id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
16542	ChimeraX bug report submission	chimerax-bug-report@…		"{{{
The following bug report has been submitted:
Platform:        macOS-14.4.1-arm64-arm-64bit
ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault

Current thread 0x00000001f540fac0 (most recent call first):
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 315 in event_loop
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1003 in init
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1166 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.surface._surface, chimerax.map._map, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, chimerax.pdb_lib._load_libs, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.pdb._pdbio, lxml._elementpath, lxml.etree, 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._minpack2, 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._cdflib, scipy.special._ufuncs, scipy.special._specfun, scipy.special._comb, scipy.special._ellip_harm_2, scipy.spatial.transform._rotation, scipy.optimize._direct, chimerax.atom_search.ast, chimerax.chem_group._chem_group, chimerax.coulombic._esp, PIL._imagingmath, PIL._webp, psutil._psutil_osx, psutil._psutil_posix (total: 124)


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  ""vmSummary"" : ""ReadOnly portion of Libraries: Total=1.5G resident=0K(0%) swapped_out_or_unallocated=1.5G(100%)\nWritable regions: Total=19.7G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=19.7G(100%)\n\n                                VIRTUAL   REGION \nREGION TYPE                        SIZE    COUNT (non-coalesced) \n===========                     =======  ======= \nAccelerate framework               384K        3 \nActivity Tracing                   256K        1 \nCG image                           704K       40 \nColorSync                          656K       31 \nCoreAnimation                     2096K      129 \nCoreGraphics                        48K        3 \nCoreUI image data                 5184K       43 \nFoundation                          48K        2 \nKernel Alloc Once                   32K        1 \nMALLOC                            18.2G      297 \nMALLOC guard page                  384K       24 \nMach message                        64K        3 \nOpenGL GLSL                        384K        4 \nSTACK GUARD                       1072K       67 \nStack                            170.8M       68 \nStack Guard                       56.0M        1 \nVM_ALLOCATE                      557.2M      349 \nVM_ALLOCATE (reserved)           832.0M        8         reserved VM address space (unallocated)\n__AUTH                            2679K      439 \n__AUTH_CONST                      32.9M      661 \n__CTF                               824        1 \n__DATA                            26.0M      891 \n__DATA_CONST                      45.2M      892 \n__DATA_DIRTY                      2050K      240 \n__FONT_DATA                        2352        1 \n__GLSLBUILTINS                    5174K        1 \n__INFO_FILTER                         8        1 \n__LINKEDIT                       562.5M      232 \n__OBJC_RO                         71.7M        1 \n__OBJC_RW                         2195K        1 \n__TEXT                             1.0G      909 \ndyld private memory                592K        7 \nmapped file                      238.8M       61 \nshared memory                     3760K       30 \n===========                     =======  ======= \nTOTAL                             21.7G     5442 \nTOTAL, minus reserved VM space    20.9G     5442 \n"",
  ""legacyInfo"" : {
  ""threadTriggered"" : {
    ""name"" : ""CrBrowserMain"",
    ""queue"" : ""com.apple.main-thread""
  }
},
  ""logWritingSignature"" : ""3e007e65458b363b257d358c43eb0e3be033561d"",
  ""trialInfo"" : {
  ""rollouts"" : [
    {
      ""rolloutId"" : ""6434420a89ec2e0a7a38bf5a"",
      ""factorPackIds"" : {

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    {
      ""rolloutId"" : ""648a2601f74c42732876cb5b"",
      ""factorPackIds"" : {
        ""SIRI_TEXT_TO_SPEECH"" : ""66b55f4e9142fa69576cb851""
      },
      ""deploymentId"" : 240000272
    }
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  ""experiments"" : [
    {
      ""treatmentId"" : ""45f4e2a5-551b-4bc2-a2dc-19c244dda8f8"",
      ""experimentId"" : ""6643969b3099cf28e049862f"",
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}
===== Log before crash start =====
UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open ""/Users/upneet/Desktop/Narlilkar Lab/Manuscript_INO80_AutoInib/Figures
> /Figure 1/Version 1/Chimera Session V2/HSa.cxs""

Log from Sat Dec 21 19:42:25 2024UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open ""/Users/upneet/Desktop/Narlilkar Lab/Manuscript_INO80_AutoInib/Figures
> /Figure 1/Version 1/Chimera Session V2/HSa.cxs""

Log from Sat Dec 21 18:53:40 2024UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open ""/Users/upneet/Desktop/Narlilkar Lab/Manuscript_INO80_AutoInib/Figures
> /Figure 1/Version 2-resubmission/Chimera Session/Figure1_HSA.cxs""

Log from Fri Dec 20 14:57:31 2024UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open ""/Users/upneet/Desktop/Narlilkar Lab/Manuscript_INO80_AutoInib/Figures
> /Figure 1/Version 2-resubmission/Chimera Session/Figure1_noRvbs'.cxs"" format
> session

