms, 5 bonds, 1 residue, 1 model selected
> select add #12/A:295
12 atoms, 10 bonds, 2 residues, 1 model selected
> show sel atoms
> color sel byhetero
> select clear
> show #!13 models
> hide #12.1 models
> color #12 cyan
> transparency #13 90
> transparency #13 75
> color #12 dim gray
> color #12 khaki
> select #12
24113 atoms, 24865 bonds, 16 pseudobonds, 2801 residues, 3 models selected
> color sel light salmon
> color sel dark goldenrod
> color sel olive
> color sel green
> color sel olive
> color sel misty rose
> color sel lavender blush
> color sel snow
> color sel dark green
> color sel white
> color sel light yellow
> color sel ghost white
> color sel mint cream
> color sel white smoke
> color sel papaya whip
> color sel moccasin
> color sel navajo white
> select clear
> color #12 byhetero
> select #12/K:6@C5'
1 atom, 1 residue, 1 model selected
> select up
11 atoms, 11 bonds, 1 residue, 1 model selected
> select up
833 atoms, 926 bonds, 43 residues, 1 model selected
> color sel pale goldenrod
> color #12 pale goldenrod
> color #12/a,i byhetero
> select clear
> color #12 ivory
> color #12 orange red
> color #12 chocolate
> select clear
> color #12 goldenrod
> select clear
> color #12/a,i byhetero
> select clear
> hide #!13 models
> show #!13 models
> hide #!13 models
> hide #!12 models
> hide #!11 models
> open "/Users/zxc755/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/Type
> I-F_HNH/Manuscript/halfcleaved_HNH_center_main_model_temp_editing.pdb"
Chain information for halfcleaved_HNH_center_main_model_temp_editing.pdb #23
---
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
> style stick
Changed 253112 atom styles
> close #23
> open "/Users/zxc755/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/Type
> I-F_HNH/Manuscript/halfcleaved_HNH_center_main_model_temp_editing.pdb"
Chain information for halfcleaved_HNH_center_main_model_temp_editing.pdb #23
---
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
> style stick
Changed 253112 atom styles
> color #23/j red
> colse #23
Unknown command: colse #23
> close #23
> open "/Users/zxc755/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/Type
> I-F_HNH/Manuscript/halfcleaved_HNH_center_main_model_temp_editing.pdb"
Chain information for halfcleaved_HNH_center_main_model_temp_editing.pdb #23
---
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
> style stu
Expected a keyword
> style stick
Changed 253111 atom styles
> select #23/J:61@P
1 atom, 1 residue, 1 model selected
> select add #23/J:60@O3'
2 atoms, 2 residues, 1 model selected
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> close #23
> show #!22 models
> hide #!22.1 models
> show #!22.1 models
> hide #!22.1 models
> show #!22.1 models
> hide #!22.1 models
> show #!22.1 models
> hide #!22.1 models
> transparency
> #22.2.1#22.3.1#22.4.1#22.5.1#22.6.1#22.7.1#22.8.1#22.9.1#22.10.1 0
> view
> lighting soft
> hide #!22.2 models
> hide #!22.6 models
> hide #!22.7 models
> hide #!22.8 models
> hide #!22.9 models
> hide #!22.10 models
> show #!22.10 models
> hide #!22.4 models
> hide #!22.5 models
> show #!22.2 models
> hide #!22.3 models
> show #!22.9 models
> hide #!22.9 models
> show #!12 models
> show #12 cartoons
> show #12/j,k,l atoms
> hide #12/j,k,l cartoons
> hide #12 cartoons
> show #!22.9 models
> hide #!22.9 models
> show #!22.7 models
> hide #!22.7 models
> show #!22.7 models
> hide #!22.7 models
> hide #12/k,l atoms
> show #!22.3 models
> show #!22.9 models
> hide #!22.9 models
> show #!22.4 models
> hide #!22.2 models
> hide #!12 models
> show #!22.9 models
> show #!22.8 models
> show #!22.7 models
> hide #!22.9 models
> hide #!22.10 models
> show #!22.10 models
> hide #!22.4 models
> hide #!22.3 models
> hide #!22.7 models
> show #!22.7 models
> show #!22.3 models
> show #!22.4 models
> hide #!22.8 models
> show #!22.9 models
> show #!22.5 models
> hide #!22.3 models
> show #!22.3 models
> hide #!22.3 models
> show #!22.3 models
> hide #!22.3 models
> show #!22.3 models
> hide #!22.3 models
> show #!22.3 models
> hide #!22.3 models
> show #!22.3 models
> hide #!22.3 models
> show #!22.3 models
> hide #!22.3 models
> show #!22.3 models
> hide #!22.3 models
> show #!22.3 models
> show #!21 models
> hide #!21 models
> show #!21 models
> hide #!21 models
> show #!22.6 models
> volume #22 copy
Expected a keyword
> volume copy #22
Opened halfcleaved_HNH_center_sharp3Å.mrc 0 copy as #23, grid size
420,420,420, pixel 0.725, shown at step 1, values float32
Opened halfcleaved_HNH_center_sharp3Å.mrc 1 copy as #24, grid size
420,420,420, pixel 0.725, shown at step 1, values float32
Opened halfcleaved_HNH_center_sharp3Å.mrc 2 copy as #25, grid size
420,420,420, pixel 0.725, shown at step 1, values float32
Opened halfcleaved_HNH_center_sharp3Å.mrc 3 copy as #26, grid size
420,420,420, pixel 0.725, shown at step 1, values float32
Opened halfcleaved_HNH_center_sharp3Å.mrc 4 copy as #27, grid size
420,420,420, pixel 0.725, shown at step 1, values float32
Opened halfcleaved_HNH_center_sharp3Å.mrc 5 copy as #28, grid size
420,420,420, pixel 0.725, shown at step 1, values float32
Opened halfcleaved_HNH_center_sharp3Å.mrc 6 copy as #29, grid size
420,420,420, pixel 0.725, shown at step 1, values float32
Opened halfcleaved_HNH_center_sharp3Å.mrc 7 copy as #30, grid size
420,420,420, pixel 0.725, shown at step 1, values float32
Opened halfcleaved_HNH_center_sharp3Å.mrc 8 copy as #31, grid size
420,420,420, pixel 0.725, shown at step 1, values float32
Opened halfcleaved_HNH_center_sharp3Å.mrc 9 copy as #32, grid size
420,420,420, pixel 0.725, shown at step 1, values float32
> close #23-27-29,30,32
Expected a models specifier or a keyword
> close #23-27,29,30,32
> select add #31
2 models selected
> select add #28
4 models selected
> ui mousemode right "rotate selected models"
Drag select of 28 halfcleaved_HNH_center_sharp3Å.mrc 5 copy , 31
halfcleaved_HNH_center_sharp3Å.mrc 8 copy
> select clear
> select add #28
2 models selected
> select add #31
4 models selected
> view matrix models
> #28,1,0,0,-15.745,0,1,0,17.233,0,0,1,35.558,#31,1,0,0,-15.745,0,1,0,17.233,0,0,1,35.558
> hide #!22 models
> show #!22 models
> hide #!22 models
> show #!22 models
> show #!22.9 models
> show #!22.6 models
Drag select of 28 halfcleaved_HNH_center_sharp3Å.mrc 5 copy
> view matrix models #28,1,0,0,-26.099,0,1,0,28.092,0,0,1,69.137
> undo
> view matrix models #28,1,0,0,-27.45,0,1,0,25.948,0,0,1,59.885
> undo
> view matrix models
> #28,1,0,0,-61.332,0,1,0,40.335,0,0,1,88.812,#31,1,0,0,-61.332,0,1,0,40.335,0,0,1,88.812
> view matrix models
> #28,0.99986,-0.0031587,-0.016157,-58.015,0.0031298,0.99999,-0.0018136,40.189,0.016163,0.0017628,0.99987,86.175,#31,0.99986,-0.0031587,-0.016157,-58.015,0.0031298,0.99999,-0.0018136,40.189,0.016163,0.0017628,0.99987,86.175
> view matrix models
> #28,0.9887,0.14469,-0.039276,-77.926,-0.05202,0.57675,0.81526,-6.0261,0.14062,-0.804,0.57776,271.07,#31,0.9887,0.14469,-0.039276,-77.926,-0.05202,0.57675,0.81526,-6.0261,0.14062,-0.804,0.57776,271.07
> view matrix models
> #28,0.9887,0.14469,-0.039276,-85.135,-0.05202,0.57675,0.81526,15.862,0.14062,-0.804,0.57776,246.68,#31,0.9887,0.14469,-0.039276,-85.135,-0.05202,0.57675,0.81526,15.862,0.14062,-0.804,0.57776,246.68
> view matrix models
> #28,0.9887,0.14469,-0.039276,-81.276,-0.05202,0.57675,0.81526,19.835,0.14062,-0.804,0.57776,247.27,#31,0.9887,0.14469,-0.039276,-81.276,-0.05202,0.57675,0.81526,19.835,0.14062,-0.804,0.57776,247.27
> view matrix models
> #28,0.9887,0.14469,-0.039276,-79.275,-0.05202,0.57675,0.81526,15.652,0.14062,-0.804,0.57776,250.56,#31,0.9887,0.14469,-0.039276,-79.275,-0.05202,0.57675,0.81526,15.652,0.14062,-0.804,0.57776,250.56
> view matrix models
> #28,0.9887,0.14469,-0.039276,-77.942,-0.05202,0.57675,0.81526,16.097,0.14062,-0.804,0.57776,249.3,#31,0.9887,0.14469,-0.039276,-77.942,-0.05202,0.57675,0.81526,16.097,0.14062,-0.804,0.57776,249.3
> hide #!28 models
> hide #!22.6 models
> select clear
> show #!28 models
> volume copy #28,31
Opened halfcleaved_HNH_center_sharp3Å.mrc 5 copy as #23, grid size
420,420,420, pixel 0.725, shown at step 1, values float32
Opened halfcleaved_HNH_center_sharp3Å.mrc 8 copy as #24, grid size
420,420,420, pixel 0.725, shown at step 1, values float32
> select add #24
2 models selected
> select add #23
4 models selected
> hide #!23 models
> view matrix models
> #23,0.9887,0.14469,-0.039276,8.0563,-0.05202,0.57675,0.81526,-113.04,0.14062,-0.804,0.57776,129.77,#24,0.9887,0.14469,-0.039276,8.0563,-0.05202,0.57675,0.81526,-113.04,0.14062,-0.804,0.57776,129.77
> view matrix models
> #23,0.043581,0.44731,-0.89332,249.71,0.41027,0.80728,0.42424,-149.29,0.91092,-0.38499,-0.14834,101.97,#24,0.043581,0.44731,-0.89332,249.71,0.41027,0.80728,0.42424,-149.29,0.91092,-0.38499,-0.14834,101.97
> view matrix models
> #23,0.31764,-0.21312,-0.92395,341.68,-0.32375,0.89148,-0.31693,58.267,0.89123,0.3998,0.21417,-119.07,#24,0.31764,-0.21312,-0.92395,341.68,-0.32375,0.89148,-0.31693,58.267,0.89123,0.3998,0.21417,-119.07
> view matrix models
> #23,0.59224,0.40091,-0.69894,170.96,-0.54032,0.8411,0.024613,71.479,0.59774,0.36308,0.71476,-154.16,#24,0.59224,0.40091,-0.69894,170.96,-0.54032,0.8411,0.024613,71.479,0.59774,0.36308,0.71476,-154.16
> view matrix models
> #23,0.69706,-0.11362,-0.70796,246.89,-0.1613,0.93721,-0.30923,51.937,0.69864,0.32974,0.63496,-158.3,#24,0.69706,-0.11362,-0.70796,246.89,-0.1613,0.93721,-0.30923,51.937,0.69864,0.32974,0.63496,-158.3
> view matrix models
> #23,0.69706,-0.11362,-0.70796,252.59,-0.1613,0.93721,-0.30923,47.072,0.69864,0.32974,0.63496,-159,#24,0.69706,-0.11362,-0.70796,252.59,-0.1613,0.93721,-0.30923,47.072,0.69864,0.32974,0.63496,-159
> view matrix models
> #23,0.69706,-0.11362,-0.70796,252.6,-0.1613,0.93721,-0.30923,49.338,0.69864,0.32974,0.63496,-154.62,#24,0.69706,-0.11362,-0.70796,252.6,-0.1613,0.93721,-0.30923,49.338,0.69864,0.32974,0.63496,-154.62
> show #!31 models
> show #!22.3 models
> hide #!22.3 models
> view matrix models
> #23,0.53219,-0.46563,-0.70708,340.77,-0.13597,0.77732,-0.61423,119.83,0.83563,0.42303,0.35037,-150.59,#24,0.53219,-0.46563,-0.70708,340.77,-0.13597,0.77732,-0.61423,119.83,0.83563,0.42303,0.35037,-150.59
> view matrix models
> #23,0.53219,-0.46563,-0.70708,348.32,-0.13597,0.77732,-0.61423,144.51,0.83563,0.42303,0.35037,-125.55,#24,0.53219,-0.46563,-0.70708,348.32,-0.13597,0.77732,-0.61423,144.51,0.83563,0.42303,0.35037,-125.55
> view matrix models
> #23,0.53219,-0.46563,-0.70708,340.03,-0.13597,0.77732,-0.61423,154.48,0.83563,0.42303,0.35037,-128.41,#24,0.53219,-0.46563,-0.70708,340.03,-0.13597,0.77732,-0.61423,154.48,0.83563,0.42303,0.35037,-128.41
> view
> view matrix models
> #23,0.53219,-0.46563,-0.70708,339.08,-0.13597,0.77732,-0.61423,161.1,0.83563,0.42303,0.35037,-130.68,#24,0.53219,-0.46563,-0.70708,339.08,-0.13597,0.77732,-0.61423,161.1,0.83563,0.42303,0.35037,-130.68
> show #!22.3 models
> view matrix models
> #23,0.53219,-0.46563,-0.70708,343.45,-0.13597,0.77732,-0.61423,159.05,0.83563,0.42303,0.35037,-136.71,#24,0.53219,-0.46563,-0.70708,343.45,-0.13597,0.77732,-0.61423,159.05,0.83563,0.42303,0.35037,-136.71
> view matrix models
> #23,0.53219,-0.46563,-0.70708,341.97,-0.13597,0.77732,-0.61423,158.87,0.83563,0.42303,0.35037,-137.21,#24,0.53219,-0.46563,-0.70708,341.97,-0.13597,0.77732,-0.61423,158.87,0.83563,0.42303,0.35037,-137.21
> view matrix models
> #23,0.53219,-0.46563,-0.70708,341.85,-0.13597,0.77732,-0.61423,158.37,0.83563,0.42303,0.35037,-137,#24,0.53219,-0.46563,-0.70708,341.85,-0.13597,0.77732,-0.61423,158.37,0.83563,0.42303,0.35037,-137
> hide #!22.3 models
> select clear
> show #!23 models
> show #!28 models
> show #!22.6 models
> hide #!28 models
> hide #!23 models
> hide #!22.6 models
> show #!22.3 models
> show #!28 models
> hide #!28 models
> show #!23 models
> show #!22.4 models
> show #!22.6 models
> show #!28 models
> hide #!28 models
> hide #!23 models
> hide #!22.3 models
> hide #!22.4 models
> show #!22.2 models
> show #!28 models
> show #!23 models
> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/figures/chimera_session.cxs"
——— End of log from Thu Mar 27 17:05:34 2025 ———
opened ChimeraX session
> hide #!22.6 models
> hide #!22.2 models
> show #!22.6 models
> hide #!22.6 models
> hide #!23 models
> hide #!28 models
> show #!28 models
> select add #28
2 models selected
> select add #31
4 models selected
> ui mousemode right "rotate selected models"
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> view matrix models
> #28,0.99705,0.030134,-0.070522,-54.036,0.023972,0.75103,0.65984,-13.412,0.072847,-0.65958,0.74809,214.74,#31,0.99705,0.030134,-0.070522,-54.036,0.023972,0.75103,0.65984,-13.412,0.072847,-0.65958,0.74809,214.74
> show #!23 models
> show #!22.6 models
> hide #!28 models
> hide #!23 models
> hide #!22.6 models
> select clear
> open "/Users/zxc755/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/Type
> I-F_HNH/Manuscript/halfcleaved_HNH_center_main_model_temp_editing.pdb"
Chain information for halfcleaved_HNH_center_main_model_temp_editing.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 | 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
> volume #22 hide
> volume #24-25 hide
> volume #31 hide
> style stick
Changed 253111 atom styles
> show #25 cartoons
> hide #25
> show #25 & nucleic
> color #25/L light gray
> color #25/K dim gray
> color #25/J dark red
> color #25/I rebecca purple
> color #25/B forest green
> color #25/C,D,E,F,G,H khaki
> color #25/A steel blue
> color #25/A:232-350 dark turquoise
> hide #25 & nucleic cartoons
> show #25
> hide #25
> show #25 & nucleic
> show #25/j
> open 3i4h
Summary of feedback from opening 3i4h fetched from pdb
---
note | Fetching compressed mmCIF 3i4h from http://files.rcsb.org/download/3i4h.cif
3i4h title:
Crystal structure of Cas6 in Pyrococcus furiosus [more info...]
Chain information for 3i4h #26
---
Chain | Description | UniProt
X | endoribonuclease | Q8U1S4_PYRFU 8-270
> hide #!22 models
> hide #!26 models
> show #!26 models
> hide #!25 models
> show #!25 models
> select #26/X:34
4 atoms, 3 bonds, 1 residue, 1 model selected
> view matrix models #26,1,0,0,11.063,0,1,0,112.94,0,0,1,76.569
Drag select of 48 residues
> view matrix models #26,1,0,0,25.302,0,1,0,250.11,0,0,1,200.98
> view matrix models #26,1,0,0,73.305,0,1,0,249.54,0,0,1,132.47
> view matrix models
> #26,0.6118,0.31311,-0.72641,89.838,-0.77626,0.41421,-0.47524,242.91,0.15208,0.85463,0.49646,158
> view matrix models
> #26,0.20919,0.21723,-0.95344,137.17,-0.96272,0.21674,-0.16184,238.54,0.17149,0.95175,0.25447,203.29
> view matrix models
> #26,-0.18257,0.38275,-0.90563,144.87,-0.7876,0.49443,0.36774,240.71,0.58852,0.78041,0.21118,199.4
> view matrix models
> #26,0.24049,0.042201,-0.96973,126.99,-0.49179,0.86663,-0.084247,255.09,0.83685,0.49716,0.22917,198.15
> view matrix models
> #26,0.24049,0.042201,-0.96973,115.81,-0.49179,0.86663,-0.084247,256.61,0.83685,0.49716,0.22917,201.79
> select #26 & name="tyr"
Expected a keyword
> select ::name="TYR"
15699 atoms, 15721 bonds, 1261 residues, 36 models selected
> select #26::name="tyr"
192 atoms, 193 bonds, 16 residues, 1 model selected
> select #26::name="tyr" #26::name=lys
390 atoms, 373 bonds, 38 residues, 1 model selected
> select #26::name="tyr" #26::name=lys,his
1913 atoms, 1970 bonds, 2 pseudobonds, 232 residues, 2 models selected
> select #26::name="tyr" #26::name=lys
390 atoms, 373 bonds, 38 residues, 1 model selected
> select #26::name=lys
198 atoms, 178 bonds, 22 residues, 1 model selected
> select #26::name=his
80 atoms, 82 bonds, 8 residues, 1 model selected
> view matrix models
> #26,-0.89794,0.08841,0.43115,111.17,0.14503,0.98434,0.10021,254.49,-0.41554,0.15251,-0.8967,209.66
> select #26::name="his,lys"
Nothing selected
> select #26::name=his,lys
1913 atoms, 1970 bonds, 2 pseudobonds, 232 residues, 2 models selected
> select #26::name=his::name=lys
278 atoms, 260 bonds, 30 residues, 1 model selected
> select #26::name=his::name=lys::name=tyr
470 atoms, 455 bonds, 46 residues, 1 model selected
> show sel
> select clear
> mmaker #26 to #25/i
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 I (#25)
with 3i4h, chain X (#26), sequence alignment score = 33.6
RMSD between 6 pruned atom pairs is 1.546 angstroms; (across all 156 pairs:
18.266)
> hide #!26 models
> hide #!25 models
> open "/Users/zxc755/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/Type
> I-F_HNH/Manuscript/halfcleaved_HNH_center_main_model_temp_editing.pdb"
Chain information for halfcleaved_HNH_center_main_model_temp_editing.pdb #27
---
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
> style stick
Changed 279140 atom styles
> hide #27
> show #27 cartoons
> show #27/j,k,l
> hide #27/j,k,l cartoons
> color #27/L light gray
> color #27/K dim gray
> color #27/J dark red
> color #27/I rebecca purple
> color #27/B forest green
> color #27/C,D,E,F,G,H khaki
> color #27/A steel blue
> color #27/A:232-350 dark turquoise
> color #27/O blue
> color #27/M red
> volume #13 show
> color zone #13 near #27 distance 10
> color zone #13 near #27 distance 6
> color zone #13 near #27 distance 4
> color zone #13 near #27 distance 8
> transparency #13 50
> volume #13 hide
> hide #27 models
> close #27
> open "/Users/zxc755/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/Type
> I-F_HNH/Manuscript/halfcleaved_HNH_center_main_model_temp_editing.pdb"
Chain information for halfcleaved_HNH_center_main_model_temp_editing.pdb #27
---
Chain | Description
A | No description available
B | No description available
C E | No description available
D | 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
> style stick
Changed 279111 atom styles
> hide #27
> show #27 cartoons
> show #27 & nucleic
> color #27/L light gray
> color #27/K dim gray
> color #27/J dark red
> color #27/I rebecca purple
> color #27/B forest green
> color #27/C,D,E,F,G,H khaki
> color #27/A steel blue
> color #27/A:232-350 dark turquoise
> color #27/O blue
> color #27/M red
> hide #27& nucleic
> hide #27& nucleic cartoons
> hide #27& nucleic
> show #27 & nucleic
> select clear
> select P
1109 atoms, 1108 residues, 15 models selected
> color sel byhetero
> select clear
> hide #!27 models
> open 3pkm
Summary of feedback from opening 3pkm fetched from pdb
---
note | Fetching compressed mmCIF 3pkm from http://files.rcsb.org/download/3pkm.cif
3pkm title:
Crystal structure of Cas6 with its substrate RNA [more info...]
