![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 3 weeks ago
Last modified 3 weeks ago
#19808 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-15.7.1-arm64-arm-64bit
ChimeraX Version: 1.10.1 (2025-07-24 20:15:27 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 0x000000020789a140 (most recent call first):
File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 368 in event_loop
File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1057 in init
File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1220 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, chimerax.surface._surface, chimerax.pdb_lib._load_libs, openmm._openmm, openmm.app.internal.xtc_utils, openmm.app.internal.compiled, psutil._psutil_osx, psutil._psutil_posix, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, lz4._version, lz4.frame._frame, msgpack._cmsgpack, PIL._imaging, 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, PIL._imagingmath, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw, 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: 120)
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"codeSigningMonitor" : 2,
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"translated" : false,
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"procLaunch" : "2026-02-04 13:02:25.8609 -0500",
"procStartAbsTime" : 21061986312168,
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"codeSigningFlags" : 570491649,
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"vmSummary" : "ReadOnly portion of Libraries: Total=2.0G resident=0K(0%) swapped_out_or_unallocated=2.0G(100%)\nWritable regions: Total=8.0G written=77.4M(1%) resident=4487K(0%) swapped_out=73.0M(1%) unallocated=7.9G(99%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 256K 2 \nActivity Tracing 256K 1 \nCG image 1440K 36 \nColorSync 704K 38 \nCoreAnimation 2144K 118 \nCoreGraphics 80K 5 \nCoreServices 624K 2 \nCoreUI image data 6432K 57 \nFoundation 144K 3 \nKernel Alloc Once 32K 1 \nMALLOC 6.7G 173 \nMALLOC guard page 288K 18 \nMach message 64K 3 \nOpenGL GLSL 384K 4 \nSTACK GUARD 1008K 63 \nStack 213.6M 64 \nStack Guard 56.0M 1 \nVM_ALLOCATE 328.9M 220 \nVM_ALLOCATE (reserved) 768.0M 3 reserved VM address space (unallocated)\n__AUTH 5517K 697 \n__AUTH_CONST 77.4M 944 \n__CTF 824 1 \n__DATA 40.4M 1182 \n__DATA_CONST 38.7M 1189 \n__DATA_DIRTY 2777K 342 \n__FONT_DATA 2352 1 \n__GLSLBUILTINS 5174K 1 \n__INFO_FILTER 8 1 \n__LINKEDIT 660.4M 240 \n__OBJC_RO 61.4M 1 \n__OBJC_RW 2396K 1 \n__TEXT 1.4G 1208 \n__TEXT (graphics) 48K 2 \n__TPRO_CONST 128K 2 \ndyld private memory 12.5M 100 \nmapped file 759.5M 107 \npage table in kernel 4487K 1 \nshared memory 3248K 30 \n=========== ======= ======= \nTOTAL 11.0G 6862 \nTOTAL, minus reserved VM space 10.3G 6862 \n",
"legacyInfo" : {
"threadTriggered" : {
"name" : "CrBrowserMain",
"queue" : "com.apple.main-thread"
}
},
"logWritingSignature" : "82c56b840f6684891fa68812616e7f0450124f05",
"trialInfo" : {
"rollouts" : [
{
"rolloutId" : "63508950b3714d3622fc77f7",
"factorPackIds" : {
"SIRI_MEMORY_SYNC_CONFIG" : "6526e111d0c9ce2f459b54a8"
},
"deploymentId" : 240000015
},
{
"rolloutId" : "661464ecda55e5192b100804",
"factorPackIds" : {
},
"deploymentId" : 240000005
}
],
"experiments" : [
]
}
}
===== Log before crash start =====
UCSF ChimeraX version: 1.10.1 (2025-07-24)
© 2016-2025 Regents of the University of California. All rights reserved.
> open "/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV
> with Terns/20260111 IVC
> manuscript/IVC_DNA_bound/IVC_DNAbound_HD_compare_apo_5.cxs"
Opened cryosparc_P38_J47_006_volume_map.mrc as #2, grid size 512,512,512,
pixel 1.07, shown at level 0.142, step 1, values float32
Opened cryosparc_P6_J91_004_volume_map.mrc as #6, grid size 384,384,384, pixel
1.07, shown at level 0.0524, step 2, values float32
Log from Tue Feb 3 15:37:02 2026UCSF ChimeraX version: 1.10.1 (2025-07-24)
© 2016-2025 Regents of the University of California. All rights reserved.
> open "/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV
> with Terns/20260111 IVC
> manuscript/IVC_DNA_bound/IVC_DNAbound_HD_compare_apo_5.cxs"
Opened cryosparc_P38_J47_006_volume_map.mrc as #2, grid size 512,512,512,
pixel 1.07, shown at level 0.142, step 1, values float32
Opened cryosparc_P6_J91_004_volume_map.mrc as #6, grid size 384,384,384, pixel
1.07, shown at level 0.0524, step 2, values float32
Log from Tue Feb 3 13:26:30 2026UCSF ChimeraX version: 1.10.1 (2025-07-24)
© 2016-2025 Regents of the University of California. All rights reserved.
> open "/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV
> with Terns/20260111 IVC
> manuscript/IVC_DNA_bound/IVC_DNAbound_HD_compare_apo_2_movie1.cxs"
Log from Mon Feb 2 10:29:38 2026UCSF ChimeraX version: 1.10.1 (2025-07-24)
© 2016-2025 Regents of the University of California. All rights reserved.
> open "/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV
> with Terns/20260111 IVC manuscript/IVC_DNA_bound/IVC_DNAbound_PAM2.cxs"
Opened cryosparc_P6_J91_004_volume_map.mrc as #4, grid size 384,384,384, pixel
1.07, shown at level 0.227, step 1, values float32
Opened cryosparc_P6_J91_004_volume_map.mrc copy as #1, grid size 384,384,384,
pixel 1.07, shown at level 0.248, step 1, values float32
Opened cryosparc_P6_J91_004_volume_map.mrc as #3, grid size 384,384,384, pixel
1.07, shown at level 0.153, step 1, values float32
Log from Sun Feb 1 21:27:29 2026UCSF ChimeraX version: 1.10.1 (2025-07-24)
© 2016-2025 Regents of the University of California. All rights reserved.
> open "/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV
> with Terns/20260111 IVC manuscript/IVC_DNA_bound/IVC_DNAbound_focus2.cxs"
Opened cryosparc_P6_J91_004_volume_map.mrc as #1, grid size 384,384,384, pixel
1.07, shown at level 0.145, step 1, values float32
Opened cryosparc_P6_J91_004_volume_map.mrc copy as #4, grid size 384,384,384,
pixel 1.07, shown at level 0.143, step 1, values float32
Log from Thu Jan 15 09:33:23 2026UCSF ChimeraX version: 1.10.1 (2025-07-24)
© 2016-2025 Regents of the University of California. All rights reserved.
> open "/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV
> with Terns/20260111 IVC manuscript/IVC_DNA_bound/IVC_DNAbound_focus1.cxs"
Opened cryosparc_P6_J91_004_volume_map.mrc as #1, grid size 384,384,384, pixel
1.07, shown at level 0.145, step 1, values float32
Opened cryosparc_P6_J91_004_volume_map.mrc copy as #4, grid size 384,384,384,
pixel 1.07, shown at level 0.138, step 1, values float32
Log from Tue Jan 13 14:05:11 2026UCSF ChimeraX version: 1.10.1 (2025-07-24)
© 2016-2025 Regents of the University of California. All rights reserved.
> open "/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV
> with Terns/20260111 IVC manuscript/IVC_DNA_bound/IVC_DNAbound_focus1.cxs"
Opened cryosparc_P6_J91_004_volume_map.mrc as #1, grid size 384,384,384, pixel
1.07, shown at level 0.145, step 1, values float32
Log from Tue Jan 13 12:34:22 2026UCSF ChimeraX version: 1.10.1 (2025-07-24)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV
> with Terns/20260111 IVC
> manuscript/IVC_DNA_bound/cryosparc_P6_J91_004_volume_map.mrc"
Opened cryosparc_P6_J91_004_volume_map.mrc as #1, grid size 384,384,384, pixel
1.07, shown at level 0.0524, step 2, values float32
> open "/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV
> with Terns/20260111 IVC
> manuscript/IVC_DNA_bound/merged_real_space_refined_007.pdb"
Chain information for merged_real_space_refined_007.pdb #2
---
Chain | Description
A | No description available
C H I J K L | No description available
D | No description available
E | No description available
F | No description available
G | No description available
M | No description available
N O P Q R | No description available
S | No description available
> hide atoms
> show cartoons
> set bgColor white
> surface dust #1 size 10.7
> volume #1 step 1
> volume #1 level 0.1467
> hide #!1 models
> select #2/D
2438 atoms, 2496 bonds, 297 residues, 1 model selected
> ui tool show "Color Actions"
> color sel hot pink
> ui tool show "Color Actions"
> color sel pink
> select #2/A
4478 atoms, 4580 bonds, 1 pseudobond, 550 residues, 2 models selected
> ui tool show "Color Actions"
> color sel light sky blue
> select #2/S,R,Q,P,O,N
5281 atoms, 5363 bonds, 1 pseudobond, 664 residues, 2 models selected
> ui tool show "Color Actions"
> color sel gold
> color sel orange
> color sel gold
> color sel orange
> select #2/M,L,K,J,I,H,C,
Expected an objects specifier or a keyword
> select #2/M,L,K,J,I,H,C
16170 atoms, 16420 bonds, 1 pseudobond, 2079 residues, 2 models selected
> ui tool show "Color Actions"
> color sel medium sea green
> color sel light green
> color sel pale green
> save "/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV
> with Terns/20260111 IVC manuscript/IVC_DNA_bound/IVC_DNAbound_color1.cxs"
> select add #2
30522 atoms, 31271 bonds, 3 pseudobonds, 3693 residues, 2 models selected
> select subtract #2
Nothing selected
> lighting soft
> lighting simple
> lighting soft
> lighting flat
> open /Volumes/CHENGTAO/cryosparc_P6_J96_005_volume_map.mrc
Opened cryosparc_P6_J96_005_volume_map.mrc as #3, grid size 256,256,256, pixel
1.61, shown at level 0.107, step 1, values float32
> surface dust #3 size 16.1
> lighting full
> lighting soft
> hide #!2 models
> open /Volumes/CHENGTAO/cryosparc_P6_J97_004_volume_map.mrc
Opened cryosparc_P6_J97_004_volume_map.mrc as #4, grid size 256,256,256, pixel
1.61, shown at level 0.11, step 1, values float32
> open /Volumes/CHENGTAO/cryosparc_P6_J98_004_volume_map.mrc
Opened cryosparc_P6_J98_004_volume_map.mrc as #5, grid size 256,256,256, pixel
1.61, shown at level 0.103, step 1, values float32
> open /Volumes/CHENGTAO/cryosparc_P6_J99_004_volume_map.mrc
Opened cryosparc_P6_J99_004_volume_map.mrc as #6, grid size 256,256,256, pixel
1.61, shown at level 0.107, step 1, values float32
> surface dust #3 size 16.1
> surface dust #4 size 16.1
> surface dust #5 size 16.1
> surface dust #6 size 16.1
> volume #3 level 0.2172
> volume #4 level 0.1954
> volume #4 level 0.2116
> volume #4 level 0.2035
> volume #5 level 0.2178
> volume #6 level 0.225
> volume #6 level 0.2054
> hide #!3 models
> show #!2 models
> show #!3 models
> select add #2
30522 atoms, 31271 bonds, 3 pseudobonds, 3693 residues, 2 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #2,-0.86578,-0.49991,0.022818,486.88,0.49898,-0.86584,-0.036613,283.9,0.03806,-0.020313,0.99907,-3.613
> undo
> select subtract #2
Nothing selected
> hide #!2 models
> show #!4 models
> show #!5 models
> show #!6 models
> hide #!3 models
> hide #!4 models
> open "/Users/xuchengtao/Documents/Building models undergoing/20251222 IVC
> intermediate/20260112 IVC
> intermediate/merged_IVC_noDNA_crRNA_TS_Cas10modified_real_space_refined_002forJ73.pdb"
Chain information for
merged_IVC_noDNA_crRNA_TS_Cas10modified_real_space_refined_002forJ73.pdb #7
---
Chain | Description
A | No description available
B E G | No description available
C | No description available
D | No description available
F H | No description available
I | No description available
J | No description available
K L M O | No description available
N | No description available
P | No description available
Q | No description available
> show #!7 cartoons
> hide #!7 atoms
> show #!4 models
> show #!3 models
> hide #!7 models
> volume #3 level 0.2008
> open "/Users/xuchengtao/Documents/Building models undergoing/20251222 IVC
> intermediate/flipped_cryosparc_P6_J90_004_volume_map.mrc"
Opened flipped_cryosparc_P6_J90_004_volume_map.mrc as #8, grid size
384,384,384, pixel 1.07, shown at level 0.0589, step 2, values float32
> surface dust #4 size 16.1
> surface dust #5 size 16.1
> surface dust #6 size 16.1
> surface dust #8 size 10.7
> ui tool show "Fit in Map"
> ui mousemode right "translate selected models"
> select add #8
2 models selected
> view matrix models
> #8,-0.71372,-0.49135,0.49917,334.98,-0.54393,0.83781,0.046962,132.29,-0.44129,-0.238,-0.86523,550.67
> view matrix models
> #8,0.97257,0.03667,-0.2297,35.228,0.058924,-0.99413,0.090782,387.87,-0.22503,-0.10183,-0.96902,451.87
> volume #8 step 1
> volume #8 level 0.09502
> fitmap #8 inMap #3
Fit map flipped_cryosparc_P6_J90_004_volume_map.mrc in map
cryosparc_P6_J96_005_volume_map.mrc using 324674 points
correlation = 0.9805, correlation about mean = 0.9142, overlap = 2.547e+04
steps = 216, shift = 16.2, angle = 21 degrees
Position of flipped_cryosparc_P6_J90_004_volume_map.mrc (#8) relative to
cryosparc_P6_J96_005_volume_map.mrc (#3) coordinates:
Matrix rotation and translation
0.97292447 0.21705585 0.07940239 -51.11804392
0.21669675 -0.97614950 0.01321611 360.31959015
0.08037724 0.00434796 -0.99675503 373.34043768
Axis -0.99320802 -0.10918025 -0.04021824
Axis point 0.00000000 183.38879293 187.30072229
Rotation angle (degrees) 179.74420803
Shift along axis -3.58402524
> select subtract #8
Nothing selected
> show #!7 models
> hide #!7 models
> volume #8 level 0.1269
> hide #!6 models
> show #!6 models
> hide #!8 models
> show #!8 models
> hide #!6 models
> volume #8 level 0.1181
> hide #!8 models
> show #!6 models
> volume #6 level 0.2054
> show #!7 models
> volume #3 level 0.2069
> volume #4 level 0.2577
> volume #5 level 0.2147
> volume #6 level 0.2229
> hide #!6 models
> show #!8 models
> hide #!7 models
> volume #8 level 0.134
> volume #6 level 0.2142
> volume #6 level 0.2287
[Repeated 1 time(s)]
> volume #5 level 0.2392
> volume #5 level 0.2178
> volume #6 level 0.2083
> volume #6 level 0.2025
> volume #4 level 0.1914
> volume #5 level 0.2055
> volume #5 level 0.1872
> volume #4 level 0.2095
> show #!7 models
> volume #3 level 0.1826
> volume #4 showOutlineBox true
> volume #4 level 0.1945
> volume #4 showOutlineBox false
> volume #4 level 0.1824
> volume #3 level 0.1673
> volume #5 level 0.1903
> hide #!7 models
> volume #5 level 0.1658
> volume #4 level 0.1794
> volume #5 level 0.1933
> volume #5 level 0.2269
> volume #4 level 0.2246
> show #!7 models
> volume #3 level 0.216
> volume #3 level 0.1978
> volume #5 level 0.2086
> hide #!7 models
> show #!5 models
> hide #!5 models
> hide #!6 models
> show #!6 models
> show #!5 models
> hide #!6 models
> hide #!5 models
> show #!4 models
> volume #4 level 0.1794
> volume #5 level 0.1719
> volume #6 level 0.1734
> volume #5 level 0.1475
> volume #4 level 0.2095
> volume #6 level 0.22
> volume #3 level 0.213
> volume #4 level 0.2155
> show #!7 models
> color #4 #b2ffffb0 models
> color #4 #f4fcfeb1 models
> color #4 #9a9fa0b1 models
> color #4 #8e9293b1 models
> color #4 #6c7070b1 models
> color #4 #9ca1a2b1 models
> color #4 #9ca1a2b0 models
> color #3 #909071ff models
> color #3 #867f90ff models
> color #3 #867f90b3 models
> hide #!4 models
> show #!5 models
> color #5 #b2b2ffba models
> color #5 #f3ecfaba models
> color #5 #95919aba models
> color #6 #faf3fbff models
> color #6 #817d82ff models
> color #6 #817d82a5 models
> color #6 #817d82a6 models
> volume #5 level 0.2422
> volume #5 level 0.1994
> hide #!5 models
> show #!6 models
> volume #6 level 0.2038
> volume #6 level 0.2394
> volume #6 level 0.2167
> volume #6 level 0.2135
> volume #4 level 0.2357
> volume #3 level 0.2333
> volume #6 level 0.233
> copy #2
Unknown command: copy #2
> duplicate #2
Unknown command: duplicate #2
> mcopy #2
Missing required "to_atoms" argument
> combine #2
> hide #!7 models
> show #!2 models
> hide #!2 models
> show #!7 models
> select add #9
30522 atoms, 31271 bonds, 3 pseudobonds, 3693 residues, 2 models selected
> view matrix models
> #9,-0.78485,0.6147,-0.07848,262.35,-0.61967,-0.77759,0.10659,471.23,0.0044959,0.13229,0.9912,-26.215
> mmaker #9 to #7
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
merged_IVC_noDNA_crRNA_TS_Cas10modified_real_space_refined_002forJ73.pdb,
chain A (#7) with copy of merged_real_space_refined_007.pdb, chain A (#9),
sequence alignment score = 2382.1
RMSD between 256 pruned atom pairs is 1.157 angstroms; (across all 517 pairs:
3.343)
> select subtract #9
Nothing selected
> hide #!9 models
> show #!9 models
> hide #!7 models
> show #!7 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> hide #!7 models
> show #!2 models
> save "/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV
> with Terns/20260111 IVC manuscript/IVC_DNA_2_states_compare.cxs"
> color zone #1
Missing required "near" argument
> color zone #1 near #2
> color zone #1 near #2 range 3
Expected a keyword
> open "/Users/xuchengtao/Documents/Building models undergoing/20251030
> 8mut_ssDNA/DNA-RNA/IscB_8mut_ssDNA_DNA_model_coloring.cxc"
> hide #!4-13 models
> select #1/A:1-54
Nothing selected
> color sel hotpink
> select #1/A:55-85,161-196,297-374
Nothing selected
> color sel royalblue
> select #1/A:86-122
Nothing selected
> color sel mediumslateblue
> select #1/A:123-160
Nothing selected
> color sel yellow
> select #1/A:197-296
Nothing selected
> color sel orange
> select #1/A:375-429
Nothing selected
> color sel lightsalmon
> select #1/A:430-496
Nothing selected
> color sel blueviolet
> select #1/D
Nothing selected
> color sel dodgerblue
> select #1/B:1-16
Nothing selected
> color sel firebrick
> select #1/B:17-256
Nothing selected
> color sel silver
executed IscB_8mut_ssDNA_DNA_model_coloring.cxc
> color zone #1 near #2 range 3
Expected a keyword
> color zone #1 near #2 distance 3
> color zone #1 near #2 distance 3.5
> hide #!2 models
> show #!2 models
> hide #!1 models
> select @2/G
4324 atoms, 4594 bonds, 395 residues, 3 models selected
> select #2/G
983 atoms, 1100 bonds, 46 residues, 1 model selected
> ui tool show "Color Actions"
> color sel wheat
> color sel khaki
> select #2/F
972 atoms, 1090 bonds, 47 residues, 1 model selected
> ui tool show "Color Actions"
> color sel deep sky blue
> color sel dodger blue
> color sel cornflower blue
> color sel dodger blue
> select #2/E
200 atoms, 222 bonds, 10 residues, 1 model selected
> ui tool show "Color Actions"
> color sel tomato
> color sel dark salmon
> color sel hot pink
> color sel pale violet red
> color sel deep pink
> color sel hot pink
> select add #2
30522 atoms, 31271 bonds, 3 pseudobonds, 3693 residues, 2 models selected
> select subtract #2
Nothing selected
> color zone #1 near #2 distance 3.5
> show #!1 models
> volume #1 level 0.1611
> hide #!2 models
> volume #1 level 0.17
> volume #1 level 0.16
> color zone #1 near #2 distance 4
> volume #1 level 0.12
> volume #1 level 0.13
> volume #1 level 0.14
> volume #1 level 0.145
> save /Users/xuchengtao/Desktop/image166.png supersample 3
> color zone #1 near #2 distance 4.5
> save /Users/xuchengtao/Desktop/image167.png supersample 3
> hide #!1 models
> show #!7 models
> show #!9 models
> hide #!7 models
> hide #!9 models
> show #!2 models
> save /Users/xuchengtao/Desktop/image168.png supersample 3
> save /Users/xuchengtao/Desktop/image169.png supersample 3
> select add #2
30522 atoms, 31271 bonds, 3 pseudobonds, 3693 residues, 2 models selected
> cartoon style (#!2 & sel) modeHelix tube sides 20
> select subtract #2
Nothing selected
> save /Users/xuchengtao/Desktop/image170.png supersample 3
> save /Users/xuchengtao/Desktop/image171.png supersample 3
> show #!1 models
> hide #!2 models
> save /Users/xuchengtao/Desktop/image172.png supersample 3
> hide #!1 models
> show #!3 models
> show #!4 models
> show #!5 models
> close #3-6,8
> show #!1 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> save "/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV
> with Terns/20260111 IVC manuscript/IVC_DNA_bound/IVC_DNAbound_color1.cxs"
——— End of log from Tue Jan 13 12:34:22 2026 ———
> view name session-start
opened ChimeraX session
> show #!7 models
> show #!9 models
> hide #!7 models
> hide #!9 models
> close #7,9
> show #!2 models
> combine #2
> hide #!1 models
> hide #!2 models
> combine #1
No structures specified
> copy #1
Unknown command: copy #1
> duplicate #1
Unknown command: duplicate #1
> open "/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV
> with Terns/20260111 IVC
> manuscript/IVC_DNA_bound/cryosparc_P6_J91_004_volume_map.mrc"
Opened cryosparc_P6_J91_004_volume_map.mrc as #4, grid size 384,384,384, pixel
1.07, shown at level 0.0524, step 2, values float32
> close #4
> select #3/S,R,q,p,o,n
5281 atoms, 5363 bonds, 1 pseudobond, 664 residues, 2 models selected
> ui tool show "Color Actions"
> color sel light gray
> color sel gray
> color sel light gray
> color sel dark gray
> color sel light gray
> select #3/m,l,k,j,i,H,C
16170 atoms, 16420 bonds, 1 pseudobond, 2079 residues, 2 models selected
> ui tool show "Color Actions"
> color sel light gray
> volume copy #1
Opened cryosparc_P6_J91_004_volume_map.mrc copy as #4, grid size 384,384,384,
pixel 1.07, shown at step 1, values float32
> color #4 #b2b2b299 models
> color zone #4 near #3 distance 4
> color #4 #b2b2b280 models
> color #4 #b2b2b299 models
> transparency
Missing or invalid "percent" argument: Expected a number
> transparency #3 60
> hide #!3 models
> show #!3 models
> transparency #4 60
> color zone #4 near #3 distance 4
> transparency #4 60
> surface dust #4 size 10.7
> hide #!3 models
> transparency #4 80
> color zone #4 near #3 distance 4
> transparency #4 90
> color zone #4 near #3 distance 4
> transparency #4 10
> lighting soft
> lighting simple
> lighting flat
> lighting soft
> lighting flat
> lighting simple
> lighting soft
> lighting full
> lighting soft
> lighting flat
> lighting full
> lighting simple
[Repeated 1 time(s)]
> lighting full
> save /Users/xuchengtao/Desktop/image186.png supersample 3
> save /Users/xuchengtao/Desktop/image187.png supersample 3
> select add #3
30522 atoms, 31271 bonds, 3 pseudobonds, 3693 residues, 2 models selected
> select subtract #3
Nothing selected
> show #!3 models
> hide #!4 models
> hide #3 cartoons
> show #3/A cartoons
> ui mousemode right select
> style #!3 stick
Changed 30522 atom styles
> show #!3 atoms
> color #!3 byhetero
> show #!4 models
> hide #!4 models
> transparency #4 20
> show #!4 models
> hide #!3 models
> show #!3 models
> transparency #4.1 0
> transparency #4 20
> transparency #4 50
> volume #4 level 0.1208
> color zone #4 near #3 distance 4
> hide #!3 atoms
> color zone #4 near #3 distance 4
> select #3/A
4478 atoms, 4580 bonds, 1 pseudobond, 550 residues, 2 models selected
> ui tool show "Color Actions"
> color sel light sky blue
> color zone #4 near #3 distance 4
> select add #3
30522 atoms, 31271 bonds, 3 pseudobonds, 3693 residues, 2 models selected
> select subtract #3
Nothing selected
> hide #!4 models
> style #!3 stick
Changed 30522 atom styles
> show #!3 atoms
> style #!3 stick
Changed 30522 atom styles
> color #!3 byhetero
> hide #3/A
> hide #!3 models
> show #!3 models
> hide #!3 models
> select #3/A:115,147,146,159,94,93,70,97,54
87 atoms, 85 bonds, 9 residues, 1 model selected
> show sel atoms
> show #!3 models
> hide #3/A cartoons
> select add #3
30522 atoms, 31271 bonds, 3 pseudobonds, 3693 residues, 2 models selected
> select subtract #3
Nothing selected
> hide #3 cartoons
> hide #3 atoms
> show sel atoms
> select #3/A:115,147,146,159,94,93,70,97,54
87 atoms, 85 bonds, 9 residues, 1 model selected
> show sel atoms
> show #!4 models
> combine #3
> hide #!3 models
> hide #!4 models
> select add #3
30522 atoms, 31271 bonds, 3 pseudobonds, 3693 residues, 2 models selected
> show #!1 models
> select subtract #3
Nothing selected
> color zone #4 near #1 distance 5
color zone: No atoms specified.