Opened 121124-a8-split_xl080.mrc as #1, grid size 480,480,480, pixel 0.835,
shown at level 0.00375, step 1, values float32  
Opened ies2-x80-lowres.mrc as #3, grid size 480,480,480, pixel 0.835, shown at
level 0.348, step 1, values float32  
Opened 041924-global-resampleonapo.mrc 0 as #5.1, grid size 480,480,480, pixel
0.835, shown at level 0.221, step 1, values float32  
Opened 041924-global-resampleonapo.mrc 1 as #5.2, grid size 480,480,480, pixel
0.835, shown at level 0.238, step 1, values float32  
Opened 041924-global-resampleonapo.mrc 2 as #5.3, grid size 480,480,480, pixel
0.835, shown at level 0.221, step 1, values float32  
Opened 041924-global-resampleonapo.mrc 3 as #5.4, grid size 480,480,480, pixel
0.835, shown at level 0.221, step 1, values float32  
Opened 041924-global-resampleonapo.mrc 4 as #5.5, grid size 480,480,480, pixel
0.835, shown at level 0.221, step 1, values float32  
Opened 041924-global-resampleonapo.mrc 5 as #5.6, grid size 480,480,480, pixel
0.835, shown at level 0.221, step 1, values float32  
Opened 041924-global-resampleonapo.mrc 6 as #5.7, grid size 480,480,480, pixel
0.835, shown at level 0.221, step 1, values float32  
Opened 041924-global-resampleonapo.mrc 7 as #5.8, grid size 480,480,480, pixel
0.835, shown at level 0.221, step 1, values float32  
Opened 041924-global-resampleonapo.mrc 8 as #5.9, grid size 480,480,480, pixel
0.835, shown at level 0.235, step 1, values float32  
Opened 041924-global-resampleonapo.mrc 9 as #5.10, grid size 480,480,480,
pixel 0.835, shown at level 0.174, step 1, values float32  
Opened 041924-nuc-resampleonapo_xl080.mrc as #6, grid size 480,480,480, pixel
0.835, shown at level 1.44, step 1, values float32  
Opened 121124-a8-split_Xl040.mrc as #4, grid size 448,448,448, pixel 0.831,
shown at level 0.0026, step 1, values float32  
Opened onlyies2-lowres-Xl040.mrc as #7, grid size 448,448,448, pixel 0.831,
shown at level 0.0519, step 1, values float32  
Opened onlynuc_Xl040.mrc as #8, grid size 448,448,448, pixel 0.831, shown at
level 0.411, step 1, values float32  
Opened inocore_Xl040.mrc as #9, grid size 448,448,448, pixel 0.831, shown at
level 0.218, step 1, values float32  
Opened 041924-global-resampleonapo.mrc as #11, grid size 480,480,480, pixel
0.835, shown at level 0.105, step 2, values float32  
Opened 041924-global-resampleonapo.mrc 0 as #12.1, grid size 480,480,480,
pixel 0.835, shown at level 0.105, step 1, values float32  
Opened 041924-global-resampleonapo.mrc 1 as #12.2, grid size 480,480,480,
pixel 0.835, shown at level 0.105, step 1, values float32  
Opened 041924-global-resampleonapo.mrc 2 as #12.3, grid size 480,480,480,
pixel 0.835, shown at level 0.105, step 1, values float32  
Opened 041924-global-resampleonapo.mrc 3 as #12.4, grid size 480,480,480,
pixel 0.835, shown at level 0.105, step 1, values float32  
Opened 041924-global-resampleonapo.mrc 4 as #12.5, grid size 480,480,480,
pixel 0.835, shown at level 0.105, step 1, values float32  
Opened 041924-global-resampleonapo.mrc 5 as #12.6, grid size 480,480,480,
pixel 0.835, shown at level 0.105, step 1, values float32  
Opened 041924-global-resampleonapo.mrc 6 as #12.7, grid size 480,480,480,
pixel 0.835, shown at level 0.105, step 1, values float32  
Opened 041924-global-resampleonapo.mrc 7 as #12.8, grid size 480,480,480,
pixel 0.835, shown at level 0.105, step 1, values float32  
Opened 041924-global-resampleonapo.mrc 8 as #12.9, grid size 480,480,480,
pixel 0.835, shown at level 0.105, step 1, values float32  
Opened 041924-global-resampleonapo.mrc 9 as #12.10, grid size 480,480,480,
pixel 0.835, shown at level 0.105, step 1, values float32  
Opened 041924-global-resampleonapo.mrc 10 as #12.11, grid size 480,480,480,
pixel 0.835, shown at level 0.105, step 1, values float32  
Log from Thu Dec 12 17:07:10 2024UCSF ChimeraX version: 1.7.1 (2024-01-23)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open ""/Users/upneet/Desktop/Narlilkar Lab/Manuscript_INO80_AutoInib/Figures
> /Figure 1/Version 2-resubmission/Chimera Session/Figure1_noRvbs'.cxs"" format
> session

Opened 121124-a8-split_xl080.mrc as #1, grid size 480,480,480, pixel 0.835,
shown at level 0.00375, step 1, values float32  
Opened ies2-x80-lowres.mrc as #3, grid size 480,480,480, pixel 0.835, shown at
level 0.348, step 1, values float32  
Opened 041924-global-resampleonapo.mrc 0 as #5.1, grid size 480,480,480, pixel
0.835, shown at level 0.221, step 1, values float32  
Opened 041924-global-resampleonapo.mrc 1 as #5.2, grid size 480,480,480, pixel
0.835, shown at level 0.238, step 1, values float32  
Opened 041924-global-resampleonapo.mrc 2 as #5.3, grid size 480,480,480, pixel
0.835, shown at level 0.221, step 1, values float32  
Opened 041924-global-resampleonapo.mrc 3 as #5.4, grid size 480,480,480, pixel
0.835, shown at level 0.221, step 1, values float32  
Opened 041924-global-resampleonapo.mrc 4 as #5.5, grid size 480,480,480, pixel
0.835, shown at level 0.221, step 1, values float32  
Opened 041924-global-resampleonapo.mrc 5 as #5.6, grid size 480,480,480, pixel
0.835, shown at level 0.221, step 1, values float32  
Opened 041924-global-resampleonapo.mrc 6 as #5.7, grid size 480,480,480, pixel
0.835, shown at level 0.221, step 1, values float32  
Opened 041924-global-resampleonapo.mrc 7 as #5.8, grid size 480,480,480, pixel
0.835, shown at level 0.221, step 1, values float32  
Opened 041924-global-resampleonapo.mrc 8 as #5.9, grid size 480,480,480, pixel
0.835, shown at level 0.235, step 1, values float32  
Opened 041924-global-resampleonapo.mrc 9 as #5.10, grid size 480,480,480,
pixel 0.835, shown at level 0.174, step 1, values float32  
Opened 041924-nuc-resampleonapo_xl080.mrc as #6, grid size 480,480,480, pixel
0.835, shown at level 1.44, step 1, values float32  
Opened 121124-a8-split_Xl040.mrc as #4, grid size 448,448,448, pixel 0.831,
shown at level 0.0026, step 1, values float32  
Opened onlyies2-lowres-Xl040.mrc as #7, grid size 448,448,448, pixel 0.831,
shown at level 0.0519, step 1, values float32  
Opened onlynuc_Xl040.mrc as #8, grid size 448,448,448, pixel 0.831, shown at
level 0.411, step 1, values float32  
Opened inocore_Xl040.mrc as #9, grid size 448,448,448, pixel 0.831, shown at
level 0.218, step 1, values float32  
Log from Thu Dec 12 15:35:36 2024 Startup Messages  
---  
warnings | Replacing fetcher for 'ngff' and format OME-Zarr from OME-Zarr bundle with that from OME-Zarr bundle  
Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR bundle with
that from NMRSTAR bundle  
  
UCSF ChimeraX version: 1.7.1 (2024-01-23)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open ""/Users/upneet/Library/CloudStorage/Box-Box/INO-yeastNCP/Map and
> Model/wtINO80-0N80-Yeast-Apo/121124-a8-split.mrc""

Opened 121124-a8-split.mrc as #1, grid size 512,512,512, pixel 0.819, shown at
level 0.000444, step 2, values float32  

> set bgColor white

> open ""/Users/upneet/Library/CloudStorage/Box-Box/INO-yeastNCP/Map and
> Model/wtINO80-0N80-Yeast-Apo/120524-inocore-nuc-3.16A.mrc""

Opened 120524-inocore-nuc-3.16A.mrc as #2, grid size 512,512,512, pixel 0.819,
shown at level 0.0802, step 2, values float32  

> volume #1 step 1

> volume #2 step 1

> volume #1 level 0.001846

> surface dust #1 size 8.19

> surface dust #2 size 8.19

> volume #2 level 0.1187

> volume #1 level 0.002828

> volume #2 level 0.1524

> volume #2 level 0.1596

> volume #2 level 0.1741

> color #2 silver models

> open ""/Users/upneet/Library/CloudStorage/Box-Box/INO-yeastNCP/Map and
> Model/wtINO80-0N80-Yeast-Apo/120524-final-ino80-0y80-apo-512box.pdb""

Chain information for 120524-final-ino80-0y80-apo-512box.pdb #3  
---  
Chain | Description  
A E | No description available  
B F | No description available  
C | No description available  
D H | No description available  
G | No description available  
I | No description available  
J | No description available  
K | No description available  
L | No description available  
M | No description available  
O | No description available  
Q | No description available  
R | No description available  
S | No description available  
T | No description available  
U | No description available  
V | No description available  
W | No description available  
X | No description available  
Y | No description available  
Z | No description available  
  