Chain information for 3pkm #29
---
Chain | Description | UniProt
A X | CRISPR-associated endoribonuclease Cas6 | CAS6_PYRFU 8-270
G | 5'-R(*AP*UP*UP*AP*CP*AP*AP*UP*AP*A)-3' |
R | 5'-R(P*UP*UP*AP*CP*AP*AP*UP*AP*A)-3' |
3pkm mmCIF Assemblies
---
1| author_defined_assembly
2| author_defined_assembly
Drag select of 237 residues, 3 pseudobonds, 27 shapes
> hide sel cartoons
> select #29/A:106
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel cartoons
Drag select of 71 atoms, 71 bonds, 27 shapes
> hide sel
Drag select of 13 atoms
> hide sel
> close #29
> show #27 models
> view
> close #27
> open "/Users/zxc755/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/Type
> I-F_HNH/Manuscript/halfcleaved_HNH_center_main_model_temp_editing.pdb"
Chain information for halfcleaved_HNH_center_main_model_temp_editing.pdb #27
---
Chain | Description
A | No description available
B | No description available
C E | No description available
D | 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
> style sty
Expected a keyword
> style stick
Changed 279111 atom styles
> hide #27
> color #27/L light gray
> color #27/K dim gray
> color #27/J dark red
> color #27/I rebecca purple
> color #27/B forest green
> color #27/C,D,E,F,G,H khaki
> color #27/A steel blue
> color #27/A:232-350 dark turquoise
> color #27/O blue
> color #27/M red
> show #27 cartoons
> show #27/j,k,l,m,o
> hide #27 & nucleic cartoons
> select P
1109 atoms, 1108 residues, 15 models selected
> select #27::P
Nothing selected
> select #27::name=P
Nothing selected
> select #27 & P
112 atoms, 111 residues, 1 model selected
> color sel byhetero
> select clear
> hide #27 models
> open /Users/zxc755/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/Phenix/eLBOW_54/elbow.001.pdb
> view
> close #29
> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/figures/chimera_session.cxs"
——— End of log from Mon Mar 31 18:07:43 2025 ———
opened ChimeraX session
> open /Users/zxc755/Downloads/J620_abinitio_map.mrc
Opened J620_abinitio_map.mrc as #29, grid size 128,128,128, pixel 2.38, shown
at level 0.218, step 1, values float32
> hide #!29 models
> show #!29 models
> view
> lighting soft
> lighting simple
> lighting soft
> ui tool show "Color Actions"
> select add #29
2 models selected
> color sel dark khaki
[Repeated 1 time(s)]
> color sel navajo white
> select clear
> lighting soft
> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/figures/structure/half_abinitio.tif" width 1984 height
> 1210 supersample 3 transparentBackground true
> open /Users/zxc755/Downloads/half_hetref_J623_map.mrc
Opened half_hetref_J623_map.mrc as #30, grid size 128,128,128, pixel 2.38,
shown at level 0.227, step 1, values float32
> select add #30
2 models selected
> color sel navajo white
> hide #!29 models
> select clear
> volume #30 level 0.5
> volume #30 level 0.3
> volume #30 level 0.35
> volume #30 level 0.33
> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/figures/structure/half_hetref.tif" width 1984 height 1210
> supersample 3
> hide #!30 models
Unsupported scale factor (0.000000) detected on Display0
[Repeated 7 time(s)]
> show #!31 models
> hide #!31 models
> show #!29 models
> show #!30 models
> hide #!30 models
> show #!30 models
> hide #!29 models
> show #!13 models
> hide #!30 models
> show #!30 models
> hide #!30 models
> color #12/L light gray
> color #12/K dim gray
> color #12/J dark red
> color #12/I rebecca purple
> color #12/B forest green
> color #12/C,D,E,F,G,H salmon
> color #12/A steel blue
> color #12/A:232-350 dark turquoise
> color #12/O blue
> color #12/M red
> color zone #13 near #12 distance 10
> show #!22.1 models
> hide #!22 models
> hide #!22.1 models
> show #!22.2 models
> hide #!22.2 models
> show #!22.2 models
> hide #!22.2 models
> show #!22.2 models
> hide #!22.2 models
> color #22.2 salmon
> show #!22.2 models
> hide #!22.2 models
> hide #!13 models
> show #!22.2 models
> show #!22.1 models
> hide #!22.2 models
> show #!22.2 models
> hide #!22.1 models
> show #!22.1 models
> hide #!22.2 models
> show #!22.2 models
> hide #!22.1 models
> show #!22.3 models
> hide #!22.2 models
> show #!22.2 models
> surface dust #22.2-9 size 10
> hide #!22.3 models
> show #!22.3 models
> hide #!22.2 models
> show #!22.4 models
> hide #!22.3 models
> show #!22.5 models
> show #!22.3 models
> hide #!22.3 models
> show #!22.2 models
> hide #!22.2 models
> show #!22.3 models
> show #!22.7 models
> hide #!22.7 models
> surface dust #22.5 size 10
> surface dust #22.4 size 10
> surface dust #22.6 size 10
> surface dust #22.7 size 10
> surface dust #22.8 size 10
> surface dust #22.9 size 10
> show #!22.6 models
> hide #!22.3 models
> surface dust #22.6 size 10
> hide #!22.4 models
> hide #!22.5 models
> show #!22.7 models
> hide #!22.6 models
> show #!22.8 models
> show #!22.9 models
> surface dust #22.7 size 10
> surface dust #22.8 size 10
> surface dust #22.9 size 10
> show #!22.10 models
> hide #!22.10 models
> view
> hide #!22.9 models
> hide #!22.8 models
> hide #!22.7 models
> show #!22.6 models
> show #!22.9 models
> hide #!22.9 models
> hide #!22.6 models
> show #!22.5 models
> show #!22.4 models
> hide #!22.5 models
> hide #!22.4 models
> show #!22.3 models
> show #!22.4 models
> show #!22.2 models
> hide #!22.4 models
> hide #!22.3 models
> show #!22.3 models
> show #!22.4 models
> hide #!22.4 models
> show #!22.4 models
> hide #!22.4 models
> show #!22.4 models
> hide #!22.4 models
> show #!22.9 models
> show #!22.8 models
> show #!22.7 models
> show #!22.4 models
> show #!22.5 models
> show #!22.6 models
> show #!22.10 models
> view
[Repeated 1 time(s)]
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!12 models
> volume #22 hide
> show #12
> hide #12
> show #12 cartoons
> show #12 & nucleic
> volume #22 hide mod
Expected a keyword
> volume #22 hide model
Expected a keyword
> hide #22 models
> show #22
> hide #!22.1 models
> hide #22 models
> show #!13 models
> hide #!13 models
> show #22 models
> hide #!22.1 models
> transparency #22 70
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> lighting flat
> show #12/A:83,85
> color #12/A byhetero
> hide #12 & nucleic cartoons
> ui tool show "Side View"
> hide #!22.10 models
> hide #!22.9 models
> hide #!22.6 models
> hide #!22.5 models
> hide #!22.3 models
> show #!22.3 models
> hide #!22.3 models
> show #!22.3 models
> hide #!22.2 models
> hide #12/c,d,e,f,g,h,i cartoons
> show #!22.9 models
> hide #!22.9 models
> hide #12/c,d,e,f,g,h,i,j cartoons
> hide #12/j
> color #12/l wheat
> color #22.7 wheat
> show #!22.2 models
> hide #!22.2 models
> show #!21 models
> hide #!21 models
> show #!11 models
> select add #11
13 pseudobonds, 2 models selected
> color sel black
> color sel slate gray
> color sel gray
> color sel dim gray
> select subtract #11
Nothing selected
> hide #!11 models
> show #!11 models
> show #!22.5 models
> show #!22.2 models
> show #!22.6 models
> show #!22.9 models
> show #!22.10 models
> hide #!12 models
> transparency #22 0
> lighting soft
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> color #22.7 gold
> color #22.7 khaki
> color #22.7 dark khaki
> color #22.7 olive
> color #22.7 dark khaki
> view
> color #22.7 goldenrod
> color #22.7 orange
> color #22.7 dark orange
> color #22.7 dark khaki
> show #!12 models
> transparency #22 70
> graphics silhouettes true
> lighting flat
[Repeated 2 time(s)]
> lighting soft
> lighting flat
> lighting soft
> lighting flat
> lighting shadows true intensity 0.5
> lighting flat
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> transparency #22 80
> transparency #22 99
> transparency #22 90
> transparency #12/l:1-6 50
> select add #11
13 pseudobonds, 2 models selected
> color sel crimson
> color sel brown
> color sel saddle brown
> color sel indian red
> color sel yellow
> color sel gold
[Repeated 1 time(s)]
> color sel orange
> color sel dark orange
> color sel goldenrod
> color sel salmon
> color sel dark khaki
> color sel peru
> color sel dark goldenrod
> select subtract #11
Nothing selected
> view
> hide #!22.2 models
> show #!22.2 models
> hide #!22.2 models
> hide #!22.5 models
> hide #!22.6 models
> hide #!22.7 models
> show #!22.7 models
> hide #!22.8 models
> show #!22.8 models
> hide #!22.9 models
> hide #!22.10 models
> show #!22.10 models
> hide #!22 models
> show #!22 models
> graphics silhouettes false
> graphics silhouettes true
> lighting flat
> volume #22.8 level 0.03
> volume #22.8 level 0.02
> volume #22 level 0.07
> volume #22 level 0.05
> hide #!22 models
> show #!22 models
> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/figures/structure/PAM/PAM_sharp_2.tif" width 1984 height
> 1210 supersample 3
> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/figures/structure/PAM/PAM_sharp_2.tif" width 1984 height
> 1210 supersample 4
> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/figures/structure/PAM/PAM_session.cxs"
[Repeated 1 time(s)]
> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/figures/structure/PAM/PAM_sharp_2.tif" width 1984 height
> 1210 supersample 3
> graphics silhouettes false
> graphics silhouettes true
> hide #12/a:83,85
> volume #22 level 0.02
> show #!22.5 models
> show #!22.9 models
> show #12/j
> hide #12/a,b
> hide #12/a,b cartoons
> hide #!22.5 models
> hide #!22.4 models
> hide #!22.3 models
> hide #!12 models
> open "/Users/zxc755/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/Type
> I-F_HNH/Manuscript/halfcleaved_HNH_center_main_model_temp.pdb"
Chain information for halfcleaved_HNH_center_main_model_temp.pdb #32
---
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
> hide #!32 models
> show #!32 models
> style ato
Expected a keyword
> style stick
Changed 303224 atom styles
> cki #32
Unknown command: cki #32
> close #32
> open "/Users/zxc755/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/Type
> I-F_HNH/Manuscript/halfcleaved_HNH_center_main_model_temp2.pdb"
Chain information for halfcleaved_HNH_center_main_model_temp2.pdb #32
---
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
> style stick
Changed 303277 atom styles
> close #32
> open "/Users/zxc755/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/Type
> I-F_HNH/Manuscript/halfcleaved_HNH_center_main_model_temp_editing.pdb"
Chain information for halfcleaved_HNH_center_main_model_temp_editing.pdb #32
---
Chain | Description
A | No description available
B | No description available
C E | No description available
D | 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
> style stick
Changed 303198 atom styles
> hide #32
> show #32 cartoons
Computing secondary structure
> cartoon style nucleic xsection oval width 1 thickness 1
> color #32/L dark khaki
> 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
> hide #32 & nucleic cartoons
> show #32 & nucleic
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!32 models
> show #!32 models
> hide #!32 models
> show #!32 models
> hide #!32 models
> show #!32 models
> hide #!32 models
> show #!32 models
> hide #!32 models
> show #!32 models
> hide #!32 models
> show #!32 models
> hide #!32 models
> hide #!22.7 models
> show #!22.7 models
> show #!32 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!12 models
> color #22.7 khaki
> color #22.7 dark khaki
> hide #!12 models
> color #32/l khaki
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> hide #!22.7 models
> show #!22.7 models
> hide #!32 models
> show #!12 models
> show #12/m,o
> hide #!22.8 models
> hide #!22.9 models
> hide #!22.7 models
> show #!22.5 models
> show #!22.4 models
> hide #!22.4 models
> show #12/a cartoons
> hide #12/j
> show #!22.4 models
> show #12/a:304,305
> hide #!22 models
> select #12/A:280
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #12/A:319
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #12/A:280
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel
> select clear
> select #12/K:2@C2'
1 atom, 1 residue, 1 model selected
> select add #12/K:2@C1'
2 atoms, 1 residue, 1 model selected
> select add #12/K:2@O4'
3 atoms, 1 residue, 1 model selected
> select add #12/K:2@O5'
4 atoms, 1 residue, 1 model selected
> select add #12/K:2@C5'
5 atoms, 1 residue, 1 model selected
> select add #12/K:2@C4'
6 atoms, 1 residue, 1 model selected
> select add #12/K:2@C3'
7 atoms, 1 residue, 1 model selected
> hide sel
> select clear
> select #12/K:3@P
1 atom, 1 residue, 1 model selected
> select up
4 atoms, 3 bonds, 1 residue, 1 model selected
> select up
833 atoms, 926 bonds, 43 residues, 1 model selected
> select down
4 atoms, 3 bonds, 1 residue, 1 model selected
> select up
833 atoms, 926 bonds, 43 residues, 1 model selected
> select down
4 atoms, 3 bonds, 1 residue, 1 model selected
> select add #12/K:2@O3'
5 atoms, 3 bonds, 2 residues, 1 model selected
> color sel byhetero
> select clear
> select #12/A:328
10 atoms, 10 bonds, 1 residue, 1 model selected
> show sel
> select clear
> show #!22 models
> hide #!22 models
> hide #!12 models
> show #!12 models
> show #!22 models
> hide #!22 models
> hide #!12 models
> show #!22 models
> show #!12 models
> transparency #22 90
> transparency #22 95
> hide #!22 models
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> lighting shadows true intensity 0.5
> graphics silhouettes false
> graphics silhouettes true
> lighting shadows false
> lighting flat
[Repeated 1 time(s)]
> graphics silhouettes false
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting flat
> lighting shadows true intensity 0.5
> lighting flat
> graphics silhouettes false
> show #!22 models
> graphics silhouettes true
> view
> view orient
[Repeated 1 time(s)]
> show #12/a
> volume #22 level 0.05
> volume #22 level 0.09
> volume #22 level 0.02
> hide #12/a
> hide #!12 models
> show #!22.2 models
> show #!22.3 models
> hide #!22.4 models
> hide #!22.5 models
> hide #!22.2 models
> show #!12 models
> hide #12/a cartoons
> show #12/b cartoons
> hide #12/k,l
> show #12/b
> hide #12/b
> hide #12/b cartoons
> hide #!22.3 models
> show #!22.2 models
> show #12/c,d,e,f,g,h
> show #12/c,d,e,f,g,h cartoons
> hide #12/c,d,e,f,g,h
> hide #!22.2 models
> hide #12/c,d,e,f,g,h cartoons
> show #!22.9 models
> show #!22.8 models
> show #!22.7 models
> show #12/j,k,l
> hide #!12 models
> show #!32 models
> hide #!32 models
> show #!12 models
> show #!32 models
> hide #!32 models
> show #!32 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!22.2 models
> show #!22.3 models
> show #!22.4 models
> show #!22.5 models
> show #!22.6 models
> hide #!22 models
> hide #!32 models
> show #!32 models
> show #32/m,o
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> select #32/l
247 atoms, 280 bonds, 1 pseudobond, 12 residues, 2 models selected
> color sel khaki
> color sel burly wood
> color sel rosy brown
> color sel midnight blue
> color sel purple
> color sel rebecca purple
> color sel cornflower blue
> color sel dodger blue
> color sel peru
> color sel dark goldenrod
> color sel dark orange
> color sel orange
> color sel dark orange
> color sel orange
> color sel dark orange
> select clear
> show #!22.1 models
> select add #22.7
2 models selected
> select subtract #22.7
Nothing selected
> select add #22.7
2 models selected
> color sel dark orange
> select clear
> hide #!22.1 models
> hide #!22 models
> show #!22 models
> hide #!22 models
> show #!13 models
> hide #!13 models
> hide #!11 models
> show #!13 models
> graphics silhouettes false
> lighting simple
> lighting soft
> color zone #13 near #32 distance 10
> hide #!13 models
> show #!22.1 models
> hide #!22 models
> select #32/K:40@N1
1 atom, 1 residue, 1 model selected
> select up
3 atoms, 1 bond, 2 residues, 1 model selected
> select up
41 atoms, 44 bonds, 2 residues, 1 model selected
> color sel indigo
> color sel peru
> color sel maroon
> color sel hot pink
> show #!22 models
> view
> select clear
> hide #32/c,d,e,f,g,h,j, car
> hide #32/c,d,e,f,g,h,j cartoons
> hide #!22 models
> show #!22 models
> hide #!22.1 models
> hide #!22.2 models
> hide #!22.6 models
> hide #!22.7 models
> show #!22.7 models
> hide #!22.8 models
> show #!22.8 models
> hide #!22.9 models
> hide #!22.10 models
> show #!22.10 models
> hide #32/m,o
> show #32/a:83,85
> color #32/a byhetero
> show #!11 models
> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/figures/chimera_session.cxs"
——— End of log from Wed Apr 23 13:09:57 2025 ———
opened ChimeraX session
> lighting flat
> graphics silhouettes false
> graphics silhouettes true
> hide #!11 models
> show #!11 models
> ui tool show Distances
> hide #!22 models
> select #32/A:85@NZ
1 atom, 1 residue, 1 model selected
> select add #32/L:6@N2
2 atoms, 2 residues, 1 model selected
> distance #32/A:85@NZ #32/L:6@N2
Distance between halfcleaved_HNH_center_main_model_temp_editing.pdb #32/A LYS
85 NZ and /L DG 6 N2: 3.258Å
> distance style radius 0.04
[Repeated 2 time(s)]
> distance style radius 0.03
[Repeated 2 time(s)]
> distance style radius 0.02
[Repeated 2 time(s)]
> distance style radius 0.01
[Repeated 2 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)]
> distance style decimalPlaces 2
[Repeated 2 time(s)]
> distance style decimalPlaces 1
[Repeated 2 time(s)]
> select #32/A:85@NZ
1 atom, 1 residue, 1 model selected
> select add #32/K:41@O2
2 atoms, 2 residues, 1 model selected
> distance #32/A:85@NZ #32/K:41@O2
Distance between halfcleaved_HNH_center_main_model_temp_editing.pdb #32/A LYS
85 NZ and /K DC 41 O2: 3.0Å
> select #32/A:83@OD1
1 atom, 1 residue, 1 model selected
> select add #32/A:85@NZ
2 atoms, 2 residues, 1 model selected
> distance #32/A:83@OD1 #32/A:85@NZ
Distance between halfcleaved_HNH_center_main_model_temp_editing.pdb #32/A ASP
83 OD1 and LYS 85 NZ: 2.9Å
> select #32/K:40@N2
1 atom, 1 residue, 1 model selected
> select #32/A:83@OD1
1 atom, 1 residue, 1 model selected
> select add #32/K:40@N2
2 atoms, 2 residues, 1 model selected
> distance #32/A:83@OD1 #32/K:40@N2
Distance between halfcleaved_HNH_center_main_model_temp_editing.pdb #32/A ASP
83 OD1 and /K DG 40 N2: 3.0Å
> distance style dashes 4
[Repeated 2 time(s)]
> distance style dashes 5
[Repeated 2 time(s)]
> distance style radius 0.04
[Repeated 2 time(s)]
> distance style radius 0.05
[Repeated 2 time(s)]
> distance style radius 0.04
[Repeated 2 time(s)]
> distance style radius 0.05
[Repeated 2 time(s)]
> select clear
> select add #11
17 pseudobonds, 2 models selected
> color sel peru
> color sel light salmon
> color sel olive
> color sel teal
> select clear
> close sel
> delete sel
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> close #32
> open "/Users/zxc755/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/Type
> I-F_HNH/Manuscript/halfcleaved_HNH_center_main_model_temp_editing.pdb"
Chain information for halfcleaved_HNH_center_main_model_temp_editing.pdb #32
---
Chain | Description
A | No description available
B | No description available
C E | No description available
D | 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
> style stick
Changed 303202 atom styles
> 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
> color #32/k:40 hot pink
> hide #32
> show #32/k,l
> show #32/a,b cartoons
Computing secondary structure
> color #32/a byhetero
> show #32/a:83-85
> select #32/A:83@OD1
1 atom, 1 residue, 1 model selected
> select add #32/K:40@N2
2 atoms, 2 residues, 1 model selected
> distance #32/A:83@OD1 #32/K:40@N2
Distance between halfcleaved_HNH_center_main_model_temp_editing.pdb #32/A ASP
83 OD1 and /K DG 40 N2: 3.0Å
> select #32/A:85@NZ
1 atom, 1 residue, 1 model selected
> select add #32/A:83@OD1
2 atoms, 2 residues, 1 model selected
> distance #32/A:85@NZ #32/A:83@OD1
Distance between halfcleaved_HNH_center_main_model_temp_editing.pdb #32/A LYS
85 NZ and ASP 83 OD1: 2.7Å
> select #32/A:85@NZ
1 atom, 1 residue, 1 model selected
> select add #32/L:6@N2
2 atoms, 2 residues, 1 model selected
> distance #32/A:85@NZ #32/L:6@N2
Distance between halfcleaved_HNH_center_main_model_temp_editing.pdb #32/A LYS
85 NZ and /L DG 6 N2: 3.1Å
> select #32/K:41@O2
1 atom, 1 residue, 1 model selected
> select add #32/A:85@NZ
2 atoms, 2 residues, 1 model selected
> distance #32/K:41@O2 #32/A:85@NZ
Distance between halfcleaved_HNH_center_main_model_temp_editing.pdb #32/K DC
41 O2 and /A LYS 85 NZ: 2.9Å
> select add #11
2 atoms, 17 pseudobonds, 2 residues, 3 models selected
> color sel dark khaki
> color sel teal
> select clear
> select #32/A:85
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel steel blue