> show #!4 models
> hide #!1 models
> color #4 #b8bfbb66 models
> color zone #4 near #1 distance 5
color zone: No atoms specified.
> color zone #4 near #2 distance 5
> volume #4 level 0.13
> volume #4 level 0.135
> lighting soft
> hide #!4 models
> show #!4 models
> hide #!5 models
> show #!5 models
> hide #!4 models
> show #!4 models
> volume #4 level 0.14
> transparency #4 20
> ui tool show "Side View"
> transparency #4 50
> volume #4 level 0.138
> color zone #4 near #2 distance 5
> transparency #4 50
[Repeated 1 time(s)]
> transparency #4 70
> save "/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV
> with Terns/20260111 IVC manuscript/IVC_DNA_bound/IVC_DNAbound_focus1.cxs"
——— End of log from Tue Jan 13 14:05:11 2026 ———
> view name session-start
opened ChimeraX session
> hide #!4 models
> hide #!5 models
> show #!3 models
> show #!4 models
> hide #!3 models
> show #!1 models
> hide #!4 models
> hide #!1 models
> show #!4 models
> show #!5 models
> hide #!4 models
> show #!4 models
> hide #!5 models
> show #!3 models
> hide #!4 models
> show #!5 models
> hide #!3 models
> show #!3 models
> hide #!5 models
> show #!5 models
> show #5 cartoons
> show #5 atoms
> hide #5 atoms
> show #!4 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> hide #!4 models
> show #!4 models
> color zone #4 near #5 distance 5
> hide #!5 atoms
> color zone #4 near #5 distance 5
> volume #4 level 0.09687
> volume #4 style mesh
> volume #4 style surface
> volume #4 level 0.1428
> color #!5 bychain
> undo
> hide #!4 models
> show #!1 models
> hide #!1 models
> show #!5 atoms
> select #5/E,F,A,D
8088 atoms, 8388 bonds, 1 pseudobond, 904 residues, 2 models selected
> hide #5 cartoons
> hide #5 atoms
> select #5/E,F,A,D
8088 atoms, 8388 bonds, 1 pseudobond, 904 residues, 2 models selected
> show sel cartoons
> select #5/A
4478 atoms, 4580 bonds, 1 pseudobond, 550 residues, 2 models selected
> ui tool show "Color Actions"
> color sel light sky blue
> select #5/F
972 atoms, 1090 bonds, 47 residues, 1 model selected
> ui tool show "Color Actions"
> color sel deep sky blue
> undo
> color sel dodger blue
[Repeated 3 time(s)]
> select #5/D
2438 atoms, 2496 bonds, 297 residues, 1 model selected
> ui tool show "Color Actions"
> color sel light pink
> select #5/E
200 atoms, 222 bonds, 10 residues, 1 model selected
> ui tool show "Color Actions"
> color sel hot pink
[Repeated 3 time(s)]
> select add #5
30522 atoms, 31271 bonds, 3 pseudobonds, 3693 residues, 2 models selected
> select subtract #5
Nothing selected
> show #!5 atoms
> hide #!5 atoms
> select #5/A,D,E,F
8088 atoms, 8388 bonds, 1 pseudobond, 904 residues, 2 models selected
> show #!4 models
> hide #!4 models
> show #!4 models
> volume zone #4 nearAtoms 5 dist 4.5
Invalid "nearAtoms" argument: invalid atoms specifier
> volume zone #4 nearAtoms #5 dist 4.5
Expected a keyword
> volume zone #4 nearAtoms #5
> volume zone #4 nearAtoms sel
> show #!4 models
> volume zone #4 nearAtoms sel dist 5
Expected a keyword
> volume zone #4 nearAtoms sel dis4
Expected a keyword
> volume zone #4 nearAtoms sel dis 4
Expected a keyword
> volume zone #4 nearAtoms sel range 4
> volume zone #4 nearAtoms sel range 3
> volume zone #4 nearAtoms sel range 2
> volume zone #4 nearAtoms sel range 2.5
> color zone #4 near sel distance 4
> select add #5
30522 atoms, 31271 bonds, 3 pseudobonds, 3693 residues, 2 models selected
> select subtract #5
Nothing selected
> hide #!5 models
> volume zone #4 nearAtoms sel range 3
no atoms specified for zone
> select #5/A,D,E,F
8088 atoms, 8388 bonds, 1 pseudobond, 904 residues, 2 models selected
> volume zone #4 nearAtoms sel range 3
> transparency #4 50
> show #!5 models
> save "/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV
> with Terns/20260111 IVC manuscript/IVC_DNA_bound/IVC_DNAbound_focus2.cxs"
Drag select of 4 cryosparc_P6_J91_004_volume_map.mrc copy , 10 residues
> select clear
> open "/Users/xuchengtao/Documents/Building models
> undergoing/20251003IVC/20251222 Xiaomeng AI
> IVC/merged_real_space_refined_009.pdb"
Chain information for merged_real_space_refined_009.pdb #6
---
Chain | Description
A | No description available
C H I J K L | No description available
D | No description available
E | No description available
F | No description available
G | No description available
M | No description available
N O P Q R | No description available
S | No description available
> hide #!4 models
> hide #!5 models
> select add #6
30522 atoms, 31271 bonds, 3 pseudobonds, 3693 residues, 2 models selected
> hide sel atoms
> show sel cartoons
> select subtract #6
Nothing selected
> hide #!6 models
> show #!5 models
> show #!4 models
> hide #!5 models
> hide #!4 models
> show #!5 models
> select #5/E:8
19 atoms, 20 bonds, 1 residue, 1 model selected
> hide #5/F:1-36
> hide #5/F:1-36 cartoons
> show #5/F:34-37 cartoons
Drag select of 9 residues
> select #5/E:6
22 atoms, 24 bonds, 1 residue, 1 model selected
Drag select of 9 residues
> select add #5/E:6
209 atoms, 24 bonds, 10 residues, 1 model selected
> select add #5/E:7
228 atoms, 44 bonds, 11 residues, 1 model selected
> select subtract #5/E:7
209 atoms, 24 bonds, 10 residues, 1 model selected
> select add #5/E:7
228 atoms, 44 bonds, 11 residues, 1 model selected
> select add #5/E:8
247 atoms, 64 bonds, 12 residues, 1 model selected
> select subtract #5/E:8
228 atoms, 44 bonds, 11 residues, 1 model selected
> select add #5/E:8
247 atoms, 64 bonds, 12 residues, 1 model selected
> select subtract #5/E:8
228 atoms, 44 bonds, 11 residues, 1 model selected
> select add #5/E:9
247 atoms, 64 bonds, 12 residues, 1 model selected
> select add #5/E:8
266 atoms, 84 bonds, 13 residues, 1 model selected
> select add #5/E:10
285 atoms, 104 bonds, 14 residues, 1 model selected
> select add #5/F:43
304 atoms, 124 bonds, 15 residues, 1 model selected
> select add #5/F:42
325 atoms, 147 bonds, 16 residues, 1 model selected
> select add #5/F:41
344 atoms, 167 bonds, 17 residues, 1 model selected
> select add #5/F:40
366 atoms, 191 bonds, 18 residues, 1 model selected
> select add #5/F:39
388 atoms, 215 bonds, 19 residues, 1 model selected
> select add #5/F:38
410 atoms, 239 bonds, 20 residues, 1 model selected
> select add #5/F:37
432 atoms, 263 bonds, 21 residues, 1 model selected
> select add #5/F:36
453 atoms, 286 bonds, 22 residues, 1 model selected
> select add #5/F:35
472 atoms, 306 bonds, 23 residues, 1 model selected
> select add #5/F:34
492 atoms, 327 bonds, 24 residues, 1 model selected
> show sel atoms
> color sel byhetero
> color sel bychain
> select add #5
30522 atoms, 31271 bonds, 3 pseudobonds, 3693 residues, 2 models selected
> select subtract #5
Nothing selected
> select #5/A:400,405,434,532,355
48 atoms, 43 bonds, 5 residues, 1 model selected
> show sel atoms
> color sel byhetero
> hbonds sel reveal true
44 hydrogen bonds found
> undo
> color sel byhetero
> hide #5/A:403
> select add #5
30522 atoms, 31271 bonds, 13 pseudobonds, 3693 residues, 3 models selected
> select subtract #5
Nothing selected
> lighting simple
> lighting soft
Drag select of 1 residues
> select #5/D:159
6 atoms, 5 bonds, 1 residue, 1 model selected
> color sel byhetero
> save "/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV
> with Terns/20260111 IVC manuscript/IVC_DNA_bound/IVC_DNAbound_focus2.cxs"
[Repeated 1 time(s)]
——— End of log from Thu Jan 15 09:33:23 2026 ———
> view name session-start
opened ChimeraX session
> close session
> open "/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV
> with Terns/20260111 IVC
> manuscript/IVC_DNA_bound/cryosparc_P6_J91_004_volume_map.mrc"
Opened cryosparc_P6_J91_004_volume_map.mrc as #1, grid size 384,384,384, pixel
1.07, shown at level 0.0524, step 2, values float32
> open "/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV
> with Terns/20260111 IVC
> manuscript/IVC_DNA_bound/merged_real_space_refined_011.pdb"
Chain information for merged_real_space_refined_011.pdb #2
---
Chain | Description
A | No description available
C H I J K L | No description available
D | No description available
E | No description available
F | No description available
G | No description available
M | No description available
N O P Q R | No description available
S | No description available
> style stick
Changed 30524 atom styles
> show cartoons
> volume #1 step 1
> surface dust #1 size 10.7
> hide #!1 models
> hide #2
> hide #2 cartoons
> show #2/E:1-10
> show #2/F:37-47
> show #2/A
> select #2/A
4478 atoms, 4582 bonds, 1 pseudobond, 550 residues, 2 models selected
> ui tool show "Color Actions"
> color sel light sky blue
> select #2/F
972 atoms, 1090 bonds, 47 residues, 1 model selected
> ui tool show "Color Actions"
> color sel cornflower blue
> ui tool show "Color Actions"
> color sel deep sky blue
> color sel royal blue
> select #2/E
200 atoms, 222 bonds, 10 residues, 1 model selected
> color sel hot pink
> select #2/D
2438 atoms, 2496 bonds, 297 residues, 1 model selected
> show
> Hide
Unknown command: Hide
> hide
> undo
> show #2/D
> color sel red
> select add #2
30524 atoms, 31273 bonds, 3 pseudobonds, 3695 residues, 2 models selected
> select subtract #2
Nothing selected
> color byhetero
> undo
> show #2/D
[Repeated 1 time(s)]
> select #2/D
2438 atoms, 2496 bonds, 297 residues, 1 model selected
> ui tool show "Color Actions"
> color sel violet
> color sel light pink
> volume copy #1
Opened cryosparc_P6_J91_004_volume_map.mrc copy as #3, grid size 384,384,384,
pixel 1.07, shown at step 1, values float32
> volume #3 level 0.1685
> volume #1 level 0.1879
> color #1 #b2b2b2ad models
> color #3 #b2b2b2a9 models
> color #3 #b2b2b2a8 models
> volume #1 near #2/D range 3
Expected a keyword
> volume zone #1 nearAtoms #2/D range 3
> select add #2
30524 atoms, 31273 bonds, 3 pseudobonds, 3695 residues, 2 models selected
> hide #!1 models
> hide #!3 models
> select subtract #2
Nothing selected
> select add #2
30524 atoms, 31273 bonds, 3 pseudobonds, 3695 residues, 2 models selected
> select subtract #2
Nothing selected
> show #!1 models
> volume #1 level 0.2145
> volume zone #3 nearAtoms #2/A range 3
> hide #!1 models
> show #!3 models
> hide #!3 models
> select add #1
2 models selected
> show #!1 models
> ui tool show "Color Actions"
> color sel light pink
> color #1 #b2b2b29e models
[Repeated 1 time(s)]
> color #1 #b2b2b284 models
> color #1 #b2b2b280 models
> color #1 hotpink
> color #1 lightpink
> select ~sel & ##selected
Nothing selected
> color #1 hotpink transparency 20
> color #1 lightpink transparency
Missing "transparency" keyword's argument
> color #1 lightpink transparency 20
> color #1 lightpink transparency 60
> color #3 cornflowerblue transparency 60
> show #!3 models
> ui tool show "Color Actions"
> color #3 lightskyblue transparency 60
> volume #3 level 0.1491
> hide #2/F:42-47
> hide #2/F:37
> hide #!3 models
> hide #!1 models
> open "/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV
> with Terns/20260111 IVC
> manuscript/IVC_DNA_bound/cryosparc_P6_J91_004_volume_map.mrc"
Opened cryosparc_P6_J91_004_volume_map.mrc as #4, grid size 384,384,384, pixel
1.07, shown at level 0.0524, step 2, values float32
> volume #4 step 1
> close #1,3
> volume copy #4
Opened cryosparc_P6_J91_004_volume_map.mrc copy as #1, grid size 384,384,384,
pixel 1.07, shown at step 1, values float32
> volume #4 level 0.1491
> volume #1 level 0.154
> color #1 lightpink transparency 60
> color #4 lightskyblue transparency 60
> volume #4 level 0.2217
> volume #1 level 0.2217
> hide #2/E:1-5
> hide #2/E:10
> volume zone #1 nearAtoms #2/D range 4
> volume zone #4 nearAtoms #2/A range 4
> volume #4 level 0.1879
> volume #4 level 0.1927
> volume #4 level 0.212
> volume zone #4 nearAtoms #2/A range 2.5
> volume zone #1 nearAtoms #2/D range 2.5
> hide #2/A
> hide #2/D
> volume #4 level 0.1854
> volume #1 level 0.1951
> nucleotides fill
> style nucleic stick
Changed 2155 atom styles
> color byhetero
> nucleotides atoms
> style nucleic stick
Changed 2155 atom styles
> volume #1 level 0.1612
> select #2/A:434
11 atoms, 10 bonds, 1 residue, 1 model selected
> show (sel-residues & sidechain) target ab
> volume #4 level 0.2
> volume #4 level 0.1927
> volume #4 level 0.1975
> select #2/A:405
9 atoms, 8 bonds, 1 residue, 1 model selected
> show (sel-residues & sidechain) target ab
> select #2/D:159
6 atoms, 5 bonds, 1 residue, 1 model selected
> show (sel-residues & sidechain) target ab
> volume zone #4 nearAtoms #2/A range 23
> volume zone #4 nearAtoms #2/A range 2.3
> volume zone #4 nearAtoms #2/A range 2
> volume zone #4 nearAtoms #2/A range 2.3
> volume zone #4 nearAtoms #2/A range 2
> select add #2
30524 atoms, 31273 bonds, 3 pseudobonds, 3695 residues, 2 models selected
> select subtract #2
Nothing selected
> lighting full
> ui tool show "Side View"
> hbonds reveal true
3027 hydrogen bonds found
> ~hbonds
> undo
[Repeated 3 time(s)]
> hide #2
> show #2/E:5-9
> show #2/F:38-41
> hide #2/E:5
> hide #2/E:6
> select #2/D:159
6 atoms, 5 bonds, 1 residue, 1 model selected
> show (sel-residues & sidechain) target ab
> select #2/A:434
11 atoms, 10 bonds, 1 residue, 1 model selected
> show (sel-residues & sidechain) target ab
> select #2/A:405
9 atoms, 8 bonds, 1 residue, 1 model selected
> show (sel-residues & sidechain) target ab
> select add #2
30524 atoms, 31273 bonds, 3 pseudobonds, 3695 residues, 2 models selected
> select subtract #2
Nothing selected
> cartoon hide
> select add #2
30524 atoms, 31273 bonds, 3 pseudobonds, 3695 residues, 2 models selected
> select subtract #2
Nothing selected
> volume #4 level 0.2175
> open "/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV
> with Terns/20260111 IVC
> manuscript/IVC_DNA_bound/cryosparc_P6_J91_004_volume_map.mrc"
Opened cryosparc_P6_J91_004_volume_map.mrc as #3, grid size 384,384,384, pixel
1.07, shown at level 0.0524, step 2, values float32
> color #3 #f7f9fbff models
> color #3 #caccce8c models
> volume #3 step 1
> volume #3 level 0.1426
> color #3 lighskyblue transparency 60
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> select add #3
4 models selected
> ui tool show "Color Actions"
> color sel light sky blue
> ui tool show "Color Actions"
> volume #3 color #87cefa66
> volume #3 level 0.1376
> volume #4 level 0.1377
> volume zone #4 nearAtoms #2/A range 3
> volume #3 level 0.1526
> volume #4 level 0.1477
> volume #4 level 0.2
> volume #1 level 0.1762
> volume #1 level 0.2484
> lighting full
> lighting flat
> volume #4 level 0.21
> volume #4 level 0.2274
> save "/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV
> with Terns/20260111 IVC manuscript/IVC_DNA_bound/IVC_DNAbound_PAM1.cxs"
——— End of log from Sun Feb 1 21:27:29 2026 ———
> view name session-start
opened ChimeraX session
> select #2/A:1-404,406-433,435-600
4458 atoms, 4560 bonds, 1 pseudobond, 548 residues, 2 models selected
> surface (#!2 & sel)
> hide #!4 models
> surface sel transparency 90
> hide #!1 models
> select #2/D:1-158, 160-500
2432 atoms, 2489 bonds, 296 residues, 1 model selected
> surface sel
> surface sel transparency 90
> undo
> surface #2/A transparecy 90
Expected a keyword
> surface #2/A transparency 90
> surface #2/D transparency 90
> ui tool show "Side View"
> hide #2/E:6
> hide #2/F:41
> select add #2
30524 atoms, 31273 bonds, 3 pseudobonds, 3695 residues, 7 models selected
> select subtract #2
2 models selected
> show #2/A:532 & ~@N,CA,C,O
> show #2/A:532 & ~@N,C,O
> save /Users/xuchengtao/Desktop/image216.png supersample 3
> save "/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV
> with Terns/20260111 IVC manuscript/IVC_DNA_bound/IVC_DNAbound_PAM3.cxs"
> save /Users/xuchengtao/Desktop/image217.png supersample 3
> lighting soft
> lighting full
> lighting simple
> lighting soft
> lighting simple
> lighting soft
> ui tool show "Color Actions"
> color #2/F dodgerblue
> color byhetero
> undo
> color #2/F byhetero
> save /Users/xuchengtao/Desktop/image218.png supersample 3
> save /Users/xuchengtao/Desktop/image219.png supersample 3
> save "/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV
> with Terns/20260111 IVC manuscript/IVC_DNA_bound/IVC_DNAbound_PAM2.cxs"
> close session
> open "/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV
> with Terns/20260111 IVC
> manuscript/IVC_DNA_bound/merged_real_space_refined_011.pdb"
Chain information for merged_real_space_refined_011.pdb #1
---
Chain | Description
A | No description available
C H I J K L | No description available
D | No description available
E | No description available
F | No description available
G | No description available
M | No description available
N O P Q R | No description available
S | No description available
> open "/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV
> with Terns/20260111 IVC manuscript/IVC_Apo/merged_ivc_apo_refine_007.pdb"
Summary of feedback from opening
/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV with
Terns/20260111 IVC manuscript/IVC_Apo/merged_ivc_apo_refine_007.pdb
---
warning | Start residue of secondary structure not found: HELIX 149 149 ILE P 16 ILE P 30 1 15
Chain information for merged_ivc_apo_refine_007.pdb #2
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E F G H | No description available
I | No description available
J | No description available
K L M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
> combine #1
> combine #2
> hide
> show #3/A
> show #4/A
> style stick
Changed 124372 atom styles
> color byhetero
> show #3/E:1-10
> show #3/F:37-47
> mmaker #4/A to #3/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 copy of merged_real_space_refined_011.pdb, chain A (#3) with copy
of merged_ivc_apo_refine_007.pdb, chain A (#4), sequence alignment score =
2305.8
RMSD between 212 pruned atom pairs is 1.103 angstroms; (across all 504 pairs:
3.208)