> volume #1 level 0.003126

> hide #!1 models

> hide #!2 models

> hide atoms

> show cartoons

> select #3/A-H,T-Y

26415 atoms, 26739 bonds, 2 pseudobonds, 3403 residues, 2 models selected  

> ui tool show ""Color Actions""

> color sel light gray

> select #3/I,J

7702 atoms, 8638 bonds, 1 pseudobond, 376 residues, 2 models selected  

> color sel slate gray

> show sel atoms

> hide sel atoms

> nucleotides sel atoms

> style nucleic & sel stick

Changed 7702 atom styles  

> nucleotides sel ladder

> show sel atoms

> select #3/Q

6141 atoms, 6266 bonds, 8 pseudobonds, 758 residues, 2 models selected  

> color sel fire brick

> select #3/Z

464 atoms, 469 bonds, 1 pseudobond, 72 residues, 2 models selected  

> color sel fire brick

> color sel orange

> select #3/R,S

4527 atoms, 4639 bonds, 2 pseudobonds, 570 residues, 2 models selected  

> color sel medium sea green

> select #3/K

5092 atoms, 5206 bonds, 628 residues, 1 model selected  

> color sel medium blue

> select #3/L

2856 atoms, 2919 bonds, 1 pseudobond, 363 residues, 2 models selected  

> color sel gold

> select #3/M

3454 atoms, 3531 bonds, 1 pseudobond, 433 residues, 2 models selected  

> color sel deep sky blue

> select #3/N

Nothing selected  

> color dim gray

> undo

> select #3/O

287 atoms, 296 bonds, 34 residues, 1 model selected  

> color sel dim gray

> select clear

> show #!2 models

> show #!1 models

> ui tool show ""Color Zone""

> color zone #1 near #3 distance 4.91

> color zone #1 near #3 distance 4.81

> color zone #1 near #3 distance 4.71

> color zone #1 near #3 distance 4.61

> color zone #1 near #3 distance 4.51

> color zone #1 near #3 distance 4.41

> color zone #1 near #3 distance 4.31

> color zone #1 near #3 distance 4.21

> color zone #1 near #3 distance 4.11

> color zone #1 near #3 distance 4.01

> color zone #1 near #3 distance 3.91

> color zone #1 near #3 distance 3.81

> color zone #1 near #3 distance 3.71

> color zone #1 near #3 distance 3.61

> color zone #1 near #3 distance 3.51

> color zone #1 near #3 distance 3.41

> color zone #1 near #3 distance 3.83

> color zone #1 near #3 distance 9.39

> color zone #1 near #3 distance 1

> color zone #1 near #3 distance 10

[Repeated 1 time(s)]

> volume #1 level 0.00344

> color zone #2 near #3 distance 4.91

> volume #1 level 0.003283

> lighting simple

> lighting soft

> lighting simple

> lighting soft

> ui tool show ""Side View""

> hide #!3 models

> color #1 #b2b2b224 models

> color #1 #b2b2b297 models

> color #1 #b2b2b296 models

> undo

[Repeated 4 time(s)]

> color zone #1 near #3 distance 10

> volume #2 level 0.1046

> volume #2 level 0.1313

> volume #2 level 0.1607

> volume #2 level 0.118

> volume #2 level 0.1287

> volume #2 level 0.15

> volume #2 level 0.1634

No map chosen to save  

> save /Users/upneet/Desktop/test.png width 3600 height 2697 supersample 3
> transparentBackground true

> hide #!2 models

> hide #!1 models

> show #!3 models

> hide #!3 models

> show #!1 models

> show #!3 models

> hide #!1 models

> show #!1 models

> open ""/Users/upneet/Library/CloudStorage/Box-Box/INO-yeastNCP/Map and
> Model/WT-0N80Xe-ADPBeF/121124-a8-split.mrc""

Opened 121124-a8-split.mrc as #4, grid size 480,480,480, pixel 0.835, shown at
level 0.000837, step 2, values float32  

> volume #4 level 0.003553

> volume #4 step 1

> hide #!3 models

> hide #!4 models

> hide #!1 models

> show #!4 models

> volume #4 level 0.003726

> volume #4 level 0.003661

> color #4 silver models

> open ""/Users/upneet/Library/CloudStorage/Box-Box/INO-yeastNCP/Map and
> Model/INO-40yeastnuc-ADPBeF/121124-a8-split.mrc""

Opened 121124-a8-split.mrc as #5, grid size 480,480,480, pixel 0.835, shown at
level 4.83e-07, step 2, values float32  

> volume #5 level 0.003775

> volume #5 level 0.003851

> hide #!4 models

> hide #!5 models

> show #!3 models

> select ::name=""ARG""

3893 atoms, 3559 bonds, 362 residues, 1 model selected  

> ui mousemode right select

> select clear

Drag select of 1 residues  

> show sel surfaces

> hide sel surfaces

> style sel stick

Changed 11 atom styles  

> show sel atoms

> color sel byhetero

> hide #!3 models

> show #!1 models

> show #!2 models

> close #1-5

> open ""/Users/upneet/Library/CloudStorage/Box-Box/INO-yeastNCP/Map and
> Model/WT-0N80Xe-ADPBeF/121124-a8-split.mrc""

Opened 121124-a8-split.mrc as #1, grid size 480,480,480, pixel 0.835, shown at
level 4.88e-06, step 2, values float32  

> open ""/Users/upneet/Library/CloudStorage/Box-Box/INO-yeastNCP/Map and
> Model/WT-0N80Xe-ADPBeF/121124-0n80-xe-wt-adpbef-final-coot-0-pymol-
> shortdna.pdb""

Chain information for 121124-0n80-xe-wt-adpbef-final-coot-0-pymol-shortdna.pdb
#2  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
F | No description available  
G | No description available  
H | No description available  
I | No description available  
J | No description available  
K | No description available  
L | No description available  
M | No description available  
O | No description available  
Q | No description available  
R | No description available  
S | No description available  
T | No description available  
U | No description available  
V | No description available  
W | No description available  
X | No description available  
Y | No description available  
Z | No description available  
  

> hide atoms

> show cartoons

> volume #1 step 1

> volume #1 level 0.004082

> hide #!2 models

> show #!2 models

> hide #!1 models

> color #2/Q firebrick

> color #2/Q firebrick, #2/R,S seagreen

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

> color #2/Q firebrick

> color #2/R,S medium seagreen

> color #2/T-Y, A-H grey

> color #2/T-Y, A-H lightr grey

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

> color #2/T-Y, A-H light grey

> color #2/Z orange

> color #2/k medium blue

> color #2/L gold

> color #2/N deep skyblue

> color #2/M deep skyblue

[Repeated 1 time(s)]

> color #2/O grey

> color #2/I,J slate blue

> color #2/I,J slate grey

> select #2/I,J

7787 atoms, 8735 bonds, 380 residues, 1 model selected  

> nucleotides sel ladder

> show sel atoms

> select clear

[Repeated 2 time(s)]