> color sel byhetero
> select clear
> select #32/K:41@O2
1 atom, 1 residue, 1 model selected
> color sel dim gray
> select clear
> select #32/L:7@C2
1 atom, 1 residue, 1 model selected
> select up
19 atoms, 20 bonds, 1 residue, 1 model selected
> color sel hot pink
> select clear
> show #!22 models
> hide #!22 models
> distance style radius 0.04
[Repeated 2 time(s)]
> distance style radius 0.05
[Repeated 2 time(s)]
> show #11.1 models
> hide #11.1 models
> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/figures/structure/PAM/PAM_nomap.tif" width 1984 height
> 1210 supersample 3
> show #!22 models
> hide #!22 models
> graphics silhouettes false
> graphics silhouettes true
> lighting flat
> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/figures/structure/PAM/PAM_session.cxs"
> close #1-10
> close #14-21
> close #23-31
> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/figures/structure/PAM/PAM_session.cxs"
> show #32 cartoons
> hide #32/a
> cartoon style nucleic xsection oval width 1 thickness 1
> show #!22 models
> show #!22.2 models
> show #!22.6 models
> show #!22.9 models
> show #32/j
> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/figures/structure/PAM/PAM_zoomout.tif" width 1984 height
> 1210 supersample 3
> hide #32/j,k,l cartoons
> select clear
> hide #!22 models
> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/figures/structure/PAM/PAM_zoomout_nomap.tif" width 1984
> height 1210 supersample 3
> show #!22 models
> hide #!22 models
> show #!22 models
> hide #!22 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 #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/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 #2
---
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
> hide #1-2
> hide #32/k:1-6
> show #1-2 cartoons
Computing secondary structure
[Repeated 1 time(s)]
> color #1,2/L dark orange
> color #1,2/K dim gray
> color #1,2/J dark red
> color #1,2/I rebecca purple
> color #1,2/B forest green
> color #1,2/C,D,E,F,G,H salmon
> color #1,2/A steel blue
> color #1,2/A:232-350 dark turquoise
> color #1,2/O blue
> color #1,2/M red
> cartoon style nucleic xsection oval width 1 thickness 1
> hide #1-2 & nucleic cartoons
> color #32/k dim gray
> color #32/l dark orange
> select clear
> mmaker #1/a:150-200 to #32/a:150-200
Computing secondary structure
[Repeated 1 time(s)] 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 halfcleaved_HNH_inwards_refined.pdb, chain A (#1), sequence alignment
score = 253.2
RMSD between 51 pruned atom pairs is 0.259 angstroms; (across all 51 pairs:
0.259)
> mmaker #2/a:150-200 to #32/a:150-200
Computing secondary structure
[Repeated 1 time(s)] 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 halfcleaved_HNH_outwards_refined.pdb, chain A (#2), sequence alignment
score = 241.2
RMSD between 51 pruned atom pairs is 0.283 angstroms; (across all 51 pairs:
0.283)
> combine #1
> combine #2
> combine #32
> morph #2 #32 #1 #5 #4
Computed 201 frame morph #6
> coordset #6 1,201
> hide #!3 models
> hide #!6 models
> show #!6 models
> show #6 & nucleic cartoons
> cartoon style nucleic xsection oval width 1 thickness 1
> nucleotides #!6 ladder
> show #6 & nucleic
> hide #!6 models
> close #1-5
> 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 #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/NTS_cleaved/halfcleaved_HNH_inwards_refined.pdb"
Chain information for halfcleaved_HNH_inwards_refined.pdb #2
---
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_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 #3
---
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
> combine #32
> hide #1-4
> show #1-4 cartoons
Computing secondary structure
[Repeated 2 time(s)]
> color #1-4/L dark orange
> color #1-4/K dim gray
> color #1-4/J dark red
> color #1-4/I rebecca purple
> color #1-4/B forest green
> color #1-4/C,D,E,F,G,H salmon
> color #1-4/A steel blue
> color #1-4/A:232-350 dark turquoise
> color #1-4/O blue
> color #1-4/M red
> hide #!4 models
> hide #!3 models
> hide #!2 models
> hide #!1 models
> morph #1 #3 #4 #32 #2
Computed 201 frame morph #5
> coordset #5 1,201
> close #5
> morph #1 #32 #2 #4 #3
Computed 201 frame morph #5
> coordset #5 1,201
> hide #5/k:1-6
> hide #5/k:1-6 cartoons
> show #5 & nucleic
> style stick
Changed 192721 atom styles
> nucleotides #!5 ladder
> cartoon style nucleic xsection oval width 1 thickness 1
> lighting flat
> graphics silhouettes false
> graphics silhouettes true
> movie record
> movie encode /Users/zxc755/Desktop/movie1.mp4 framerate 25.0
Movie saved to /Users/zxc755/Desktop/movie1.mp4
> hide #!5 models
> show #!32 models
> show #!22 models
> show #32/k
> hide #!22 models
> select #32/K:2@O5'
1 atom, 1 residue, 1 model selected
> select add #32/K:2@C4'
2 atoms, 1 residue, 1 model selected
> select add #32/K:2@O4'
3 atoms, 1 residue, 1 model selected
> select add #32/K:2@C1'
4 atoms, 1 residue, 1 model selected
> select add #32/K:2@C2'
5 atoms, 1 residue, 1 model selected
> select add #32/K:2@C3'
6 atoms, 1 residue, 1 model selected
> hide sel
> select #32/K:2@C5'
1 atom, 1 residue, 1 model selected
> hide sel
> show #32/m,o
> select clear
> show #32/a:280,305,304
> select #32/K:3@P
1 atom, 1 residue, 1 model selected
> select add #32/K:2@O3'
2 atoms, 2 residues, 1 model selected
> select add #32/K:3@OP1
3 atoms, 2 residues, 1 model selected
> select add #32/K:3@OP2
4 atoms, 2 residues, 1 model selected
> select add #32/K:3@O5'
5 atoms, 2 residues, 1 model selected
> color sel byhetero
> select clear
> hide #32.1 models
> select #32/A:328
10 atoms, 10 bonds, 1 residue, 1 model selected
> show sel
> select clear
> select #32/A:304@ND1
1 atom, 1 residue, 1 model selected
> select add #32/M:2@MG
2 atoms, 2 residues, 1 model selected
> distance #32/A:304@ND1 #32/M:2@MG
Distance between halfcleaved_HNH_center_main_model_temp_editing.pdb #32/A HIS
304 ND1 and /M MG 2 MG: 2.3Å
> select #32/A:328@NE2
1 atom, 1 residue, 1 model selected
> select add #32/M:2@MG
2 atoms, 2 residues, 1 model selected
> distance #32/A:328@NE2 #32/M:2@MG
Distance between halfcleaved_HNH_center_main_model_temp_editing.pdb #32/A HIS
328 NE2 and /M MG 2 MG: 1.8Å
> hide #11.1 models
> select #32/O:1@O
1 atom, 1 residue, 1 model selected
> select add #32/K:3@OP2
2 atoms, 2 residues, 1 model selected
> distance #32/O:1@O #32/K:3@OP2
Distance between halfcleaved_HNH_center_main_model_temp_editing.pdb #32/O HOH
1 O and /K DA 3 OP2: 2.9Å
> select #32/A:280@NH2
1 atom, 1 residue, 1 model selected
> select add #32/K:3@OP2
2 atoms, 2 residues, 1 model selected
> distance #32/A:280@NH2 #32/K:3@OP2
Distance between halfcleaved_HNH_center_main_model_temp_editing.pdb #32/A ARG
280 NH2 and /K DA 3 OP2: 2.7Å
> select #32/A:308
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #32/A:309
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel
> hide sel cartoons
> select #32/A:309@N
1 atom, 1 residue, 1 model selected
> select add #32/O:1@O
2 atoms, 2 residues, 1 model selected
> distance #32/A:309@N #32/O:1@O
Distance between halfcleaved_HNH_center_main_model_temp_editing.pdb #32/A LEU
309 N and /O HOH 1 O: 3.0Å
> select #32/A:309@CA
1 atom, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel cartoons
> hide sel
> select #32/M:2@MG
1 atom, 1 residue, 1 model selected
> select add #32/K:3@OP1
2 atoms, 2 residues, 1 model selected
> distance #32/M:2@MG #32/K:3@OP1
Distance between halfcleaved_HNH_center_main_model_temp_editing.pdb #32/M MG 2
MG and /K DA 3 OP1: 2.5Å
> color #11 teal
> select clear
> select #32/A:305@ND1
1 atom, 1 residue, 1 model selected
> select add #32/K:3@OP2
2 atoms, 2 residues, 1 model selected
> distance sel
Distance between halfcleaved_HNH_center_main_model_temp_editing.pdb #32/A HIS
305 ND1 and /K DA 3 OP2: 2.9Å
> color #11 teal
> distance style radius 0.04
[Repeated 2 time(s)]
> distance style radius 0.05
[Repeated 2 time(s)]
> distance style dashes 4
[Repeated 2 time(s)]
> distance style dashes 5
[Repeated 2 time(s)]
> distance style dashes 4
[Repeated 2 time(s)]
> distance style dashes 3
[Repeated 2 time(s)]
> distance style dashes 2
[Repeated 2 time(s)]
> distance style dashes 1
[Repeated 2 time(s)]
> distance style dashes 2
[Repeated 2 time(s)]
> distance style dashes 3
[Repeated 2 time(s)]
> distance style dashes 4
[Repeated 2 time(s)]
> distance style dashes 5
[Repeated 2 time(s)]
> distance style dashes 6
[Repeated 2 time(s)]
> distance style dashes 7
[Repeated 2 time(s)]
> distance style dashes 8
[Repeated 2 time(s)]
> distance style dashes 7
[Repeated 2 time(s)]
> distance style dashes 8
[Repeated 2 time(s)]
> distance style dashes 7
[Repeated 2 time(s)]
> distance style dashes 6
[Repeated 2 time(s)]
> distance style dashes 5
[Repeated 2 time(s)]
> select clear
> show #!22 models
> hide #!22 models
> show #!22 models
> hide #!22 models
> show #!22 models
> hide #!22 models
> show #!22 models
> hide #!22 models
> show #!22 models
> hide #!22 models
> show #!22 models
> hide #!22 models
> show #!22 models
> hide #!22 models
> show #!22 models
> hide #!22 models
> show #32/a:319
> show #!22 models
> hide #!22 models
> select #32/A:320
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #32/A:320
8 atoms, 7 bonds, 1 residue, 1 model selected
> select clear
> ~distance #12/A:85@NZ #12/A:83@OD1
> ~distance #12/K:3@OP2 #12/A:305@ND1
> ~distance #12/M:2@MG #12/A:304@ND1
> ~distance #12/K:40@N2 #12/A:83@OD1
> ~distance #12/A:85@NZ #12/K:41@O2
> ~distance #12/A:193@OD1 #12/L:9@N2
> ~distance #12/A:280@NH2 #12/K:3@OP2
> ~distance #12/A:85@NZ #12/L:6@N2
> ~distance #12/A:191@OG #12/K:39@OP1
> ~distance #12/A:328@NE2 #12/M:2@MG
> ~distance #12/A:309@N #12/O:1@O
> ~distance #12/K:3@OP1 #12/M:2@MG
> ~distance #12/O:1@O #12/K:3@OP2
> select #32/A:305@ND1
1 atom, 1 residue, 1 model selected
> select add #32/K:3@OP2
2 atoms, 2 residues, 1 model selected
> select ~sel & ##selected
24089 atoms, 24845 bonds, 12 pseudobonds, 2799 residues, 3 models selected
> select clear
> select #32/A:305@ND1
1 atom, 1 residue, 1 model selected
> select add #32/K:3@OP2
2 atoms, 2 residues, 1 model selected
> ~distance sel
> select #32/K:3@O5'
1 atom, 1 residue, 1 model selected
> select add #32/A:305@ND1
2 atoms, 2 residues, 1 model selected
> distance sel
Distance between halfcleaved_HNH_center_main_model_temp_editing.pdb #32/K DA 3
O5' and /A HIS 305 ND1: 2.9Å
> distance style radius 0.04
[Repeated 2 time(s)]
> distance style radius 0.05
[Repeated 2 time(s)]
> color #11 teal
> select clear
> hide #32 cartoons
> hide #32/j
> show #32/a cartoons
> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/figures/structure/HNH/HNH_cat_nomap.tif" width 1984
> height 1210 supersample 3
> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/figures/structure/HNH/HNH_cat_session.cxs"
> show #32 cartoons
> hide #32/k:1-6 cartoons
> select #32/J:48
23 atoms, 25 bonds, 1 residue, 1 model selected
> show #32/j
> show #32/k:6 cartoons
> select clear
> hide #!11 models
> hide #32/a
> hide #32/m,o
> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/figures/structure/HNH/HNH_cat_zoomout_nomap.tif" width
> 1984 height 1210 supersample 3
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!13 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> show #!13 models
> surface dust #13 size 10
> hide #!32 models
> lighting soft
> lighting full
> lighting soft
> lighting simple
> lighting soft
> view
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting soft
> lighting flat
> lighting soft
> set bgColor gray
> set bgColor white
> view #13
> show #!32 models
> hide #!13 models
> hide #!32 models
> show #!12 models
> color #12/L dark orange
> color #12/K dim gray
> color #12/J dark red
> color #12/I rebecca purple
> color #12/B forest green
> color #12/C,D,E,F,G,H salmon
> color #12/A steel blue
> color #12/A:232-350 dark turquoise
> color #12/O dark turquoise
> color #12/M dark turquoise
> color #12/k:1-3 dark turquoise
> hide #!12 models
> show #!13 models
> color zone #13 near #12 distance 10
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> volume #13 level 0.05
> volume #13 change image level 0.0001303,0 level 0.002946,0.8 level 1.983,1
> volume #13 level 0.09
> volume #13 level 0.06
> volume #13 level 0.05
> volume #13 level 0.03
> turn x 90
[Repeated 3 time(s)]
> hide #!13 models
> show #!32 models
> hide #!32 models
> show #!22 models
> lighting soft
> graphics silhouettes true
> graphics silhouettes false
> lighting soft
> lighting full
> lighting soft
> lighting simple
> lighting soft
> show #!32 models
> graphics silhouettes true
> lighting flat
> hide #!32 models
> hide #!22 models
> show #!22 models
> hide #!22 models
> show #!22 models
> hide #!22 models
> show #!32 models
> hide #!32 models
> show #!32 models
> cd "/Users/zxc755/Library/CloudStorage/OneDrive-UniversityofCopenhagen/Type
> I-F_HNH/Manuscript"
Current working directory is: /Users/zxc755/Library/CloudStorage/OneDrive-
UniversityofCopenhagen/Type I-F_HNH/Manuscript
> save "/Users/zxc755/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/Type I-F_HNH/Manuscript/chimerax_session.cxs"
——— End of log from Fri Apr 25 19:29:02 2025 ———
opened ChimeraX session
> hide #!32 models
> show #!32 models
> graphics silhouettes false
> graphics silhouettes true
> hide #!32 models
> show #!1 models
> show #!2 models
> show #!3 models
> hide #!3 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> show #!32 models
> hide #1,2,32 cartoons
> hide #1,2,32
> show #1,2,32/a
> show #1,2,32/a cartoons
> hide #1,2,32
> show #!22 models
> hide #!22 models
> show #!22 models
> hide #!22 models
> open "/Users/zxc755/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/Type
> I-F_HNH/Manuscript/IFhnh_Manuscript/maps_and_models/NTS_cleaved/halfcleaved_HNH_center_fullTS_sharp.mrc"
Opened halfcleaved_HNH_center_fullTS_sharp.mrc as #7, grid size 420,420,420,
pixel 0.725, shown at level 0.00325, step 2, values float32
> open "/Users/zxc755/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/Type
> I-F_HNH/Manuscript/IFhnh_Manuscript/maps_and_models/NTS_cleaved/halfcleaved_HNH_center_main_map_sharp.mrc"
Opened halfcleaved_HNH_center_main_map_sharp.mrc as #8, grid size 420,420,420,
pixel 0.725, shown at level 0.00305, step 2, values float32
> 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 #9, grid size 420,420,420, pixel 0.725,
shown at level 0.00277, step 2, values float32
> 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 #10, grid size 420,420,420, pixel
0.725, shown at level 0.0029, step 2, values float32
> close #7,8
> hide #!2 models
> hide #!1 models
> color zone #9 near #2 distance 10
> color zone #10 near #1 distance 10
> ui tool show "Color Zone"
> volume splitbyzone #9
Opened halfcleaved_HNH_in_sharp.mrc 0 as #7.1, grid size 420,420,420, pixel
0.725, shown at level 0.00277, 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 0.00277, 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 0.00277, 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 0.00277, 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 0.00277, 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 0.00277, 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 0.00277, 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 0.00277, 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 0.00277, step 1, values float32
> volume splitbyzone #10
Opened halfcleaved_HNH_out_sharp.mrc 0 as #8.1, grid size 420,420,420, pixel
0.725, shown at level 0.0029, 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 0.0029, 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 0.0029, 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 0.0029, 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 0.0029, 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 0.0029, 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 0.0029, 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 0.0029, 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 0.0029, step 1, values float32
> hide #!7.1 models
> show #!7.1 models
> hide #!7.1 models
> hide #!7.4 models
> hide #!7.5 models
> hide #!7.6 models
> hide #!7.7 models
> hide #!7.8 models
> hide #!7.9 models
> hide #!8.1 models
> hide #!8.4 models
> hide #!8.5 models
> hide #!8.6 models
> hide #!8.7 models
> hide #!8.8 models
> hide #!8.9 models
> hide #!8 models
> show #!2 models
> transparency #7,8 90
> volume dus #7,8 siz 10
Expected a density maps specifier or a keyword
> surface dust #7.2 size 7.25
> surface dust #7.3 size 7.25
> surface dust #8 size 10
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> hide #!7 models
> show #!7 models
> volume #7.2 level 0.002
> volume #7 level 0.002
> volume #8 level 0.002
> hide #!2 models
> hide #!7 models
> show #!8 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!32 models
> show #!7 models
> show #!2 models
> hide #!1 models
> hide #!8 models
> surface dust #7 size 10
> show #!1 models
> hide #!2 models
> show #!8 models
> hide #!7 models
> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/figures/structure/subunits_with_map/Cas8_out.tif" width
> 1984 height 1210 supersample 3 transparentBackground true
> show #!2 models
> hide #!1 models
> show #!7 models
> hide #!8 models
> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/figures/structure/subunits_with_map/Cas8_in.tif" width
> 1984 height 1210 supersample 3
> hide #!2 models
> hide #!7 models
> show #!22 models
> show #!32 models
> hide #!22.2 models
> hide #!22.3 models
> hide #!22.6 models
> hide #!22.7 models
> hide #!22.8 models
> hide #!22.9 models
> hide #!22.10 models
> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/figures/structure/subunits_with_map/Cas8_cent.tif" width
> 1984 height 1210 supersample 3
> hide #!32 models
> hide #!22.5 models
> show #!22.5 models
> hide #!22 models
> show #!7 models
> show #!8 models
> hide #!7 models
> show #!7 models
> hide #!8 models
> show #!7.4 models
> show #!7.5 models
> show #!7.6 models
> show #!7.7 models
> show #!7.8 models
> show #!7.9 models
> hide #!7.9 models
> show #!7.9 models
> hide #!7.4 models
> hide #!7.5 models
> hide #!7.6 models
> hide #!7.7 models
> hide #!7.8 models
> hide #!7.9 models
> show #!2 models
> show #!1 models
> show #!8 models
> hide #!7 models
> hide #!2 models
> hide #!1 models
> hide #!8 models
> show #!22 models
> show #!32 models
> hide #!32 models
> hide #!22 models
> show #!7 models
> show #!8 models
> hide #!7 models
> show #!1 models
> hide #!1 models
> show #!1 models
> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/figures/structure/subunits_with_map/Cas8_out_2.tif" width
> 1984 height 1210 supersample 3
> hide #!8 models
> show #!7 models
> show #!2 models
> hide #!1 models
> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/figures/structure/subunits_with_map/Cas8_in_2.tif" width
> 1984 height 1210 supersample 3
> hide #!2 models
> hide #!7 models
> show #!22 models
> show #!32 models
> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/figures/structure/subunits_with_map/Cas8_cent_2.tif"
> width 1984 height 1210 supersample 3
> hide #!32 models
> hide #!22 models
> show #!22 models
> show #!32 models
> hide #!32 models
> hide #!22 models
> show #!1 models
> show #!2 models
> hide #!2 models
> hide #!1 models
> open "/Users/zxc755/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/Type
> I-F_HNH/Manuscript/IFhnh_Manuscript/maps_and_models/apo/apo_HNH_center_refined.pdb"
Chain information for apo_HNH_center_refined.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
> 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 #15
---
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_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 #16
---
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_cent_sharp.mrc"
Opened apo_HNH_cent_sharp.mrc as #17, grid size 420,420,420, pixel 0.725,
shown at level 0.00199, step 2, values float32
> 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 #18, grid size 420,420,420, pixel 0.725, shown
at level 0.00173, step 2, values float32
> 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 #19, grid size 420,420,420, pixel 0.725, shown
at level 0.00214, step 2, values float32
> hide #!19 models
> hide #!18 models
> hide #!17 models
> color ##14/L dark orange;col ##14/K dim gray;col ##14/J dark red;col ##14/I
> rebecca purple;col ##14/B forest green;col ##14/C,D,E,F,G,H salmon;col