> show cartoons
> undo
> hide #!4 models
> show #!4 models
> hide #!4 models
> hide #!2 models
> hide #!1 models
> select #3/A
4478 atoms, 4582 bonds, 1 pseudobond, 550 residues, 2 models selected
> show sel cartoons
> ui tool show "Color Actions"
> color sel light sky blue
> color sel byhetero
> cartoon style (#!3 & sel) xsection oval modeHelix default
> cartoon style (#!3 & sel) modeHelix tube sides 20
> hide (#!3 & sel) target a
> color #3/A transparency 10
> select #3/E,F
1172 atoms, 1312 bonds, 57 residues, 1 model selected
> show sel cartoons
> undo
> select #3/E:1-10
200 atoms, 222 bonds, 10 residues, 1 model selected
> show sel cartoons
> select #3/F:37-47
232 atoms, 261 bonds, 11 residues, 1 model selected
> show sel cartoons
> ui tool show "Color Actions"
> color sel dodger blue
> color sel byhetero
> select #3/E:1-10
200 atoms, 222 bonds, 10 residues, 1 model selected
> ui tool show "Color Actions"
> color sel hot pink
> color sel byhetero
> nucleotides sel fill
> style nucleic & sel stick
Changed 200 atom styles
> select #3/F:37-47
232 atoms, 261 bonds, 11 residues, 1 model selected
> nucleotides sel fill
> style nucleic & sel stick
Changed 232 atom styles
> select #4/A
4099 atoms, 4193 bonds, 3 pseudobonds, 504 residues, 2 models selected
> show #!3 cartoons
> undo
> show sel cartoons
> show #!4 models
> hide sel atoms
> color sel white transcparency 70
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> color sel white transparency 70
> lighting soft
> select add #4
31662 atoms, 32360 bonds, 17 pseudobonds, 3888 residues, 2 models selected
> select subtract #4
Nothing selected
> mmaker #4/A: 70, 93, 94, 115,146,147,159
> matchmaker #4/A: 70, 93, 94, 115,146,147,159
Missing required "to" argument
> mmaker #4/A: 70, 93, 94, 115,146,147,159 to #3/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 copy of merged_real_space_refined_011.pdb, chain A (#3) with copy
of merged_ivc_apo_refine_007.pdb, chain A (#4), sequence alignment score =
45.3
RMSD between 7 pruned atom pairs is 0.873 angstroms; (across all 7 pairs:
0.873)
> select #4/A
4099 atoms, 4193 bonds, 3 pseudobonds, 504 residues, 2 models selected
> cartoon style (#!4 & sel) modeHelix tube sides 20
> select add #4
31662 atoms, 32360 bonds, 17 pseudobonds, 3888 residues, 2 models selected
> select subtract #4
Nothing selected
> select #3/A
4478 atoms, 4582 bonds, 1 pseudobond, 550 residues, 2 models selected
> color sel transparency 30
> select add #3
30524 atoms, 31273 bonds, 3 pseudobonds, 3695 residues, 2 models selected
> select subtract #3
Nothing selected
> save /Users/xuchengtao/Desktop/image220.png supersample 3
> save "/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV
> with Terns/20260111 IVC
> manuscript/IVC_DNA_bound/IVC_DNAbound_HD_compare_apo_1.cxs"
> measure motion #3/A toModel #4/A showVectors true color cyan
Missing or invalid "surface" argument: Require 1 surface, got 0
> measure rotation #3/A toModel #4/A showVectors true color cyan
Expected a keyword
> measure rotation #3/A toModel #4/A showAxis true color cyan
Position of copy of merged_real_space_refined_011.pdb #3 relative to copy of
merged_ivc_apo_refine_007.pdb #4 coordinates:
Matrix rotation and translation
-0.99736182 -0.00562907 0.07237203 460.06370117
0.01683128 0.95188599 0.30598983 -17.09119514
-0.07061236 0.30640068 -0.94928000 404.90437477
Axis 0.00283863 0.98788229 0.15517902
Axis point 237.34717297 0.00000000 195.36024542
Rotation angle (degrees) 175.84992537
Shift along axis 47.25452561
> measure rotation #3/A toModel #4/A coordinateSystem#4/A showAxis true color
> cyan
Expected a keyword
> measure rotation #3/A toModel #4/A coordinateSystem #4/A showAxis true color
> cyan
Position of copy of merged_real_space_refined_011.pdb #3 relative to copy of
merged_ivc_apo_refine_007.pdb #4 in copy of merged_ivc_apo_refine_007.pdb #4
coordinate system:
Matrix rotation and translation
-0.99736182 -0.00562907 0.07237203 460.06370117
0.01683128 0.95188599 0.30598983 -17.09119514
-0.07061236 0.30640068 -0.94928000 404.90437477
Axis 0.00283863 0.98788229 0.15517902
Axis point 237.34717297 0.00000000 195.36024542
Rotation angle (degrees) 175.84992537
Shift along axis 47.25452561
> measure rotation #3/A toModel #4/A coordinateSystem #4/A showSlabs true
> color cyan
Position of copy of merged_real_space_refined_011.pdb #3 relative to copy of
merged_ivc_apo_refine_007.pdb #4 in copy of merged_ivc_apo_refine_007.pdb #4
coordinate system:
Matrix rotation and translation
-0.99736182 -0.00562907 0.07237203 460.06370117
0.01683128 0.95188599 0.30598983 -17.09119514
-0.07061236 0.30640068 -0.94928000 404.90437477
Axis 0.00283863 0.98788229 0.15517902
Axis point 237.34717297 0.00000000 195.36024542
Rotation angle (degrees) 175.84992537
Shift along axis 47.25452561
> measure rotation #3/A toModel #4/A showSlabs true color cyan
Position of copy of merged_real_space_refined_011.pdb #3 relative to copy of
merged_ivc_apo_refine_007.pdb #4 coordinates:
Matrix rotation and translation
-0.99736182 -0.00562907 0.07237203 460.06370117
0.01683128 0.95188599 0.30598983 -17.09119514
-0.07061236 0.30640068 -0.94928000 404.90437477
Axis 0.00283863 0.98788229 0.15517902
Axis point 237.34717297 0.00000000 195.36024542
Rotation angle (degrees) 175.84992537
Shift along axis 47.25452561
> measure rotation #3 toModel #4/A showSlabs true color cyan
Position of copy of merged_real_space_refined_011.pdb #3 relative to copy of
merged_ivc_apo_refine_007.pdb #4 coordinates:
Matrix rotation and translation
-0.99736182 -0.00562907 0.07237203 460.06370117
0.01683128 0.95188599 0.30598983 -17.09119514
-0.07061236 0.30640068 -0.94928000 404.90437477
Axis 0.00283863 0.98788229 0.15517902
Axis point 237.34717297 0.00000000 195.36024542
Rotation angle (degrees) 175.84992537
Shift along axis 47.25452561
> measure rotation #3 toModel #4 showSlabs true color cyan
Position of copy of merged_real_space_refined_011.pdb #3 relative to copy of
merged_ivc_apo_refine_007.pdb #4 coordinates:
Matrix rotation and translation
-0.99736182 -0.00562907 0.07237203 460.06370117
0.01683128 0.95188599 0.30598983 -17.09119514
-0.07061236 0.30640068 -0.94928000 404.90437477
Axis 0.00283863 0.98788229 0.15517902
Axis point 237.34717297 0.00000000 195.36024542
Rotation angle (degrees) 175.84992537
Shift along axis 47.25452561
> measure rotation #3 toModel #4 showSlabs true color cyan
Position of copy of merged_real_space_refined_011.pdb #3 relative to copy of
merged_ivc_apo_refine_007.pdb #4 coordinates:
Matrix rotation and translation
-0.99736182 -0.00562907 0.07237203 460.06370117
0.01683128 0.95188599 0.30598983 -17.09119514
-0.07061236 0.30640068 -0.94928000 404.90437477
Axis 0.00283863 0.98788229 0.15517902
Axis point 237.34717297 0.00000000 195.36024542
Rotation angle (degrees) 175.84992537
Shift along axis 47.25452561
> measure rotation #3 toModel #4 showSlabs true color cyan
Position of copy of merged_real_space_refined_011.pdb #3 relative to copy of
merged_ivc_apo_refine_007.pdb #4 coordinates:
Matrix rotation and translation
-0.99736182 -0.00562907 0.07237203 460.06370117
0.01683128 0.95188599 0.30598983 -17.09119514
-0.07061236 0.30640068 -0.94928000 404.90437477
Axis 0.00283863 0.98788229 0.15517902
Axis point 237.34717297 0.00000000 195.36024542
Rotation angle (degrees) 175.84992537
Shift along axis 47.25452561
> measure rotation #3 toModel #4 showSlabs true color cyan
Position of copy of merged_real_space_refined_011.pdb #3 relative to copy of
merged_ivc_apo_refine_007.pdb #4 coordinates:
Matrix rotation and translation
-0.99736182 -0.00562907 0.07237203 460.06370117
0.01683128 0.95188599 0.30598983 -17.09119514
-0.07061236 0.30640068 -0.94928000 404.90437477
Axis 0.00283863 0.98788229 0.15517902
Axis point 237.34717297 0.00000000 195.36024542
Rotation angle (degrees) 175.84992537
Shift along axis 47.25452561
> measure rotation #3 toModel #4 showSlabs true color cyan
Position of copy of merged_real_space_refined_011.pdb #3 relative to copy of
merged_ivc_apo_refine_007.pdb #4 coordinates:
Matrix rotation and translation
-0.99736182 -0.00562907 0.07237203 460.06370117
0.01683128 0.95188599 0.30598983 -17.09119514
-0.07061236 0.30640068 -0.94928000 404.90437477
Axis 0.00283863 0.98788229 0.15517902
Axis point 237.34717297 0.00000000 195.36024542
Rotation angle (degrees) 175.84992537
Shift along axis 47.25452561
> close #5-22
> morph #4/A,#3/A frames 2 showVectors true
Missing or invalid "structures" argument: only initial part "#4/A" of atom
specifier valid
> morph #4/A #3/A frames 2 showVectors true
Expected a keyword
> morph #4/A #3/A frames 60
models have different number of chains, 19 (Morph - copy of
merged_ivc_apo_refine_007.pdb #/A,Morph - copy of
merged_ivc_apo_refine_007.pdb #/B,Morph - copy of
merged_ivc_apo_refine_007.pdb #/C,Morph - copy of
merged_ivc_apo_refine_007.pdb #/D,Morph - copy of
merged_ivc_apo_refine_007.pdb #/E,Morph - copy of
merged_ivc_apo_refine_007.pdb #/F,Morph - copy of
merged_ivc_apo_refine_007.pdb #/G,Morph - copy of
merged_ivc_apo_refine_007.pdb #/H,Morph - copy of
merged_ivc_apo_refine_007.pdb #/I,Morph - copy of
merged_ivc_apo_refine_007.pdb #/J,Morph - copy of
merged_ivc_apo_refine_007.pdb #/K,Morph - copy of
merged_ivc_apo_refine_007.pdb #/L,Morph - copy of
merged_ivc_apo_refine_007.pdb #/M,Morph - copy of
merged_ivc_apo_refine_007.pdb #/N,Morph - copy of
merged_ivc_apo_refine_007.pdb #/O,Morph - copy of
merged_ivc_apo_refine_007.pdb #/P,Morph - copy of
merged_ivc_apo_refine_007.pdb #/Q,Morph - copy of
merged_ivc_apo_refine_007.pdb #/R,Morph - copy of
merged_ivc_apo_refine_007.pdb #/S) and 18 (copy of
merged_real_space_refined_011.pdb #3/A,copy of
merged_real_space_refined_011.pdb #3/C,copy of
merged_real_space_refined_011.pdb #3/D,copy of
merged_real_space_refined_011.pdb #3/E,copy of
merged_real_space_refined_011.pdb #3/F,copy of
merged_real_space_refined_011.pdb #3/G,copy of
merged_real_space_refined_011.pdb #3/H,copy of
merged_real_space_refined_011.pdb #3/I,copy of
merged_real_space_refined_011.pdb #3/J,copy of
merged_real_space_refined_011.pdb #3/K,copy of
merged_real_space_refined_011.pdb #3/L,copy of
merged_real_space_refined_011.pdb #3/M,copy of
merged_real_space_refined_011.pdb #3/N,copy of
merged_real_space_refined_011.pdb #3/O,copy of
merged_real_space_refined_011.pdb #3/P,copy of
merged_real_space_refined_011.pdb #3/Q,copy of
merged_real_space_refined_011.pdb #3/R,copy of
merged_real_space_refined_011.pdb #3/S)
> morph #4/A,#3/A frames 60
Missing or invalid "structures" argument: only initial part "#4/A" of atom
specifier valid
> select #3/A
4478 atoms, 4582 bonds, 1 pseudobond, 550 residues, 2 models selected
> save "/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV
> with Terns/20260111 IVC manuscript/IVC_DNA_bound/Cas10_bound.pdb" models #3
> selectedOnly true relModel #3
> select #4/A
4099 atoms, 4193 bonds, 3 pseudobonds, 504 residues, 2 models selected
> save "/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV
> with Terns/20260111 IVC manuscript/IVC_DNA_bound/Cas10_apo.pdb" models #4
> selectedOnly true relModel #3
> open "/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV
> with Terns/20260111 IVC manuscript/IVC_DNA_bound/Cas10_apo.pdb"
Summary of feedback from opening
/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV with
Terns/20260111 IVC manuscript/IVC_DNA_bound/Cas10_apo.pdb
---
warnings | Start residue of secondary structure not found: HELIX 19 19 LEU B 30 ASN B 46 1 17
Start residue of secondary structure not found: HELIX 20 20 ARG B 51 THR B 60
1 10
Start residue of secondary structure not found: HELIX 21 21 LYS B 135 LEU B
143 1 9
Start residue of secondary structure not found: HELIX 22 22 GLN B 187 LYS B
199 1 13
Start residue of secondary structure not found: HELIX 23 23 PRO B 249 THR B
257 1 9
209 messages similar to the above omitted
Chain information for Cas10_apo.pdb #5
---
Chain | Description
A | No description available
> open "/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV
> with Terns/20260111 IVC manuscript/IVC_DNA_bound/Cas10_bound.pdb"
Summary of feedback from opening
/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV with
Terns/20260111 IVC manuscript/IVC_DNA_bound/Cas10_bound.pdb
---
warnings | Start residue of secondary structure not found: HELIX 20 20 GLY C 46 SER C 72 1 27
Start residue of secondary structure not found: HELIX 21 21 ILE C 81 PHE C 88
1 8
Start residue of secondary structure not found: HELIX 22 22 ILE C 105 LYS C
111 1 7
Start residue of secondary structure not found: HELIX 23 23 LEU C 117 MET C
122 1 6
Start residue of secondary structure not found: HELIX 24 24 MET C 180 MET C
184 1 5
203 messages similar to the above omitted
Chain information for Cas10_bound.pdb #6
---
Chain | Description
A | No description available
> hide #!3 models
> hide #!4 models
> select add #4
31662 atoms, 32360 bonds, 17 pseudobonds, 3888 residues, 2 models selected
> select subtract #4
Nothing selected
> select add #6
4478 atoms, 4582 bonds, 1 pseudobond, 550 residues, 2 models selected
> ui tool show "Color Actions"
> color sel light sky blue
> select add #5
8577 atoms, 8775 bonds, 4 pseudobonds, 1054 residues, 4 models selected
> select subtract #6
4099 atoms, 4193 bonds, 3 pseudobonds, 504 residues, 2 models selected
> ui tool show "Color Actions"
> color sel white
> color #5 #ffffffb3
> color #5 #ffffff4d
> select add #6
8577 atoms, 8775 bonds, 4 pseudobonds, 1054 residues, 4 models selected
> cartoon style (#!5-6 & sel) modeHelix tube sides 20
> select subtract #5
4478 atoms, 4582 bonds, 1 pseudobond, 550 residues, 2 models selected
> select subtract #6
Nothing selected
> morph #5,#6 frames 60
Missing or invalid "structures" argument: only initial part "#5" of atom
specifier valid
> morph #5 #6 frames 60
Computed 61 frame morph #7
> coordset #7 1,61
> morph #5 #6 frames 30
Computed 31 frame morph #8
> coordset #8 1,31
> close #7
> select add #8
4095 atoms, 4189 bonds, 3 pseudobonds, 504 residues, 2 models selected
> ui tool show "Color Actions"
> color sel light sky blue
> select subtract #8
Nothing selected
> save "/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV
> with Terns/20260111 IVC
> manuscript/IVC_DNA_bound/IVC_DNAbound_HD_compare_apo_2_movie1.cxs"
——— End of log from Mon Feb 2 10:29:38 2026 ———
> view name session-start
opened ChimeraX session
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!1 models
> show #1
> hide #!1 models
> show #!2 models
> show #2
> mmaker #2 to #1
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 merged_real_space_refined_011.pdb, chain A (#1) with
merged_ivc_apo_refine_007.pdb, chain A (#2), sequence alignment score = 2305.8
RMSD between 212 pruned atom pairs is 1.103 angstroms; (across all 504 pairs:
3.208)
> show #!1 models
> hide #!1 models
> hide #!2 models
> show #!1 models
> show #!2 models
> hide #!1 models
> hide #!2 models
> open "/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV
> with Terns/20260111 IVC manuscript/IVC_DNA_bound/Cas10_bound.pdb"
Summary of feedback from opening
/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV with
Terns/20260111 IVC manuscript/IVC_DNA_bound/Cas10_bound.pdb
---
warnings | Start residue of secondary structure not found: HELIX 20 20 GLY C 46 SER C 72 1 27
Start residue of secondary structure not found: HELIX 21 21 ILE C 81 PHE C 88
1 8
Start residue of secondary structure not found: HELIX 22 22 ILE C 105 LYS C
111 1 7
Start residue of secondary structure not found: HELIX 23 23 LEU C 117 MET C
122 1 6
Start residue of secondary structure not found: HELIX 24 24 MET C 180 MET C
184 1 5
203 messages similar to the above omitted
Chain information for Cas10_bound.pdb #7
---
Chain | Description
A | No description available
> close session
> open "/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV
> with Terns/20260111 IVC manuscript/IVC_DNA_bound/Cas10_bound.pdb" format pdb
Summary of feedback from opening
/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV with
Terns/20260111 IVC manuscript/IVC_DNA_bound/Cas10_bound.pdb
---
warnings | Start residue of secondary structure not found: HELIX 20 20 GLY C 46 SER C 72 1 27
Start residue of secondary structure not found: HELIX 21 21 ILE C 81 PHE C 88
1 8
Start residue of secondary structure not found: HELIX 22 22 ILE C 105 LYS C
111 1 7
Start residue of secondary structure not found: HELIX 23 23 LEU C 117 MET C
122 1 6
Start residue of secondary structure not found: HELIX 24 24 MET C 180 MET C
184 1 5
203 messages similar to the above omitted
Chain information for Cas10_bound.pdb #1
---
Chain | Description
A | No description available
> select #1/A:1-335
2374 atoms, 2430 bonds, 1 pseudobond, 290 residues, 2 models selected
> save "/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV
> with Terns/20260111 IVC manuscript/IVC_DNA_bound/Cas10_bound_1_335.pdb"
> selectedOnly true relModel #1
> select #1/A:335-437
801 atoms, 815 bonds, 103 residues, 1 model selected
> save "/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV
> with Terns/20260111 IVC manuscript/IVC_DNA_bound/Cas10_bound_335_437.pdb"
> selectedOnly true relModel #1
> select #1/A:437-900
1314 atoms, 1347 bonds, 159 residues, 1 model selected
> save "/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV
> with Terns/20260111 IVC manuscript/IVC_DNA_bound/Cas10_bound_437_Cterm.pdb"
> relModel #1
> view matrix models #1,1,0,0,0.00059032,0,1,0,-0.020052,0,0,1,0.0076704
> select #1/A:50-180
1058 atoms, 1086 bonds, 131 residues, 1 model selected
> save "/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV
> with Terns/20260111 IVC manuscript/IVC_DNA_bound/Cas10_bound_50_180.pdb"
> selectedOnly true relModel #1
> open 7tr8
7tr8 title:
Cascade complex from type I-A CRISPR-Cas system [more info...]