> show #!1 models

> ui tool show ""Color Zone""

> color zone #1 near #2 distance 5.01

> color zone #1 near #2 distance 5.19

> color zone #1 near #2 distance 11.56

> color zone #1 near #2 distance 11.7

[Repeated 1 time(s)]

> color zone #1 near #2 distance 1

> color zone #1 near #2 distance 10

[Repeated 1 time(s)]

> color zone #1 near #2 distance 1

> color zone #1 near #2 distance 15

[Repeated 1 time(s)]

> volume #1 level 0.004276

> volume #1 level 0.004216

> volume #1 level 0.003992

> open ""/Users/upneet/Library/CloudStorage/Box-Box/INO-yeastNCP/Map and
> Model/WT-0N80Xe-ADPBeF/ies2-x80-lowres.mrc""

Opened ies2-x80-lowres.mrc as #3, grid size 480,480,480, pixel 0.835, shown at
level 5.64e-05, step 2, values float32  

> volume #3 step 1

> volume #3 level 0.3484

> hide #!3 models

> volume #1 level 0.003664

> surface dust #1 size 8.35

> volume #1 level 0.003843

> volume #1 level 0.003873

> ui tool show ""Side View""

> volume #1 level 0.003754

> volume #1 level 0.003664

> surface dust #1 size 8.35

> volume #1 level 0.003754

> select #2/L

2862 atoms, 2925 bonds, 1 pseudobond, 364 residues, 2 models selected  

> ui tool show ""Color Actions""

> color sel sandy brown

> color zone #1 near #2 distance 15

> color sel navajo white

> color zone #1 near #2 distance 15

> hide #!1 models

> show #!1 models

> color sel goldenrod

> color zone #1 near #2 distance 15

> color sel orange

> color zone #1 near #2 distance 15

> color (#!2 & sel) #ffd479ff

> color zone #1 near #2 distance 15

> color (#!2 & sel) #ffd778ff

> color (#!2 & sel) #ffd87aff

> color (#!2 & sel) #ffdb82ff

> color (#!2 & sel) #ffdc89ff

> color (#!2 & sel) #ffe296ff

> color (#!2 & sel) #ffe396ff

> color (#!2 & sel) #ffea91ff

> color (#!2 & sel) #ffe482ff

> color (#!2 & sel) #ffe077ff

> color (#!2 & sel) #ffe370ff

> color (#!2 & sel) #ffea6cff

> color (#!2 & sel) #fff26aff

> color (#!2 & sel) #fff36aff

> color (#!2 & sel) #fff36dff

> color (#!2 & sel) #fff475ff

> color zone #1 near #2 distance 15

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> select #2/O

347 atoms, 356 bonds, 40 residues, 1 model selected  

> color sel #011993ff

> color zone #1 near #2 distance 15

> color sel #9437ffff

> color zone #1 near #2 distance 15

> color sel #76d6ffff

> color zone #1 near #2 distance 15

> color sel #79b8ffff

> color zone #1 near #2 distance 15

> color sel #00fdffff

> color sel #73fdffff

> color zone #1 near #2 distance 15

> color sel #ffd479ff

> color zone #1 near #2 distance 15

> color sel #011993ff

> color sel #005493ff

> color zone #1 near #2 distance 15

> select clear

> select #2/Z

467 atoms, 472 bonds, 1 pseudobond, 72 residues, 2 models selected  

> color (#!2 & sel) #ff2600ff

> color (#!2 & sel) #ff7e79ff

> select clear

> select #2/M

3430 atoms, 3507 bonds, 1 pseudobond, 429 residues, 2 models selected  

> select #2/L

2862 atoms, 2925 bonds, 1 pseudobond, 364 residues, 2 models selected  

> select #2/L

2862 atoms, 2925 bonds, 1 pseudobond, 364 residues, 2 models selected  

> select #2/K

5614 atoms, 5735 bonds, 1 pseudobond, 692 residues, 2 models selected  

> ui tool show ""Color Actions""

> color sel cornflower blue

> color zone #1 near #2 distance 15

> color sel royal blue

> color zone #1 near #2 distance 15

> select #2/M

3430 atoms, 3507 bonds, 1 pseudobond, 429 residues, 2 models selected  

> ui tool show ""Color Actions""

> color sel light pink

> color zone #1 near #2 distance 15

> color sel plum

> color zone #1 near #2 distance 15

> color sel pink

> color zone #1 near #2 distance 15

> color sel light pink

> color zone #1 near #2 distance 15

> hide #!1 models

> cartoon style (#!2 & sel) modeHelix tube sides 20

> cartoon style modeHelix tube radius 1.5

> select clear

> show #!1 models

> select #2/L

2862 atoms, 2925 bonds, 1 pseudobond, 364 residues, 2 models selected  

> select #2/K

5614 atoms, 5735 bonds, 1 pseudobond, 692 residues, 2 models selected  

> ui tool show ""Color Actions""

> color sel cornflower blue

> color sel blue

> color zone #1 near #2 distance 15

> color sel medium blue

> color zone #1 near #2 distance 15

> select #2/M

3430 atoms, 3507 bonds, 1 pseudobond, 429 residues, 2 models selected  

> ui tool show ""Color Actions""

> color sel deep sky blue

> color zone #1 near #2 distance 15

> select clear

> hide #!1 models

> show #!1 models

> open ""/Users/upneet/Library/CloudStorage/Box-Box/INO-yeastNCP/Map and
> Model/WT-0N80Xe-ADPBeF/041924-global-resampleonapo.mrc""

Opened 041924-global-resampleonapo.mrc as #4, grid size 480,480,480, pixel
0.835, shown at level 0.105, step 2, values float32  

> volume #4 step 1

> volume #4 level 0.1559

> volume #4 level 0.2387

> volume #4 level 0.3295

> volume #4 level 0.2569

> volume #4 level 0.2205

> color zone #4 near #2 distance 5.01

> hide #!2 models

> lighting soft

> lighting simple

> lighting soft

> volume splitbyzone #4

Opened 041924-global-resampleonapo.mrc 0 as #5.1, grid size 480,480,480, pixel
0.835, shown at level 0.221, step 1, values float32  
Opened 041924-global-resampleonapo.mrc 1 as #5.2, grid size 480,480,480, pixel
0.835, shown at level 0.221, step 1, values float32  
Opened 041924-global-resampleonapo.mrc 2 as #5.3, grid size 480,480,480, pixel
0.835, shown at level 0.221, step 1, values float32  
Opened 041924-global-resampleonapo.mrc 3 as #5.4, grid size 480,480,480, pixel
0.835, shown at level 0.221, step 1, values float32  
Opened 041924-global-resampleonapo.mrc 4 as #5.5, grid size 480,480,480, pixel
0.835, shown at level 0.221, step 1, values float32  
Opened 041924-global-resampleonapo.mrc 5 as #5.6, grid size 480,480,480, pixel
0.835, shown at level 0.221, step 1, values float32  
Opened 041924-global-resampleonapo.mrc 6 as #5.7, grid size 480,480,480, pixel
0.835, shown at level 0.221, step 1, values float32  
Opened 041924-global-resampleonapo.mrc 7 as #5.8, grid size 480,480,480, pixel
0.835, shown at level 0.221, step 1, values float32  
Opened 041924-global-resampleonapo.mrc 8 as #5.9, grid size 480,480,480, pixel
0.835, shown at level 0.221, step 1, values float32  
Opened 041924-global-resampleonapo.mrc 9 as #5.10, grid size 480,480,480,
pixel 0.835, shown at level 0.221, step 1, values float32  