> ##14/A steel blue;col ##14/A:232-350 dark turquoise; col ##14/O blue; col
> ##14/M red
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color #14/L dark orange
> color #14/K dim gray
> color #14/J dark red
> color #14/I rebecca purple
> color #14/B forest green
> color #14/C,D,E,F,G,H salmon
> color #14/A steel blue
> color #14/A:232-350 dark turquoise
> color #14/O blue
> color #14/M red
> color #15/L dark orange
> color #15/K dim gray
> color #15/J dark red
> color #15/I rebecca purple
> color #15/B forest green
> color #15/C,D,E,F,G,H salmon
> color #15/A steel blue
> color #15/A:232-350 dark turquoise
> color #15/O blue
> color #15/M red
> color #16/L dark orange
> color #16/K dim gray
> color #16/J dark red
> color #16/I rebecca purple
> color #16/B forest green
> color #16/C,D,E,F,G,H salmon
> color #16/A steel blue
> color #16/A:232-350 dark turquoise
> color #16/O blue
> color #16/M red
> color zone #17 near #14 distance 10
> color zone #18 near #15 distance 10
> color zone #19 near #16 distance 10
> hide #!16 models
> show #!16 models
> hide #!16 models
> hide #!15 models
> hide #!14 models
> show #!17 models
> show #!18 models
> show #!19 models
> hide #!19 models
> hide #!18 models
> hide #!17 models
> 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 #20
---
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/postcleavage_HNH_inwards_refined.pdb"
Chain information for postcleavage_HNH_inwards_refined.pdb #21
---
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/postcleavage_HNH_outwards.pdb"
Chain information for postcleavage_HNH_outwards.pdb #23
---
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_cent_sharp.mrc"
Opened post_HNH_cent_sharp.mrc as #24, grid size 420,420,420, pixel 0.725,
shown at level 0.00328, step 2, values float32
> 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 #25, grid size 420,420,420, pixel 0.725, shown
at level 0.0257, step 2, values float32
> 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 #26, grid size 420,420,420, pixel 0.725,
shown at level 0.00342, step 2, values float32
> hide #!20 models
> hide #!21 models
> hide #!23 models
> color #20/L dark orange
> color #20/K dim gray
> color #20/J dark red
> color #20/I rebecca purple
> color #20/B forest green
> color #20/C,D,E,F,G,H salmon
> color #20/A steel blue
> color #20/A:232-350 dark turquoise
> color #20/O blue
> color #20/M red
> color #21/L dark orange
> color #21/K dim gray
> color #21/J dark red
> color #21/I rebecca purple
> color #21/B forest green
> color #21/C,D,E,F,G,H salmon
> color #21/A steel blue
> color #21/A:232-350 dark turquoise
> color #21/O blue
> color #21/M red
> color #23/L dark orange
> color #23/K dim gray
> color #23/J dark red
> color #23/I rebecca purple
> color #23/B forest green
> color #23/C,D,E,F,G,H salmon
> color #23/A steel blue
> color #23/A:232-350 dark turquoise
> color #23/O blue
> color #23/M red
> color zone #24 near #20 distance 10
> color zone #25 near #21 distance 10
> color zone #26 near #23 distance 10
> hide #!26 models
> hide #!25 models
> hide #!24 models
> show #!17 models
> hide #!17 models
> volume splitbyzone #17
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_cent_sharp.mrc 6 as #27.7, grid size 420,420,420, pixel 0.725,
shown at level 0.00199, step 1, values float32
> hide #!27.1 models
> hide #!27.4 models
> hide #!27.5 models
> hide #!27.6 models
> hide #!27.7 models
> volume splitbyzone #18
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_in_sharp.mrc 6 as #28.7, grid size 420,420,420, pixel 0.725,
shown at level 0.00173, step 1, values float32
> hide #!28.1 models
> hide #!28.4 models
> hide #!28.5 models
> hide #!28.6 models
> hide #!28.7 models
> volume splitbyzone #19
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 apo_HNH_out_sharp.mrc 6 as #29.7, grid size 420,420,420, pixel 0.725,
shown at level 0.00214, step 1, values float32
> hide #!29.1 models
> hide #!29.4 models
> show #!29.4 models
> hide #!29.4 models
> hide #!29.5 models
> hide #!29.6 models
> hide #!29.7 models
> hide #!27 models
> hide #!28 models
> hide #!29 models
> volume splitbyzone #24
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_cent_sharp.mrc 8 as #30.9, grid size 420,420,420, pixel 0.725,
shown at level 0.00328, step 1, values float32
> volume splitbyzone #25
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 0.0257, 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_in_sharp.mrc 8 as #31.9, grid size 420,420,420, pixel 0.725,
shown at level 0.0257, step 1, values float32
> volume splitbyzone #26
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
Opened post_HNH_out_sharp.mrc 8 as #33.9, grid size 420,420,420, pixel 0.725,
shown at level 0.00342, step 1, values float32
> hide #!30.1 models
> hide #!30.4 models
> hide #!30.5 models
> hide #!30.6 models
> hide #!30.7 models
> hide #!30.8 models
> hide #!30.9 models
> hide #!31.1 models
> hide #!31.4 models
> hide #!31.5 models
> hide #!31.6 models
> hide #!31.7 models
> hide #!31.8 models
> hide #!31.9 models
> hide #!33.1 models
> hide #!33.4 models
> hide #!33.5 models
> hide #!33.6 models
> hide #!33.7 models
> hide #!33.8 models
> hide #!33.9 models
> show #!32 models
> hide #!32 models
> show #!22 models
> hide #!22 models
> show #!29 models
> show #!28 models
> show #!27 models
> transparency 90
> surface dust siz 10
Missing or invalid "surfaces" argument: invalid surfaces specifier
> surface dust #27-31 #33 size 10
> hide #!33 models
> hide #!31 models
> hide #!30 models
> hide #!29 models
> hide #!28 models
Must specify one map, got 10
> fitmap #27.2 inMap #22.4
Fit map apo_HNH_cent_sharp.mrc 1 in map halfcleaved_HNH_center_sharp3Å.mrc 3
using 53530 points
correlation = 0, correlation about mean = 0, overlap = 0
steps = 24, shift = 0, angle = 0 degrees
Position of apo_HNH_cent_sharp.mrc 1 (#27.2) relative to
halfcleaved_HNH_center_sharp3Å.mrc 3 (#22.4) coordinates:
Matrix rotation and translation
1.00000000 0.00000000 0.00000000 0.00000000
0.00000000 1.00000000 0.00000000 0.00000000
0.00000000 0.00000000 1.00000000 0.00000000
Axis 0.00000000 0.00000000 1.00000000
Axis point 0.00000000 0.00000000 0.00000000
Rotation angle (degrees) 0.00000000
Shift along axis 0.00000000
> hide #!27.2 models
> show #!27.2 models
> hide #!27.2 models
> show #!27.2 models
> show #!22 models
> hide #!22.4 models
> show #!22.4 models
> hide #!22.4 models
> show #!22.4 models
> hide #!22.4 models
> show #!22.4 models
> hide #!27.2 models
> show #!27.2 models
> fitmap #27.2 inMap #22.4
Fit map apo_HNH_cent_sharp.mrc 1 in map halfcleaved_HNH_center_sharp3Å.mrc 3
using 53530 points
correlation = 0, correlation about mean = 0, overlap = 0
steps = 24, shift = 0, angle = 0 degrees
Position of apo_HNH_cent_sharp.mrc 1 (#27.2) relative to
halfcleaved_HNH_center_sharp3Å.mrc 3 (#22.4) coordinates:
Matrix rotation and translation
1.00000000 0.00000000 0.00000000 0.00000000
0.00000000 1.00000000 0.00000000 0.00000000
0.00000000 0.00000000 1.00000000 0.00000000
Axis 0.00000000 0.00000000 1.00000000
Axis point 0.00000000 0.00000000 0.00000000
Rotation angle (degrees) 0.00000000
Shift along axis 0.00000000
> select #27.2
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #27.2,-0.90481,-0.32416,-0.27613,332.21,0.31284,-0.94596,0.085389,229.16,-0.28888,-0.0091226,0.95732,44.701
> view matrix models
> #27.2,-0.97923,-0.19279,0.06285,325.19,0.18122,-0.97109,-0.15536,293.34,0.090985,-0.14075,0.98586,0.54729
> undo
[Repeated 2 time(s)]
> close #27-31
> close #33
> color #14-16/a steel blue
> show #!14 models
> hide #!14 models
> show #!14 models
> show #!15 models
> hide #!15 models
> hide #!14 models
> show #!14 models
> hide #!14 models
> show #!14 models
> hide #!14 models
> color #20,21,23/a steel blue
> color zone #17 near #14 distance 10
> color zone #18 near #15 distance 10
> color zone #19 near #16 distance 10
> color #24 nea #20 dis 10
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color zone #24 near #20 distance 10
> color zone #25 near #21 distance 10
> color zone #26 near #23 distance 10
> volume splitbyzone #17
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
> volume splitbyzone #18
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
> volume splitbyzone #19
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
> volume splitbyzone #24
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
> volume splitbyzone #25
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 0.0257, 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
> volume splitbyzone #26
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
> hide #!33 models
> hide #!33.1 models
> hide #!33.3 models
> show #!33 models
> hide #!33.4 models
> hide #!33.5 models
> hide #!33.6 models
> hide #!33.7 models
> hide #!33.8 models
> hide #!31.8 models
> hide #!31.7 models
> hide #!31.6 models
> hide #!31.5 models
> hide #!31.4 models
> hide #!31.3 models
> hide #!31.1 models
> hide #!30.8 models
> hide #!30.7 models
> hide #!30.6 models
> hide #!30.5 models
> hide #!30.4 models
> hide #!30.3 models
> hide #!30.1 models
> hide #!29.6 models
> hide #!29.5 models
> hide #!29.4 models
> hide #!29.3 models
> hide #!29.1 models
> hide #!28.6 models
> hide #!28.5 models
> hide #!28.4 models
> hide #!28.3 models
> hide #!28.1 models
> hide #!27.6 models
> hide #!27.5 models
> hide #!27.4 models
> hide #!27.3 models
> hide #!27.1 models
> hide #!22 models
> transparency #27-31,33 90
> show #!22 models
> hide #!28 models
> hide #!29 models
> hide #!30 models
> hide #!31 models
> hide #!33 models
> fitmap #27.2 inMap #22.4
Fit map apo_HNH_cent_sharp.mrc 1 in map halfcleaved_HNH_center_sharp3Å.mrc 3
using 82885 points
correlation = 0, correlation about mean = 0, overlap = 0
steps = 24, shift = 0, angle = 0 degrees
Position of apo_HNH_cent_sharp.mrc 1 (#27.2) relative to
halfcleaved_HNH_center_sharp3Å.mrc 3 (#22.4) coordinates:
Matrix rotation and translation
1.00000000 0.00000000 0.00000000 0.00000000
0.00000000 1.00000000 0.00000000 0.00000000
0.00000000 0.00000000 1.00000000 0.00000000
Axis 0.00000000 0.00000000 1.00000000
Axis point 0.00000000 0.00000000 0.00000000
Rotation angle (degrees) 0.00000000
Shift along axis 0.00000000
> select #27.2
2 models selected
> select add #27
13 models selected
> view matrix models
> #27,-0.9851,0.028378,0.1696,261.6,0.012815,-0.97143,0.23698,244.5,0.17148,0.23562,0.9566,-52.331
Drag select of 27.2 apo_HNH_cent_sharp.mrc 1
> view matrix models
> #27.2,1,4.8572e-17,6.1062e-16,-14.27,8.32e-32,1,4.1633e-16,-23.71,3.8858e-16,1.6653e-16,1,-1.3138
> view matrix models
> #27.2,1,4.8572e-17,6.1062e-16,10.218,8.32e-32,1,4.1633e-16,-19.262,3.8858e-16,1.6653e-16,1,-23.993
> color #27.2 red
> view matrix models
> #27.2,1,0.0011286,0.00024256,-17.671,-0.0011282,1,-0.001653,-23.156,-0.00024442,0.0016527,1,0.99344
> view matrix models
> #27.2,0.98647,0.15904,0.039716,-44.71,-0.15822,0.86043,0.48439,-45.115,0.042865,-0.48412,0.87395,80.037
> surface dust #27-31,33 size 10
> hide #!27 models
> select add #27
13 models selected
> select subtract #27
Nothing selected
> hide #!22 models
> show #!22 models
> show #!30 models
> select add #30
17 models selected
> color #30.2 green
> view matrix models
> #30,0.99278,0.11969,0.0075487,-17.819,-0.11662,0.97821,-0.17177,45.003,-0.027942,0.16965,0.98511,-26.609
> select subtract #30
Nothing selected
> hide #!30 models
> hide #!22 models
> show #!2 models
> hide #!2 models
> show #!7 models
> show #!28 models
> color #28.2 red
> color #29.2 red
> color #31.2 green
> color #33.2 green
> select add #28
13 models selected
> view matrix models
> #28,-0.93864,-0.18774,0.28933,282.81,0.11817,-0.96316,-0.24158,292.86,0.32402,-0.19257,0.92624,-7.1144
> view matrix models
> #28,-0.93864,-0.18774,0.28933,281.83,0.11817,-0.96316,-0.24158,308.33,0.32402,-0.19257,0.92624,-20.3
> view matrix models
> #28,-0.94765,-0.24867,0.20033,309.6,0.18207,-0.93615,-0.30078,306.85,0.26233,-0.24856,0.93242,-0.83323
> view matrix models
> #28,-0.95707,-0.19669,0.2129,302.83,0.13597,-0.95335,-0.26952,311.55,0.25597,-0.229,0.93917,-4.0077
> view matrix models
> #28,-0.95956,-0.22645,0.1672,313.45,0.18549,-0.95546,-0.22952,299.35,0.21173,-0.18923,0.95883,-5.8084
> view matrix models
> #28,-0.95956,-0.22645,0.1672,313,0.18549,-0.95546,-0.22952,299.82,0.21173,-0.18923,0.95883,-5.8642
> view matrix models
> #28,-0.94956,-0.28011,0.14095,322.64,0.23523,-0.93354,-0.2705,294.86,0.20736,-0.2237,0.95235,0.5275
> select subtract #28
Nothing selected
> hide #!28 models
> show #!31 models
> select add #31
17 models selected
> view matrix models
> #31,0.95745,0.28853,-0.0061963,-39.992,-0.2858,0.94498,-0.15916,77.745,-0.040066,0.15415,0.98723,-22.047
> view matrix models
> #31,0.98495,0.16362,0.055651,-31.707,-0.14812,0.9651,-0.21598,59.788,-0.089048,0.20449,0.97481,-20.953
> view matrix models
> #31,0.98502,0.15503,0.075475,-31.759,-0.13914,0.9732,-0.18309,50.935,-0.10184,0.16984,0.98019,-13.582
> view matrix models
> #31,0.98251,0.17881,0.052001,-31.724,-0.16394,0.96301,-0.21385,60.765,-0.088316,0.20159,0.97548,-20.561
> view matrix models
> #31,0.98782,0.1293,0.086525,-28.788,-0.10934,0.97261,-0.20513,49.258,-0.11068,0.19317,0.9749,-15.438
> select subtract #31
Nothing selected
> hide #!31 models
> hide #!7 models
> show #!8 models
> show #!29 models
> select add #29
13 models selected
> view matrix models
> #29,-0.96301,-0.11026,0.24587,268.61,0.020435,-0.93971,-0.34137,320.74,0.26869,-0.32372,0.9072,1.2682
> view matrix models
> #29,-0.92586,-0.36935,0.079794,337.56,0.33423,-0.89898,-0.28307,279.15,0.17629,-0.23541,0.95577,1.8338
> view matrix models
> #29,-0.9501,-0.28304,0.13113,324.32,0.24497,-0.93725,-0.24809,292.2,0.19312,-0.20359,0.95982,-2.6028
> view matrix models
> #29,-0.94885,-0.296,0.10988,328.51,0.25817,-0.9277,-0.26968,291.73,0.18176,-0.22752,0.95666,1.6234
> view matrix models
> #29,-0.95084,-0.25098,0.18144,313.28,0.21054,-0.95351,-0.21564,295.36,0.22712,-0.16684,0.95947,-11.512
> view matrix models
> #29,-0.94437,-0.26912,0.18906,314.35,0.22158,-0.94541,-0.23894,296.14,0.24304,-0.18376,0.95245,-10.94
> hide #!29 models
> select subtract #29
Nothing selected
> show #!33 models
> select add #33
17 models selected
> view matrix models
> #33,0.95382,0.29041,-0.076702,-29.712,-0.30037,0.92263,-0.24193,98.778,0.0005105,0.25379,0.96726,-42.939
> view matrix models
> #33,0.96865,0.24664,-0.029782,-31.412,-0.24842,0.96286,-0.10577,62.659,0.0025886,0.10985,0.99394,-24.767
> view matrix models
> #33,0.9728,0.17623,-0.15036,-2.5415,-0.20302,0.96116,-0.18696,65.208,0.11158,0.2124,0.97079,-60.099
> view matrix models
> #33,0.98074,0.15825,0.11447,-37.799,-0.13348,0.97094,-0.19866,54.576,-0.14258,0.17955,0.97336,-11.971
> view matrix models
> #33,0.98222,0.15787,0.10163,-34.87,-0.13329,0.96753,-0.21473,54.252,-0.13223,0.19737,0.97137,-14.291
> view matrix models
> #33,0.98222,0.15787,0.10163,-35.019,-0.13329,0.96753,-0.21473,54.238,-0.13223,0.19737,0.97137,-13.879
> fitmap #33.2 inMap #8.4
Fit map post_HNH_out_sharp.mrc 1 in map halfcleaved_HNH_out_sharp.mrc 3 using
87660 points
correlation = 0.2302, correlation about mean = 0.1069, overlap = 657.4
steps = 364, shift = 12.6, angle = 27.8 degrees
Position of post_HNH_out_sharp.mrc 1 (#33.2) relative to
halfcleaved_HNH_out_sharp.mrc 3 (#8.4) coordinates:
Matrix rotation and translation
0.88487665 -0.11856540 -0.45048370 86.96048472
0.12698700 0.99183644 -0.01160897 -10.81407486
0.44818257 -0.04693306 0.89270917 -57.31875206
Axis -0.03789003 -0.96394524 0.26338929
Axis point 159.50208814 0.00000000 151.60629729
Rotation angle (degrees) 27.78400581
Shift along axis -7.96790445
> fitmap #33.2 inMap #8.2
Fit map post_HNH_out_sharp.mrc 1 in map halfcleaved_HNH_out_sharp.mrc 1 using
87660 points
correlation = 0.7507, correlation about mean = 0.6577, overlap = 3498
steps = 300, shift = 13.1, angle = 25.8 degrees
Position of post_HNH_out_sharp.mrc 1 (#33.2) relative to
halfcleaved_HNH_out_sharp.mrc 1 (#8.2) coordinates:
Matrix rotation and translation
0.99883251 0.02105205 -0.04347916 3.28381267
-0.01860045 0.99825524 0.05604021 -3.01589348
0.04458306 -0.05516605 0.99748136 2.36658331
Axis -0.75501980 -0.59788649 -0.26921525
Axis point 0.00000000 33.34610426 68.86626768
Rotation angle (degrees) 4.22334809
Shift along axis -1.31330194
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!33 models
> show #!29 models
> fitmap #29.2 inMap #8.2
Fit map apo_HNH_out_sharp.mrc 1 in map halfcleaved_HNH_out_sharp.mrc 1 using
83162 points
correlation = 0.6154, correlation about mean = 0.4909, overlap = 1988
steps = 108, shift = 0.371, angle = 3.89 degrees
Position of apo_HNH_out_sharp.mrc 1 (#29.2) relative to
halfcleaved_HNH_out_sharp.mrc 1 (#8.2) coordinates:
Matrix rotation and translation
0.99774720 -0.00616969 0.06680170 -7.75363432
0.00547813 0.99992955 0.01053061 -2.15873626
-0.06686197 -0.01014094 0.99771070 11.37852778
Axis -0.15227290 0.98460707 0.08580135
Axis point 165.97569556 0.00000000 121.59503582
Rotation angle (degrees) 3.89203832
Shift along axis 0.03145444
> select subtract #33
Nothing selected
> hide #!29 models
> hide #!8 models
> show #!7 models
> show #!28 models
> fitmap #28.2 inMap #7.2
Fit map apo_HNH_in_sharp.mrc 1 in map halfcleaved_HNH_in_sharp.mrc 1 using
78989 points
correlation = 0.6568, correlation about mean = 0.5566, overlap = 1483
steps = 100, shift = 1.93, angle = 2.75 degrees
Position of apo_HNH_in_sharp.mrc 1 (#28.2) relative to
halfcleaved_HNH_in_sharp.mrc 1 (#7.2) coordinates:
Matrix rotation and translation
0.99894275 -0.01608144 0.04306693 -3.27929226
0.01666443 0.99977384 -0.01321212 -2.52037376
-0.04284472 0.01391584 0.99898482 4.13599960
Axis 0.28299722 0.89622541 0.34160298
Axis point 109.08725783 0.00000000 67.16502763
Rotation angle (degrees) 2.74722295
Shift along axis -1.77398382
> hide #!28 models
> show #!31 models
> fitmap #31.2 inMap #7.2
Fit map post_HNH_in_sharp.mrc 1 in map halfcleaved_HNH_in_sharp.mrc 1 using
83790 points
correlation = 0.5948, correlation about mean = 0.441, overlap = 2814
steps = 152, shift = 1.12, angle = 4.52 degrees
Position of post_HNH_in_sharp.mrc 1 (#31.2) relative to
halfcleaved_HNH_in_sharp.mrc 1 (#7.2) coordinates:
Matrix rotation and translation
0.99726035 0.04676217 -0.05731570 1.19747961
-0.04518981 0.99857380 0.02842974 4.02672915
0.05856339 -0.02576177 0.99795123 -4.59092844
Axis -0.34397877 -0.73553868 -0.58366211
Axis point 85.75257186 0.00000000 12.62773521
Rotation angle (degrees) 4.51795970
Shift along axis -0.69417165
> hide #!31 models
> show #!22 models
> hide #!22.4 models
> show #!22.4 models
> hide #!22.4 models
> show #!22.4 models
> hide #!7 models
> show #!30 models
> fitmap #30.2 inMap #22.4
Fit map post_HNH_cent_sharp.mrc 1 in map halfcleaved_HNH_center_sharp3Å.mrc 3
using 86342 points
correlation = 0.7861, correlation about mean = 0.6973, overlap = 3404
steps = 84, shift = 0.298, angle = 2.98 degrees
Position of post_HNH_cent_sharp.mrc 1 (#30.2) relative to
halfcleaved_HNH_center_sharp3Å.mrc 3 (#22.4) coordinates:
Matrix rotation and translation
0.99880892 0.03024374 0.03828920 -9.33094617
-0.03093378 0.99936719 0.01755928 3.13913491
-0.03773391 -0.01872279 0.99911241 9.35512683
Axis -0.34850229 0.73022926 -0.58763201
Axis point 242.75204382 0.00000000 250.82225024
Rotation angle (degrees) 2.98383902
Shift along axis 0.04677237
> hide #!30 models
> show #!27 models
> fitmap #27.2 inMap #22.4
Fit map apo_HNH_cent_sharp.mrc 1 in map halfcleaved_HNH_center_sharp3Å.mrc 3
using 82885 points
correlation = 0.608, correlation about mean = 0.4719, overlap = 1708
steps = 124, shift = 1.2, angle = 3.81 degrees
Position of apo_HNH_cent_sharp.mrc 1 (#27.2) relative to
halfcleaved_HNH_center_sharp3Å.mrc 3 (#22.4) coordinates:
Matrix rotation and translation
0.97832698 0.19020262 0.08184916 -54.13025495
-0.20662179 0.87084737 0.44601826 -34.04774174
0.01355572 -0.45326352 0.89127348 78.28203288
Axis -0.91268658 0.06931143 -0.40273953
Axis point 0.00000000 156.71923356 124.12929737
Rotation angle (degrees) 29.51532960
Shift along axis 15.51679105
> show #!14 models
> style stick
Changed 332211 atom styles
> hide #14
> show #14/a cartoons
Computing secondary structure
> color #14/a red
> fitmap #14/a inMap #27.2
Fit molecule apo_HNH_center_refined.pdb (#14) to map apo_HNH_cent_sharp.mrc 1
(#27.2) using 2728 atoms
average map value = 0.0141, steps = 2000