Chain information for 7tr8 #2
---
Chain | Description | UniProt
A | CRISPR-associated helicase Cas3 | A0A5C0XNV5_PYRFU 10-516
C | Cas8 | Q8U338_PYRFU 2-342
D E F G H | Cas11a | Q8U332_PYRFU 2-109
I J K L M N O | Cas7a | Q8U333_PYRFU 1-336
P | Cas5a | A0A5C0XNV9_PYRFU 1-256
Q | CRISPR-associated endonuclease Cas3-HD | CS3HD_PYRFU 2-216
R | crRNA (45-MER) |
Non-standard residues in 7tr8 #2
---
NI — nickel (II) ion
> select add #1
4478 atoms, 4582 bonds, 1 pseudobond, 550 residues, 2 models selected
> hide #!1 models
> select subtract #1
Nothing selected
> style #!2 stick
Changed 33581 atom styles
> show #!2 atoms
> show #!2 cartoons
> color #!2 byhetero
> hide #!2 atoms
> cartoon style #2 modeHelix tube sides 20
> show #!2 cartoons
> show #!2 atoms
> hide #!2 cartoons
> show #!2 atoms
> show #!2 cartoons
> hide #!2 atoms
> open "/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV
> with Terns/20260111 IVC manuscript/IVC_DNA_bound/Cas10_bound_335_437.pdb"
Summary of feedback from opening
/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV with
Terns/20260111 IVC manuscript/IVC_DNA_bound/Cas10_bound_335_437.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 SER A 40 SER A 44 1 5
Start residue of secondary structure not found: HELIX 2 2 LEU A 67 PHE A 81 1
15
Start residue of secondary structure not found: HELIX 3 3 GLY A 84 ILE A 92 1
9
Start residue of secondary structure not found: HELIX 4 4 GLN A 120 PHE A 130
1 11
Start residue of secondary structure not found: HELIX 5 5 LYS A 138 LYS A 144
1 7
18 messages similar to the above omitted
Cannot find LINK/SSBOND residue CYS (152 )
Chain information for Cas10_bound_335_437.pdb #3
---
Chain | Description
A | No description available
> mmaker #3 to #2
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 7tr8, chain A (#2) with Cas10_bound_335_437.pdb, chain A (#3),
sequence alignment score = 65.9
RMSD between 7 pruned atom pairs is 1.051 angstroms; (across all 100 pairs:
14.603)
> close #2
> open /Users/xuchengtao/Downloads/AF-A0A7V6NIE4-F1-model_v6.pdb
Summary of feedback from opening
/Users/xuchengtao/Downloads/AF-A0A7V6NIE4-F1-model_v6.pdb
---
warning | Ignored bad PDB record found on line 38
DBREF XXXX A 1 478 UNP A0A7V6NIE4 A0A7V6NIE4_9CLOT 1 478
AF-A0A7V6NIE4-F1-model_v6.pdb title:
Alphafold monomer V2.0 prediction for type I-B crispr-associated protein
CAS8B1/CST1 (A0A7V6NIE4) [more info...]
Chain information for AF-A0A7V6NIE4-F1-model_v6.pdb #2
---
Chain | Description
A | type I-B crispr-associated protein CAS8B1/CST1
Computing secondary structure
> mmaker #3 to #2
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 AF-A0A7V6NIE4-F1-model_v6.pdb, chain A (#2) with
Cas10_bound_335_437.pdb, chain A (#3), sequence alignment score = 104.6
RMSD between 26 pruned atom pairs is 0.744 angstroms; (across all 98 pairs:
9.407)
> ui tool show "Selection Inspector"
> center #2
Unknown command: center #2
> center
Unknown command: center
> cofr
Center of rotation: -9.0432 -2.4508 11.129 front center
> cofr #2
> show #!1 models
> hide #!1 models
> show #!1 models
> select #1/A:55-150
785 atoms, 809 bonds, 96 residues, 1 model selected
> save "/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV
> with Terns/20260111 IVC manuscript/IVC_DNA_bound/Cas10_bound_55_150.pdb"
> models #1 selectedOnly true relModel #1
> select #1/A:437-500
539 atoms, 550 bonds, 64 residues, 1 model selected
> save "/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV
> with Terns/20260111 IVC manuscript/IVC_DNA_bound/Cas10_bound_437_Cterm.pdb"
> models #1 selectedOnly true relModel #1
> open 6TH
'6TH' has no suffix
> open 6THH
Summary of feedback from opening 6THH fetched from pdb
---
note | Fetching compressed mmCIF 6thh from http://files.rcsb.org/download/6thh.cif
6thh title:
Crystal structure of type I-D CRISPR-Cas nuclease Cas10d in complex with the
SIRV3 AcrID1 (gp02) anti-CRISPR protein [more info...]
Chain information for 6thh #4
---
Chain | Description | UniProt
A B | SIRV3 AcrID1 (gp02) anti-CRISPR protein | A0A1B3SN05_9VIRU 1-96
C | CRISPR-associated protein, CscA | M9U4Y8_SULIS 1-847
Non-standard residues in 6thh #4
---
PO4 — phosphate ion
ZN — zinc ion
6thh mmCIF Assemblies
---
1| author_defined_assembly
> select add #1
4478 atoms, 4582 bonds, 1 pseudobond, 550 residues, 2 models selected
> select add #4
12721 atoms, 12994 bonds, 8 pseudobonds, 1560 residues, 6 models selected
> mmaker #1 to #4
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 6thh, chain C (#4) with Cas10_bound.pdb, chain A (#1), sequence
alignment score = 154.1
RMSD between 22 pruned atom pairs is 1.050 angstroms; (across all 409 pairs:
40.667)
> select subtract #4
4478 atoms, 4582 bonds, 1 pseudobond, 550 residues, 2 models selected
> select subtract #1
Nothing selected
> cofr #4/C
> open 6Yes
Summary of feedback from opening 6Yes fetched from pdb
---
note | Fetching compressed mmCIF 6yes from http://files.rcsb.org/download/6yes.cif
6yes title:
Crystal structure of type I-D CRISPR-Cas nuclease Cas10d [more info...]
Chain information for 6yes #5
---
Chain | Description | UniProt
A B | CRISPR-associated protein, CscA | M9U4Y8_SULIS 1-847
Non-standard residues in 6yes #5
---
ZN — zinc ion
6yes mmCIF Assemblies
---
1| author_defined_assembly
2| author_defined_assembly
> select #5/A:14-847
6325 atoms, 6448 bonds, 3 pseudobonds, 791 residues, 2 models selected
> hide #2 models
> hide #3 models
> mmaker #1 to #5
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 6yes, chain A (#5) with Cas10_bound.pdb, chain A (#1), sequence
alignment score = 135.7
RMSD between 11 pruned atom pairs is 1.193 angstroms; (across all 431 pairs:
32.783)
> hide #!1 models
> select add #5
12534 atoms, 12775 bonds, 10 pseudobonds, 1569 residues, 4 models selected
> show #!1 models
> select subtract #5
Nothing selected
> select #5/B:14-844
6207 atoms, 6327 bonds, 2 pseudobonds, 776 residues, 2 models selected
> hide #5/B cartoons
> hide #5/B
> select add #1
10685 atoms, 10909 bonds, 3 pseudobonds, 1326 residues, 4 models selected
> select add #5
17012 atoms, 17357 bonds, 11 pseudobonds, 2119 residues, 6 models selected
> select subtract #5
4478 atoms, 4582 bonds, 1 pseudobond, 550 residues, 2 models selected
> view matrix models
> #1,0.66911,0.7076,-0.22714,-278.82,-0.74159,0.61589,-0.26594,125.06,-0.048282,0.34639,0.93685,-320.82
> view matrix models
> #1,0.10857,0.58169,-0.80613,28.689,-0.99406,0.069538,-0.083697,235.53,0.0073718,0.81043,0.58578,-325.5
> view matrix models
> #1,-0.049471,0.44584,-0.89374,113.79,-0.99529,0.052664,0.081364,193.82,0.083344,0.89356,0.44114,-318.66
> view matrix models
> #1,0.21172,0.80335,-0.5566,-104.87,-0.96736,0.091101,-0.23648,267.3,-0.13927,0.5885,0.79641,-308.2
> view matrix models
> #1,0.30895,0.91561,-0.25732,-216.38,-0.8958,0.18925,-0.40214,261.48,-0.31951,0.35475,0.87867,-230.9
> select subtract #1
Nothing selected
> select add #1
4478 atoms, 4582 bonds, 1 pseudobond, 550 residues, 2 models selected
> select subtract #1
Nothing selected
> cofr #1
> select add #1
4478 atoms, 4582 bonds, 1 pseudobond, 550 residues, 2 models selected
> view matrix models
> #1,0.30895,0.91561,-0.25732,-257.59,-0.8958,0.18925,-0.40214,262.52,-0.31951,0.35475,0.87867,-278.37
> ui tool show "Show Sequence Viewer"
> sequence chain #4/C #5/A #5/B
Alignment identifier is 1
> close #4
> ui tool show "Show Sequence Viewer"
> sequence chain #5/A #5/B
Alignment identifier is 1
> select #5/A-B:93
20 atoms, 20 bonds, 2 residues, 1 model selected
> select #5/A-B:93-94
36 atoms, 36 bonds, 4 residues, 1 model selected
> show sel atoms
> select add #5
12534 atoms, 12775 bonds, 10 pseudobonds, 1569 residues, 4 models selected
> show sel atoms
> close #5
> open 7SBA
Summary of feedback from opening 7SBA fetched from pdb
---
note | Fetching compressed mmCIF 7sba from http://files.rcsb.org/download/7sba.cif
7sba title:
Structure of type I-D Cascade bound to a dsDNA target [more info...]
Chain information for 7sba #4
---
Chain | Description | UniProt
A B C D E F G | Cas7d | Q6ZEI6_SYNY3 1-329
H | Cas5d | Q6ZEI5_SYNY3 1-254
I | Cas10d | Q6ZEI7_SYNY3 1-975
J K | Cas11d | Q6ZEI7_SYNY3 1-146
X | DNA target strand |
Y | DNA non-target strand |
Z | crRNA |
> sequence chain #4/I
Alignment identifier is 4/I
> mmaker #1 to #4/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 7sba, chain I (#4) with Cas10_bound.pdb, chain A (#1), sequence
alignment score = 131.1
RMSD between 14 pruned atom pairs is 1.230 angstroms; (across all 409 pairs:
37.869)
> cofr #4/I
> show #!1,4 atoms
> hide #!1,4 atoms
> show #!1,4 cartoons
> select #4/I:975
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #4/I:767-975
1719 atoms, 1747 bonds, 209 residues, 1 model selected
> select add #4
30651 atoms, 31399 bonds, 35 pseudobonds, 3741 residues, 3 models selected
> select subtract #4
Nothing selected
> select clear
> select #4/I:2-226
1300 atoms, 1329 bonds, 3 pseudobonds, 159 residues, 2 models selected
> select #4/I:115-116
18 atoms, 18 bonds, 2 residues, 1 model selected
> select #4/I:115-116
18 atoms, 18 bonds, 2 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 18 atom styles
> color sel byhetero
> select #4/I:210
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #4/I:210-211
15 atoms, 14 bonds, 2 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 15 atom styles
> color sel byhetero
> select #4/I:81
10 atoms, 10 bonds, 1 residue, 1 model selected
> select #4/I:81-83
26 atoms, 26 bonds, 3 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 26 atom styles
> color sel byhetero
> select add #1
4504 atoms, 4608 bonds, 1 pseudobond, 553 residues, 3 models selected
> select subtract #1
26 atoms, 26 bonds, 3 residues, 1 model selected
> select add #4
30651 atoms, 31399 bonds, 35 pseudobonds, 3741 residues, 3 models selected
> select subtract #4
Nothing selected
> select add #1
4478 atoms, 4582 bonds, 1 pseudobond, 550 residues, 2 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #1,-0.92899,-0.15763,0.33486,365.26,0.26402,-0.9163,0.30113,305.54,0.25937,0.36815,0.89286,-130.81
> view matrix models
> #1,-0.92168,0.011683,0.38778,316.88,0.0013436,-0.99944,0.033304,453.28,0.38795,0.031217,0.92115,-103.03
> view matrix models
> #1,-0.97299,-0.20139,0.11281,444.21,0.17741,-0.96509,-0.19269,469.37,0.14768,-0.16747,0.97475,-26.294
> view matrix models
> #1,-0.95377,-0.085947,0.28798,372.04,0.068101,-0.99512,-0.071442,471.83,0.29272,-0.048527,0.95497,-83.653
> view matrix models
> #1,-0.95377,-0.085947,0.28798,372.22,0.068101,-0.99512,-0.071442,471.54,0.29272,-0.048527,0.95497,-83.902
> view matrix models
> #1,-0.95377,-0.085947,0.28798,372.37,0.068101,-0.99512,-0.071442,467.5,0.29272,-0.048527,0.95497,-81.992
> view matrix models
> #1,-0.92916,-0.3413,0.14206,455.49,0.36415,-0.77877,0.51079,200.84,-0.063704,0.52634,0.84789,-82.728
> view matrix models
> #1,-0.92916,-0.3413,0.14206,455.32,0.36415,-0.77877,0.51079,188.2,-0.063704,0.52634,0.84789,-75.666
> view matrix models
> #1,-0.92916,-0.3413,0.14206,451.36,0.36415,-0.77877,0.51079,174.97,-0.063704,0.52634,0.84789,-54.964
> view matrix models
> #1,-0.92916,-0.3413,0.14206,455.29,0.36415,-0.77877,0.51079,178.31,-0.063704,0.52634,0.84789,-63.121
> view matrix models
> #1,-0.86919,-0.39526,0.29711,409.74,0.49112,-0.75998,0.42572,169.72,0.057532,0.51595,0.85469,-90.031
> select #1/A:94,93,159,115
37 atoms, 36 bonds, 4 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 37 atom styles
> color sel byhetero
> view matrix models
> #1,-0.86919,-0.39526,0.29711,405.12,0.49112,-0.75998,0.42572,166.84,0.057532,0.51595,0.85469,-75.68
> view matrix models
> #1,-0.86919,-0.39526,0.29711,405.72,0.49112,-0.75998,0.42572,169.37,0.057532,0.51595,0.85469,-78.05
> view matrix models
> #1,-0.87411,-0.48334,0.048136,491.77,0.45718,-0.78522,0.41763,183.96,-0.16406,0.38706,0.90734,-18.514
> view matrix models
> #1,-0.87491,-0.482,0.047025,492.94,0.45544,-0.78588,0.41829,184.36,-0.16466,0.38738,0.90709,-21.008
> view matrix models
> #1,-0.87491,-0.482,0.047025,492.77,0.45544,-0.78588,0.41829,184.58,-0.16466,0.38738,0.90709,-20.838
> view matrix models
> #1,-0.88733,-0.45747,-0.058039,519.63,0.3877,-0.80823,0.44324,197.11,-0.24968,0.37079,0.89452,4.7181
> view matrix models
> #1,-0.88334,-0.46707,-0.039382,515.36,0.40537,-0.80343,0.4361,193.64,-0.23533,0.36926,0.89904,0.93621
> view matrix models
> #1,-0.89367,-0.4487,0.0058692,501.77,0.40237,-0.79548,0.45312,188.13,-0.19864,0.4073,0.89143,-12.406
> view matrix models
> #1,-0.86852,-0.49445,-0.034478,515.93,0.43488,-0.79355,0.42562,188.05,-0.23781,0.35467,0.90424,2.8431
> view matrix models
> #1,-0.86852,-0.49445,-0.034478,517.42,0.43488,-0.79355,0.42562,188.02,-0.23781,0.35467,0.90424,1.6296
> view matrix models
> #1,-0.78923,-0.58513,-0.18638,558.61,0.48029,-0.77727,0.40641,180.06,-0.38267,0.23123,0.89448,60.114
> view matrix models
> #1,-0.78129,-0.59771,-0.17979,558.76,0.50063,-0.77212,0.39142,178.15,-0.37278,0.2158,0.90248,57.532
> view matrix models
> #1,-0.78129,-0.59771,-0.17979,558.66,0.50063,-0.77212,0.39142,178.63,-0.37278,0.2158,0.90248,57.646
> select #1/A:94,93,159,115,70
47 atoms, 46 bonds, 5 residues, 1 model selected
> show sel atoms
> view matrix models
> #1,-0.80502,-0.59205,0.037748,503.3,0.57171,-0.75722,0.31587,180.64,-0.15843,0.27586,0.94805,-14.063
> view matrix models
> #1,-0.80502,-0.59205,0.037748,503.39,0.57171,-0.75722,0.31587,182.05,-0.15843,0.27586,0.94805,-14.885
> view matrix models
> #1,-0.81791,-0.57123,-0.068667,531.44,0.51406,-0.77917,0.35866,187.37,-0.25838,0.25805,0.93094,15.477
> view matrix models
> #1,-0.81791,-0.57123,-0.068667,531,0.51406,-0.77917,0.35866,185.96,-0.25838,0.25805,0.93094,14.32
> view matrix models
> #1,-0.81791,-0.57123,-0.068667,530.06,0.51406,-0.77917,0.35866,188.55,-0.25838,0.25805,0.93094,13.985
> view matrix models
> #1,-0.77362,-0.6252,-0.1032,539.92,0.57011,-0.75783,0.31728,183.31,-0.27657,0.18662,0.9427,28.429
> view matrix models
> #1,-0.76784,-0.63464,-0.087455,536.13,0.57323,-0.74157,0.34853,170.97,-0.28605,0.21749,0.93321,27.261
> view matrix models
> #1,-0.76784,-0.63464,-0.087455,535.05,0.57323,-0.74157,0.34853,169.78,-0.28605,0.21749,0.93321,28.598
> view matrix models
> #1,-0.76784,-0.63464,-0.087455,535.06,0.57323,-0.74157,0.34853,170.38,-0.28605,0.21749,0.93321,28.285
> view matrix models
> #1,-0.76784,-0.63464,-0.087455,534.8,0.57323,-0.74157,0.34853,170.74,-0.28605,0.21749,0.93321,28.066
> view matrix models
> #1,-0.75284,-0.64687,-0.12158,543.13,0.56806,-0.73187,0.37639,162.41,-0.33246,0.2143,0.91845,43.062
> view matrix models
> #1,-0.75284,-0.64687,-0.12158,542.71,0.56806,-0.73187,0.37639,162.76,-0.33246,0.2143,0.91845,42.834
> view matrix models
> #1,-0.75284,-0.64687,-0.12158,542.66,0.56806,-0.73187,0.37639,162.54,-0.33246,0.2143,0.91845,43.02
> view matrix models
> #1,-0.75838,-0.63698,-0.13826,546.58,0.5545,-0.74197,0.37685,167.36,-0.34263,0.20913,0.9159,46.971
> view matrix models
> #1,-0.7596,-0.63718,-0.13043,544.75,0.54112,-0.7304,0.41678,157.21,-0.36083,0.24601,0.8996,48.465
> view matrix models
> #1,-0.7596,-0.63718,-0.13043,544.49,0.54112,-0.7304,0.41678,155.79,-0.36083,0.24601,0.8996,48.75
> select add #1
4478 atoms, 4582 bonds, 1 pseudobond, 550 residues, 2 models selected
> select subtract #1
Nothing selected
> save "/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV
> with Terns/20260111 IVC manuscript/IVC_DNA_bound/Cas10_bound_ID.cxs"
> hide #!1 models
> show #!1 models
> hide #!4 models
> combine #1
> hide #!1 models
> open 8BMW
Summary of feedback from opening 8BMW fetched from pdb
---
note | Fetching compressed mmCIF 8bmw from http://files.rcsb.org/download/8bmw.cif
8bmw title:
SsoCsm [more info...]