> hide #!5 models

> show #!5 models

> hide #!5.2 models

> show #!5.2 models

> hide #!5.3 models

> hide #5.2.1 models

> show #5.2.1 models

> volume #5.2 level 0.2383

> volume #5.8 level 0.2205

> volume #5.9 level 0.2241

> volume #5.10 level 0.164

> volume #5.10 level 0.174

> surface dust #1 size 8.35

> surface dust #5.1 size 8.35

> surface dust #5.2 size 8.35

> surface dust #5.4 size 8.35

> surface dust #5.5 size 8.35

> surface dust #5.6 size 8.35

> surface dust #5.7 size 8.35

> surface dust #5.8 size 8.35

> surface dust #5.9 size 8.35

> surface dust #5.10 size 8.35

> open ""/Users/upneet/Library/CloudStorage/Box-Box/INO-yeastNCP/Map and
> Model/WT-0N80Xe-ADPBeF/041924-nuc-resampleonapo.mrc""

Opened 041924-nuc-resampleonapo.mrc as #6, grid size 480,480,480, pixel 0.835,
shown at level 0.188, step 2, values float32  

> color zone #6 near #2 distance 5.01

> surface dust #1 size 8.35

> surface dust #5.1 size 8.35

> surface dust #5.2 size 8.35

> surface dust #5.4 size 8.35

> surface dust #5.5 size 8.35

> surface dust #5.6 size 8.35

> surface dust #5.7 size 8.35

> surface dust #5.8 size 8.35

> surface dust #5.9 size 8.35

> surface dust #5.10 size 8.35

> surface dust #6 size 8.35

> volume #6 step 1

> volume #6 level 0.7474

> volume #6 level 0.9057

> color zone #6 near #2 distance 5.01

[Repeated 1 time(s)]

> volume #6 level 1.127

> volume #6 level 1.233

> color zone #6 near #2 distance 5.11

> color zone #6 near #2 distance 5.21

> color zone #6 near #2 distance 5.31

> color zone #6 near #2 distance 5.41

> color zone #6 near #2 distance 5.51

> color zone #6 near #2 distance 5.61

> color zone #6 near #2 distance 5.71

> color zone #6 near #2 distance 5.81

> color zone #6 near #2 distance 5.91

> color zone #6 near #2 distance 6.01

> color zone #6 near #2 distance 6.11

> color zone #6 near #2 distance 6.21

> volume #6 level 1.444

> volume #5.9 level 0.2348

> show #!3 models

> color zone #3 near #2 distance 5.01

> select clear

> save /Users/upneet/Desktop/test.png width 3600 height 2671 supersample 3
> transparentBackground true

> close #4

> rename #5 ""041924-global-resampleonapo_xl080.mrc split""

> rename #6 041924-nuc-resampleonapo_xl080.mrc

> rename #1 121124-a8-split_xl080.mrc

> open ""/Users/upneet/Library/CloudStorage/Box-Box/INO-yeastNCP/Map and
> Model/INO-40Xenuc-ADPBe/121124-a8-split.mrc""

Opened 121124-a8-split.mrc as #4, grid size 448,448,448, pixel 0.831, shown at
level 0.0002, step 2, values float32  

> open ""/Users/upneet/Library/CloudStorage/Box-Box/INO-yeastNCP/Map and
> Model/INO-40Xenuc-ADPBe/onlyies2-lowres.mrc""

Opened onlyies2-lowres.mrc as #7, grid size 448,448,448, pixel 0.831, shown at
level 2.07e-05, step 2, values float32  

> open ""/Users/upneet/Library/CloudStorage/Box-Box/INO-yeastNCP/Map and
> Model/INO-40Xenuc-ADPBe/onlynuc.mrc""

Opened onlynuc.mrc as #8, grid size 448,448,448, pixel 0.831, shown at level
9.79e-05, step 2, values float32  

> open ""/Users/upneet/Library/CloudStorage/Box-Box/INO-yeastNCP/Map and
> Model/INO-40Xenuc-ADPBe/inocore.mrc""

Opened inocore.mrc as #9, grid size 448,448,448, pixel 0.831, shown at level
3.68e-05, step 2, values float32  

> open ""/Users/upneet/Library/CloudStorage/Box-Box/INO-yeastNCP/Map and
> Model/INO-40Xenuc-ADPBe/nuc-resample.mrc""

Opened nuc-resample.mrc as #10, grid size 448,448,448, pixel 0.831, shown at
level 0.326, step 2, values float32  

> surface dust #1 size 8.35

> surface dust #3 size 8.35

> surface dust #5.1 size 8.35

> surface dust #5.2 size 8.35

> surface dust #5.4 size 8.35

> surface dust #5.5 size 8.35

> surface dust #5.6 size 8.35

> surface dust #5.7 size 8.35

> surface dust #5.8 size 8.35

> surface dust #5.9 size 8.35

> surface dust #5.10 size 8.35

> surface dust #6 size 8.35

> surface dust #4 size 8.31

> surface dust #7 size 8.31

> surface dust #8 size 8.31

> surface dust #9 size 8.31

> surface dust #10 size 8.31

> hide #!7 models

> hide #!8 models

> hide #!9 models

> hide #!10 models

> rename #7 onlyies2-lowres-Xl040.mrc

> rename #8 onlynuc_Xl040.mrc

> rename #9 inocore_Xl040.mrc

> rename #10 nuc-resample_Xl040.mrc

> surface dust #1 size 8.35

> surface dust #3 size 8.35

> surface dust #5.1 size 8.35

> surface dust #5.2 size 8.35

> surface dust #5.4 size 8.35

> surface dust #5.5 size 8.35

> surface dust #5.6 size 8.35

> surface dust #5.7 size 8.35

> surface dust #5.8 size 8.35

> surface dust #5.9 size 8.35

> surface dust #5.10 size 8.35

> surface dust #6 size 8.35

> surface dust #4 size 8.31

> surface dust #10 size 8.31

> volume #7 step 1

> volume #8 step 1

> volume #9 step 1

> volume #10 step 1

> volume #7 level 0.00766

> volume #7 level 0.04253

> volume #8 level 0.1849

> volume #9 level 0.1834

> hide #!1 models

> hide #!3 models

> hide #!4 models

> hide #!5 models

> hide #!6 models

> show #!4 models

> hide #!4 models

> volume #10 level 0.6999

> volume #8 level 0.4115

> volume #7 level 0.05194

> volume #9 level 0.2181

> surface dust #7 size 8.31

> surface dust #8 size 8.31

> surface dust #9 size 8.31

> show #!4 models

> volume #4 step 1

> volume #4 level 0.002465

> lighting simple

> lighting soft

> volume #4 level 0.0026

> close #10

> rename #4 121124-a8-split_Xl040.mrc

> open ""/Users/upneet/Library/CloudStorage/Box-Box/INO-yeastNCP/Map and
> Model/Final-withADPBeF/042624-x40-wt-adpbef-withadpbef-final.pdb""