shifted from previous position = 21.7
rotated from previous position = 19 degrees
atoms outside contour = 2485, contour level = 0.0019908
Position of apo_HNH_center_refined.pdb (#14) relative to
apo_HNH_cent_sharp.mrc 1 (#27.2) coordinates:
Matrix rotation and translation
0.87515076 -0.42346707 0.23406577 55.94220375
0.48348878 0.74666401 -0.45687137 70.79007602
0.01870149 0.51299950 0.85818516 -55.77887122
Axis 0.72097898 0.16009669 0.67420944
Axis point 0.00000000 146.26043027 68.91682292
Rotation angle (degrees) 42.26858727
Shift along axis 14.05976817
> select #14/A:169
8 atoms, 7 bonds, 1 residue, 1 model selected
> view matrix models
> #14,-0.60187,-0.59648,-0.531,396.65,0.776,-0.27978,-0.56529,167.42,0.18862,-0.75229,0.63126,115.81
> fitmap #14/a inMap #27.2
Fit molecule apo_HNH_center_refined.pdb (#14) to map apo_HNH_cent_sharp.mrc 1
(#27.2) using 2728 atoms
average map value = 0.04066, steps = 124
shifted from previous position = 2.25
rotated from previous position = 10.1 degrees
atoms outside contour = 1852, contour level = 0.0019908
Position of apo_HNH_center_refined.pdb (#14) relative to
apo_HNH_cent_sharp.mrc 1 (#27.2) coordinates:
Matrix rotation and translation
-0.82083116 -0.46116689 -0.33698869 392.52408221
0.45571980 -0.17311548 -0.87312688 269.72015669
0.34431924 -0.87026214 0.35226145 171.58912907
Axis 0.00250785 -0.59643049 0.80266081
Axis point 145.87352872 275.32026651 0.00000000
Rotation angle (degrees) 145.16922813
Shift along axis -22.15706392
> view matrix models
> #14,-0.91976,-0.13361,0.36905,259.57,0.12723,-0.991,-0.041693,295.14,0.3713,0.0086066,0.92847,-56.6
> view matrix models
> #14,-0.94601,-0.32105,-0.044503,348.25,0.30157,-0.82153,-0.48389,302.66,0.1188,-0.47119,0.874,58.735
> fitmap #14/a inMap #27.2
Fit molecule apo_HNH_center_refined.pdb (#14) to map apo_HNH_cent_sharp.mrc 1
(#27.2) using 2728 atoms
average map value = 0.1677, steps = 128
shifted from previous position = 5.27
rotated from previous position = 18.3 degrees
atoms outside contour = 544, contour level = 0.0019908
Position of apo_HNH_center_refined.pdb (#14) relative to
apo_HNH_cent_sharp.mrc 1 (#27.2) coordinates:
Matrix rotation and translation
-0.98941113 -0.04220312 0.13886890 304.43360331
-0.05300114 -0.78565708 -0.61638777 392.25034981
0.13511682 -0.61722111 0.77510102 112.81565364
Axis -0.07270707 0.32735899 -0.94209860
Axis point 148.46002111 215.26270714 0.00000000
Rotation angle (degrees) 179.67164584
Shift along axis -0.01126639
> select clear
> hide #!14 models
> show #!14 models
> hide #!14 models
> hide #!27 models
> show #!30 models
> show #!20 models
> hide #20
> show #20/a
> color #20/a green
> hide #20
> show #20/a cartoons
Computing secondary structure
> fitmap #20/a inMap #30.2
Fit molecule postcleavage_HNH_center_refined.pdb (#20) to map
post_HNH_cent_sharp.mrc 1 (#30.2) using 2728 atoms
average map value = 0.2822, steps = 108
shifted from previous position = 5.73
rotated from previous position = 12.7 degrees
atoms outside contour = 221, contour level = 0.0032808
Position of postcleavage_HNH_center_refined.pdb (#20) relative to
post_HNH_cent_sharp.mrc 1 (#30.2) coordinates:
Matrix rotation and translation
0.99338756 0.11381514 0.01507534 -17.65419683
-0.10945975 0.97851549 -0.17471692 44.27616892
-0.03463688 0.17191148 0.98450329 -25.68733743
Axis 0.83464546 0.11970190 -0.53762293
Axis point 0.00000000 156.57774257 231.16518944
Rotation angle (degrees) 11.98467665
Shift along axis 4.37504802
> show #!32 models
> show #!14 models
> show #!17 models
> hide #!17 models
> show #!27 models
> hide #!20 models
> hide #!22 models
> hide #!27 models
> hide #!30 models
> hide #!32 models
> hide #!14 models
> show #!15 models
> hide #15-6
> hide #15
> hide #15,16
> show #15,16/a cartoons
Computing secondary structure
[Repeated 1 time(s)]
> color #15,16/a red
> show #!28 models
> select #15/A:341
14 atoms, 15 bonds, 1 residue, 1 model selected
> view matrix models
> #15,-0.93405,-0.34831,-0.078927,345.57,0.30616,-0.66712,-0.67913,293.42,0.1839,-0.65851,0.72976,90.717
> fitmap #15/a nea #28.2
Expected a keyword
> fitmap #15/a inMap #28.2
Fit molecule apo_HNH_inwards_refined.pdb (#15) to map apo_HNH_in_sharp.mrc 1
(#28.2) using 2728 atoms
average map value = 0.02958, steps = 260
shifted from previous position = 11.6
rotated from previous position = 23.4 degrees
atoms outside contour = 2054, contour level = 0.0017272
Position of apo_HNH_inwards_refined.pdb (#15) relative to apo_HNH_in_sharp.mrc
1 (#28.2) coordinates:
Matrix rotation and translation
-0.79630665 -0.43561221 -0.41968766 386.18629814
0.58540743 -0.38030007 -0.71600978 230.23651908
0.15229535 -0.81585162 0.55784610 144.52477351
Axis -0.08500291 -0.48697238 0.86927120
Axis point 158.93131778 227.39289934 0.00000000
Rotation angle (degrees) 144.03543017
Shift along axis -19.31456020
> view matrix models
> #15,-0.94602,-0.14843,-0.28813,357.26,0.24355,-0.9121,-0.32979,304.65,-0.21385,-0.38217,0.89901,84.308
> fitmap #15/a inMap #28.2
Fit molecule apo_HNH_inwards_refined.pdb (#15) to map apo_HNH_in_sharp.mrc 1
(#28.2) using 2728 atoms
average map value = 0.1223, steps = 184
shifted from previous position = 7.42
rotated from previous position = 24 degrees
atoms outside contour = 707, contour level = 0.0017272
Position of apo_HNH_inwards_refined.pdb (#15) relative to apo_HNH_in_sharp.mrc
1 (#28.2) coordinates:
Matrix rotation and translation
-0.96127242 -0.26981301 0.05618076 335.20428011
0.25014099 -0.93972629 -0.23311799 292.00968965
0.11569280 -0.21003679 0.97082425 10.38879106
Axis 0.04406009 -0.11360351 0.99254871
Axis point 147.82603778 169.13090853 0.00000000
Rotation angle (degrees) 164.81546446
Shift along axis -8.09281367
> select clear
> hide #!15 models
> hide #!28 models
> show #!31 models
> show #!15 models
> hide #!15 models
> show #!21 models
> show #!20 models
> hide #!20 models
> show #!23 models
> hide #!23 models
> hide #21,23
> show #21,23/a cartoons
Computing secondary structure
[Repeated 1 time(s)]
> color #21,23/a green
> fitmap #21/a inMap #31.2
Fit molecule postcleavage_HNH_inwards_refined.pdb (#21) to map
post_HNH_in_sharp.mrc 1 (#31.2) using 2703 atoms
average map value = 0.2685, steps = 112
shifted from previous position = 5.5
rotated from previous position = 13.7 degrees
atoms outside contour = 520, contour level = 0.025678
Position of postcleavage_HNH_inwards_refined.pdb (#21) relative to
post_HNH_in_sharp.mrc 1 (#31.2) coordinates:
Matrix rotation and translation
0.98616651 0.13380918 0.09783004 -31.07144516
-0.11332146 0.97498229 -0.19122706 47.65695927
-0.12097049 0.17749548 0.97665833 -11.51991642
Axis 0.74507872 0.44213088 -0.49937760
Axis point 0.00000000 84.76781023 229.63504986
Rotation angle (degrees) 14.32599614
Shift along axis 3.67272934
> hide #!31 models
> show #!33 models
> show #!23 models
> hide #!21 models
> fitmap #23/a inMap #33.2
Fit molecule postcleavage_HNH_outwards.pdb (#23) to map post_HNH_out_sharp.mrc
1 (#33.2) using 2728 atoms
average map value = 0.2713, steps = 180
shifted from previous position = 7.21
rotated from previous position = 13.7 degrees
atoms outside contour = 230, contour level = 0.003418
Position of postcleavage_HNH_outwards.pdb (#23) relative to
post_HNH_out_sharp.mrc 1 (#33.2) coordinates:
Matrix rotation and translation
0.98012633 0.16191619 0.11461028 -37.06976884
-0.13594647 0.96898777 -0.20635229 53.55638420
-0.14446774 0.18667045 0.97174236 -10.17466150
Axis 0.70553647 0.46508503 -0.53470946
Axis point 0.00000000 78.56032267 238.27779114
Rotation angle (degrees) 16.17234589
Shift along axis 4.19468674
> show #!20 models
> hide #!23 models
> hide #!33 models
> show #!30 models
> show #!33 models
> hide #!33 models
> show #!33 models
> hide #!33 models
> show #!33 models
> hide #!33 models
> hide #!30 models
> show #!21 models
> hide #!21 models
> show #!21 models
> show #!23 models
> hide #!23 models
> hide #!21 models
> show #!14 models
> show #!32 models
> hide #!32 models
> hide #!20 models
> hide #!14 models
> show #!15 models
> show #!21 models
> show #!2 models
> hide #!2 models
> hide #!15 models
> hide #!21 models
> show #!16 models
> show #!23 models
> show #!1 models
> show #!29 models
> select #16/A:287
5 atoms, 4 bonds, 1 residue, 1 model selected
> view matrix models
> #16,0.62757,-0.044878,-0.77726,162.91,0.38861,0.88314,0.26278,-73.948,0.67464,-0.46696,0.57167,26.566
> view matrix models
> #16,-0.40419,-0.68046,-0.61123,393.44,0.90481,-0.39532,-0.15824,86.915,-0.13395,-0.617,0.77548,143.78
> view matrix models
> #16,-0.39826,-0.68007,-0.61555,393.45,0.90771,-0.38883,-0.1577,112.35,-0.1321,-0.62154,0.77216,126.84
> fitmap #23/a inMap #29.2
Fit molecule postcleavage_HNH_outwards.pdb (#23) to map apo_HNH_out_sharp.mrc
1 (#29.2) using 2728 atoms
average map value = 0.1546, steps = 40
shifted from previous position = 0.0804
rotated from previous position = 0.183 degrees
atoms outside contour = 645, contour level = 0.0021375
Position of postcleavage_HNH_outwards.pdb (#23) relative to
apo_HNH_out_sharp.mrc 1 (#29.2) coordinates:
Matrix rotation and translation
0.98502518 0.17240574 0.00128825 -22.90899269
-0.16981904 0.97148276 -0.16547731 53.93769403
-0.02978076 0.16278055 0.98621276 -24.79677780
Axis 0.69074579 0.06537784 -0.72013610
Axis point 285.26360326 179.92837540 0.00000000
Rotation angle (degrees) 13.74559352
Shift along axis 5.55909429
> view matrix models
> #16,-0.89523,-0.41361,-0.16578,367.07,0.41729,-0.64769,-0.63747,283.05,0.15628,-0.63986,0.75243,90.762
> fitmap #23/a inMap #29.2
Fit molecule postcleavage_HNH_outwards.pdb (#23) to map apo_HNH_out_sharp.mrc
1 (#29.2) using 2728 atoms
average map value = 0.1546, steps = 40
shifted from previous position = 0.0116
rotated from previous position = 0.0128 degrees
atoms outside contour = 644, contour level = 0.0021375
Position of postcleavage_HNH_outwards.pdb (#23) relative to
apo_HNH_out_sharp.mrc 1 (#29.2) coordinates:
Matrix rotation and translation
0.98500387 0.17252839 0.00115057 -22.91842576
-0.16996614 0.97147812 -0.16535350 53.95165575
-0.02964593 0.16267828 0.98623369 -24.80251774
Axis 0.69024031 0.06480160 -0.72067265
Axis point 285.13190470 179.83196787 0.00000000
Rotation angle (degrees) 13.74619735
Shift along axis 5.55142851
> hide #!29 models
> show #!29 models
> view matrix models
> #16,-0.88458,-0.38657,-0.26093,381.82,0.46041,-0.81307,-0.35627,265.27,-0.074434,-0.43529,0.89721,76.738
> fitmap #23/a inMap #29.2
Fit molecule postcleavage_HNH_outwards.pdb (#23) to map apo_HNH_out_sharp.mrc
1 (#29.2) using 2728 atoms
average map value = 0.1546, steps = 28
shifted from previous position = 0.0105
rotated from previous position = 0.016 degrees
atoms outside contour = 645, contour level = 0.0021375
Position of postcleavage_HNH_outwards.pdb (#23) relative to
apo_HNH_out_sharp.mrc 1 (#29.2) coordinates:
Matrix rotation and translation
0.98502926 0.17238229 0.00130491 -22.90911466
-0.16979162 0.97147864 -0.16552961 53.94066736
-0.02980207 0.16282995 0.98620396 -24.80004337
Axis 0.69090730 0.06545276 -0.71997434
Axis point 285.31689662 179.95179673 0.00000000
Rotation angle (degrees) 13.74665869
Shift along axis 5.55788562
> fitmap #16/A inMap #29.2
Fit molecule apo_HNH_outwards_refined.pdb (#16) to map apo_HNH_out_sharp.mrc 1
(#29.2) using 2684 atoms
average map value = 0.1709, steps = 164
shifted from previous position = 5.87
rotated from previous position = 25 degrees
atoms outside contour = 433, contour level = 0.0021375
Position of apo_HNH_outwards_refined.pdb (#16) relative to
apo_HNH_out_sharp.mrc 1 (#29.2) coordinates:
Matrix rotation and translation
-0.96402236 -0.25980162 0.05624954 334.31569824
0.23888339 -0.93953169 -0.24538732 293.59018493
0.11660025 -0.22312178 0.96779185 12.48674161
Axis 0.04428161 -0.12002525 0.99178278
Axis point 148.03200436 169.10595691 0.00000000
Rotation angle (degrees) 165.43913121
Shift along axis -8.05006265
Must specify one map, got 0
> fitmap #23/a inMap #33.2
Fit molecule postcleavage_HNH_outwards.pdb (#23) to map post_HNH_out_sharp.mrc
1 (#33.2) using 2728 atoms
average map value = 0.2714, steps = 60
shifted from previous position = 0.085
rotated from previous position = 0.177 degrees
atoms outside contour = 229, contour level = 0.003418
Position of postcleavage_HNH_outwards.pdb (#23) relative to
post_HNH_out_sharp.mrc 1 (#33.2) coordinates:
Matrix rotation and translation
0.98009236 0.16199252 0.11479281 -37.09053836
-0.13597963 0.96897219 -0.20640359 53.56869743
-0.14466688 0.18668509 0.97170992 -10.14527457
Axis 0.70529698 0.46553397 -0.53463472
Axis point 0.00000000 78.41673669 238.26776560
Rotation angle (degrees) 16.18077713
Shift along axis 4.20221993
> show #!33 models
> show #!8 models
> select clear
> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/figures/structure/cas8_movement/cas8_out_overlap_maps.tif"
> width 1984 height 1210 supersample 3
> hide #!33 models
> hide #!29 models
> hide #!8 models
> color #1/a steel blue
> color #8.3 steel blue
> show #!8 models
> hide #!8.3 models
> show #!8.3 models
> hide #!8 models
> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/figures/structure/cas8_movement/cas8_out_overlap.tif"
> width 1984 height 1210 supersample 3
> show #!8 models
> show #!29 models
> show #!33 models
> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/figures/structure/cas8_movement/cas8_out_overlap_maps.tif"
> width 1984 height 1210 supersample 3
> hide #!33 models
> hide #!29 models
> hide #!23 models
> hide #!16 models
> hide #!8 models
> hide #!1 models
> show #!32 models
> color #32/a steel blue
> show #!22 models
> color #22.4 steel blue
> color #22.5 steel blue
> show #!30 models
> show #!29 models
> hide #!29 models
> show #!27 models
> show #!14 models
> show #!15 models
> hide #!15 models
> show #!20 models
> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/figures/structure/cas8_movement/cas8_cent_overlap_maps.tif"
> width 1984 height 1210 supersample 3
> hide #!30 models
> hide #!27 models
> hide #!22 models
> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/figures/structure/cas8_movement/cas8_cent_overlap.tif"
> width 1984 height 1210 supersample 3
> hide #!32 models
> hide #!20 models
> hide #!14 models
> show #!2 models
> color #2/a steel blue
> show #!16 models
> hide #!16 models
> show #!15 models
> show #!21 models
> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/figures/structure/cas8_movement/cas8_in_overlap.tif"
> width 1984 height 1210 supersample 3
> show #!31 models
> show #!28 models
> volume step 1
> volume #31.2 level 0.03
> volume #31.2 level 0.07
> show #!7 models
> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/figures/structure/cas8_movement/cas8_in_overlap_maps.tif"
> width 1984 height 1210 supersample 3
> hide #!2 models
> hide #!7 models
> hide #!31 models
> hide #!28 models
> hide #!21 models
> hide #!15 models
> show #!14 models
> show #!32 models
> show #!20 models
> show #!30 models
> show #!27 models
> show #!22 models
> hide #!22 models
> show #!22 models
> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/figures/structure/cas8_movement/cas8_cent_overlap_maps.tif"
> width 1984 height 1210 supersample 3
> hide #!20 models
> hide #!22 models
> hide #!27 models
> hide #!30 models
> hide #!32 models
> hide #!14 models
> show #!16 models
> show #!1 models
> show #!23 models
> show #!29 models
> show #!33 models
> show #!8 models
> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/figures/structure/cas8_movement/cas8_out_overlap_maps.tif"
> width 1984 height 1210 supersample 3
> hide #!8 models
> hide #!16 models
> hide #!23 models
> hide #!29 models
> hide #!33 models
> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/chimerax_session.cxs"
> show #!32 models
> hide #!1 models
> show #!22 models
> transparency #22 100
> transparency #22 90
> hide #!22 models
> hide #!32 models
> show #!2 models
> show #!7 models
> color #7.3 steel blue
> show #!15 models
> show #!31 models
> show #!28 models
> show #!21 models
> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/figures/structure/cas8_movement/cas8_in_overlap.tif"
> width 1984 height 1210 supersample 3
> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/figures/structure/cas8_movement/cas8_in_overlap_maps.tif"
> width 1984 height 1210 supersample 3
> hide #!31 models
> hide #!28 models
> hide #!7 models
> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/figures/structure/cas8_movement/cas8_in_overlap.tif"
> width 1984 height 1210 supersample 3
> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/chimerax_session.cxs"
——— End of log from Thu May 1 15:38:06 2025 ———
opened ChimeraX session
> hide #!2 models
> hide #!15 models
> hide #!21 models
> show #!32 models
> select #32/a:283
9 atoms, 8 bonds, 1 residue, 1 model selected
> select ::name="ASN"
15560 atoms, 13797 bonds, 1945 residues, 14 models selected
> select clear
> show #!16 models
> hide #!16 models
> show #!14 models
> show #!16 models
> hide #!16 models
> show #!16 models
> hide #!16 models
> show #!20 models
> color #14/a salmon
> ui tool show "Color Actions"
> color #20/a orchid
> color #20/a aquamarine
> color #20/a sea green
> color #20/a pale green
> color #15/a salmon
> color #16/a salmon
> color #21/a pale green
> color #23/a pale green
> color #30.2 #31.2 #33.2 pale green
> color #27.2 #28.2 #29.2 salmon
> show #!27 models
> show #!30 models
> hide #!30 models
> show #!30 models
> hide #!30 models
> show #!30 models
> hide #!30 models
> show #!30 models
> color #27.2 #28.2 #29.2 #14-16/a salmon
> color #30.2 #31.2 #33.2 #20-21/a #23/a pale green
> show #!22 models
> color #27.2 #28.2 #29.2 #14-16/a hot pink
> color #30.2 #31.2 #33.2 #20-21/a #23/a forest green
> hide #!27 models
> show #!27 models
> hide #!27 models
> show #!27 models
> hide #!27 models
> show #!27 models
> hide #!27 models
> show #!27 models
> hide #!27 models
> show #!27 models
> color #27.2 #28.2 #29.2 #14-16/a plum
> color #30.2 #31.2 #33.2 #20-21/a #23/a dark sea green
> color #27.2 #28.2 #29.2 #14-16/a vermilion
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color #27.2 #28.2 #29.2 #14-16/a dark orange
> color #30.2 #31.2 #33.2 #20-21/a #23/a bluish green
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color #27.2 #28.2 #29.2 #14-16/a warm beige
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color #27.2 #28.2 #29.2 #14-16/a beige
> color #30.2 #31.2 #33.2 #20-21/a #23/a sof gra
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color #30.2 #31.2 #33.2 #20-21/a #23/a dim gray
> color #30.2 #31.2 #33.2 #20-21/a #23/a light gray
> color #30.2 #31.2 #33.2 #20-21/a #23/a gray
> color #27.2 #28.2 #29.2 #14-16/a plum
> transparency 70
> transparency 100
> transparency 80
> color #27.2 #28.2 #29.2 #14-16/a dark gray
> color #30.2 #31.2 #33.2 #20-21/a #23/a medium sea green
> color #27.2 #28.2 #29.2 #14-16/a plum
> color #30.2 #31.2 #33.2 #20-21/a #23/a pale green
> color #30.2 #31.2 #33.2 #20-21/a #23/a dark gray
> color #27.2 #28.2 #29.2 #14-16/a orange
> color #30.2 #31.2 #33.2 #20-21/a #23/a teal
> color #30.2 #31.2 #33.2 #20-21/a #23/a cyan
> color #30.2 #31.2 #33.2 #20-21/a #23/a turquoise
> color #27.2 #28.2 #29.2 #14-16/a chocolate
> color #27.2 #28.2 #29.2 #14-16/a coral
> color #30.2 #31.2 #33.2 #20-21/a #23/a olive
> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/figures/structure/cas8_movement/cas8_cent_overlap_maps2.tif"
> width 1984 height 1210 supersample 3
> hide #!14 models
> hide #!20 models
> hide #!22 models
> hide #!27 models
> hide #!30 models
> hide #!32 models
> show #!15 models
> show #!2 models
> show #!21 models
> show #!7 models
> show #!28 models
> show #!31 models
> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/figures/structure/cas8_movement/cas8_in_overlap_maps2.tif"
> width 1984 height 1210 supersample 3
> hide #!31 models
> hide #!28 models
> hide #!21 models
> hide #!15 models
> hide #!7 models
> hide #!2 models
> show #!1 models
> show #!8 models
> show #!16 models
> show #!26 models
> hide #!26 models
> show #!29 models
> show #!33 models
> show #!23 models
> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/figures/structure/cas8_movement/cas8_out_overlap_maps2.tif"
> width 1984 height 1210 supersample 3
> hide #!8 models
> hide #!16 models
> hide #!23 models
> hide #!29 models
> hide #!33 models
> hide #!1 models
> show #!22 models