Chain information for 8bmw #6
---
Chain | Description | UniProt
A B C D E | CRISPR-associated small subunit protein (Type III-D) | A0A157T170_SACSO 1-139
F G | CRISPR-associated Cas7 paralog (Type III-D) | A0A157T0X8_SACSO 1-248
H I | CRISPR-associated Cas7 paralog (Type III-D) | A0A157T120_SACSO 1-278
J | CRISPR-associated Cas7 paralog (Type III-D) | A0A157T1A2_SACSO 3-274
K | CRISPR-associated protein Cas10 (Type III-D) | A0A157T112_SACSO 1-829
L | CRISPR-associated Cas7 paralog (Type III-D) | A0A157T2I3_SACSO 1-202
M | CRISPR-associated protein Cas5 (Type III-D) | A0A157T1I2_SACSO 1-300
N | CRISPR-associated Cas7 paralog (Type III-D) | A0A157T1J6_SACSO 1-252
R | RNA (48-MER) |
> select add #6
28658 atoms, 29252 bonds, 3 pseudobonds, 3523 residues, 2 models selected
> show sel cartoons
> hide sel atoms
> select #6/K:1-829
6678 atoms, 6805 bonds, 829 residues, 1 model selected
> mmaker #5 to #6/K
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 8bmw, chain K (#6) with copy of Cas10_bound.pdb, chain A (#5),
sequence alignment score = 185.2
RMSD between 25 pruned atom pairs is 1.021 angstroms; (across all 419 pairs:
31.068)
> hide #!5 models
> select add #6
28658 atoms, 29252 bonds, 3 pseudobonds, 3523 residues, 2 models selected
> select subtract #6
Nothing selected
> cofr #6
> open "/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV
> with Terns/20260111 IVC
> manuscript/IVC_DNA_bound/merged_real_space_refined_011.pdb"
Chain information for merged_real_space_refined_011.pdb #7
---
Chain | Description
A | No description available
C H I J K L | No description available
D | No description available
E | No description available
F | No description available
G | No description available
M | No description available
N O P Q R | No description available
S | No description available
> select add #7
30524 atoms, 31273 bonds, 3 pseudobonds, 3695 residues, 2 models selected
> show sel atoms
> style sel stick
Changed 30524 atom styles
> hide sel cartoons
> show sel cartoons
> hide sel atoms
[Repeated 1 time(s)]
> view matrix models #7,1,0,0,13.762,0,1,0,40.121,0,0,1,-62.573
> view matrix models
> #7,-0.64946,0.021277,-0.7601,502.79,0.039004,0.99922,-0.0053566,33.191,0.7594,-0.033126,-0.64979,109.51
> view matrix models
> #7,-0.64946,0.021277,-0.7601,532.01,0.039004,0.99922,-0.0053566,-59.316,0.7594,-0.033126,-0.64979,98.523
> view matrix models
> #7,0.40297,0.91334,0.058558,-49.62,0.80765,-0.32479,-0.49215,160.87,-0.43048,0.24562,-0.86854,307.91
> view matrix models
> #7,0.051556,0.95685,0.28596,-29.803,0.88581,0.088412,-0.45554,53.02,-0.46117,0.27679,-0.84304,302.94
> view matrix models
> #7,-0.0029515,0.95165,0.30718,-42.665,0.90473,0.1334,-0.40456,25.462,-0.42598,0.27672,-0.86137,309.92
> view matrix models
> #7,-0.53098,0.81849,0.2194,111.93,0.79275,0.57127,-0.21258,-78.241,-0.29934,0.061054,-0.95219,345.35
> view matrix models
> #7,-0.53098,0.81849,0.2194,77.406,0.79275,0.57127,-0.21258,-90.854,-0.29934,0.061054,-0.95219,352.18
> view matrix models
> #7,-0.8291,0.55788,0.037085,228.61,0.5408,0.81702,-0.20006,-90.982,-0.14191,-0.14581,-0.97908,367.19
> view matrix models
> #7,-0.8291,0.55788,0.037085,228.55,0.5408,0.81702,-0.20006,-87.866,-0.14191,-0.14581,-0.97908,380.33
> view matrix models
> #7,-0.85422,0.50761,-0.11238,273.39,0.51975,0.82842,-0.20876,-84.094,-0.01287,-0.23674,-0.97149,370.47
> view matrix models
> #7,-0.96768,0.25114,-0.023036,331.89,0.25206,0.9601,-0.12111,-72.32,-0.0082982,-0.123,-0.99237,350.4
> view matrix models
> #7,-0.70511,0.64449,0.29573,126.28,0.63304,0.76003,-0.14699,-101.62,-0.3195,0.083564,-0.9439,358.76
> view matrix models
> #7,-0.65421,0.65946,0.37029,97.966,0.59449,0.75105,-0.28724,-64.214,-0.46753,0.032215,-0.88339,388.26
> view matrix models
> #7,-0.65961,0.62754,0.41365,97.099,0.4846,0.77577,-0.40415,-23.387,-0.57452,-0.066127,-0.81582,417.4
> view matrix models
> #7,-0.65961,0.62754,0.41365,89.815,0.4846,0.77577,-0.40415,-26.954,-0.57452,-0.066127,-0.81582,416.99
> view matrix models
> #7,-0.65961,0.62754,0.41365,89.768,0.4846,0.77577,-0.40415,-27.843,-0.57452,-0.066127,-0.81582,415.91
> view matrix models
> #7,-0.21793,0.93874,0.26696,-37.188,0.86475,0.31254,-0.3931,-14.808,-0.45246,0.14518,-0.87989,359.85
> view matrix models
> #7,-0.21793,0.93874,0.26696,-36.18,0.86475,0.31254,-0.3931,-15.08,-0.45246,0.14518,-0.87989,359.07
> select subtract #7
Nothing selected
> color #6 #e49e9eff
> color #6 #e4e4e0ff
> color #7 #6e7cf9ff
> color #6 #8c8d8bff
> color #6 #fefffdff
> color #6 #f0ff73ff
> select add #7
30524 atoms, 31273 bonds, 3 pseudobonds, 3695 residues, 2 models selected
> view matrix models
> #7,-0.21793,0.93874,0.26696,-34.672,0.86475,0.31254,-0.3931,-15.515,-0.45246,0.14518,-0.87989,358.27
> view matrix models
> #7,-0.29187,0.88991,0.35052,-25.674,0.67377,0.45141,-0.58503,33.657,-0.67886,0.065411,-0.73135,392.65
> view matrix models
> #7,-0.29187,0.88991,0.35052,67.353,0.67377,0.45141,-0.58503,97.803,-0.67886,0.065411,-0.73135,380.41
> view matrix models
> #7,0.12179,0.95469,0.27155,-16.692,0.79285,0.071016,-0.60526,154.58,-0.59712,0.28901,-0.74828,321.03
> view matrix models
> #7,0.12179,0.95469,0.27155,-77.534,0.79285,0.071016,-0.60526,142.09,-0.59712,0.28901,-0.74828,314.91
> view matrix models
> #7,-0.234,0.83803,0.4929,-22.917,0.69423,0.49895,-0.51874,58.323,-0.68066,0.2208,-0.69854,336.51
> view matrix models
> #7,-0.234,0.83803,0.4929,-34.186,0.69423,0.49895,-0.51874,25.983,-0.68066,0.2208,-0.69854,350.78
> view matrix models
> #7,-0.62708,0.76066,0.16784,127.43,0.6775,0.63893,-0.36437,-29.398,-0.3844,-0.11478,-0.916,400.14
> view matrix models
> #7,-0.70238,0.68776,0.18344,149.83,0.60673,0.71324,-0.35096,-50.542,-0.37221,-0.13521,-0.91825,400.1
> view matrix models
> #7,-0.69971,0.63699,0.32348,132.15,0.59564,0.77016,-0.22816,-83.951,-0.39447,0.033031,-0.91831,370.41
> view matrix models
> #7,-0.69971,0.63699,0.32348,125.08,0.59564,0.77016,-0.22816,-76.844,-0.39447,0.033031,-0.91831,378.06
> view matrix models
> #7,-0.69971,0.63699,0.32348,117.6,0.59564,0.77016,-0.22816,-76.942,-0.39447,0.033031,-0.91831,379.71
> view matrix models
> #7,-0.83123,0.42438,0.35909,181.46,0.45119,0.89237,-0.010192,-114.53,-0.32477,0.15355,-0.93325,343.49
> view matrix models
> #7,-0.88372,0.30166,0.35783,217.72,0.35464,0.93053,0.091374,-122.1,-0.3054,0.20765,-0.92931,327.63
> view matrix models
> #7,-0.88372,0.30166,0.35783,211.66,0.35464,0.93053,0.091374,-122.07,-0.3054,0.20765,-0.92931,324.25
> view matrix models
> #7,-0.56247,0.70283,0.43549,47.486,0.70514,0.6828,-0.19122,-89.18,-0.43175,0.19953,-0.87965,342.53
> mmaker #7 to #6
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 8bmw, chain K (#6) with merged_real_space_refined_011.pdb, chain A
(#7), sequence alignment score = 185.2
RMSD between 25 pruned atom pairs is 1.021 angstroms; (across all 419 pairs:
31.068)
> view matrix models
> #7,0.30911,0.95069,0.025143,-88.754,0.88584,-0.27821,-0.37134,98.811,-0.34604,0.13706,-0.92816,340.69
> view matrix models
> #7,0.30911,0.95069,0.025143,-90.701,0.88584,-0.27821,-0.37134,94.742,-0.34604,0.13706,-0.92816,346.99
> view matrix models
> #7,-0.59825,0.78378,0.16671,104.93,0.78192,0.61649,-0.092444,-120.96,-0.17523,0.075052,-0.98166,334.5
> view matrix models
> #7,-0.59825,0.78378,0.16671,98.447,0.78192,0.61649,-0.092444,-120.88,-0.17523,0.075052,-0.98166,337.15
> view matrix models
> #7,-0.56838,0.80004,0.19201,83.93,0.77689,0.59871,-0.19489,-96.101,-0.27088,0.038403,-0.96185,360.7
> select subtract #7
Nothing selected
> select add #7
30524 atoms, 31273 bonds, 3 pseudobonds, 3695 residues, 2 models selected
> view matrix models
> #7,-0.56838,0.80004,0.19201,123.42,0.77689,0.59871,-0.19489,-29.729,-0.27088,0.038403,-0.96185,321.74
> view matrix models
> #7,-0.81366,0.51412,0.27137,216.79,0.4764,0.8572,-0.19558,-20.449,-0.33317,-0.029854,-0.94239,344.64
> view matrix models
> #7,-0.81292,0.51564,0.27069,170.28,0.47811,0.8563,-0.19535,-67.438,-0.33253,-0.029381,-0.94264,371.27
> view matrix models
> #7,-0.81292,0.51564,0.27069,164.44,0.47811,0.8563,-0.19535,-70.198,-0.33253,-0.029381,-0.94264,377.77
> view matrix models
> #7,-0.6748,0.63257,0.38012,92.37,0.6264,0.76328,-0.15819,-91.803,-0.39021,0.13137,-0.91131,350.78
> view matrix models
> #7,-0.6748,0.63257,0.38012,105.27,0.6264,0.76328,-0.15819,-106.57,-0.39021,0.13137,-0.91131,348.68
> view matrix models
> #7,-0.6748,0.63257,0.38012,102.03,0.6264,0.76328,-0.15819,-106.9,-0.39021,0.13137,-0.91131,344.75
> view matrix models
> #7,-0.73464,0.5535,0.39235,128.26,0.6362,0.76291,0.11497,-162.48,-0.2357,0.33407,-0.9126,271.38
> view matrix models
> #7,-0.73464,0.5535,0.39235,123.54,0.6362,0.76291,0.11497,-161.88,-0.2357,0.33407,-0.9126,275.9
> view matrix models
> #7,-0.92912,0.23184,0.28807,250.25,0.23464,0.97175,-0.025291,-93.191,-0.2858,0.044095,-0.95727,354.33
> view matrix models
> #7,-0.92912,0.23184,0.28807,250.78,0.23464,0.97175,-0.025291,-92.605,-0.2858,0.044095,-0.95727,360
> view matrix models
> #7,-0.92912,0.23184,0.28807,250.51,0.23464,0.97175,-0.025291,-94.297,-0.2858,0.044095,-0.95727,360.58
> view matrix models
> #7,-0.86677,0.46943,0.16836,212.49,0.47815,0.87818,0.013035,-133.53,-0.14173,0.091799,-0.98564,326.35
> view matrix models
> #7,-0.75369,0.55111,0.3581,134.98,0.59561,0.80308,0.017645,-143.61,-0.27786,0.22659,-0.93352,317.01
> view matrix models
> #7,-0.75369,0.55111,0.3581,134.9,0.59561,0.80308,0.017645,-139.03,-0.27786,0.22659,-0.93352,317.56
> view matrix models
> #7,-0.75562,0.53048,0.38422,134.39,0.61149,0.78155,0.12352,-158.73,-0.23476,0.32828,-0.91494,284.16
> view matrix models
> #7,-0.87839,0.1055,0.46616,230.69,0.23165,0.94709,0.22217,-132.62,-0.41806,0.30314,-0.85635,316.04
> view matrix models
> #7,-0.87839,0.1055,0.46616,233.2,0.23165,0.94709,0.22217,-133.27,-0.41806,0.30314,-0.85635,318.67
> view matrix models
> #7,-0.87839,0.1055,0.46616,227.55,0.23165,0.94709,0.22217,-131.84,-0.41806,0.30314,-0.85635,320.35
> view matrix models
> #7,-0.93225,-0.14612,0.33099,316.69,-0.11028,0.98605,0.12469,-49.31,-0.34459,0.079745,-0.93536,366.13
> view matrix models
> #7,-0.92482,0.31305,0.21613,243.94,0.26945,0.94012,-0.20873,-53.736,-0.26853,-0.1348,-0.95379,397.68
> view matrix models
> #7,-0.92482,0.31305,0.21613,245.77,0.26945,0.94012,-0.20873,-54.196,-0.26853,-0.1348,-0.95379,393.98
> view matrix models
> #7,-0.91926,0.28285,0.27379,239.46,0.2527,0.95729,-0.14052,-67.592,-0.30184,-0.059985,-0.95147,385.2
> view matrix models
> #7,-0.87025,0.40939,0.27398,203.36,0.38118,0.91193,-0.15192,-82.905,-0.31205,-0.027772,-0.94966,380.4
> select subtract #7
Nothing selected
> color #!6-7 bychain
> hide #!6 models
> show #!6 models
> hide #!7 models
> show #!7 models
> hide #!6 models
> hide #!7 models
> show #!6 models
> hide #!6 models
> show #!7 models
> show #!6 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!6 models
> show #!6 models
> hide #!7 models
> hide #!6 models
> show #!7 models
> show #!6 models
> select add #7
30524 atoms, 31273 bonds, 3 pseudobonds, 3695 residues, 2 models selected
> view matrix models
> #7,-0.82295,0.51309,0.24391,178.13,0.50778,0.85685,-0.089235,-110.38,-0.25478,0.050415,-0.96568,355.72
> view matrix models
> #7,-0.78408,0.52693,0.32797,150.7,0.521,0.84596,-0.11358,-106.14,-0.3373,0.081817,-0.93783,361.06
> view matrix models
> #7,-0.89777,0.38001,0.22271,225.07,0.38215,0.92343,-0.035182,-108.37,-0.21903,0.053522,-0.97425,349.31
> view matrix models
> #7,-0.89849,0.35157,0.2629,223.14,0.33404,0.9361,-0.11019,-86.193,-0.28484,-0.011191,-0.95851,373.16
> view matrix models
> #7,-0.89999,0.33607,0.27763,223.72,0.34879,0.93719,-0.0037997,-110.38,-0.26147,0.093416,-0.96068,347.35
> view matrix models
> #7,-0.86687,0.36718,0.33723,198.77,0.38136,0.92407,-0.025835,-110.17,-0.32111,0.10621,-0.94107,353.34
> view matrix models
> #7,-0.85053,0.42931,0.3038,189.23,0.44771,0.89412,-0.010102,-120.99,-0.27597,0.12742,-0.95268,341.87
> view matrix models
> #7,-0.85053,0.42931,0.3038,188.25,0.44771,0.89412,-0.010102,-122.75,-0.27597,0.12742,-0.95268,342.46
> select subtract #7
Nothing selected
> hide #!6 models
> show #!6 models
> hide #!7 models
> show #!7 models
> save "/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV
> with Terns/20260111 IVC manuscript/IVC_DNA_bound/Cas10_bound_IIIA.cxs"
> open 7uzz
Summary of feedback from opening 7uzz fetched from pdb
---
note | Fetching compressed mmCIF 7uzz from http://files.rcsb.org/download/7uzz.cif
7uzz title:
Staphylococcus epidermidis RP62a CRISPR tall effector complex [more info...]