Chain information for 042624-x40-wt-adpbef-withadpbef-final.pdb #10  
---  
Chain | Description  
A | No description available  
B | No description available  
C G | No description available  
D | No description available  
E | No description available  
F | No description available  
H | No description available  
I | No description available  
J | No description available  
L | No description available  
M | No description available  
N | No description available  
O | No description available  
Q | No description available  
R | No description available  
S | No description available  
T | No description available  
U | No description available  
V | No description available  
W | No description available  
X | No description available  
Y | No description available  
Z | No description available  
  

> hide #!10 cartoons

> hide #!10 atoms

> show #!10 cartoons

> hide #!7 models

> hide #!8 models

> hide #!9 models

> hide #!10 models

> hide #!4 models

> show #!10 models

> color #10/Q firebrick

Drag select of 808 residues  

> color #10/R,S medium seagreen

> color #10/T-Y,A-H medium seagreen

> color #10/T-Y,A-H light gray

> select clear

> color #10/T-Y,I,J light slate gray

> color #10/I,J light slate gray

> nucleotides #!10 ladder

> show #!10 atoms

> undo

> select #10/I,J

6601 atoms, 7404 bonds, 322 residues, 1 model selected  

> show sel atoms

> select clear

> select #10/K

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

> color #10/N medium blue

[Repeated 1 time(s)]

> select #10/L

2824 atoms, 2886 bonds, 1 pseudobond, 361 residues, 2 models selected  

> ui tool show ""Color Actions""

> color sel sandy brown

> color sel goldenrod

[Repeated 1 time(s)]

> show #!2 models

> cartoon style (#!10 & sel) modeHelix tube sides 20

> select up

55996 atoms, 57633 bonds, 12 pseudobonds, 6600 residues, 2 models selected  

> select up

55996 atoms, 57633 bonds, 14 pseudobonds, 6600 residues, 3 models selected  

> select up

55996 atoms, 57633 bonds, 14 pseudobonds, 6600 residues, 3 models selected  

> select up

114335 atoms, 117752 bonds, 14 pseudobonds, 13459 residues, 19 models selected  

> select down

55996 atoms, 57633 bonds, 14 pseudobonds, 6600 residues, 3 models selected  

> select down

14 pseudobonds, 2 models selected  

> cartoon style modeHelix tube radius 1.5

> select #10/Z

467 atoms, 472 bonds, 1 pseudobond, 72 residues, 2 models selected  

> color sel salmon

[Repeated 1 time(s)]

> color sel dark salmon

> color sel salmon

> select #10/L

2824 atoms, 2886 bonds, 1 pseudobond, 361 residues, 2 models selected  

> color (#!10 & sel) #ffd479ff

> color (#!10 & sel) #feff80ff

[Repeated 1 time(s)]

> select clear

> select #10/M

3422 atoms, 3498 bonds, 1 pseudobond, 431 residues, 2 models selected  

> color sel deep sky blue

> select #10/O\

Nothing selected  

> select #10/O

287 atoms, 296 bonds, 34 residues, 1 model selected  

> color sel royal blue

> color sel #2163a6ff

[Repeated 1 time(s)]

> select clear

> hide #!2 models

> show #!9 models

> show #!8 models

> show #!4 models

> show #!7 models

> ui tool show ""Color Zone""

> color zone #4 near #10 distance 4.99

> color zone #4 near #10 distance 1

> color zone #4 near #10 distance 10

> color zone #7 near #10 distance 4.99

> color zone #8 near #10 distance 4.99

> color zone #9 near #10 distance 4.99

> hide #!4 models

> show #!4 models

> hide #!10 models

> ui tool show ""Side View""

> show #!2 models

> hide #!2 models

> show #!1 models

> hide #!1 models

> show #!6 models

> hide #!6 models

> show #!5 models

> hide #!5 models

> show #!1 models

> hide #!7 models

> hide #!8 models

> hide #!9 models

> hide #!4 models

> show #!3 models

> show #!4 models

> hide #!4 models

> show #!5 models

> show #!6 models

> save ""/Users/upneet/Desktop/Narlilkar Lab/Manuscript_INO80_AutoInib/Figures
> /Figure 1/Version 2/xl_080_map.png"" width 3600 height 2934 supersample 3
> transparentBackground true

> hide #!1 models

> hide #!3 models

> hide #!5 models

> hide #!6 models

> show #!8 models

> show #!9 models

> show #!7 models

> show #!4 models

> save ""/Users/upneet/Desktop/Narlilkar Lab/Manuscript_INO80_AutoInib/Figures
> /Figure 1/Version 2/xl_040_map.png"" width 3600 height 2934 supersample 3
> transparentBackground true

> save ""/Users/upneet/Desktop/Narlilkar Lab/Manuscript_INO80_AutoInib/Figures
> /Figure 1/Version 2-resubmission/Chimera Session/Figure1.cxs"" includeMaps
> true

> show #!10 models

> select #10/L

2824 atoms, 2886 bonds, 1 pseudobond, 361 residues, 2 models selected  

> ui tool show ""Color Actions""

> color sel gold

[Repeated 1 time(s)]

> color zone #9 near #10 distance 4.99

> color zone #4 near #10 distance 10

> select clear

> hide #!10 models

> save ""/Users/upneet/Desktop/Narlilkar Lab/Manuscript_INO80_AutoInib/Figures
> /Figure 1/Version 2-resubmission/Chimera Session/Xl_0N40_map.png"" width 3600
> height 2700 supersample 3 transparentBackground true

> save ""/Users/upneet/Desktop/Narlilkar Lab/Manuscript_INO80_AutoInib/Figures
> /Figure 1/Version 2-resubmission/Chimera Session/Xl_0N40_map.png"" width 3600
> height 2700 supersample 4 transparentBackground true

> select clear

> save ""/Users/upneet/Desktop/Narlilkar Lab/Manuscript_INO80_AutoInib/Figures
> /Figure 1/Version 2-resubmission/Chimera Session/Xl_0N40_map.png"" width 3600
> height 2700 supersample 1 transparentBackground true

> graphics silhouettes true

> save ""/Users/upneet/Desktop/Narlilkar Lab/Manuscript_INO80_AutoInib/Figures
> /Figure 1/Version 2-resubmission/Chimera Session/Xl_0N40_map.png"" width 3600
> height 2700 supersample 3 transparentBackground true

> graphics silhouettes false

> save ""/Users/upneet/Desktop/Narlilkar Lab/Manuscript_INO80_AutoInib/Figures
> /Figure 1/Version 2-resubmission/Chimera Session/Xl_0N40_map.png"" width 3600
> height 2700 supersample 3 transparentBackground true

> hide #!4 models

> hide #!7 models

> hide #!8 models

> hide #!9 models

> show #!1 models

> show #!3 models

> show #!5 models

> show #!6 models

> save ""/Users/upneet/Desktop/Narlilkar Lab/Manuscript_INO80_AutoInib/Figures
> /Figure 1/Version 2-resubmission/Chimera Session/Xl_0N80_map.png"" width 3600
> height 2700 supersample 3 transparentBackground true