> show #!22.3 models
> show #!22.2 models
> show #!22.6 models
> show #!22.7 models
> show #!22.8 models
> show #!22.9 models
> transparency 100
> show #!22.1 models
> hide #!22.1 models
> hide #!22.2 models
> hide #!22.3 models
> hide #!22.4 models
> hide #!22.5 models
> hide #!22.6 models
> hide #!22.7 models
> hide #!22.8 models
> hide #!22.9 models
> show #!22.4 models
> show #!22.5 models
> hide #!22.5 models
> show #!22.5 models
> hide #!22.5 models
> show #!22.5 models
> show #!22.3 models
> hide #!22.5 models
> hide #!22.4 models
> show #!22.9 models
> hide #!22.9 models
> show #!22.9 models
> hide #!22.9 models
> show #!22.2 models
> hide #!22.2 models
> show #!22.2 models
> hide #!22.2 models
> show #!22.2 models
> transparency 80
> show #!22.4 models
> hide #!22.4 models
> show #!22.4 models
> hide #!22.3 models
> hide #!22.4 models
> show #!22.3 models
> hide #!22.3 models
> hide #!22.2 models
> show #!22.6 models
> show #!22.9 models
> hide #!22.9 models
> show #!22.9 models
> show #!22.7 models
> show #!22.8 models
> hide #!22.9 models
> show #!22.2 models
> show #!22.5 models
> show #!22.4 models
> show #!22.3 models
> show #!22.9 models
> transparency #22.2 100
> transparency #22 100
> show #!32 models
> show #32 cartoons
> hide #32 cartoons
> hide #!22.9 models
> hide #!22.8 models
> hide #!22.7 models
> hide #!22.6 models
> hide #!22.3 models
> hide #!22.2 models
> show #!22.2 models
> show #!22.3 models
> hide #!22.3 models
> hide #!22.2 models
> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/figures/structure/subunits_with_map/silhouette_cas8.tif"
> width 1984 height 1210 supersample 3 transparentBackground true
> hide #!22.5 models
> hide #!22.4 models
> show #!22.3 models
> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/figures/structure/subunits_with_map/silhouette_cas5.tif"
> width 1984 height 1210 supersample 3
> hide #!22.3 models
> show #!22.6 models
> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/figures/structure/subunits_with_map/silhouette_cas6.tif"
> width 1984 height 1210 supersample 3 transparentBackground true
> hide #!22.6 models
> show #!22.3 models
> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/figures/structure/subunits_with_map/silhouette_cas5.tif"
> width 1984 height 1210 supersample 3 transparentBackground true
> hide #!22.3 models
> show #!22.2 models
> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/figures/structure/subunits_with_map/silhouette_cas7_6x.tif"
> width 1984 height 1210 supersample 3 transparentBackground true
> hide #!22.2 models
> show #!22.7 models
> show #!22.8 models
> show #!22.9 models
> hide #!22.8 models
> hide #!22.7 models
> show #!22.7 models
> hide #!22.7 models
> show #!22.2 models
> show #32/c cartoons
> color #32/c green
> color zone #22.2 near #32 distance 10
> volume splitbyzone #22.2
Opened halfcleaved_HNH_center_sharp3Å.mrc 1 0 as #34.1, grid size
420,420,420, pixel 0.725, shown at level 0.02, step 1, values float32
Opened halfcleaved_HNH_center_sharp3Å.mrc 1 1 as #34.2, grid size
420,420,420, pixel 0.725, shown at level 0.02, 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 0.02, 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 0.02, 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 0.02, 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 0.02, 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 0.02, 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 0.02, 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 0.02, 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 0.02, 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 0.02, 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 0.02, 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 0.02, step 1, values float32
> hide #!22 models
> hide #!34.1 models
> hide #!34.2 models
> hide #!34.4 models
> show #!34.4 models
> hide #!34.4 models
> hide #!34.5 models
> hide #!34.6 models
> hide #!34.8 models
> hide #!34.7 models
> hide #!34.9 models
> hide #!34.10 models
> hide #!34.11 models
> hide #!34.12 models
> hide #!34.13 models
> transparency 100
> surface dust siz 10
Missing or invalid "surfaces" argument: invalid surfaces specifier
> dus siz 10
Unknown command: dus siz 10
> surface dust #34.3 size 7.25
> hide #!32 models
> show #!22 models
> show #!22.8 models
> hide #!22.9 models
> hide #!22.8 models
> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/figures/structure/subunits_with_map/silhouette_cas7.tif"
> width 1984 height 1210 supersample 3 transparentBackground true
> show #!22.2 models
> show #!22.3 models
> show #!22.4 models
> show #!22.5 models
> show #!22.6 models
> show #!22.9 models
> hide #!22.9 models
> show #!22.9 models
> hide #!22.9 models
> show #!22.9 models
> hide #!22.9 models
> show #!22.8 models
> show #!22.7 models
> hide #!22.7 models
> hide #!22.8 models
> hide #!22.6 models
> hide #!22.5 models
> hide #!22.4 models
> hide #!22.3 models
> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/figures/structure/subunits_with_map/silhouette_cas7_6x_2.tif"
> width 1984 height 1210 supersample 3 transparentBackground true
> show #!22.4 models
> show #!22.5 models
> show #!22.3 models
> show #!22.6 models
> transparency 0
> lighting soft
> lighting simple
> lighting soft
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> show #!22.7 models
> show #!22.8 models
> show #!22.9 models
> show (#22.2-9#34.3#!22,34 & sidechain) target ab
> ui tool show "Side View"
> turn x 90
[Repeated 3 time(s)]
> view
> turn x -90
> turn x 90
> show #!17 models
> hide #!17 models
> show #!18 models
> hide #!18 models
> show #!26 models
> hide #!26 models
> show #!26 models
> hide #!26 models
> show #!26 models
> hide #!26 models
> lighting soft
> lighting simple
> lighting soft
> lighting simple
> lighting soft
> view
> turn x 90
[Repeated 3 time(s)]
> turn x -90
> turn x 90
> turn x -90
> turn x 90
> turn x -90
> turn x 90
> turn x -90
> turn x 90
> turn x -90
[Repeated 1 time(s)]
> turn x 90
[Repeated 1 time(s)]
> turn x -90
> hide #!34.3 models
> hide #!34 models
> hide #!22 models
> show #!22 models
> show #!1 models
> show #!2 models
> hide #!22 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!1 models
> show #!32 models
> hide #32/b cartoons
> hide #32/c cartoons
> show #32/a cartoons
> hide #!32 models
> show #!32 models
> hide #!32 models
> show #!32 models
> hide #!32 models
> show #!32 models
> hide #!32 models
> show #!32 models
> hide #!32 models
> show #!22 models
> hide #!22 models
> show #!22 models
> hide #!22 models
> show #!22 models
> hide #!22 models
> hide #!2 models
> show #!32 models
> show #!1 models
> hide #!32 models
> show #!32 models
> hide #!1 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!32 models
> show #!32 models
> hide #!32 models
> show #!32 models
> hide #!32 models
> show #!32 models
> hide #!32 models
> show #!32 models
> hide #!32 models
> show #!32 models
> hide #!32 models
> show #!32 models
> hide #!2 models
> show #!1 models
> hide #!32 models
> show #!2 models
> hide #!2 models
> show #!32 models
> hide #!32 models
> show #!32 models
> hide #!32 models
> show #!32 models
> hide #!32 models
> show #!32 models
> hide #!32 models
> show #!32 models
> hide #!32 models
> show #!32 models
> hide #!32 models
> show #!32 models
> hide #!32 models
> show #!32 models
> select ~sel & ##selected
Nothing selected
> show #32/a cartoons
> hide #1/a cartoons
> show #1/a cartoons
> hide #32/a cartoons
> show #32/a cartoons
> hide #1/a cartoons
> show #1/a cartoons
> hide #32/a cartoons
> show #32/a cartoons
> hide #1/a cartoons
> show #1/a cartoons
> hide #32/a cartoons
> show #32/a cartoons
> hide #1/a cartoons
> show #1/a cartoons
> hide #32/a cartoons
> show #32/a cartoons
> hide #1/a cartoons
> show #1/a cartoons
> hide #32/a cartoons
> show #32/a cartoons
> hide #1/a cartoons
> show #1/a cartoons
> hide #32/a cartoons
> show #32/a cartoons
> hide #1/a cartoons
> show #1/a cartoons
> hide #32/a cartoons
> show #32/a cartoons
> hide #1/a cartoons
> show #1/a cartoons
> hide #32/a cartoons
> show #32/a cartoons
> hide #1/a cartoons
> show #1/a cartoons
> hide #32/a cartoons
> show #32/a cartoons
> hide #1/a cartoons
> show #1/a cartoons
> hide #32/a cartoons
> show #32/a cartoons
> hide #1/a cartoons
> show #1/a cartoons
> hide #32/a cartoons
> show #32/a cartoons
> hide #1/a cartoons
> show #1/a cartoons
> hide #32/a cartoons
> show #32/a cartoons
> hide #1/a cartoons
> show #1/a cartoons
> hide #32/a cartoons
> show #32/a cartoons
> hide #1/a cartoons
> show #1/a cartoons
> hide #32/a cartoons
> show #32/a cartoons
> hide #!1 models
> show #!33 models
> hide #!33 models
> hide #!32 models
> show #!25 models
> view
> surface dust siz 10
Missing or invalid "surfaces" argument: invalid surfaces specifier
> surface dust #25 size 10
> volume level 0.05
> volume level 0.06
> hide #!25 models
> show #!24 models
> hide #!24 models
> show #!26 models
> lighting simple
> lighting soft
> lighting simple
> lighting soft
> graphics silhouettes true
> graphics silhouettes false
> transparency 0
> hide #!26 models
> show #!22 models
> volume #22 show
> hide #!22.2 models
> show #!22.2 models
> hide #!22.3 models
> show #!22.3 models
> hide #!22.4 models
> show #!22.4 models
> hide #!22.5 models
> show #!22.5 models
> hide #!22.6 models
> show #!22.6 models
> hide #!22.7 models
> show #!22.7 models
> hide #!22.8 models
> show #!22.8 models
> hide #!22.9 models
> show #!22.9 models
> hide #!22.2 models
> show #!22.2 models
> hide #!22.2 models
> show #!22.2 models
> hide #!22.2 models
> show #!22.2 models
> lighting soft
> lighting simple
> lighting soft
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> transparency 0
> volume level 0.05
> hide #!22.1 models
> transparency 90
> transparency 10
> transparency 1
> transparency 0
> lighting simple
> lighting shadows true
> lighting shadows false
> graphics silhouettes true
> graphics silhouettes false
> lighting full
> lighting simple
> hide #!22.2 models
> hide #!22.3 models
> hide #!22.4 models
> hide #!22.5 models
> hide #!22.6 models
> hide #!22.10 models
> show #!22.10 models
> hide #!22.10 models
> show #!32 models
> hide #32 cartoons
> show #32/j,k,l
> hide #32/k:1-3
> transparency 90
> lighting flat
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> volume #22 level 0.03
> volume #22 level 0.02
> volume #22 level 0.01
> volume #22 level 0.005
> volume #22 level 0.001
> volume #22 level 0.0001
> volume #22 level 0.02
> hide #32
> hide #!22.9 models
> hide #!22.8 models
> hide #!22.7 models
> show #!22.6 models
> hide #!22.6 models
> show #!22.5 models
> show #!22.4 models
> show #32/a
> hide #32
> hide #!22.5 models
> hide #!22.4 models
> show #!22.3 models
> show #32/b
> hide #!22.3 models
> show #!22.2 models
> hide #32
> show #32/c
> color #32/c salmon
> show #32/c-h
> hide #32
> hide #!22.2 models
> show #!22.6 models
> hide #!22.6 models
> show #!22.6 models
> show #32/i
> hide #!22.6 models
> show #!22.6 models
> show #32/d,b
> show #32/j:41-60
> show #32/j:41-65
> hide #32
> hide #!22.6 models
> show #!22.2 models
> show #!22.3 models
> show #!22.4 models
> show #!22.5 models
> show #!22.6 models
> show #!22.7 models
> show #!22.8 models
> show #!22.9 models
> show #!22.10 models
> hide #!22.10 models
> hide #!22 models
> hide #!32 models
> show #!32 models
> show #32 cartoons
> hide #32/k:1-3 cartoons
> show #32/a:304
> show #32/a:305
> show #32/m,o
> graphics silhouettes false
> graphics silhouettes true
> select ~sel & ##selected
Nothing selected
> show #32/a:328,319
> show #32/a:328,319,280
> show #32/k
> select #32/A:281
9 atoms, 8 bonds, 1 residue, 1 model selected
> select clear
> show #!11 models
> show #32/a:83-85
> show #32/l
> color #32/k:40 #32/l:6 hot pink
> color #32/k:40 #32/l:7 hot pink
> color #32/l:7 orange
> color #32/l:6 orange
> color #32/l:7 hot pink
> hide #32 & nucleic cartoons
> show #32/j
> show #!22 models
> show #!22.10 models
> hide #!22 models
> hide #!32 models
> show #!8 models
> show #!8.4 models
> show #!8.5 models
> show #!8.6 models
> show #!8.7 models
> show #!8.8 models
> show #!8.9 models
> hide #!8.9 models
> show #!8.9 models
> show #!1 models
> show #1 cartoons
> hide #!8 models
> select #1/I:140
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel
> show #1/a:295
> show #!8 models
> show #1/a:319,304,305,328,280
> color #1/a:319,304,305,328,280 byhetero
> show #!2 models
> hide #!1 models
> hide #!8 models
> show #!7 models
> color #2/a:319,304,305,328,280 byhetero
> show #2/a:319,304,305,328,280
> show #2/a:295
> volume #7 level 0.02
> show #!7.4 models
> show #!7.5 models
> show #!7.6 models
> show #!7.7 models
> show #!7.8 models
> show #!7.9 models
> show #!7.1 models
> hide #!7.1 models
> volume #7 level 0.01
> volume #7 level 0.02
> hide #!7 models
> show #!9 models
> volume #9 level 0.02
> volume #9 level 0.01
> volume #9 level 0.002
> show #2 cartoons
> surface dust siz 5
Missing or invalid "surfaces" argument: invalid surfaces specifier
> surface dust #9 size 5
> hide #!2 models
> show #!2 models
> hide #!9 models
Drag select of 3 atoms, 57 residues, 2 bonds
> show sel
> hide #!2 models
> show #!1 models
Drag select of 2 atoms, 16 residues
> show sel
> hide #!1 models
> show #!12 models
> hide #!12 models
> show #!2 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!9 models
> hide #!9 models
> show #!7 models
> hide #!7 models
> show #!7 models
> show #2/i
> color #2/i,a byhetero
> hide #!2 models
> show #!1 models
> show #!10 models
> hide #!10 models
> show #!8 models
> hide #!7 models
> hide sel
> select clear
> show #1-2/j
> hide #1-2 & nucleic cartoons
> select clear
> show #!2 models
> hide #!1 models
> show #!7 models
> hide #!8 models
> hide #1-2
> show #1-2 cartoons
> show #!1 models
> show #!3 models
> hide #!7 models
> show #!8 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> hide #!2 models
> hide #!8 models
> hide #!1 models
> show #!19 models
> hide #!19 models
> show #!10 models
> hide #!10 models
> show #!32 models
> select #32/A:193
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #32/A:192
14 atoms, 12 bonds, 2 residues, 1 model selected
> show sel
> select clear
> hide #32/k 1-33
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide #32/k:1-33
> select #32/K:34@P
1 atom, 1 residue, 1 model selected
> select add #32/K:34@OP1
2 atoms, 1 residue, 1 model selected
> select add #32/K:34@OP2
3 atoms, 1 residue, 1 model selected
> select add #32/K:34@O5'
4 atoms, 1 residue, 1 model selected
> select add #32/K:34@C5'
5 atoms, 1 residue, 1 model selected
> hide sel
> select #32/a:220-243
196 atoms, 197 bonds, 24 residues, 1 model selected
> show #32/k
> select clear
> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/chimerax_session.cxs"
——— End of log from Mon May 12 14:04:47 2025 ———
opened ChimeraX session
> hide #!11 models
> hide #!32 models
> show #!16 models
> hide #16 cartoons
> show #16/j
> show #!29 models
> hide #!29 models
> show #!29 models
> show #!28 models
> hide #!28 models
> show #!19 models
> hide #!19 models
> show #!19 models
> hide #!19 models
> show #!19 models
> hide #!19 models
> show #!19 models
> hide #!19 models
> select #29.2
2 models selected
> hide #!29.2 models
> show #!29.2 models
> hide #!29.2 models
> show #!29.6 models
> volume #29 level 0.02
> hide #!29.6 models
> show #!27 models
> hide #!27 models
> show #!26 models
> hide #!26 models
> show #!19 models
> hide #!16 models
> hide #!19 models
> show #!29.6 models
> show #!16 models
> show #!15 models
> hide #!15 models
> show #!14 models
> show #!15 models
> hide #!15 models
> hide #!14 models
> combine #16
> hide #!16 models
> hide #!35 models
> show #!35 models
> fitmap #35/j inMap #29.6
Fit molecule copy of apo_HNH_outwards_refined.pdb (#35) to map
apo_HNH_out_sharp.mrc 5 (#29.6) using 1288 atoms
average map value = 0.3487, steps = 184
shifted from previous position = 2.25
rotated from previous position = 3.92 degrees
atoms outside contour = 340, contour level = 0.02
Position of copy of apo_HNH_outwards_refined.pdb (#35) relative to
apo_HNH_out_sharp.mrc 5 (#29.6) coordinates:
Matrix rotation and translation
-0.94445333 -0.26862857 0.18933201 314.24147225
0.22085794 -0.94540525 -0.23964699 296.35999000
0.24337151 -0.18451992 0.95221989 -10.86743333
Axis 0.11124727 -0.10905253 0.98779127
Axis point 138.91057616 167.65489171 0.00000000
Rotation angle (degrees) 165.65451579
Shift along axis -8.09505614
> volume #29 level 0.002
> volume #29 level 0.0002
> volume #29 level 0.002
> hide #!35 models
> hide #!29 models
> show #!30 models
> hide #!30.2 models
> show #!30.8 models
> show #!30.7 models
> show #!30.6 models
> hide #!30.6 models
> show #!30.5 models
> show #!1 models
> show #!3 models
> hide #!3 models
> hide #1 cartoons
> show #1/j-l
> hide #!1 models
> show #!20 models
> hide #20 cartoons
> show #20/j-l
> fitmap #20/j inMap #30.8
Fit molecule postcleavage_HNH_center_refined.pdb (#20) to map
post_HNH_cent_sharp.mrc 7 (#30.8) using 1288 atoms
average map value = 0.3259, steps = 228
shifted from previous position = 2.32
rotated from previous position = 3 degrees
atoms outside contour = 457, contour level = 0.05
Position of postcleavage_HNH_center_refined.pdb (#20) relative to
post_HNH_cent_sharp.mrc 7 (#30.8) coordinates:
Matrix rotation and translation
0.99292341 0.11846591 0.00830222 -17.69757193
-0.11532901 0.97858172 -0.17051988 44.51738269
-0.02832520 0.16835570 0.98531926 -26.31185417
Axis 0.81987504 0.08861632 -0.56564306
Axis point 0.00000000 162.56775146 238.40498938
Rotation angle (degrees) 11.92686357
Shift along axis 4.31828685
> volume #30 level 0.002
> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/figures/structure/subunits_with_map/nucleotides_post.tif"
> width 1984 height 1210 supersample 3
> hide #!30 models
> hide #!20 models
> show #!35 models
> show #!19 models
> hide #!19 models
> show #!29 models
> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/figures/structure/subunits_with_map/nucleotides_apo.tif"
> width 1984 height 1210 supersample 3
> hide #!29 models
> hide #!35 models
> show #!30 models
> show #!20 models
> select #20/l:1
17 atoms, 19 bonds, 1 residue, 1 model selected
> select clear
> hide #!30 models
> show #20 cartoons
> cartoon style nucleic xsection oval width 1 thickness 1
> color #20/L dark orange
> color #20/K dim gray
> color #20/J dark red
> color #20/I rebecca purple
> color #20/B forest green
> color #20/C,D,E,F,G,H salmon
> color #20/A steel blue
> color #20/A:232-350 dark turquoise
> color #20/O blue
> color #20/M red
> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/figures/structure/post_full_cartoon.tif" width 1984
> height 1210 supersample 3
> hide #!20 models
> show #!16 models
> show #16 cartoons
> color #16/L dark orange
> color #16/K dim gray
> color #16/J dark red
> color #16/I rebecca purple
> color #16/B forest green
> color #16/C,D,E,F,G,H salmon
> color #16/A steel blue
> color #16/A:232-350 dark turquoise
> color #16/O blue
> color #16/M red
> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/figures/structure/apo_full_cartoon.tif" width 1984 height
> 1210 supersample 3
> hide #!16 models
> show #!32 models
> 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
> show #32/m,o
> show #32 cartoons
> save "/Users/zxc755/OneDrive - University of Copenhagen/Type
> I-F_HNH/Manuscript/figures/structure/half_full_cartoon.tif" width 1984
> height 1210 supersample 3
> hide #!32 models
> show #!13 models
> hide #!13 models
> show #!13 models
> lighting simple
> graphics silhouettes false
> ui tool show "Surface Color"
> color sample #13.1 map #13 palette #ff0000:#ffffff:#0000ff
Map values for surface "surface": minimum 0.04997, mean 0.05, maximum 0.05003
> 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 #36, grid size
420,420,420, pixel 0.725, shown at level 0.0319, step 2, values float32
> hide #!13 models
> hide #!36 models
> open "/Users/zxc755/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/Type
> I-F_HNH/Manuscript/maps_models/fsc_and_halfmaps/halfcleaved_HNH_center/J635_005_volume_map_half_A.mrc"
Opened J635_005_volume_map_half_A.mrc as #37, grid size 420,420,420, pixel
0.725, shown at level 0.138, step 2, values float32
> color sample #13.1 map #37 palette
> 0.04997,#ff0000:0.05,#ffffff:0.05003,#0000ff