Chain information for 7uzz #8
---
Chain | Description | UniProt
A B C D | CRISPR system Cms endoribonuclease Csm3 | Q5HK91_STAEQ 1-214
E | CRISPR system Cms protein Csm5 | Q5HK93_STAEQ 1-340
F | CRISPR system single-strand-specific deoxyribonuclease Cas10/Csm1 (subtype III-A) | Q5HK89_STAEQ 1-757
G | RNA (37-MER) |
H | CRISPR system Cms protein Csm4 | Q5HK92_STAEQ 1-304
I J K | CRISPR system Cms protein Csm2 | Q5HK90_STAEQ 14-141
> select add #8
19967 atoms, 20391 bonds, 20 pseudobonds, 2410 residues, 2 models selected
> show sel cartoons
> hide sel atoms
> mmaker #8 to #6
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 8bmw, chain K (#6) with 7uzz, chain F (#8), sequence alignment
score = 511.8
RMSD between 93 pruned atom pairs is 1.318 angstroms; (across all 573 pairs:
19.490)
> hide #!6 models
> hide #!7 models
> select subtract #8
Nothing selected
> show #!7 models
> select add #8
19967 atoms, 20391 bonds, 20 pseudobonds, 2410 residues, 2 models selected
> view matrix models
> #8,0.0845,-0.98012,-0.1795,412.25,0.90669,0.00092228,0.4218,-142.16,-0.41325,-0.19839,0.88875,35.585
> undo
> select subtract #8
Nothing selected
> select add #7
30524 atoms, 31273 bonds, 3 pseudobonds, 3695 residues, 2 models selected
> view matrix models
> #7,-0.81633,0.44067,0.37339,165.14,0.45487,0.88888,-0.054584,-114.45,-0.35596,0.12529,-0.92607,354.36
> view matrix models
> #7,-0.81662,0.49226,0.30135,168.81,0.46376,0.87044,-0.16511,-90.847,-0.34358,0.0049201,-0.93911,378.91
> view matrix models
> #7,-0.81662,0.49226,0.30135,172.72,0.46376,0.87044,-0.16511,-86.119,-0.34358,0.0049201,-0.93911,377.93
> view matrix models
> #7,-0.81662,0.49226,0.30135,172.89,0.46376,0.87044,-0.16511,-82.532,-0.34358,0.0049201,-0.93911,372.99
> view matrix models
> #7,-0.82887,0.49346,0.26357,182.62,0.47056,0.86977,-0.14859,-87.056,-0.30257,0.00086647,-0.95313,368.01
> view matrix models
> #7,-0.82416,0.50826,0.24988,181.3,0.47514,0.86059,-0.18336,-79.315,-0.30824,-0.032389,-0.95076,375.52
> view matrix models
> #7,-0.83782,0.38323,0.38884,182.4,0.3359,0.92331,-0.18621,-62.502,-0.43038,-0.0254,-0.90229,390.07
> view matrix models
> #7,-0.86925,0.25505,0.4235,207.88,0.18583,0.96239,-0.19816,-33.763,-0.45811,-0.093551,-0.88396,406.02
> view matrix models
> #7,-0.88198,0.25193,0.3983,216.12,0.1757,0.95997,-0.21814,-27.234,-0.43731,-0.12241,-0.89094,408.95
> view matrix models
> #7,-0.90652,0.17807,0.38277,239.36,0.088975,0.96691,-0.23911,-6.4377,-0.41268,-0.1827,-0.89237,416.39
> view matrix models
> #7,-0.90652,0.17807,0.38277,245.13,0.088975,0.96691,-0.23911,-7.8887,-0.41268,-0.1827,-0.89237,419.89
> view matrix models
> #7,-0.90652,0.17807,0.38277,245.84,0.088975,0.96691,-0.23911,-4.2885,-0.41268,-0.1827,-0.89237,420.93
> view matrix models
> #7,-0.90652,0.17807,0.38277,246.4,0.088975,0.96691,-0.23911,-5.0303,-0.41268,-0.1827,-0.89237,419.99
> view matrix models
> #7,-0.89684,0.24239,0.37004,233.75,0.15668,0.95634,-0.24671,-15.509,-0.41368,-0.16328,-0.89566,416.88
> select subtract #7
Nothing selected
> select add #6
28658 atoms, 29252 bonds, 3 pseudobonds, 3523 residues, 2 models selected
> show #!6 models
> hide #!8 models
> select subtract #6
Nothing selected
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> save "/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV
> with Terns/20260111 IVC manuscript/IVC_DNA_bound/Cas10_bound_IIIA_2.cxs"
[Repeated 1 time(s)]
> close session
> open "/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV
> with Terns/20260111 IVC
> manuscript/IVC_DNA_bound/cryosparc_P6_J91_004_volume_map.mrc"
Opened cryosparc_P6_J91_004_volume_map.mrc as #1, grid size 384,384,384, pixel
1.07, shown at level 0.0524, step 2, values float32
> close
> open "/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV
> with Terns/20260111 IVC manuscript/IVC_Apo/merged_ivc_apo_refine_007.pdb"
Summary of feedback from opening
/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV with
Terns/20260111 IVC manuscript/IVC_Apo/merged_ivc_apo_refine_007.pdb
---
warning | Start residue of secondary structure not found: HELIX 149 149 ILE P 16 ILE P 30 1 15
Chain information for merged_ivc_apo_refine_007.pdb #1
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E F G H | No description available
I | No description available
J | No description available
K L M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
> open "/Users/xuchengtao/Documents/Building models undergoing/20260114 IVC
> apo/cryosparc_P38_J47_006_volume_map.mrc"
Opened cryosparc_P38_J47_006_volume_map.mrc as #2, grid size 512,512,512,
pixel 1.07, shown at level 0.0338, step 2, values float32
> volume #2 step 1
> surface dust #2 size 10.7
> volume #2 level 0.1238
> hide cartoons
> hide atoms
> volume #2 level 0.1508
> volume #2 color #8d8d8d81
> volume #2 color #7d8d8d81
> volume #2 color #7d8d8d82
> select add #2
2 models selected
> ui tool show "Color Actions"
> color sel light sky blue
> volume #2 color #87cefa60
> select subtract #2
Nothing selected
> volume #2 color #87cefa61
> combine #1
> select add #2
2 models selected
> select add #1
31662 atoms, 32360 bonds, 17 pseudobonds, 3888 residues, 4 models selected
> select add #3
63324 atoms, 64720 bonds, 34 pseudobonds, 7776 residues, 6 models selected
> ui tool show "Color Actions"
> color sel white
> color #2 #ffffff6c models
> color #2 #ffffff6b models
> lighting soft
> color #2 #e6e8e86b models
> color #2 #e6e8e8d0 models
> color #2 #969797d0 models
> color #2 #aeb0b0d0 models
> lighting full
> select subtract #1
31662 atoms, 32360 bonds, 17 pseudobonds, 3888 residues, 4 models selected
> select subtract #3
2 models selected
> select subtract #2
Nothing selected
> select #1/A:54,70,93,97,115,146,159
69 atoms, 66 bonds, 7 residues, 1 model selected
> show (sel-residues & sidechain) target ab
> style sel stick
Changed 69 atom styles
> color sel byhetero
> cofr #1/A
> volume #2 level 0.2093
> volume #2 level 0.18
> volume #2 level 0.15
> volume #2 color #aeb0b03b
> select add #1
31662 atoms, 32360 bonds, 17 pseudobonds, 3888 residues, 2 models selected
> select subtract #1
Nothing selected
> volume #2 level 0.14
> select /S:2-31
1232 atoms, 1380 bonds, 60 residues, 2 models selected
> select /R:1-46
1960 atoms, 2194 bonds, 92 residues, 2 models selected
> select /Q:43-121
452 atoms, 460 bonds, 2 pseudobonds, 56 residues, 4 models selected
> select /P:17-124
1552 atoms, 1570 bonds, 4 pseudobonds, 196 residues, 4 models selected
> select /O:15-124
1674 atoms, 1698 bonds, 4 pseudobonds, 210 residues, 4 models selected
> select /N:15-124
1728 atoms, 1754 bonds, 2 pseudobonds, 218 residues, 4 models selected
> select /B:1-297
4712 atoms, 4822 bonds, 2 pseudobonds, 570 residues, 4 models selected
> select /C:1-303
4576 atoms, 4646 bonds, 2 pseudobonds, 588 residues, 4 models selected
> select /D:1-303
4608 atoms, 4678 bonds, 2 pseudobonds, 592 residues, 4 models selected
> select /I:1-303
4578 atoms, 4648 bonds, 2 pseudobonds, 586 residues, 4 models selected
> select /J:1-303
4056 atoms, 4124 bonds, 2 pseudobonds, 524 residues, 4 models selected
> select /K:16-124
1710 atoms, 1736 bonds, 2 pseudobonds, 216 residues, 4 models selected
> select /L:16-124
1710 atoms, 1736 bonds, 2 pseudobonds, 216 residues, 4 models selected
> select /H:1-303
4716 atoms, 4788 bonds, 606 residues, 2 models selected
> select /G:1-303
4716 atoms, 4788 bonds, 606 residues, 2 models selected
> select /F:1-303
4716 atoms, 4788 bonds, 606 residues, 2 models selected
> select /E:1-303
4716 atoms, 4788 bonds, 606 residues, 2 models selected
> select /C:1-303
4576 atoms, 4646 bonds, 2 pseudobonds, 588 residues, 4 models selected
> select /B:1-297
4712 atoms, 4822 bonds, 2 pseudobonds, 570 residues, 4 models selected
> select /A:40-593
8198 atoms, 8386 bonds, 6 pseudobonds, 1008 residues, 4 models selected
> select /S:2-31
1232 atoms, 1380 bonds, 60 residues, 2 models selected
> select /R:1-46
1960 atoms, 2194 bonds, 92 residues, 2 models selected
> select /Q:43-121
452 atoms, 460 bonds, 2 pseudobonds, 56 residues, 4 models selected
> select /P:17-124
1552 atoms, 1570 bonds, 4 pseudobonds, 196 residues, 4 models selected
> show #1/T
> select #1/T
2 atoms, 2 residues, 1 model selected
> ui tool show "Color Actions"
> color sel slate gray
> select add #1
31662 atoms, 32360 bonds, 17 pseudobonds, 3888 residues, 2 models selected
> select subtract #1
Nothing selected
> ui tool show "Side View"
> select #3/A:94,147
18 atoms, 17 bonds, 2 residues, 1 model selected
> show (sel-residues & sidechain) target ab
> style sel stick
Changed 18 atom styles
> color sel byhetero
> select add #3
31662 atoms, 32360 bonds, 17 pseudobonds, 3888 residues, 2 models selected
> select subtract #3
Nothing selected
> volume #2 level 0.135
> volume #2 level 0.138
> volume #2 level 0.139
> volume #2 color #8585872e
> volume #2 color #7272732e
> volume #2 color #7368732e
> volume #2 color #d5c1d62e
> volume #2 color #e5cfe62e
> volume #2 color #d6c2d72e
> lighting soft
> lighting simple
> lighting full
> volume #2 color #e1769a2e
> volume #2 color #e87a9f1b
> volume #2 level 0.142
> select add #1
31662 atoms, 32360 bonds, 17 pseudobonds, 3888 residues, 2 models selected
> select add #3
63324 atoms, 64720 bonds, 34 pseudobonds, 7776 residues, 4 models selected
> ui tool show "Color Actions"
> color sel pale violet red
> color sel plum
> color sel pink
> color sel light pink
> color sel byhetero
> select #1/T
2 atoms, 2 residues, 1 model selected
> ui tool show "Color Actions"
> color sel slate gray
> select add #1
31662 atoms, 32360 bonds, 17 pseudobonds, 3888 residues, 2 models selected
> select subtract #1
Nothing selected
> save /Users/xuchengtao/Desktop/image221.png supersample 3
> save /Users/xuchengtao/Desktop/image222.png supersample 3
> save "/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV
> with Terns/20260111 IVC manuscript/IVC_Apo/IVC_apo_HD_1.cxs"
> lighting full
> lighting soft
> volume zone #2 nearAtoms #1range 3
Invalid "nearAtoms" argument: only initial part "#1" of atom specifier valid
> volume zone #2 nearAtoms #1/A range 3
> volume zone #2 nearAtoms #1/A range 4
> save /Users/xuchengtao/Desktop/image223.png supersample 3
> save "/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV
> with Terns/20260111 IVC manuscript/IVC_Apo/IVC_apo_HD_1.cxs"
> hide #!1 models
> hide #!3 models
> show #!3 models
> show #!1 models
> hide #!2 models
> open "/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV
> with Terns/20260111 IVC
> manuscript/IVC_DNA_bound/merged_real_space_refined_011.pdb"
Chain information for merged_real_space_refined_011.pdb #4
---
Chain | Description
A | No description available
C H I J K L | No description available
D | No description available
E | No description available
F | No description available
G | No description available
M | No description available
N O P Q R | No description available
S | No description available
> mmaker #4/A: 54, 70,93,94,115,146,147,97
> matchmaker #4/A: 54, 70,93,94,115,146,147,97
Missing required "to" argument
> mmaker #4/A: 54, 70,93,94,115,146,147,97 to #1
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 merged_ivc_apo_refine_007.pdb, chain A (#1) with
merged_real_space_refined_011.pdb, chain A (#4), sequence alignment score =
49.4
RMSD between 8 pruned atom pairs is 0.822 angstroms; (across all 8 pairs:
0.822)
> style stick
Changed 93848 atom styles
> hide atoms
[Repeated 1 time(s)]
> show atoms
> undo
[Repeated 3 time(s)]
> style stick
Changed 93848 atom styles
> color byhetero
> hide #4
> show #4/A:54,70,93,94,115,146,147,159
> select #4/A:54,70,93,97,115,146,159
69 atoms, 66 bonds, 7 residues, 1 model selected
> show (sel-residues & sidechain) target ab
> select #4/A
4478 atoms, 4582 bonds, 1 pseudobond, 550 residues, 2 models selected
> ui tool show "Color Actions"
> color sel light sky blue
> color sel byhetero
> combine #4/A
> select add #4
30524 atoms, 31273 bonds, 3 pseudobonds, 3695 residues, 2 models selected
> hide #!5 models
> show #!5 models
> hide #5
> show #5/A:94,147
> select #5/A:94,147
18 atoms, 17 bonds, 2 residues, 1 model selected
> show (sel-residues & sidechain) target ab
> color #1 #ffb6c17c
[Repeated 1 time(s)]
> color sel byhetero
> color #1 #ffb6c17d
> select add #1
31680 atoms, 32377 bonds, 17 pseudobonds, 3890 residues, 3 models selected
> color sel byhetero
> select subtract #1
18 atoms, 17 bonds, 2 residues, 1 model selected
> color #3 #f1c3caff
> color #3 #f1c3ca81
> color #3 #f1c3ca82
> select add #3
31680 atoms, 32377 bonds, 17 pseudobonds, 3890 residues, 3 models selected
> color sel byhetero
> select subtract #3
18 atoms, 17 bonds, 2 residues, 1 model selected
> hide #1/T
> select #1/T
2 atoms, 2 residues, 1 model selected
> show (sel-residues & sidechain) target ab
> show #1/T
> ui tool show "Color Actions"
> color sel slate gray
> select add #1
31662 atoms, 32360 bonds, 17 pseudobonds, 3888 residues, 2 models selected
> select subtract #1
Nothing selected
> save "/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV
> with Terns/20260111 IVC
> manuscript/IVC_DNA_bound/IVC_DNAbound_HD_compare_apo_5.cxs"
> show #4/A:67-81, 86-96,112-118,136-160 cartoons
> select #4/A:67-81, 86-96,112-118,136-160 cartoon
Expected a keyword
> select #4/A:67-81, 86-96,112-118,136-160
470 atoms, 480 bonds, 58 residues, 1 model selected
> cartoon style sel modeHelix tube sides 20
> select #4/A:67-81, 86-98,112-118,136-160
486 atoms, 497 bonds, 60 residues, 1 model selected
> show sel cartoons
> select add #4
30524 atoms, 31273 bonds, 3 pseudobonds, 3695 residues, 2 models selected
> select subtract #4
Nothing selected
> hide #1/T
> show #4/B
> select #4/B
2 atoms, 2 residues, 1 model selected
> ui tool show "Color Actions"
> color sel slate gray
> select add #4
30524 atoms, 31273 bonds, 3 pseudobonds, 3695 residues, 2 models selected
> select subtract #4
Nothing selected
> select #4/B
2 atoms, 2 residues, 1 model selected
> color sel byhetero
> undo
> color sel bychain
> undo
> style sel sphere
Changed 2 atom styles
> select add #4
30524 atoms, 31273 bonds, 3 pseudobonds, 3695 residues, 2 models selected
> select subtract #4
Nothing selected
> save /Users/xuchengtao/Desktop/image224.png supersample 3
> open "/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV
> with Terns/20260111 IVC
> manuscript/IVC_DNA_bound/cryosparc_P6_J91_004_volume_map.mrc"
Opened cryosparc_P6_J91_004_volume_map.mrc as #6, grid size 384,384,384, pixel
1.07, shown at level 0.0524, step 2, values float32
> save /Users/xuchengtao/Desktop/image225.png supersample 3
> save "/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV
> with Terns/20260111 IVC
> manuscript/IVC_DNA_bound/IVC_DNAbound_HD_compare_apo_5.cxs"
——— End of log from Tue Feb 3 13:26:30 2026 ———
> view name session-start
opened ChimeraX session
> hide #!3 models
> show #!3 models
> show #1/A:136-160 cartoons
> show #1/A:136-180 cartoons
[Repeated 1 time(s)]
> show #4/A:136-180 cartoons
> select #4/A:136-180
352 atoms, 357 bonds, 45 residues, 1 model selected
> cartoon style sel xsection oval modeHelix default
> select add #4
30524 atoms, 31273 bonds, 3 pseudobonds, 3695 residues, 2 models selected
> select subtract #4
Nothing selected
>
Unknown command: measure #1/A:159@CA #4/A:159@CA
> ui tool show Distances
> select #1/A:159@CA #4/A:159@CA
2 atoms, 2 residues, 2 models selected
> distance #1/A:159@CA #4/A:159@CA
Distance between merged_ivc_apo_refine_007.pdb #1/A GLU 159 CA and
merged_real_space_refined_011.pdb #4/A GLU 159 CA: 1.998Å
> hide #1/A:59
> hide #1/A:59 atoms
> hide #1/A:54 atoms
> hide #4/A:54 atoms
> mmaker #4/A:115,94,146,147 to #1/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 merged_ivc_apo_refine_007.pdb, chain A (#1) with
merged_real_space_refined_011.pdb, chain A (#4), sequence alignment score =
25.8
RMSD between 4 pruned atom pairs is 0.509 angstroms; (across all 4 pairs:
0.509)
> mmaker #4/A:115,94,146,147,70 to #1/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 merged_ivc_apo_refine_007.pdb, chain A (#1) with
merged_real_space_refined_011.pdb, chain A (#4), sequence alignment score =
33.2
RMSD between 5 pruned atom pairs is 0.579 angstroms; (across all 5 pairs:
0.579)
> save "/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV
> with Terns/20260111 IVC
> manuscript/IVC_DNA_bound/IVC_DNAbound_HD_compare_apo_5.cxs"
——— End of log from Tue Feb 3 15:37:02 2026 ———
> view name session-start
opened ChimeraX session
> show #!2 models
> hide #!2 models
> hide #!1 models
> hide #!3 models
> hide #!4 models
> hide #!5 models
> close #7#1-6
> open "/Users/xuchengtao/Documents/Building models undergoing/20260114 IVC
> apo/merged_ivc_apo_refine_007.pdb"
Summary of feedback from opening /Users/xuchengtao/Documents/Building models
undergoing/20260114 IVC apo/merged_ivc_apo_refine_007.pdb
---
warning | Start residue of secondary structure not found: HELIX 149 149 ILE P 16 ILE P 30 1 15
Chain information for merged_ivc_apo_refine_007.pdb #1
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E F G H | No description available
I | No description available
J | No description available
K L M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
> style stick
Changed 31663 atom styles
> hide atoms
> show atoms
> style stick
Changed 31663 atom styles
> show cartoons
> hide cartoons
> hide #1
> open "/Users/xuchengtao/Documents/Building models
> undergoing/20251003IVC/20251222 Xiaomeng AI
> IVC/merged_real_space_refined_014.pdb"
Chain information for merged_real_space_refined_014.pdb #2
---
Chain | Description
A | No description available
C H I J K L | No description available
D | No description available
E | No description available
F | No description available
G | No description available
M | No description available
N O P Q R | No description available
S | No description available
> hide atoms
> mmaker #1/A:70,93,94,146,147 to #2/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 merged_real_space_refined_014.pdb, chain A (#2) with
merged_ivc_apo_refine_007.pdb, chain A (#1), sequence alignment score = 33.2
RMSD between 5 pruned atom pairs is 0.530 angstroms; (across all 5 pairs:
0.530)
> show #1/A:70,93,94,146,147
> select #1/A:70,93,94,146,147
48 atoms, 49 bonds, 5 residues, 1 model selected
> style sel stick
Changed 48 atom styles
> color sel byhetero
> select #2/A:70,93,94,146,147