> save ""/Users/upneet/Desktop/Narlilkar Lab/Manuscript_INO80_AutoInib/Figures
> /Figure 1/Version 2-resubmission/Chimera Session/Figure1.cxs"" includeMaps
> true

> undo

> show #!6 models

> hide #!6 models

> hide #!5 models

> hide #!3 models

> hide #!1 models

> show #!10 models

> select #10/T-Y, Q:1022-1200

1186 atoms, 1210 bonds, 1 pseudobond, 147 residues, 2 models selected  

> hide sel atoms

> hide sel cartoons

> select #10/T-Y

20471 atoms, 20720 bonds, 2 pseudobonds, 2649 residues, 2 models selected  

> hide sel cartoons

Drag select of 98 residues  

> select up

910 atoms, 932 bonds, 115 residues, 1 model selected  

> hide sel cartoons

> select #10/Z

467 atoms, 472 bonds, 1 pseudobond, 72 residues, 2 models selected  

> hide sel cartoons

> select clear

> show #!4 models

> color #4 silver models

> color #4 #d6d6d6ff models

> color #4 silver models

> color #4 #c0c0c023 models

> color #4 #c0c0c000 models

> color #4 #c0c0c00e models

> graphics silhouettes true

> graphics silhouettes false

> lighting shadows true intensity 0.5

> lighting shadows false

> lighting shadows true

> lighting soft

> color #4 #c0c0c01b models

> color #4 white models

> color #4 #ffffff25 models

> color #4 #d6d6d6ff models

> color #4 #d6d6d605 models

> color #4 #d6d6d619 models

> save ""/Users/upneet/Desktop/Narlilkar Lab/Manuscript_INO80_AutoInib/Figures
> /Figure 1/Version 2-resubmission/Chimera Session/Figure1_noRvbs'.cxs""
> includeMaps true

——— End of log from Thu Dec 12 15:35:36 2024 ———

opened ChimeraX session  

> hide #!4 models

> hide #!10 models

> show #!2 models

> select #2/T-Y,Z

20950 atoms, 21202 bonds, 3 pseudobonds, 2723 residues, 2 models selected  

> hide sel cartoons

> ui mousemode right select

Drag select of 18 residues  

> select up

248 atoms, 246 bonds, 49 residues, 1 model selected  

> select up

651 atoms, 649 bonds, 130 residues, 1 model selected  

> select up

724 atoms, 722 bonds, 140 residues, 1 model selected  

> select up

2940 atoms, 2998 bonds, 427 residues, 1 model selected  

> select down

724 atoms, 722 bonds, 140 residues, 1 model selected  

> hide sel cartoons

[Repeated 1 time(s)]Drag select of 7 residues, 1 pseudobonds  

> select up

120 atoms, 119 bonds, 1 pseudobond, 24 residues, 2 models selected  

> select up

130 atoms, 129 bonds, 1 pseudobond, 26 residues, 2 models selected  

> select up

194 atoms, 194 bonds, 1 pseudobond, 33 residues, 2 models selected  

> select up

1894 atoms, 1922 bonds, 1 pseudobond, 278 residues, 2 models selected  

> select down

194 atoms, 194 bonds, 1 pseudobond, 33 residues, 2 models selected  

> hide sel cartoons

> select #2/Q:1022-1294

1922 atoms, 1967 bonds, 1 pseudobond, 241 residues, 2 models selected  

> color (#!2 & sel) orange

> select #2/L

2862 atoms, 2925 bonds, 1 pseudobond, 364 residues, 2 models selected  

> ui tool show ""Color Actions""

> color sel gold

> select clear

> open ""/Users/upneet/Library/CloudStorage/Box-Box/INO-yeastNCP/Map and
> Model/WT-0N80Xe-ADPBeF/041924-global-resampleonapo.mrc""

Opened 041924-global-resampleonapo.mrc as #11, grid size 480,480,480, pixel
0.835, shown at level 0.105, step 2, values float32  

> ui tool show ""Color Zone""

> color zone #11 near #2 distance 5.01

> volume splitbyzone #11

Opened 041924-global-resampleonapo.mrc 0 as #12.1, grid size 480,480,480,
pixel 0.835, shown at level 0.105, step 1, values float32  
Opened 041924-global-resampleonapo.mrc 1 as #12.2, grid size 480,480,480,
pixel 0.835, shown at level 0.105, step 1, values float32  
Opened 041924-global-resampleonapo.mrc 2 as #12.3, grid size 480,480,480,
pixel 0.835, shown at level 0.105, step 1, values float32  
Opened 041924-global-resampleonapo.mrc 3 as #12.4, grid size 480,480,480,
pixel 0.835, shown at level 0.105, step 1, values float32  
Opened 041924-global-resampleonapo.mrc 4 as #12.5, grid size 480,480,480,
pixel 0.835, shown at level 0.105, step 1, values float32  
Opened 041924-global-resampleonapo.mrc 5 as #12.6, grid size 480,480,480,
pixel 0.835, shown at level 0.105, step 1, values float32  
Opened 041924-global-resampleonapo.mrc 6 as #12.7, grid size 480,480,480,
pixel 0.835, shown at level 0.105, step 1, values float32  
Opened 041924-global-resampleonapo.mrc 7 as #12.8, grid size 480,480,480,
pixel 0.835, shown at level 0.105, step 1, values float32  
Opened 041924-global-resampleonapo.mrc 8 as #12.9, grid size 480,480,480,
pixel 0.835, shown at level 0.105, step 1, values float32  
Opened 041924-global-resampleonapo.mrc 9 as #12.10, grid size 480,480,480,
pixel 0.835, shown at level 0.105, step 1, values float32  
Opened 041924-global-resampleonapo.mrc 10 as #12.11, grid size 480,480,480,
pixel 0.835, shown at level 0.105, step 1, values float32  

> hide #!12.1 models

> hide #!12.2 models

> hide #!12.9 models

> hide #!12.4 models

> hide #!12.5 models

> hide #!12.6 models

> hide #!12.7 models

> hide #!12.11 models

> hide #!12.3 models

> select #2/Q:1022-1294

1922 atoms, 1967 bonds, 1 pseudobond, 241 residues, 2 models selected  

> hide sel cartoons

> show #!1 models

> hide #!1 models

> hide #!2 models

> hide #!12 models

> show #!2 models

> save ""/Users/upneet/Desktop/Narlilkar Lab/Manuscript_INO80_AutoInib/Figures
> /Figure 1/Version 2-resubmission/Chimera Session/Xl_0N80_model_noRvbs.png""
> width 3600 height 3420 supersample 3 transparentBackground true

> show #!1 models

> show #!12 models

> show #!6 models

> hide #!2 models

> color #1 white models

> color #1 #ffffff00 models

> graphics silhouettes true

> color #6 white models

> color #6 #ffffff00 models

> color #12 white models

> color #12 #ffffff00 models

> save ""/Users/upneet/Desktop/Narlilkar Lab/Manuscript_INO80_AutoInib/Figures
> /Figure 1/Version 2-resubmission/Chimera Session/Xl_0N80_map_noRvbs.png""
> width 3600 height 3420 supersample 3 transparentBackground true