Map values for surface "surface": minimum -0.3311, mean 0.05689, maximum
0.4275
> show #!13 models
> hide #!37 models
> key red-white-blue :0.05 :0.05 :0.05 showTool true
> ui mousemode right "color key"
> color sample #13.1 map #37 palette 2,#ff0000:2.5,#ffffff:3,#0000ff
Map values for surface "surface": minimum -0.3311, mean 0.05689, maximum
0.4275
> color sample #13.1 map #37 palette 2.1,#ff0000:2.3,#ffffff:2.8,#0000ff
Map values for surface "surface": minimum -0.3311, mean 0.05689, maximum
0.4275
> show #!37 models
> hide #!37 models
> show #!37 models
> hide #!37 models
> hide #38 models
> show #38 models
> hide #!13 models
> show #!36 models
> color sample #36.1 map #37 palette 2.1,#ff0000:2.3,#ffffff:2.8,#0000ff
Map values for surface "surface": minimum -0.3316, mean 0.02939, maximum
0.3335
> key red-white-blue :2.1 :2.3 :2.8 showTool true
> key red-white-blue :2.1 :2.5 :3.0 showTool true
[Repeated 1 time(s)]
> color sample #36.1 map #37 palette 2.1,#ff0000:2.5,#ffffff:3,#0000ff
Map values for surface "surface": minimum -0.3316, mean 0.02939, maximum
0.3335
> color single #36.1
> color sample #36.1 map #37 palette 2.1,#ff0000:2.5,#ffffff:3,#0000ff
Map values for surface "surface": minimum -0.3316, mean 0.02939, maximum
0.3335
> color single #36.1
> color sample #36.1 map #37 palette 2.5,#ff0000:3,#ffffff:3.5,#0000ff
Map values for surface "surface": minimum -0.3316, mean 0.02939, maximum
0.3335
> color sample #36.1 map #37 palette 3,#ff0000:3,#ffffff:3.5,#0000ff
Map values for surface "surface": minimum -0.3316, mean 0.02939, maximum
0.3335
> color sample #36.1 map #37 palette 3,#ff0000:3.5,#ffffff:3.5,#0000ff
Map values for surface "surface": minimum -0.3316, mean 0.02939, maximum
0.3335
> color sample #36.1 map #37 palette 3,#ff0000:3.5,#ffffff:4,#0000ff
Map values for surface "surface": minimum -0.3316, mean 0.02939, maximum
0.3335
> key red-white-blue :3.0 :3.5 :4.0 showTool true
> color sample #36.1 map #37 palette 3,#ff0000:3.5,#ffffff:4,#0000ff
Map values for surface "surface": minimum -0.3316, mean 0.02939, maximum
0.3335
> color sample #36.1 map #37 palette 3,#ff0000:3.5,#ffffff:4,#0000ff
Map values for surface "surface": minimum -0.3316, mean 0.02939, maximum
0.3335
> color sample #36.1 map #37 palette 2,#ff0000:3.5,#ffffff:4,#0000ff
Map values for surface "surface": minimum -0.3316, mean 0.02939, maximum
0.3335
> color single #36.1
> key red-white-blue :2.0 :3.5 :4.0 showTool true
> color sample #36.1 map #37 palette 2,#0433ff:2.5,#ffffff:3,#ff2600
Map values for surface "surface": minimum -0.3316, mean 0.02939, maximum
0.3335
> hide #38 models
> hide #!36 models
> ui mousemode right translate
Unsupported scale factor (0.000000) detected on Display0
[Repeated 9 time(s)]
> show #!32 models
> show #!22 models
> color #32/a byhetero
> hide #!32 models
> show #!13 models
> show #!32 models
> hide #!22 models
> hide #!13 models
> volume zone #13 nearAtoms #32/a:304,305,328,319,280 #32/k:2-3 #32/o range 2
> newMap true
Opened halfcleaved_HNH_center_sharp3Å.mrc zone as #39, grid size 420,420,420,
pixel 0.725, shown at step 1, values float32
Unknown or unsupported skia image format
> transparency #39 90
> close #39
> volume zone #13 nearAtoms #32/a:304,305,328,319,280 #32/k:2-3 #32/o range
> 1.5 newMap true
Opened halfcleaved_HNH_center_sharp3Å.mrc zone as #39, grid size 420,420,420,
pixel 0.725, shown at step 1, values float32
> transparency #39 90
> hide #32/k cartoons
> volume zone #13 nearAtoms #32/o range 2 newMap true
Opened halfcleaved_HNH_center_sharp3Å.mrc zone as #40, grid size 420,420,420,
pixel 0.725, shown at step 1, values float32
> volume #40 level 0.02
> close #40
> volume zone #13 nearAtoms #32/o range 0.5 newMap true
Opened halfcleaved_HNH_center_sharp3Å.mrc zone as #40, grid size 420,420,420,
pixel 0.725, shown at step 1, values float32
> volume #40 level 0.02
> close #40
> volume zone #13 nearAtoms #32/o range 1 newMap true
Opened halfcleaved_HNH_center_sharp3Å.mrc zone as #40, grid size 420,420,420,
pixel 0.725, shown at step 1, values float32
> volume #40 level 0.02
> transparency #40 90
> color #40 blue
> color #39 turquoise
> lighting flat
> graphics silhouettes false
> graphics silhouettes true
> color #32/k:3 byhetero
> hide #!39 models
> show #!39 models
> hide #!39 models
> show #!39 models
> hide #!39 models
> show #!39 models
> hide #!39 models
> show #!39 models
> hide #!39 models
> show #!39 models
> close #39
> hide #!40 models
> show #!40 models
> select #32/A:280@CG
1 atom, 1 residue, 1 model selected
> select add #32/A:305@ND1
2 atoms, 2 residues, 1 model selected
> select add #32/A:319@CG
3 atoms, 3 residues, 1 model selected
> select add #32/A:304@ND1
4 atoms, 4 residues, 1 model selected
> select add #32/M:2@MG
5 atoms, 1 bond, 5 residues, 1 model selected
> select add #32/K:2@O5'
6 atoms, 1 bond, 6 residues, 1 model selected
> select add #32/K:3@P
7 atoms, 1 bond, 7 residues, 1 model selected
> select up
9 atoms, 1 bond, 8 residues, 1 model selected
> select up
62 atoms, 60 bonds, 8 residues, 1 model selected
> volume zone nea sel range 1.5 newmap tru
Missing or invalid "volumes" argument: invalid density maps specifier
> volume zone #13 nearAtoms sel range 1.5 newMap true
Opened halfcleaved_HNH_center_sharp3Å.mrc zone as #39, grid size 420,420,420,
pixel 0.725, shown at step 1, values float32
> select clear
> transparency #39 90
> volume #39 level 0.03
> volume #39 level 0.02
> volume #39 level 0.002
> surface dust #40 size 7.25
> surface dust #39 size 7.25
> surface dust siz 0
Missing or invalid "surfaces" argument: invalid surfaces specifier
> surface dust #39-40 size 0
> volume #39 level 0.09
> show #!11 models
> volume #39 level 0.04054
> hide #!39 models
> hide #!40 models
> select #32/A:280,304,305,319,328
49 atoms, 48 bonds, 5 residues, 1 model selected
> select #32/A:280,304,305,319,328 #32/k:1-3
61 atoms, 60 bonds, 2 pseudobonds, 7 residues, 2 models selected
> volume zone #13 nearAtoms sel range 1.5 newMap true
Opened halfcleaved_HNH_center_sharp3Å.mrc zone as #41, grid size 420,420,420,
pixel 0.725, shown at step 1, values float32
> close #41
> show #!39 models
> show #!40 models
> volume #39 level 0.04
> volume #39 level 0.05
> volume #49 level .03
No volumes specified
> volume #39 level .03
> volume #39 level .04
> volume #40 level .04
> volume #40 level .03
> volume #40 level .025
> volume #40 level .021
> volume #40 level .02
> volume #40 level .01
> volume #40 level .02
> select clear
> 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
> save "/Users/zxc755/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/Type
> I-F_HNH/Manuscript/figures/structure/HNH/cat_pocket_with_nucleotide.tif"
> width 1938 height 1210 supersample 3
> save cat_pocket_with_nucleotide_test.tif supersample 3
> save "/Users/zxc755/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/Type
> I-F_HNH/Manuscript/figures/structure/HNH/HNH_cat_session.cxs" includeMaps
> true
> close #1-10,12,14-31,33-38
> save HNH_cat_session.cxs includeMaps true
——— End of log from Wed May 14 12:43:12 2025 ———
opened ChimeraX session
> hide #!39 models
> select add /M:2@MG
1 atom, 1 residue, 1 model selected
> select add /A:304@ND1
2 atoms, 2 residues, 1 model selected
> select add /A:304@CE1
3 atoms, 2 residues, 1 model selected
> select add /A:304@NE2
4 atoms, 2 residues, 1 model selected
> select add /A:304@CD2
5 atoms, 2 residues, 1 model selected
> select add /A:304@CG
6 atoms, 2 residues, 1 model selected
> select add /A:304@CB
7 atoms, 2 residues, 1 model selected
> select add /A:328@CD2
8 atoms, 3 residues, 1 model selected
> select add /A:328@NE2
9 atoms, 3 residues, 1 model selected
> select add /A:328@CE1
10 atoms, 3 residues, 1 model selected
> select add /A:328@ND1
11 atoms, 3 residues, 1 model selected
> select add /A:328@CG
12 atoms, 3 residues, 1 model selected
> select add /A:328@CB
13 atoms, 3 residues, 1 model selected
> select add /A:319@ND2
14 atoms, 4 residues, 1 model selected
> select add /A:319@OD1
15 atoms, 4 residues, 1 model selected
> select add /A:319@CB
16 atoms, 4 residues, 1 model selected
> select add /A:305@CB
17 atoms, 5 residues, 1 model selected
> select add /A:305@CG
18 atoms, 5 residues, 1 model selected
> select add /A:305@CD2
19 atoms, 5 residues, 1 model selected
> select add /A:305@NE2
20 atoms, 5 residues, 1 model selected
> select add /A:305@CE1
21 atoms, 5 residues, 1 model selected
> select add /A:305@ND1
22 atoms, 5 residues, 1 model selected
> select add /K:3@OP2
23 atoms, 6 residues, 1 model selected
> select add /K:3@P
24 atoms, 6 residues, 1 model selected
> select add /K:3@O5'
25 atoms, 6 residues, 1 model selected
> select add /K:3@OP1
26 atoms, 6 residues, 1 model selected
> select subtract /K:3@P
25 atoms, 6 residues, 1 model selected
> select add /K:3@P
26 atoms, 6 residues, 1 model selected
> select add /K:2@O3'
27 atoms, 7 residues, 1 model selected
> select add /K:2@C3'
28 atoms, 7 residues, 1 model selected
> select add /K:2@C4'
29 atoms, 7 residues, 1 model selected
> select add /K:2@C5'
30 atoms, 7 residues, 1 model selected
> select add /K:2@O5'
31 atoms, 7 residues, 1 model selected
> select add /K:2@O4'
32 atoms, 7 residues, 1 model selected
> select add /K:2@C2'
33 atoms, 7 residues, 1 model selected
> select add /K:2@C1'
34 atoms, 7 residues, 1 model selected
> select add /A:280@NH2
35 atoms, 8 residues, 1 model selected
> select add /A:280@NH1
36 atoms, 8 residues, 1 model selected
> select add /A:280@CZ
37 atoms, 8 residues, 1 model selected
> select add /A:280@NE
38 atoms, 8 residues, 1 model selected
> select add /A:280@CD
39 atoms, 8 residues, 1 model selected
> volume zone #13 nearAtoms sel range 1.5 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 add /A:280@CG
40 atoms, 8 residues, 1 model selected
> select add /A:280@CB
41 atoms, 8 residues, 1 model selected
> close #1
> volume zone #13 nearAtoms sel range 1.5 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 clear
> volume #1 level 0.02
> show (#1,40#!11,32 & sidechain) target ab
> ui tool show "Side View"
> hide #32
> show #32/a:280,304,305,319
> show #32/a:280,304,305,319,328 #32/o,m
> show #32/a:280,304,305,319,328 #32/o,m #32/k:1-3
> hide #32 cartoons
> show #32/a cartoons
> cd /Users/zxc755/Library/CloudStorage/OneDrive-UniversityofCopenhagen/Type
> I-F_HNH/Manuscript/figures/structure/HNH
Expected name of a folder to open/read; a name of 'browse' will bring up a
file browser or a keyword
> cd /Users/zxc755/Library/CloudStorage/OneDrive-UniversityofCopenhagen/Type
> I-F_HNH/Manuscript/figures/structure/HNH/
Expected name of a folder to open/read; a name of 'browse' will bring up a
file browser or a keyword
> cd "/Users/zxc755/OneDrive - University of Copenhagen/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
> 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
> save cat_pocket_with_nucleotide_2.tif supersample 3
> 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 #2
---
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 #3, grid size 420,420,420, pixel
0.725, shown at level 0.0029, step 2, values float32
> hide #!1 models
> hide #!2 models
> hide #!3 models
> hide #!32 models
> hide #!40 models
> show #!3 models
> show #!2 models
> style stick
Changed 48201 atom styles
> hide #2
> show #2 cartoons
Computing secondary structure
> transparency #3 90
> color #2/L dark orange
> color #2/K dim gray
> color #2/J dark red
> color #2/I rebecca purple
> color #2/B forest green
> color #2/C,D,E,F,G,H salmon
> color #2/A steel blue
> color #2/A:232-350 dark turquoise
> color #2/O blue
> color #2/M red
> show #2/a:319,280,304,305
> color #2/a byhetero
> volume #3 level 0.005
> volume #3 level 0.05
> volume #3 level 0.09
> show #2/a:328
> hide #2 cartoons
> show #2/a cartoons
> hide #!3 models
> hide #!2 models
> show #!32 models
> select #32/A:332
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel
> select #32/A:333
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel
> show #!13 models
> volume #13 level 0.02
> hide #!11 models
> hide #!13 models
> hide #!32 models
> 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 #!5 models
> style stick
Changed 71932 atom styles
> hide #4
> show #4/a cartoons
Computing secondary structure
> show #4/m
> color #4/L dark orange
> color #4/K dim gray
> color #4/J dark red
> color #4/I rebecca purple
> color #4/B forest green
> color #4/C,D,E,F,G,H salmon
> color #4/A steel blue
> color #4/A:232-350 dark turquoise
> color #4/O blue
> color #4/M red
> color #4/a byhetero
> show #4/a:280,319,304,305
> show #4/a:280,319,304,305,328
> select #4/a280,319,304,305,328 #4/m
1 atom, 1 residue, 1 model selected
> select #4/a:280,319,304,305,328 #4/m
50 atoms, 48 bonds, 6 residues, 1 model selected
> volume zone #5 nearAtoms sel range 1.5 newMap true
Opened post_HNH_cent_sharp.mrc zone as #6, grid size 420,420,420, pixel 0.725,
shown at step 1, values float32
> transparency #6 90
> volume #6 level 0.02
> hide #!6 models
> show #!5 models
> hide #!5 models
> show #!6 models
> volume #6 level 0.09
> 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
> hide #!6 models
> transparency #7 90
> hide #!7 models
> show #!6 models
> volume #6 level 0.12
> volume #6 level 0.1
> volume #6 level 0.08
> volume #6 level 0.06
> select clear
> show #!32 models
> hide #!32 models
> combine #4
> hide #!4 models
> hide #!6 models
> show #!32 models
> mmaker #8/a:220-350 to #32/a:220-350
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 (#8), sequence
alignment score = 600
RMSD between 122 pruned atom pairs is 0.599 angstroms; (across all 123 pairs:
0.646)
> color #8/a salmon
> hide #!32 models
> hide #!8 models
> show #!6 models
> show #!4 models
> show #!5 models
> hide #!5 models
> hide #!6 models
> select add #4/A:328@NE2
1 atom, 1 residue, 1 model selected
> select add #4/A:304@ND1
2 atoms, 2 residues, 1 model selected
> select add #4/A:280@CZ
3 atoms, 3 residues, 1 model selected
> select add #4/A:305@CE1
4 atoms, 4 residues, 1 model selected
> select add #4/A:319@CG
5 atoms, 5 residues, 1 model selected
> select add #4/A:332
12 atoms, 6 bonds, 6 residues, 1 model selected
> select up
56 atoms, 54 bonds, 6 residues, 1 model selected
> volume zone #5 nearAtoms sel range 1.5 newMap true
Opened post_HNH_cent_sharp.mrc zone as #9, grid size 420,420,420, pixel 0.725,
shown at step 1, values float32
> close #9
> select add #4/M:1@MG
57 atoms, 54 bonds, 7 residues, 1 model selected
> select up
407 atoms, 415 bonds, 50 residues, 1 model selected
> select down
57 atoms, 54 bonds, 7 residues, 1 model selected
> volume zone #5 nearAtoms sel range 1.5 newMap true
Opened post_HNH_cent_sharp.mrc zone as #9, grid size 420,420,420, pixel 0.725,
shown at step 1, values float32
> transparency #9 90
> volume #9 level 0.06
> select clear
> hide #!9 models
> select #4/A:332
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel
> select clear
> show #!9 models
> 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
> color #9 #ffcc99ff models
> color #9 #ffd479ff models
> color #9 white
> transparency #9 90
> ui tool show "Color Actions"
> color #9 lavender
> color #9 violet
> color #9 navy
> color #9 navajowhite
> color #9 blanchedalmond
> save cat_pocket_empty.tif supersample 3
> hide #!9 models
> show #!8 models
> hide #!4 models
> show #!32 models
> color #8 salmon
> select #32/K:2@C3'
1 atom, 1 residue, 1 model selected
> select add #32/K:2@C4'
2 atoms, 1 residue, 1 model selected
> select #32/K:2@C4'
1 atom, 1 residue, 1 model selected
> select add #32/K:2@C3'
2 atoms, 1 residue, 1 model selected
> select add #32/K:2@C5'
3 atoms, 1 residue, 1 model selected
> select add #32/K:2@O5'
4 atoms, 1 residue, 1 model selected
> select add #32/K:2@O4'
5 atoms, 1 residue, 1 model selected
> select add #32/K:2@C1'
6 atoms, 1 residue, 1 model selected
> select add #32/K:2@C2'
7 atoms, 1 residue, 1 model selected
> hide sel
> select #32/K:2@O3'
1 atom, 1 residue, 1 model selected
> color sel byhetero
> select clear
> select #32/O:1@O
1 atom, 1 residue, 1 model selected
> hide sel
> hide #!8 models
> show #!8 models
> select #8/A:332
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel
> select clear
> select add #8/A:332@CG2
1 atom, 1 residue, 1 model selected
> select up
3 atoms, 1 bond, 2 residues, 2 models selected
> select up
14 atoms, 12 bonds, 2 residues, 2 models selected
> hide sel
> select clear
> combine #8
> hide #!8 models
> mmaker #10/a to #32/a
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 copy of postcleavage_HNH_center_refined.pdb, chain A (#10),
sequence alignment score = 1678.6
RMSD between 328 pruned atom pairs is 0.795 angstroms; (across all 340 pairs:
0.913)
> mmaker #10/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 copy of postcleavage_HNH_center_refined.pdb, chain A (#10),
sequence alignment score = 542.1
RMSD between 110 pruned atom pairs is 0.556 angstroms; (across all 111 pairs:
0.605)
> save cat_half_post_superimpose.tif supersample 3
> hide #!10 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> close #10
> show #!4 models
> hide #!4 models
> hide #!32 models
> show #!4 models
> close #4
> 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 #10, grid size 420,420,420, pixel 0.725,
shown at level 0.00328, step 2, values float32
> color #4/L dark orange
> color #4/K dim gray
> color #4/J dark red
> color #4/I rebecca purple
> color #4/B forest green
> color #4/C,D,E,F,G,H salmon
> color #4/A steel blue
> color #4/A:232-350 dark turquoise
> color #4/O blue
> color #4/M red
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!10 models
> hide #!4 models
> show #!4 models
> style stick
Changed 95663 atom styles
> hide #4
> show #4/a cartoons
Computing secondary structure
> show #4/a:319,280,304,305 #4/m
> show #4/a:319,280,304,305,328 #4/m
> color #4/a byhetero
> combine #4
> hide #!4 models
> mmaker #12/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 (#12), sequence
alignment score = 542.1
RMSD between 110 pruned atom pairs is 0.556 angstroms; (across all 111 pairs:
0.605)
> color #12 salmon
> show #!32 models
> select #32/A:333@CG
1 atom, 1 residue, 1 model selected
> select up
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel
> save cat_half_post_superimpose_2.tif supersample 3
> hide #!32 models
> hide #!12 models
> show #!12 models
> show #!4 models
> hide #!12 models
> show #!8 models
> hide #!8 models
> show #!6 models
> hide #!6 models
> show #!7 models
> hide #!7 models
> show #!5 models
> hide #!5 models
> show #!6 models
> show #!9 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> ui tool show Distances
> show #!11 models
> select #4/A:304@ND1
1 atom, 1 residue, 1 model selected
> select add #4/M:1@MG
2 atoms, 2 residues, 1 model selected
> distance #4/A:304@ND1 #4/M:1@MG
Distance between postcleavage_HNH_center_refined.pdb #4/A HIS 304 ND1 and /M
MG 1 MG: 3.141Å
> distance style dashes 5
[Repeated 2 time(s)]
> distance style radius 0.09
[Repeated 2 time(s)]
> distance style radius 0.08
[Repeated 2 time(s)]
> distance style radius 0.07
[Repeated 2 time(s)]
> distance style radius 0.06
[Repeated 2 time(s)]
> distance style radius 0.05
[Repeated 2 time(s)]
> color #11 teal
> select clear
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!9 models
> save cat_pocket_empty_2.tif supersample 3
> graphics silhouettes false
> graphics silhouettes true
> lighting simple
> lighting soft
> lighting flat
> lighting shadows true intensity 0.5
> lighting full
> graphics silhouettes false
> lighting full
> lighting shadows false
> lighting shadows true
> lighting shadows false
> graphics silhouettes true
> graphics silhouettes false
> lighting flat
> graphics silhouettes false
> graphics silhouettes true
> hide #!4 models
> hide #!9 models
> show #!32 models
> show #32/a:232
> show #!10 models
> hide #!10 models
> show #11.1 models
> hide #11.1 models
> hide #!32 models
> show #!32 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!8 models
> combine #32
> hide #!32 models
> hide #!14 models
> show #!14 models
> morph#8 #14
Unknown command: morph#8 #14
> morph #8 #14
Computed 51 frame morph #15
> coordset #15 1,51
> show #!32 models
> hide #!32 models
> close #15
> show #!12 models
> hide #!12 models
> show #!14 models
> hide #!14 models
> show #!14 models
> close #14
> open "/Users/zxc755/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/Type