48 atoms, 49 bonds, 5 residues, 1 model selected
> color sel byhetero
> show sel atoms
> style sel stick
Changed 48 atom styles
> cofr sel
> select #2/A:70,93,94,146,147,115
58 atoms, 59 bonds, 6 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 58 atom styles
> color sel byhetero
> select #1/A:70,93,94,146,147,115
58 atoms, 59 bonds, 6 residues, 1 model selected
> show sel atoms
> color sel byhetero
> mmaker #1/A:70,93,94,146,147,115 to #2/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 merged_real_space_refined_014.pdb, chain A (#2) with
merged_ivc_apo_refine_007.pdb, chain A (#1), sequence alignment score = 40
RMSD between 6 pruned atom pairs is 0.637 angstroms; (across all 6 pairs:
0.637)
> select #1/A:159
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel byhetero
> select #1/A:159, #2/A:159
Expected an objects specifier or a keyword
> show sel atoms
> select #2/A:159
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 9 atom styles
> color sel byhetero
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> color #1 #eceeedff
> open "/Users/xuchengtao/Documents/Building models undergoing/20260114 IVC
> apo/merged_ivc_apo_refine_008.pdb"
Summary of feedback from opening /Users/xuchengtao/Documents/Building models
undergoing/20260114 IVC apo/merged_ivc_apo_refine_008.pdb
---
warning | Start residue of secondary structure not found: HELIX 149 149 ILE P 16 ILE P 30 1 15
Chain information for merged_ivc_apo_refine_008.pdb #3
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E F G H | No description available
I | No description available
J | No description available
K L M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
> mmaker #3 to #1
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 merged_ivc_apo_refine_007.pdb, chain A (#1) with
merged_ivc_apo_refine_008.pdb, chain A (#3), sequence alignment score = 2572.9
RMSD between 504 pruned atom pairs is 0.004 angstroms; (across all 504 pairs:
0.004)
> style sel stick
Changed 9 atom styles
> hide sel atoms
> undo
> hide #!3 models
> select add #2
30525 atoms, 31271 bonds, 7 pseudobonds, 3696 residues, 3 models selected
> select subtract #2
Nothing selected
> select add #3
31663 atoms, 32359 bonds, 18 pseudobonds, 3889 residues, 2 models selected
> hide #3
> show #!3 models
> select subtract #3
Nothing selected
> show #3/A:70, 115,146,147,93,94,159
> style stick
Changed 93851 atom styles
> hide #!1 models
> color #3 #e1e4eeff
> color #3 #b2b5bdff
> mmaker #3/A:70, 115,146,147,93,94,159 to #2/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 merged_real_space_refined_014.pdb, chain A (#2) with
merged_ivc_apo_refine_008.pdb, chain A (#3), sequence alignment score = 45.3
RMSD between 7 pruned atom pairs is 0.851 angstroms; (across all 7 pairs:
0.851)
> show #1/A:97
> show #!1 models
> hide #!1 models
> show #2/A:97
> show #3/A:97
> hide #!3 models
> show #!3 models
> open "/Users/xuchengtao/Documents/Building models
> undergoing/20251003IVC/20251222 Xiaomeng AI
> IVC/cryosparc_P6_J91_004_volume_map.mrc"
Opened cryosparc_P6_J91_004_volume_map.mrc as #4, grid size 384,384,384, pixel
1.07, shown at level 0.0524, step 2, values float32
> volume #4 step 1
> volume #4 level 0.1661
> ui tool show "Hide Dust"
> surface dust #4 size 11.38
> surface dust #4 size 12.58
> surface dust #4 size 10.12
> volume #4 color #b2b2b2ab
> ui tool show "Color Actions"
> color light sky blue
> hide #!4 models
> hide #!3 models
> show #!3 models
> select #2
30525 atoms, 31271 bonds, 7 pseudobonds, 3696 residues, 3 models selected
> color sel byhetero
> select #3
31663 atoms, 32359 bonds, 18 pseudobonds, 3889 residues, 2 models selected
> ui tool show "Color Actions"
> color sel pink
> color sel byhetero
> select subtract #3
Nothing selected
> open "/Users/xuchengtao/Documents/Building models undergoing/20260114 IVC
> apo/cryosparc_P38_J47_006_volume_map.mrc"
Opened cryosparc_P38_J47_006_volume_map.mrc as #5, grid size 512,512,512,
pixel 1.07, shown at level 0.0338, step 2, values float32
> volume #5 step 1
> surface dust #5 size 9.46
> mmaker #5 to #4
No 'to' model specified
> mmaker #5 to #3
No molecules/chains to match specified
> surface dust #5 size 9.3
> surface dust #5 size 11.38
> surface dust #5 size 9.62
> surface dust #5 size 10.29
> surface dust #5 size 13.23
> volume #5 level 0.09228
> ui tool show "Fit in Map"
> ui mousemode right "translate selected models"
> select add #5
2 models selected
> view matrix models
> #5,-0.97381,-0.031588,0.22517,490.36,-0.071884,0.98228,-0.17308,73.711,-0.21571,-0.18473,-0.95882,664.68
> view matrix models
> #5,-0.97381,-0.031588,0.22517,436.09,-0.071884,0.98228,-0.17308,0.20124,-0.21571,-0.18473,-0.95882,557.69
> volume #5 level 0.1173
> view matrix models
> #5,-0.93478,0.30346,0.18464,345.57,0.2887,0.95188,-0.10282,-106.34,-0.20696,-0.042808,-0.97741,523.25
> fitmap #5 inMap #4
Fit map cryosparc_P38_J47_006_volume_map.mrc in map
cryosparc_P6_J91_004_volume_map.mrc using 310271 points
correlation = 0.9347, correlation about mean = 0.7922, overlap = 1.556e+04
steps = 220, shift = 18.3, angle = 17.3 degrees
Position of cryosparc_P38_J47_006_volume_map.mrc (#5) relative to
cryosparc_P6_J91_004_volume_map.mrc (#4) coordinates:
Matrix rotation and translation
-0.97760466 0.20023007 -0.06478454 435.09526992
0.19862444 0.97960384 0.03040797 -118.87262867
0.06955178 0.01685918 -0.99743587 434.81572276
Axis -0.10034105 -0.99488204 -0.01189115
Axis point 216.14301063 0.00000000 225.62653040
Rotation angle (degrees) 176.12880575
Shift along axis 69.43586944
> view matrix models
> #5,-0.99043,0.12889,-0.049357,453.43,0.1291,0.99163,-0.0012337,-93.971,0.048785,-0.0075941,-0.99878,447.49
> volume #5 level 0.1674
> view matrix models
> #5,-0.98693,0.15429,-0.046578,444.85,0.15422,0.98802,0.0051166,-101.57,0.04681,-0.0021338,-0.9989,446.59
> view matrix models
> #5,-0.99436,0.088993,0.057707,435.97,0.099112,0.97336,0.20674,-137.79,-0.037772,0.21129,-0.97669,405.88
> view matrix models
> #5,-0.99438,0.087718,0.059321,435.88,0.098341,0.97272,0.21009,-138.33,-0.039274,0.21474,-0.97588,405.13
> undo
> view matrix models
> #5,-0.98265,0.16324,-0.088032,452.62,0.16414,0.98643,-0.0029871,-101.62,0.08635,-0.017385,-0.99611,439.18
> volume #5 level 0.2085
> color sel pink
> volume #5 color #ffc0cbad
> volume #4 level 0.12
> show #2/B
> select #2/B
2 atoms, 2 residues, 1 model selected
> style sel sphere
Changed 2 atom styles
> ui tool show "Color Actions"
> color sel slate gray
> hide #!3 models
> volume #4 level 0.13
> volume #4 level 0.14
> matchmaker #4 to #2
No molecules/chains to match specified
> select add #2
30525 atoms, 31271 bonds, 7 pseudobonds, 3696 residues, 3 models selected
> select subtract #2
Nothing selected
> hide #!2 models
> close #2
> open "/Users/xuchengtao/Documents/Building models
> undergoing/20251003IVC/20251222 Xiaomeng AI
> IVC/merged_real_space_refined_015.pdb"
Chain information for merged_real_space_refined_015.pdb #2
---
Chain | Description
A | No description available
C H I J K L | No description available
D | No description available
E | No description available
F | No description available
G | No description available
M | No description available
N O P Q R | No description available
S | No description available
> hide #2
> combine #2
> color #2 lightskyblue
> color #6 lightskyblue
> select #2/A:70,93,94,97,115,146,159
66 atoms, 64 bonds, 7 residues, 1 model selected
> show (sel-residues & sidechain) target ab
> style sel stick
Changed 66 atom styles
> color sel byhetero
> select #2/B
2 atoms, 2 residues, 1 model selected
> style sel sphere
Changed 2 atom styles
> show sel atoms
> color sel gray
> ui tool show "Color Actions"
> color sel slate gray
> volume #4 color #87cefa27
> volume #4 color #87cefa26
> lighting full
> lighting soft
> lighting full
> hide #2/A:94
> select #5/A:94,147
Nothing selected
> show #5/A:94,147 & ~@N,C,O
> show #!5 models
> hide #!5 models
> show #6/A:94,147 & ~@N,C,O
> select #6/A
4478 atoms, 4580 bonds, 1 pseudobond, 550 residues, 2 models selected
> style sel stick
Changed 4478 atom styles
> color sel byhetero
> select add #6
30525 atoms, 31271 bonds, 7 pseudobonds, 3696 residues, 3 models selected
> select subtract #6
Nothing selected
> combine #3
> hide #3
> hide #7
> show #!5 models
> volume #5 level 0.1566
> volume #5 color #ffc0cb2b
> select #3/A:70,93,97,115,146,159
58 atoms, 56 bonds, 6 residues, 1 model selected
> show (#2,4,6-7 & sidechain) target ab
> select #3/A:70,93,97,115,146,159
58 atoms, 56 bonds, 6 residues, 1 model selected
> show #3/A:70,93,97,115,146,159& ~@N,,C,O
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> show #3/A:70,93,97,115,146,159& ~@N,C,O
> show #!3 models
> hide #2/A:97
> hide #3/A:97
> mmaker #3/A:70,93,94,115 to #2/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 merged_real_space_refined_015.pdb, chain A (#2) with
merged_ivc_apo_refine_008.pdb, chain A (#3), sequence alignment score = 26.4
RMSD between 4 pruned atom pairs is 0.646 angstroms; (across all 4 pairs:
0.646)
> mmaker #3/A:70,93,94,115,146 to #2/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 merged_real_space_refined_015.pdb, chain A (#2) with
merged_ivc_apo_refine_008.pdb, chain A (#3), sequence alignment score = 33.2
RMSD between 5 pruned atom pairs is 0.680 angstroms; (across all 5 pairs:
0.680)
> close #7
> combine #3
> hide #7
> show #7/A:94,147 & ~@N,CA,C,O
> show #7/A:94,147 & ~@N,,C,O
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> show #7/A:94,147 & ~@N,C,O
> select add #3
31663 atoms, 32359 bonds, 18 pseudobonds, 3889 residues, 2 models selected
> select subtract #3
Nothing selected
> hide #!2 models
> show #!2 models
> hide #!4 models
> show #!5 models
> show #!4 models
> select add #5
2 models selected
> view matrix models
> #5,-0.97841,0.20197,-0.043758,428.89,0.20245,0.97927,-0.0068224,-109.08,0.041473,-0.015534,-0.99902,451.71
> undo
> select subtract #5
Nothing selected
> select add #4
2 models selected
> select subtract #4
Nothing selected
> hide #!4 models
> hide #!2 models
> hide #!6 models
> select add #5
2 models selected
> view matrix models
> #5,-0.95877,0.093992,-0.2682,514.11,0.090359,0.99557,0.025885,-91.881,0.26944,0.00058378,-0.96302,375.36
> volume #5 level 0.1727
> view matrix models
> #5,-0.97116,0.2003,-0.12934,450.76,0.20327,0.97907,-0.010053,-108.32,0.12462,-0.036052,-0.99155,432.49
> cofr @3/A
> cofr #3/A
> view matrix models
> #5,-0.96897,0.21997,-0.11274,440.16,0.22373,0.97441,-0.021689,-109.42,0.10508,-0.046238,-0.99339,440.91
> view matrix models
> #5,-0.98673,0.16214,0.0085692,427.41,0.16178,0.98627,-0.033106,-92.633,-0.013819,-0.03128,-0.99942,470.88
> view matrix models
> #5,-0.99996,-0.0010926,-0.0093869,480.02,-0.0013883,0.9995,0.031557,-69.497,0.0093478,0.031569,-0.99946,447.61
> view matrix models
> #5,-0.99994,-0.010838,0.0021348,479.5,-0.010849,0.99993,-0.0051597,-56.987,-0.0020787,-0.0051825,-0.99998,460.79
> view matrix models
> #5,-0.99926,-0.0041216,0.038311,467.59,-0.0039274,0.99998,0.0051435,-61.705,-0.038331,0.0049892,-0.99925,467.71
> view matrix models
> #5,-0.99926,-0.0041216,0.038311,467.58,-0.0039274,0.99998,0.0051435,-61.937,-0.038331,0.0049892,-0.99925,467.37
> volume #5 level 0.16
> volume #5 color #ffc0cbd6
> volume #5 level 0.17
> view matrix models
> #5,-0.9987,-0.049666,0.011361,487.1,-0.049572,0.99873,0.0084327,-50.07,-0.011765,0.0078586,-0.9999,459.55
> view matrix models
> #5,-0.9987,-0.049666,0.011361,486.96,-0.049572,0.99873,0.0084327,-49.824,-0.011765,0.0078586,-0.9999,459.82
> volume #5 level 0.15
> volume #5 level 0.175
> view matrix models
> #5,-0.9987,-0.049666,0.011361,487.47,-0.049572,0.99873,0.0084327,-50.955,-0.011765,0.0078586,-0.9999,458.34
> view matrix models
> #5,-0.99639,-0.068145,-0.0506,508.8,-0.077294,0.97481,0.20922,-91.913,0.035067,0.21238,-0.97656,383.96
> undo
> view matrix models
> #5,-0.90445,-0.37278,0.20738,495.44,-0.36083,0.92786,0.094206,29.42,-0.22754,0.010378,-0.97371,509.22
> view matrix models
> #5,-0.90445,-0.37278,0.20738,496,-0.36083,0.92786,0.094206,27.507,-0.22754,0.010378,-0.97371,509.24
> view matrix models
> #5,-0.90445,-0.37278,0.20738,506.69,-0.36083,0.92786,0.094206,29.176,-0.22754,0.010378,-0.97371,509.83
> view matrix models
> #5,-0.90435,-0.36259,0.22513,499.05,-0.35913,0.93151,0.05762,37.745,-0.2306,-0.028742,-0.97262,520.93
> view matrix models
> #5,-0.90435,-0.36259,0.22513,500.51,-0.35913,0.93151,0.05762,36.126,-0.2306,-0.028742,-0.97262,518.8
> view matrix models
> #5,-0.90384,-0.33625,0.2646,482.45,-0.35563,0.93422,-0.027601,57.769,-0.23792,-0.11905,-0.96396,542.81
> view matrix models
> #5,-0.90384,-0.33625,0.2646,487.46,-0.35563,0.93422,-0.027601,49.35,-0.23792,-0.11905,-0.96396,540.04
> view matrix models
> #5,-0.9033,-0.31727,0.28876,475.58,-0.3537,0.93169,-0.082759,64.605,-0.24278,-0.17689,-0.95382,554.21
> view matrix models
> #5,-0.9033,-0.31727,0.28876,479.2,-0.3537,0.93169,-0.082759,57.847,-0.24278,-0.17689,-0.95382,553.3
> volume #5 level 0.1947
> volume #5 level 0.175
> show #!2 models
> hide #!2 models
> show #!4 models
> view matrix models
> #5,-0.90789,-0.32005,0.27076,486.12,-0.35802,0.92795,-0.1036,65.738,-0.21809,-0.19099,-0.95706,551.27
> fitmap #5 inMap #4
Fit map cryosparc_P38_J47_006_volume_map.mrc in map
cryosparc_P6_J91_004_volume_map.mrc using 186216 points
correlation = 0.9452, correlation about mean = 0.7716, overlap = 1.379e+04
steps = 380, shift = 27.5, angle = 38 degrees
Position of cryosparc_P38_J47_006_volume_map.mrc (#5) relative to
cryosparc_P6_J91_004_volume_map.mrc (#4) coordinates:
Matrix rotation and translation
-0.97747656 0.20090883 -0.06461583 434.82603912
0.19929299 0.97946158 0.03061556 -119.07093066
0.06943966 0.01704851 -0.99744046 434.80014734
Axis -0.10068315 -0.99484628 -0.01199138
Axis point 216.05419591 0.00000000 225.60664569
Rotation angle (degrees) 176.13677177
Shift along axis 69.46376469
> hide #!4 models
> volume #5 level 0.1589
> volume #5 level 0.15
> view matrix models
> #5,-0.97451,0.21473,-0.064928,430.36,0.21213,0.97622,0.044705,-125.65,0.072984,0.029792,-0.99689,430.23
> undo
> view matrix models
> #5,-0.97748,0.20091,-0.064616,436.21,0.19929,0.97946,0.030616,-119.26,0.06944,0.017049,-0.99744,436.08
> view matrix models
> #5,-0.97239,0.22414,-0.065027,428.65,0.22083,0.9738,0.054308,-130.26,0.075496,0.038448,-0.9964,428.35
> view matrix models
> #5,-0.97239,0.22414,-0.065027,428.82,0.22083,0.9738,0.054308,-127.24,0.075496,0.038448,-0.9964,428.69
> undo
> hide #!4 models
> volume #5 level 0.1661
> view matrix models
> #5,-0.96662,0.25053,-0.05365,415.47,0.24919,0.96798,0.030408,-129.49,0.05955,0.016024,-0.9981,437.95
> view matrix models
> #5,-0.96653,0.25013,-0.056982,416.46,0.2497,0.96821,0.01465,-125.38,0.058835,-6.834e-05,-0.99827,442.54
> view matrix models
> #5,-0.96653,0.25013,-0.056982,416.26,0.2497,0.96821,0.01465,-126.49,0.058835,-6.834e-05,-0.99827,443.79
> undo
> view matrix models
> #5,-0.97268,0.22126,-0.070311,429.58,0.21796,0.97459,0.051693,-128.6,0.079962,0.034956,-0.99618,426.75
> view matrix models
> #5,-0.97268,0.22126,-0.070311,430.14,0.21796,0.97459,0.051693,-126.95,0.079962,0.034956,-0.99618,427.81
> view matrix models
> #5,-0.97268,0.22126,-0.070311,430.12,0.21796,0.97459,0.051693,-127.05,0.079962,0.034956,-0.99618,427.18
> volume #5 level 0.1589
> view matrix models
> #5,-0.97111,0.22523,-0.078833,430.95,0.22249,0.97403,0.042032,-125.48,0.086252,0.023278,-0.996,428.57
> undo
> view matrix models
> #5,-0.96202,0.25857,-0.087537,421.85,0.25149,0.96419,0.084256,-142.27,0.10619,0.059042,-0.99259,412.55
> view matrix models
> #5,-0.96202,0.25857,-0.087537,422.58,0.25149,0.96419,0.084256,-138.97,0.10619,0.059042,-0.99259,414.88
> volume #5 level 0.1446
> undo
> volume #5 level 0.1607
> volume #5 level 0.1446
> view matrix models
> #5,-0.9737,0.21948,-0.061119,428.33,0.21816,0.97552,0.027604,-120.53,0.065681,0.013544,-0.99775,437.95
> view matrix models
> #5,-0.9737,0.21948,-0.061119,429.45,0.21816,0.97552,0.027604,-123.69,0.065681,0.013544,-0.99775,436.46
> view matrix models
> #5,-0.9737,0.21948,-0.061119,430.1,0.21816,0.97552,0.027604,-123.83,0.065681,0.013544,-0.99775,436.76
> view matrix models
> #5,-0.96936,0.23489,-0.071894,427.76,0.23263,0.9718,0.038497,-129.84,0.07891,0.020593,-0.99667,430.93
> view matrix models
> #5,-0.96936,0.23489,-0.071894,427.42,0.23263,0.9718,0.038497,-128.58,0.07891,0.020593,-0.99667,431.63
> view matrix models
> #5,-0.96792,0.23643,-0.085073,430.29,0.23421,0.97154,0.035438,-128.09,0.091031,0.014376,-0.99574,429.72
> view matrix models
> #5,-0.96792,0.23643,-0.085073,430.23,0.23421,0.97154,0.035438,-127.81,0.091031,0.014376,-0.99574,429.7
> view matrix models
> #5,-0.96792,0.23643,-0.085073,430.59,0.23421,0.97154,0.035438,-127.05,0.091031,0.014376,-0.99574,429.19
> view matrix models
> #5,-0.96792,0.23643,-0.085073,430.19,0.23421,0.97154,0.035438,-128.03,0.091031,0.014376,-0.99574,428.89
> view matrix models
> #5,-0.96792,0.23643,-0.085073,429.53,0.23421,0.97154,0.035438,-128.27,0.091031,0.014376,-0.99574,428.38
> view matrix models
> #5,-0.96792,0.23643,-0.085073,429.63,0.23421,0.97154,0.035438,-128.15,0.091031,0.014376,-0.99574,429.1
> view matrix models
> #5,-0.96792,0.23643,-0.085073,429.59,0.23421,0.97154,0.035438,-128.12,0.091031,0.014376,-0.99574,428.9
> view matrix models
> #5,-0.96958,0.23531,-0.067362,425.42,0.23325,0.97171,0.037075,-128.3,0.074181,0.020235,-0.99704,432.33
> view matrix models
> #5,-0.9663,0.24851,-0.0672,420.91,0.24554,0.96813,0.049372,-134.15,0.077327,0.031207,-0.99652,428.36
> view matrix models
> #5,-0.9663,0.24851,-0.0672,422.24,0.24554,0.96813,0.049372,-132.3,0.077327,0.031207,-0.99652,429.54
> view matrix models
> #5,-0.9663,0.24851,-0.0672,422.17,0.24554,0.96813,0.049372,-132.3,0.077327,0.031207,-0.99652,429.18
> view matrix models
> #5,-0.9663,0.24851,-0.0672,422.48,0.24554,0.96813,0.049372,-132.23,0.077327,0.031207,-0.99652,429.48
> view matrix models
> #5,-0.96297,0.26101,-0.067585,418.3,0.25702,0.96439,0.062399,-138.01,0.081465,0.042718,-0.99576,425.02
> view matrix models
> #5,-0.96297,0.26101,-0.067585,418.54,0.25702,0.96439,0.062399,-136.93,0.081465,0.042718,-0.99576,425.35
> undo
> volume #5 level 0.1339
> volume #5 color #ffc0cb29
> volume #5 color #ffc0cb61
> show #!4 models
> view matrix models
> #5,-0.96792,0.23643,-0.085073,429.64,0.23421,0.97154,0.035438,-128.16,0.091031,0.014376,-0.99574,429.11
> view matrix models
> #5,-0.96792,0.23643,-0.085073,429.59,0.23421,0.97154,0.035438,-128.26,0.091031,0.014376,-0.99574,429.29
> view matrix models
> #5,-0.96792,0.23643,-0.085073,429.69,0.23421,0.97154,0.035438,-128.37,0.091031,0.014376,-0.99574,429.46
> view matrix models
> #5,-0.96792,0.23643,-0.085073,429.4,0.23421,0.97154,0.035438,-128.44,0.091031,0.014376,-0.99574,429.31
> view matrix models
> #5,-0.96792,0.23643,-0.085073,429.37,0.23421,0.97154,0.035438,-128.43,0.091031,0.014376,-0.99574,429.16
> view matrix models
> #5,-0.96792,0.23643,-0.085073,429.43,0.23421,0.97154,0.035438,-128.61,0.091031,0.014376,-0.99574,429.7
> view matrix models
> #5,-0.96792,0.23643,-0.085073,429.22,0.23421,0.97154,0.035438,-128.65,0.091031,0.014376,-0.99574,429.53
> view matrix models
> #5,-0.96792,0.23643,-0.085073,429.16,0.23421,0.97154,0.035438,-128.43,0.091031,0.014376,-0.99574,429.54
> hide #!3 models
> show #!3 models
> hide #!4 models
> view matrix models
> #5,-0.96792,0.23643,-0.085073,429.36,0.23421,0.97154,0.035438,-128.09,0.091031,0.014376,-0.99574,429.64
> view matrix models
> #5,-0.96792,0.23643,-0.085073,429.21,0.23421,0.97154,0.035438,-127.78,0.091031,0.014376,-0.99574,429.58
> view matrix models
> #5,-0.96792,0.23643,-0.085073,428.37,0.23421,0.97154,0.035438,-127.04,0.091031,0.014376,-0.99574,429.41
> view matrix models
> #5,-0.96792,0.23643,-0.085073,428.35,0.23421,0.97154,0.035438,-126.11,0.091031,0.014376,-0.99574,429.73
> view matrix models
> #5,-0.96792,0.23643,-0.085073,428.3,0.23421,0.97154,0.035438,-126,0.091031,0.014376,-0.99574,429.7
> view matrix models
> #5,-0.96792,0.23643,-0.085073,428.24,0.23421,0.97154,0.035438,-126.37,0.091031,0.014376,-0.99574,429.57
> volume #5 level 0.1464
> view matrix models
> #5,-0.96792,0.23643,-0.085073,428.2,0.23421,0.97154,0.035438,-126.21,0.091031,0.014376,-0.99574,429.4
> view matrix models
> #5,-0.96792,0.23643,-0.085073,428.13,0.23421,0.97154,0.035438,-125.77,0.091031,0.014376,-0.99574,429.31
> show #3/T
> select #3/T
2 atoms, 2 residues, 1 model selected
> style sel sphere
Changed 2 atom styles
> ui tool show "Color Actions"
> color sel slate gray
> select add #3
31663 atoms, 32359 bonds, 18 pseudobonds, 3889 residues, 2 models selected
> select subtract #3
Nothing selected
> ui tool show "Side View"
> hide #!3 models
> hide #!5 models
> hide #!7 models
> show #!4 models
> show #!6 models
> show #!2 models
> volume #4 level 0.12
> volume #4 level 0.125
> lighting full
> lighting soft
> lighting simple
> lighting full
> lighting flat
> lighting full
> lighting simple
> lighting full
> volume #4 level 0.13
> save /Users/xuchengtao/Desktop/image275.png supersample 3
> hide #!4 models
> hide #!2 models
> show #!3 models
> show #!5 models
> hide #!6 models
> show #!7 models
> save "/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV
> with Terns/20260111 IVC
> manuscript/IVC_DNA_bound/IVC_DNAbound_HD_compare_apo_6.cxs"
> save /Users/xuchengtao/Desktop/image276.png supersample 3
> hide #!3 models
> hide #!5 models
> hide #!7 models
> show #!3 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #3/T
> show #!4 models
> hide #!4 models
> show #!2 models
> show #!6 models
> show #2/A:86-96 cartoons
> cartoon style #2-3,6-7 modeHelix tube sides 20
> cartoon style (#2-3,6-7 & coil) xsection oval
> cartoon style #2-3,6-7 xsection barbell modeHelix default
> cartoon style #2-3,6-7 modeHelix tube sides 20
> show #2/A:136-160 cartoons
> combine #7
> color #8 white
> color #8 #ffffffb4
> color #8 #ffffff82
> color #8 #ffffff80
> color #8 #f5f4f680
> show #8/A:136-160 cartoons
> show #8/A:86-96 cartoons
> show #8/A:136-180 cartoons
> show #2/A:136-180 cartoons
> show #2/A:136-160 cartoons
> save "/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV
> with Terns/20260111 IVC
> manuscript/IVC_DNA_bound/IVC_DNAbound_HD_compare_apo_6.cxs"
> hide #2/A:161-180 cartoons
> hide #8/A:161-180 cartoons
> save "/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV
> with Terns/20260111 IVC
> manuscript/IVC_DNA_bound/IVC_DNAbound_HD_compare_apo_7.cxs"
> hide #8/A:147
> hide #8/A:94]
> hide #8/A:94
> save "/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV
> with Terns/20260111 IVC
> manuscript/IVC_DNA_bound/IVC_DNAbound_HD_compare_apo_7.cxs"
> lighting full
> lighting soft
> hide #!2 models
> hide #!6 models
> show #!2 models
> show #!6 models
> lighting shadows true intensity 0.5
> lighting full
> lighting shadows false
> save /Users/xuchengtao/Desktop/image277.png supersample 3
> ui tool show Distances
> select #2/A:159
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #3/A:159
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #3/A:159, #2/A:159
Expected an objects specifier or a keyword
Exactly two atoms must be selected!
> select #2,3/A:159@CA
2 atoms, 2 residues, 2 models selected
> distance #3/A:159@CA #2/A:159@CA
Distance between merged_ivc_apo_refine_008.pdb #3/A GLU 159 CA and
merged_real_space_refined_015.pdb #2/A GLU 159 CA: 2.124Å
> undo
> ~distance #3/A:159@CA #2/A:159@CA
> lighting shadows true
> lighting full
> lighting soft
> depthCue true
Unknown command: depthCue true
> depthCue true
Unknown command: depthCue true
> depthCue true
Unknown command: depthCue true
> depthCue
Unknown command: depthCue
> lighting depthCue true
> lighting depthCueStart 0.4 depthCueEnd 0.9
> lighting depthCueStart 0.4 depthCueEnd 0.8
> lighting depthCueStart 0.2 depthCueEnd 0.8
> lighting depthCueStart 0.1 depthCueEnd 0.8
> lighting depthCueStart 0.1 depthCueEnd 0.4
> lighting depthCueStart 0.2 depthCueEnd 0.4
> lighting depthCueStart 0.3 depthCueEnd 0.4
> lighting simple
> lighting flat
> lighting full
> lighting soft
> lighting depthCueStart 0.3 depthCueEnd 0.4
> lighting depthCueStart 0.4 depthCueEnd 0.9
> lighting depthCueStart 0.4 depthCueEnd 0.5
> lighting depthCueStart 0.3 depthCueEnd 0.5
> lighting depthCueStart 0.3 depthCueEnd 0.4
> lighting depthCueStart 0.4
> lighting depthCueStart 0.9
> lighting depthCueStart 0.
> lighting depthCueStart 0.5
> lighting depthCueStart 0.4
> show #!2 models
> save "/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV
> with Terns/20260111 IVC
> manuscript/IVC_DNA_bound/IVC_DNAbound_HD_compare_apo_7.cxs"
> open "/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV
> with Terns/20260111 IVC manuscript/IVC_DNA_bound/IVC_DNAbound_PAM6.cxs"
Opened cryosparc_P6_J91_004_volume_map.mrc as #4, grid size 384,384,384, pixel
1.07, shown at level 0.227, step 1, values float32
Opened cryosparc_P6_J91_004_volume_map.mrc copy as #1, grid size 384,384,384,
pixel 1.07, shown at level 0.266, step 1, values float32
Opened cryosparc_P6_J91_004_volume_map.mrc as #3, grid size 384,384,384, pixel
1.07, shown at level 0.153, step 1, values float32
> view name session-start
opened ChimeraX session
> open "/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV
> with Terns/20260111 IVC
> manuscript/IVC_DNA_bound/IVC_DNAbound_HD_compare_apo_6.cxs"
Opened cryosparc_P6_J91_004_volume_map.mrc as #4, grid size 384,384,384, pixel
1.07, shown at level 0.13, step 1, values float32
Opened cryosparc_P38_J47_006_volume_map.mrc as #5, grid size 512,512,512,
pixel 1.07, shown at level 0.146, step 1, values float32
> view name session-start
opened ChimeraX session
> open "/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV
> with Terns/20260111 IVC
> manuscript/IVC_DNA_bound/IVC_DNAbound_HD_compare_apo_7.cxs"
Opened cryosparc_P6_J91_004_volume_map.mrc as #4, grid size 384,384,384, pixel
1.07, shown at level 0.13, step 1, values float32
Opened cryosparc_P38_J47_006_volume_map.mrc as #5, grid size 512,512,512,
pixel 1.07, shown at level 0.146, step 1, values float32
> view name session-start
opened ChimeraX session
> lighting depthCueStart 0.4 depthCueStart 0.9
Repeated keyword argument "depthCueStart"
> lighting depthCueStart 0.4 depthCueEnd 0.9
> lighting depthCueStart 0.4 depthCueEnd 0.6
> lighting depthCueStart 0.1 depthCueEnd 0.6
> lighting depthCueStart 0.2 depthCueEnd 0.6
> lighting depthCueStart 0.2 depthCueEnd 0.3
> save "/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV
> with Terns/20260111 IVC
> manuscript/IVC_DNA_bound/IVC_DNAbound_HD_compare_apo_7.cxs"
> lighting depthCueStart 0.2 depthCueEnd 0.25
> lighting depthCueStart 0.2 depthCueEnd 0.5
> lighting depthCueStart 0.2 depthCueEnd 0.25
> lighting depthCueStart 0.2 depthCueEnd 0.28
> lighting depthCueStart 0.2 depthCueEnd 0.3
> lighting depthCueStart 0.2 depthCueEnd 0.34
> save /Users/xuchengtao/Desktop/image278.png supersample 3
> save /Users/xuchengtao/Desktop/image279.png supersample 3
> lighting depthCueStart 0.2 depthCueEnd 0.33
> lighting depthCueStart 0.2 depthCueEnd 0.3
> save /Users/xuchengtao/Desktop/image280.png supersample 3
> save "/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV
> with Terns/20260111 IVC
> manuscript/IVC_DNA_bound/IVC_DNAbound_HD_compare_apo_7.cxs"
> lighting depthCue false
> save "/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV
> with Terns/20260111 IVC
> manuscript/IVC_DNA_bound/IVC_DNAbound_HD_compare_apo_7.cxs"
> close session
> open
> /Users/xuchengtao/Downloads/cryosparc_P9_J31_00162_volumes/J31_class_00_00162_volume.mrc
Opened J31_class_00_00162_volume.mrc as #1, grid size 128,128,128, pixel 3.01,
shown at level 0.108, step 1, values float32
> open
> /Users/xuchengtao/Downloads/cryosparc_P9_J31_00162_volumes/J31_class_01_00162_volume.mrc
Opened J31_class_01_00162_volume.mrc as #2, grid size 128,128,128, pixel 3.01,
shown at level 0.126, step 1, values float32
> open
> /Users/xuchengtao/Downloads/cryosparc_P9_J31_00162_volumes/J31_class_02_00162_volume.mrc
Opened J31_class_02_00162_volume.mrc as #3, grid size 128,128,128, pixel 3.01,
shown at level 0.0868, step 1, values float32
> open
> /Users/xuchengtao/Downloads/cryosparc_P9_J31_00162_volumes/J31_class_03_00162_volume.mrc
Opened J31_class_03_00162_volume.mrc as #4, grid size 128,128,128, pixel 3.01,
shown at level 0.241, step 1, values float32
> open
> /Users/xuchengtao/Downloads/cryosparc_P9_J31_00162_volumes/J31_class_04_00162_volume.mrc
Opened J31_class_04_00162_volume.mrc as #5, grid size 128,128,128, pixel 3.01,
shown at level 0.105, step 1, values float32
> open
> /Users/xuchengtao/Downloads/cryosparc_P9_J31_00162_volumes/J31_class_05_00162_volume.mrc
Opened J31_class_05_00162_volume.mrc as #6, grid size 128,128,128, pixel 3.01,
shown at level 0.27, step 1, values float32
> color #1-6 lightgrey
> ui tool show "Hide Dust"
> surface dust #1 size 18.06
> surface dust #1 size 30.1
> surface dust #2 size 30.1
> surface dust #3 size 30.1
> surface dust #4 size 30.1
> surface dust #5 size 30.1
> surface dust #6 size 30.1
> hide #!2 models
> hide #!3 models
> hide #!4 models
> hide #!5 models
> hide #!6 models
> hide #!1 models
> show #!2 models
> show #!3 models
> show #!4 models
> hide #!3 models
> hide #!2 models
> hide #!4 models
> show #!5 models
> hide #!5 models
> show #!6 models
> show #!1 models
> show #!2 models
> show #!3 models
> show #!4 models
> show #!5 models
> hide #!5 models
> hide #!6 models
> hide #!4 models
> hide #!3 models
> hide #!2 models
> save /Users/xuchengtao/Desktop/image281.png supersample 3
> lighting full
> lighting soft
> save /Users/xuchengtao/Desktop/image282.png supersample 3
> hide #!1 models
> show #!2 models
> save /Users/xuchengtao/Desktop/image283.png supersample 3
> hide #!2 models
> show #!3 models
> save /Users/xuchengtao/Desktop/image284.png supersample 3
> hide #!3 models
> show #!4 models
> save /Users/xuchengtao/Desktop/image285.png supersample 3
> hide #!4 models
> show #!5 models
> save /Users/xuchengtao/Desktop/image286.png supersample 3
> hide #!5 models
> show #!6 models
> save /Users/xuchengtao/Desktop/image287.png supersample 3
> hide #!6 models
> open /Users/xuchengtao/Downloads/cryosparc_P9_J32_007_volume_map.mrc
Opened cryosparc_P9_J32_007_volume_map.mrc as #7, grid size 360,360,360, pixel
1.07, shown at level 0.0564, step 2, values float32
> color #7 #f4f6fcff models
> volume #7 step 1
> volume #7 level 0.07916
> surface dust #7 size 10.7
> volume #7 level 0.11
> lighting full
> volume #7 color #cecfd4
> lighting simple
> volume #7 color #a3a4a7
> color #7 lightgrey
> color #7 grey
> volume #7 color #b6b6b6
> save /Users/xuchengtao/Desktop/image288.png supersample 3
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.10.1 (2025-07-24)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 Metal - 89.4
OpenGL renderer: Apple M4 Pro
OpenGL vendor: Apple
Python: 3.11.4
Locale: en_US.UTF-8
Qt version: PyQt6 6.8.1, Qt 6.8.2
Qt runtime version: 6.8.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: Mac16,8
Model Number: Z1FF000ENLL/A
Chip: Apple M4 Pro
Total Number of Cores: 14 (10 performance and 4 efficiency)
Memory: 48 GB
System Firmware Version: 13822.1.2
OS Loader Version: 11881.140.96
Software:
System Software Overview:
System Version: macOS 15.7.1 (24G231)
Kernel Version: Darwin 24.6.0
Time since boot: 26 days, 11 hours, 19 minutes
Graphics/Displays:
Apple M4 Pro:
Chipset Model: Apple M4 Pro
Type: GPU
Bus: Built-In
Total Number of Cores: 20
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3024 x 1964 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
HP 23f:
Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
UI Looks like: 1920 x 1080 @ 75.00Hz
Mirror: Off
Online: Yes
Rotation: Supported
Installed Packages:
alabaster: 1.0.0
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.0
babel: 2.17.0
beautifulsoup4: 4.13.3
blockdiag: 3.0.0
blosc2: 3.6.1
build: 1.2.2.post1
certifi: 2023.11.17
cftime: 1.6.4.post1
charset-normalizer: 3.4.2
ChimeraX-AddCharge: 1.5.19
ChimeraX-AddH: 2.2.7
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.6.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.20.2
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Aniso: 1.1.4
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.60.7
ChimeraX-AtomicLibrary: 14.1.19
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.3
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-Boltz: 1.0
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.2
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.5.1
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.5
ChimeraX-ChemGroup: 2.0.2
ChimeraX-Clashes: 2.3
ChimeraX-Clipper: 0.25.2
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.8
ChimeraX-CommandLine: 1.3
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.10.1
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.5
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.4
ChimeraX-Dicom: 1.2.7
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.4
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.4.1
ChimeraX-Hbonds: 2.5.1
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.3
ChimeraX-ISOLDE: 1.10.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.6.2
ChimeraX-Label: 1.1.14
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.3
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.2.2
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.10.1
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.16
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.19
ChimeraX-ModelPanel: 1.5.1
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-MutationScores: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.14.1
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.10
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.3
ChimeraX-ProfileGrids: 1.1.3
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.3
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.3
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.7
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.17.1
ChimeraX-Shape: 1.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-SimilarStructures: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.19.1
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5.2
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.2.3
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.45.2
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.4
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.5
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.3.2
coverage: 7.10.0
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.12
debugpy: 1.8.15
decorator: 5.2.1
docutils: 0.21.2
executing: 2.2.0
filelock: 3.18.0
fonttools: 4.59.0
funcparserlib: 2.0.0a0
glfw: 2.9.0
grako: 3.16.5
h5py: 3.14.0
html2text: 2024.2.26
idna: 3.10
ihm: 2.2
imagecodecs: 2024.6.1
imagesize: 1.4.1
iniconfig: 2.1.0
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.7
jedi: 0.19.1
Jinja2: 3.1.6
jupyter_client: 8.6.3
jupyter_core: 5.8.1
jupyterlab_widgets: 3.0.15
kiwisolver: 1.4.8
line_profiler: 4.2.0
lxml: 5.3.1
lz4: 4.3.2
MarkupSafe: 3.0.2
matplotlib: 3.10.1
matplotlib-inline: 0.1.7
msgpack: 1.1.0
ndindex: 1.10.0
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.11.0
numpy: 1.26.4
OpenMM: 8.2.0
openvr: 1.26.701
packaging: 24.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pickleshare: 0.7.5
pillow: 10.4.0
pip: 25.0.1
pkginfo: 1.11.1
platformdirs: 4.3.8
pluggy: 1.6.0
prompt_toolkit: 3.0.51
psutil: 7.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
Pygments: 2.18.0
pynmrstar: 3.3.5
pynrrd: 1.0.0
PyOpenGL: 3.1.9
PyOpenGL-accelerate: 3.1.9
pyopenxr: 1.1.4501
pyparsing: 3.2.3
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.8.1
PyQt6-Qt6: 6.8.2
PyQt6-WebEngine-commercial: 6.8.0
PyQt6-WebEngine-Qt6: 6.8.2
PyQt6_sip: 13.10.0
pytest: 8.4.1
pytest-cov: 6.2.1
python-dateutil: 2.9.0.post0
pytz: 2025.2
pyzmq: 27.0.0
qtconsole: 5.5.2
QtPy: 2.4.3
qtshim: 1.1
RandomWords: 0.4.0
requests: 2.32.3
roman-numerals-py: 3.1.0
scipy: 1.14.0
setuptools: 78.1.0
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 3.0.1
sortedcontainers: 2.4.0
soupsieve: 2.7
Sphinx: 8.2.3
sphinx-autodoc-typehints: 3.1.0
sphinxcontrib-applehelp: 2.0.0
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 2.0.0
sphinxcontrib-htmlhelp: 2.1.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 2.0.0
sphinxcontrib-serializinghtml: 2.0.0
stack-data: 0.6.3
superqt: 0.7.1
tables: 3.10.2
tcia_utils: 1.5.1
tifffile: 2025.3.13
tinyarray: 1.2.4
tornado: 6.5.1
traitlets: 5.14.3
typing_extensions: 4.14.1
tzdata: 2025.2
urllib3: 2.5.0
wcwidth: 0.2.13
webcolors: 24.11.1
wheel: 0.45.1
wheel-filename: 1.4.2
widgetsnbextension: 4.0.14
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