> I-F_HNH/Manuscript/maps_models/postcleavage_HNH_center_with_TS_for_morph.pdb"
Summary of feedback from opening /Users/zxc755/Library/CloudStorage/OneDrive-
UniversityofCopenhagen/Type
I-F_HNH/Manuscript/maps_models/postcleavage_HNH_center_with_TS_for_morph.pdb
---
warning | Ignored bad PDB record found on line 59
SSBOND 1 CYS Aa 295 CYS Ca 140
Chain information for postcleavage_HNH_center_with_TS_for_morph.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
K | No description available
L | No description available
> color #14/L dark orange
> color #14/K dim gray
> color #14/J dark red
> color #14/I rebecca purple
> color #14/B forest green
> color #14/C,D,E,F,G,H salmon
> color #14/A steel blue
> color #14/A:232-350 dark turquoise
> color #14/O blue
> color #14/M red
> style stick
Changed 142917 atom styles
> hide #14
> show #14/a cartoons
Computing secondary structure
> show #14/k:1-3
> show #!32 models
> mmaker #14/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 postcleavage_HNH_center_with_TS_for_morph.pdb, chain A (#14), sequence
alignment score = 542.1
RMSD between 110 pruned atom pairs is 0.556 angstroms; (across all 111 pairs:
0.605)
> show #14/a:280,304,305,317,328
> show #14/a:280,304,305,319,328
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel
> select clear
> morph #14 #32
Computed 51 frame morph #15
> coordset #15 1,51
> show #15/k:1-3
> show #15/k
> open "/Users/zxc755/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/Type
> I-F_HNH/Manuscript/maps_models/halfcleaved_HNH_center_main_model_for_cat_morph.pdb"
Chain information for halfcleaved_HNH_center_main_model_for_cat_morph.pdb #16
---
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
k | No description available
> style stick
Changed 190521 atom styles
> hide #16
> close #15
> show #16/a cartoons
> hide #!16 models
> show #!16 models
> show #16/a
> view
> hide #!16 models
> show #!16 models
> show #!14 models
> hide #!14 models
> hide #!16 models
> show #!16 models
> close #16
> open "/Users/zxc755/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/Type
> I-F_HNH/Manuscript/maps_models/halfcleaved_HNH_center_main_model_for_cat_morph.pdb"
Chain information for halfcleaved_HNH_center_main_model_for_cat_morph.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
k | No description available
> style stick
Changed 167030 atom styles
> hide #16
> hide #15
> show #15/a cartoons
> hide #!15 models
> show #!15 models
> show #15
> show #15/A cartoons
Computing secondary structure
> hide #15
> show #15/Kk
> show #15
> select #15/k:2@C4'
1 atom, 1 residue, 1 model selected
> select up
8 atoms, 8 bonds, 1 residue, 1 model selected
> select up
12 atoms, 12 bonds, 2 residues, 1 model selected
> hide #15
> show sel
> select clear
> color #15/L dark orange
> color #15/K dim gray
> color #15/J dark red
> color #15/I rebecca purple
> color #15/B forest green
> color #15/C,D,E,F,G,H salmon
> color #15/A steel blue
> color #15/A:232-350 dark turquoise
> color #15/O blue
> color #15/M red
> show #!14 models
> hide #!14 models
> show #!14 models
> select #15/k:2@O5'
1 atom, 1 residue, 1 model selected
> select add #15/k:2@C5'
2 atoms, 1 residue, 1 model selected
> delete sel
> morph #14 #15
models have different number of chains, 12 (Morph -
postcleavage_HNH_center_with_TS_for_morph.pdb #/A,Morph -
postcleavage_HNH_center_with_TS_for_morph.pdb #/B,Morph -
postcleavage_HNH_center_with_TS_for_morph.pdb #/C,Morph -
postcleavage_HNH_center_with_TS_for_morph.pdb #/D,Morph -
postcleavage_HNH_center_with_TS_for_morph.pdb #/E,Morph -
postcleavage_HNH_center_with_TS_for_morph.pdb #/F,Morph -
postcleavage_HNH_center_with_TS_for_morph.pdb #/G,Morph -
postcleavage_HNH_center_with_TS_for_morph.pdb #/H,Morph -
postcleavage_HNH_center_with_TS_for_morph.pdb #/I,Morph -
postcleavage_HNH_center_with_TS_for_morph.pdb #/J,Morph -
postcleavage_HNH_center_with_TS_for_morph.pdb #/K,Morph -
postcleavage_HNH_center_with_TS_for_morph.pdb #/L) and 13
(halfcleaved_HNH_center_main_model_for_cat_morph.pdb
#15/A,halfcleaved_HNH_center_main_model_for_cat_morph.pdb
#15/B,halfcleaved_HNH_center_main_model_for_cat_morph.pdb
#15/C,halfcleaved_HNH_center_main_model_for_cat_morph.pdb
#15/D,halfcleaved_HNH_center_main_model_for_cat_morph.pdb
#15/E,halfcleaved_HNH_center_main_model_for_cat_morph.pdb
#15/F,halfcleaved_HNH_center_main_model_for_cat_morph.pdb
#15/G,halfcleaved_HNH_center_main_model_for_cat_morph.pdb
#15/H,halfcleaved_HNH_center_main_model_for_cat_morph.pdb
#15/I,halfcleaved_HNH_center_main_model_for_cat_morph.pdb
#15/J,halfcleaved_HNH_center_main_model_for_cat_morph.pdb
#15/K,halfcleaved_HNH_center_main_model_for_cat_morph.pdb
#15/L,halfcleaved_HNH_center_main_model_for_cat_morph.pdb #15/k)
> morph #14/A,Kk #15/A,Kk
models have different number of chains, 12 (Morph -
postcleavage_HNH_center_with_TS_for_morph.pdb #/A,Morph -
postcleavage_HNH_center_with_TS_for_morph.pdb #/B,Morph -
postcleavage_HNH_center_with_TS_for_morph.pdb #/C,Morph -
postcleavage_HNH_center_with_TS_for_morph.pdb #/D,Morph -
postcleavage_HNH_center_with_TS_for_morph.pdb #/E,Morph -
postcleavage_HNH_center_with_TS_for_morph.pdb #/F,Morph -
postcleavage_HNH_center_with_TS_for_morph.pdb #/G,Morph -
postcleavage_HNH_center_with_TS_for_morph.pdb #/H,Morph -
postcleavage_HNH_center_with_TS_for_morph.pdb #/I,Morph -
postcleavage_HNH_center_with_TS_for_morph.pdb #/J,Morph -
postcleavage_HNH_center_with_TS_for_morph.pdb #/K,Morph -
postcleavage_HNH_center_with_TS_for_morph.pdb #/L) and 13
(halfcleaved_HNH_center_main_model_for_cat_morph.pdb
#15/A,halfcleaved_HNH_center_main_model_for_cat_morph.pdb
#15/B,halfcleaved_HNH_center_main_model_for_cat_morph.pdb
#15/C,halfcleaved_HNH_center_main_model_for_cat_morph.pdb
#15/D,halfcleaved_HNH_center_main_model_for_cat_morph.pdb
#15/E,halfcleaved_HNH_center_main_model_for_cat_morph.pdb
#15/F,halfcleaved_HNH_center_main_model_for_cat_morph.pdb
#15/G,halfcleaved_HNH_center_main_model_for_cat_morph.pdb
#15/H,halfcleaved_HNH_center_main_model_for_cat_morph.pdb
#15/I,halfcleaved_HNH_center_main_model_for_cat_morph.pdb
#15/J,halfcleaved_HNH_center_main_model_for_cat_morph.pdb
#15/K,halfcleaved_HNH_center_main_model_for_cat_morph.pdb
#15/L,halfcleaved_HNH_center_main_model_for_cat_morph.pdb #15/k)
> close #14
> open "/Users/zxc755/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/Type
> I-F_HNH/Manuscript/maps_models/postcleavage_HNH_center_with_TS_for_morph.pdb"
Summary of feedback from opening /Users/zxc755/Library/CloudStorage/OneDrive-
UniversityofCopenhagen/Type
I-F_HNH/Manuscript/maps_models/postcleavage_HNH_center_with_TS_for_morph.pdb
---
warning | Ignored bad PDB record found on line 59
SSBOND 1 CYS Aa 295 CYS Ca 140
Chain information for postcleavage_HNH_center_with_TS_for_morph.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
K | No description available
L | No description available
> hide #!14 models
> color #14/L dark orange
> color #14/K dim gray
> color #14/J dark red
> color #14/I rebecca purple
> color #14/B forest green
> color #14/C,D,E,F,G,H salmon
> color #14/A steel blue
> color #14/A:232-350 dark turquoise
> color #14/O blue
> color #14/M red
> show #!14 models
> hide #!14 models
> style #14 stick
Changed 23523 atom styles
> hide #14
> show #14/A cartoons
Computing secondary structure
> show #!14 models
> hide #!14 models
> show #!14 models
> mmaker #14/A:232-350 to #15/A:232-250
Computing secondary structure
[Repeated 1 time(s)] 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_for_cat_morph.pdb, chain A (#15)
with postcleavage_HNH_center_with_TS_for_morph.pdb, chain A (#14), sequence
alignment score = 94.9
RMSD between 19 pruned atom pairs is 0.653 angstroms; (across all 19 pairs:
0.653)
> show #14,15/A:280
> show #14,15/A:280,319,304,305,329
> show #14,15/A:280,319,304,305,328
> hide #14-15/A:329
> show #14/Kk:1-3
> morph #14 #15
models have different number of chains, 12 (Morph -
postcleavage_HNH_center_with_TS_for_morph.pdb #/A,Morph -
postcleavage_HNH_center_with_TS_for_morph.pdb #/B,Morph -
postcleavage_HNH_center_with_TS_for_morph.pdb #/C,Morph -
postcleavage_HNH_center_with_TS_for_morph.pdb #/D,Morph -
postcleavage_HNH_center_with_TS_for_morph.pdb #/E,Morph -
postcleavage_HNH_center_with_TS_for_morph.pdb #/F,Morph -
postcleavage_HNH_center_with_TS_for_morph.pdb #/G,Morph -
postcleavage_HNH_center_with_TS_for_morph.pdb #/H,Morph -
postcleavage_HNH_center_with_TS_for_morph.pdb #/I,Morph -
postcleavage_HNH_center_with_TS_for_morph.pdb #/J,Morph -
postcleavage_HNH_center_with_TS_for_morph.pdb #/K,Morph -
postcleavage_HNH_center_with_TS_for_morph.pdb #/L) and 13
(halfcleaved_HNH_center_main_model_for_cat_morph.pdb
#15/A,halfcleaved_HNH_center_main_model_for_cat_morph.pdb
#15/B,halfcleaved_HNH_center_main_model_for_cat_morph.pdb
#15/C,halfcleaved_HNH_center_main_model_for_cat_morph.pdb
#15/D,halfcleaved_HNH_center_main_model_for_cat_morph.pdb
#15/E,halfcleaved_HNH_center_main_model_for_cat_morph.pdb
#15/F,halfcleaved_HNH_center_main_model_for_cat_morph.pdb
#15/G,halfcleaved_HNH_center_main_model_for_cat_morph.pdb
#15/H,halfcleaved_HNH_center_main_model_for_cat_morph.pdb
#15/I,halfcleaved_HNH_center_main_model_for_cat_morph.pdb
#15/J,halfcleaved_HNH_center_main_model_for_cat_morph.pdb
#15/K,halfcleaved_HNH_center_main_model_for_cat_morph.pdb
#15/L,halfcleaved_HNH_center_main_model_for_cat_morph.pdb #15/k)
> close #15
> open "/Users/zxc755/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/Type
> I-F_HNH/Manuscript/maps_models/halfcleaved_HNH_center_main_model_for_cat_morph.pdb"
Chain information for halfcleaved_HNH_center_main_model_for_cat_morph.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
k | No description available
> close #15
> hide #!14 models
> show #!32 models
> hide #!32 models
> show #!14 models
> hide #!14 models
> show #!32 models
> hide #32
> show #32/b cartoons
> hide #32/b cartoons
> show #32/k,l
> show #32/a:83,85
> color #32/k:40 #32/l:7 hot pink
> select add #32/A:85@CE
1 atom, 1 residue, 1 model selected
> select up
3 atoms, 1 bond, 2 residues, 1 model selected
> select up
17 atoms, 15 bonds, 2 residues, 1 model selected
> volume zone #13 nearAtoms rang 1 new tru
Invalid "nearAtoms" argument: invalid atoms specifier
> volume zone #13 nearAtoms sel range 1 newMap true
Opened halfcleaved_HNH_center_sharp3Å.mrc zone as #15, grid size 420,420,420,
pixel 0.725, shown at step 1, values float32
> transparency #15 90
> hide #32/a:200-350 cartoons
> hide #32/k:1-38
> hide #32/l:9-12
> select #32/L:7@N3
1 atom, 1 residue, 1 model selected
> select add #32/K:40@O6
2 atoms, 2 residues, 1 model selected
> select up
41 atoms, 44 bonds, 2 residues, 1 model selected
> volume zone #13 nearAtoms sel range 1 newMap true
Opened halfcleaved_HNH_center_sharp3Å.mrc zone as #16, grid size 420,420,420,
pixel 0.725, shown at step 1, values float32
> select up
4 atoms, 2 bonds, 2 residues, 1 model selected
> select up
41 atoms, 44 bonds, 2 residues, 1 model selected
> volume zone #13 nearAtoms sel range 1 newMap true
Opened halfcleaved_HNH_center_sharp3Å.mrc zone as #17, grid size 420,420,420,
pixel 0.725, shown at step 1, values float32
> transparency 16-17 90
Missing or invalid "percent" argument: Expected a number
> transparency #16-17 90
> hide #11.1 models
> hide #32/a:1-20
> hide #32/a:1-20 cartoons
> hide #32/a:87-200 cartoons
Drag select of 163 atoms, 183 bonds
> select up
169 atoms, 185 bonds, 10 residues, 1 model selected
> select up
202 atoms, 225 bonds, 10 residues, 1 model selected
Drag select of 133 atoms, 152 bonds
> select up
142 atoms, 154 bonds, 8 residues, 1 model selected
> select up
161 atoms, 179 bonds, 8 residues, 1 model selected
> hide sel
> select #15
2 models selected
> color sel steel blue
> select #16
2 models selected
> color sel hot pink
> select clear
> select #17
2 models selected
> color zone sel near #32
> transparency sel 90
> select clear
> select #32/L:5@C4'
1 atom, 1 residue, 1 model selected
> select add #32/K:42@C4
2 atoms, 2 residues, 1 model selected
> select up
41 atoms, 44 bonds, 2 residues, 1 model selected
> hide sel
Drag select of 8 residues
> 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:46
21 atoms, 18 bonds, 3 residues, 1 model selected
> select add #32/A:49
28 atoms, 25 bonds, 4 residues, 1 model selected
> show sel
> select clear
> show #32/b:95
> select #32/K:39@C4
1 atom, 1 residue, 1 model selected
> select up
3 atoms, 1 bond, 2 residues, 1 model selected
> select up
41 atoms, 44 bonds, 2 residues, 1 model selected
> hide sel
> volume zone #13 nearAtoms #32 range 1 newMap true
Opened halfcleaved_HNH_center_sharp3Å.mrc zone as #18, grid size 420,420,420,
pixel 0.725, shown at step 1, values float32
> color zone #18 near #32 distance 10
> volume #18 level 0.01
> hide #!32 models
> hide #!17 models
> hide #!16 models
> hide #!15 models
> show #!15 models
> show #!16 models
> show #!17 models
> show #!32 models
> volume #18 level 0.0001
> lighting soft
> lighting flat
> close #18
> select #32/A:47@CG
1 atom, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel
> show #32/b:90-100 cartoons
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
10 atoms, 10 bonds, 1 residue, 1 model selected
> color byhetero
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select add #32/A:49@CD
3 atoms, 1 bond, 2 residues, 1 model selected
> select up
13 atoms, 13 bonds, 2 residues, 1 model selected
> hide sel
> show #32/a:32
> show #32/a:42
> select clear
[Repeated 1 time(s)]
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel
> select clear
> show #32/a:82
> show #32/K:42
> hide #!16 models
> show #!16 models
> hide #!16 models
> show #!16 models
> hide #!15 models
> show #!15 models
> hide #!17 models
> show #!17 models
> hide #!17 models
> select add #32/K:41@P
1 atom, 1 residue, 1 model selected
> select up
3 atoms, 1 bond, 2 residues, 1 model selected
> select #32/K:41@C1'
1 atom, 1 residue, 1 model selected
> select up
3 atoms, 1 bond, 2 residues, 1 model selected
> select up
41 atoms, 44 bonds, 2 residues, 1 model selected
> select add #32/K:42@P
42 atoms, 44 bonds, 3 residues, 1 model selected
> select add #32/K:42@OP1
43 atoms, 44 bonds, 3 residues, 1 model selected
> select add #32/K:42@OP2
44 atoms, 44 bonds, 3 residues, 1 model selected
> select add #32/K:42@O5'
45 atoms, 44 bonds, 3 residues, 1 model selected
> select up
61 atoms, 66 bonds, 3 residues, 1 model selected
> select down
45 atoms, 44 bonds, 3 residues, 1 model selected
> volume zone #13 nearAtoms sel range 1 newMap true
Opened halfcleaved_HNH_center_sharp3Å.mrc zone as #18, grid size 420,420,420,
pixel 0.725, shown at step 1, values float32
> hide #!18 models
> show #!17 models
> hide #!17 models
> show #!18 models
> hide #!18 models
> show #!17 models
> show #!18 models
> hide #!17 models
> transparency #18 90
> hide #!18 models
> select #32/K:42@C4
1 atom, 1 residue, 1 model selected
> select up
20 atoms, 21 bonds, 1 residue, 1 model selected
> select subtract #32/K:42@OP2
19 atoms, 20 bonds, 1 residue, 1 model selected
> select subtract #32/K:42@OP1
18 atoms, 19 bonds, 1 residue, 1 model selected
> select subtract #32/K:42@P
17 atoms, 18 bonds, 1 residue, 1 model selected
> select subtract #32/K:42@O5'
16 atoms, 17 bonds, 1 residue, 1 model selected
> hide sel
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
22 atoms, 24 bonds, 1 residue, 1 model selected
> color sel orange
> color sel dark orange
> select #32/K:41@C4
1 atom, 1 residue, 1 model selected
> select up
19 atoms, 20 bonds, 1 residue, 1 model selected
> select add #32/K:42@P
20 atoms, 20 bonds, 2 residues, 1 model selected
> select up
39 atoms, 42 bonds, 2 residues, 1 model selected
> color sel dim gray
> hide #!16 models
> select add #32/K:40@C6
1 atom, 1 bond, 1 residue, 1 model selected
> select up
3 atoms, 1 bond, 2 residues, 1 model selected
> select up
41 atoms, 44 bonds, 2 residues, 1 model selected
> color sel hot pink
> select clear
> show #!16 models
> show #!18 models
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select down
1 bond, 1 model selected
> select #32/B:95@CB
1 atom, 1 residue, 1 model selected
> select add #32/B:95@CG
2 atoms, 1 residue, 1 model selected
> select add #32/B:95@ND1
3 atoms, 1 residue, 1 model selected
> select add #32/B:95@CE1
4 atoms, 1 residue, 1 model selected
> select add #32/B:95@NE2
5 atoms, 1 residue, 1 model selected
> select add #32/B:95@CD2
6 atoms, 1 residue, 1 model selected
> volume zone #13 nearAtoms sel range 1 newMap true
Opened halfcleaved_HNH_center_sharp3Å.mrc zone as #19, grid size 420,420,420,
pixel 0.725, shown at step 1, values float32
> color zone #19 near #32
> hide #!19 models
> show #!19 models
> select ~sel & ##selected
24085 atoms, 24839 bonds, 13 pseudobonds, 2799 residues, 3 models selected
> color #19 forest green
> transparency #19 90
> select clear
> select add #32/A:82@OD1
1 atom, 1 residue, 1 model selected
> select add #32/A:82@ND2
2 atoms, 1 residue, 1 model selected
> select add #32/A:82@CG
3 atoms, 1 residue, 1 model selected
> select add #32/A:82@CB
4 atoms, 1 residue, 1 model selected
> select add #32/A:42@NZ
5 atoms, 2 residues, 1 model selected
> select add #32/A:42@CE
6 atoms, 2 residues, 1 model selected
> select add #32/A:42@CD
7 atoms, 2 residues, 1 model selected
> select add #32/A:42@CG
8 atoms, 2 residues, 1 model selected
> select add #32/A:42@CB
9 atoms, 2 residues, 1 model selected
> select add #32/A:46@OG1
10 atoms, 3 residues, 1 model selected
> select add #32/A:46@CB
11 atoms, 3 residues, 1 model selected
> select add #32/A:46@CG2
12 atoms, 3 residues, 1 model selected
> hide #!15 models
> select add #32/A:85@NZ
13 atoms, 4 residues, 1 model selected
> select add #32/A:85@CE
14 atoms, 4 residues, 1 model selected
> select add #32/A:85@CD
15 atoms, 4 residues, 1 model selected
> select add #32/A:85@CG
16 atoms, 4 residues, 1 model selected
> select add #32/A:85@CB
17 atoms, 4 residues, 1 model selected
> select add #32/A:83@CB
18 atoms, 5 residues, 1 model selected
> select add #32/A:83@CG
19 atoms, 5 residues, 1 model selected
> select add #32/A:83@OD2
20 atoms, 5 residues, 1 model selected
> select add #32/A:83@OD1
21 atoms, 5 residues, 1 model selected
> volume zone #13 nearAtoms sel range 1 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
> color #20 steel blue
> transparency #20 90
> select #18
2 models selected
> color zone sel near #32
> color #32/:l dar ora
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color #32/:L dark ora
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color #32/:L ora
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> hide #!18 models
> select #32/L:6@OP2
1 atom, 1 residue, 1 model selected
> select up
22 atoms, 24 bonds, 1 residue, 1 model selected
> color sel orange
> color sel dark orange
> color #32/L dark orange
> color #32/L:7 hot pink
> show #!18 models
> select #18
2 models selected
> color zone sel near #32
> transparency sel 90
> select clear
> ui tool show Distances
> hide #!16 models
> show #!16 models
> hide #!16 models
> hide #!18 models
> hide #!19 models
> hide #!20 models
> show #!17 models
> hide #!17 models
> select #32/A:82@ND2
1 atom, 1 residue, 1 model selected
> select add #32/K:42@OP1
2 atoms, 2 residues, 1 model selected
> distance #32/A:82@ND2 #32/K:42@OP1
Distance between halfcleaved_HNH_center_main_model_temp_editing.pdb #32/A ASN
82 ND2 and /K DT 42 OP1: 2.690Å
> distance style radius 0.04
[Repeated 2 time(s)]
> distance style radius 0.05
[Repeated 2 time(s)]
> select #32/A:42@NZ
1 atom, 1 residue, 1 model selected
> select add #32/K:41@OP1
2 atoms, 2 residues, 1 model selected
> distance #32/A:42@NZ #32/K:41@OP1
Distance between halfcleaved_HNH_center_main_model_temp_editing.pdb #32/A LYS
42 NZ and /K DC 41 OP1: 2.885Å
> select #32/A:46@OG1
1 atom, 1 residue, 1 model selected
> select add #32/K:40@OP1
2 atoms, 2 residues, 1 model selected
> distance #32/A:46@OG1 #32/K:40@OP1
Distance between halfcleaved_HNH_center_main_model_temp_editing.pdb #32/A THR
46 OG1 and /K DG 40 OP1: 2.817Å
> select #32/B:95@ND1
1 atom, 1 residue, 1 model selected
> select add #32/K:40@OP1
2 atoms, 2 residues, 1 model selected
> distance #32/B:95@ND1 #32/K:40@OP1
Distance between halfcleaved_HNH_center_main_model_temp_editing.pdb #32/B HIS
95 ND1 and /K DG 40 OP1: 2.646Å
> 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
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