> save ""/Users/upneet/Desktop/Narlilkar Lab/Manuscript_INO80_AutoInib/Figures
> /Figure 1/Version 2-resubmission/Chimera Session/Figure1_noRvbs'.cxs""
> includeMaps true

——— End of log from Thu Dec 12 17:07:10 2024 ———

opened ChimeraX session  

> close #2-5

> close #1,6-9

> show #!11 models

> close #11-12

> show #!10 models

> graphics silhouettes false

> show surfaces

> select #10/T-Y

20471 atoms, 20720 bonds, 2 pseudobonds, 2649 residues, 2 models selected  

> hide sel surfaces

> select #10/Q:1022-1294

1916 atoms, 1961 bonds, 1 pseudobond, 241 residues, 2 models selected  

> hide sel surfaces

> select #10/z

467 atoms, 472 bonds, 1 pseudobond, 72 residues, 2 models selected  

> hide sel surfaces

> select #10/R,S

4562 atoms, 4675 bonds, 2 pseudobonds, 567 residues, 2 models selected  

> hide sel surfaces

> hide sel cartoons

[Repeated 1 time(s)]

> select #10

55996 atoms, 57633 bonds, 14 pseudobonds, 6600 residues, 15 models selected  

> color (#!10 & sel) light gray

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> select #10/Q:0-700

1105 atoms, 1118 bonds, 130 residues, 1 model selected  

> ui tool show ""Color Actions""

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> color sel fire brick

> transparency (#!10 & sel) 80

> hide sel surfaces

[Repeated 1 time(s)]

> show sel surfaces

[Repeated 1 time(s)]

> select #10/R,S

4562 atoms, 4675 bonds, 2 pseudobonds, 567 residues, 2 models selected  

> hide sel cartoons

> hide sel surfaces

> select up

55996 atoms, 57633 bonds, 12 pseudobonds, 6600 residues, 4 models selected  

> select up

55996 atoms, 57633 bonds, 14 pseudobonds, 6600 residues, 27 models selected  

> select #10/z

467 atoms, 472 bonds, 1 pseudobond, 72 residues, 2 models selected  

> hide sel surfaces

> select #10/Q:1022-1294

1916 atoms, 1961 bonds, 1 pseudobond, 241 residues, 2 models selected  

> hide sel surfaces

[Repeated 1 time(s)]

> select #10/T-Y

20471 atoms, 20720 bonds, 2 pseudobonds, 2649 residues, 2 models selected  

> hide sel surfaces

> transparency (#!10 & sel) 40

> select #10

55996 atoms, 57633 bonds, 14 pseudobonds, 6600 residues, 15 models selected  

> transparency (#!10 & sel) 80

> select clear

> select #10

55996 atoms, 57633 bonds, 14 pseudobonds, 6600 residues, 15 models selected  

> color (#!10 & sel) light gray

> transparency (#!10 & sel) 30

> transparency (#!10 & sel) 80

> hide sel cartoons

> hide sel atoms

> show sel atoms

> hide sel atoms

> show sel surfaces

> show sel cartoons

> select #10/T-Y

20471 atoms, 20720 bonds, 2 pseudobonds, 2649 residues, 2 models selected  

> hide sel surfaces

> hide sel cartoons

> select #10/Q:1022-1294

1916 atoms, 1961 bonds, 1 pseudobond, 241 residues, 2 models selected  

> hide sel cartoons

> hide sel surfaces

> select #10/z

467 atoms, 472 bonds, 1 pseudobond, 72 residues, 2 models selected  

> select #10/z

467 atoms, 472 bonds, 1 pseudobond, 72 residues, 2 models selected  

> hide sel surfaces

> hide sel cartoons

> select #10/R,S

4562 atoms, 4675 bonds, 2 pseudobonds, 567 residues, 2 models selected  

> hide sel surfaces

> hide sel cartoons

> select #10/Q:0-700

1105 atoms, 1118 bonds, 130 residues, 1 model selected  

> color (#!10 & sel) red

> transparency #10/Q:0-700 0 surfaces

> hide sel surfaces

> select #10/Q:700-3000

5289 atoms, 5408 bonds, 3 pseudobonds, 660 residues, 2 models selected  

> hide sel cartoons

> select #10/K,L,M,O

6565 atoms, 6712 bonds, 4 pseudobonds, 829 residues, 3 models selected  

> hide sel cartoons

> select #10/N

5060 atoms, 5173 bonds, 626 residues, 1 model selected  

> hide sel surfaces

> show sel surfaces

> hide sel cartoons

> select clear

> select #10/Q:545, 544, 537, 534, 533, 526, 523 , 482, 483, 487, 490, 504,
> 505, 512, 515, 522, 523, 526,

Expected a keyword  

> select #10/Q:545, 544, 537, 534, 533, 526, 523, 482, 483, 487, 490, 504,
> 505, 512, 515, 522, 523, 526,

Expected an objects specifier or a keyword  

> select #10/Q:482, 483, 487, 490, 504, 505, 512, 515, 522, 545, 544, 537,
> 534, 533, 526, 523,

Expected an objects specifier or a keyword  

> select #10/Q:482, 483, 487, 490, 504, 505, 512, 515, 522, 545, 544, 537,
> 534, 533, 526, 523

160 atoms, 150 bonds, 16 residues, 1 model selected  

> style sel sphere

Changed 160 atom styles  

> show sel surfaces

> hide sel surfaces

> show sel atoms

> style sel ball

Changed 160 atom styles  

> style sel stick

Changed 160 atom styles  

> select clear

> save ""/Users/upneet/Desktop/Narlilkar Lab/Manuscript_INO80_AutoInib/Figures
> /Figure 1/Version 2-resubmission/Chimera Session/Figure1_HSA.cxs""
> includeMaps true

> save ""/Users/upneet/Desktop/Narlilkar Lab/Manuscript_INO80_AutoInib/Figures
> /Figure 1/Version 2-resubmission/Chimera Session/Figure1_HSA.cxs""

——— End of log from Fri Dec 20 14:57:31 2024 ———

opened ChimeraX session  

> ui mousemode right ""translate selected models""

> select #10/Q:482, 483, 487, 490, 504, 505, 512, 515, 522, 545, 544, 537,
> 534, 533, 526, 523

160 atoms, 150 bonds, 16 residues, 1 model selected  

> show sel surfaces

> transparency (#!10 & sel) 90

> view matrix models #10,1,0,0,38.985,0,1,0,21.605,0,0,1,42.977

> surface #10/K,L,M,O

> hide sel surfaces

> select #10/K,L,M,O

6565 atoms, 6712 bonds, 4 pseudobonds, 829 residues, 3 models selected  

> hide sel surfaces

> ui mousemode right select

Drag select of 042624-x40-wt-adpbef-withadpbef-final.pdb_N SES surface, 64778
of 571650 triangles, cap near, 178 of 1639 triangles  

> select up

5060 atoms, 626 residues, 3 models selected  

> select up

55996 atoms, 57633 bonds, 6600 residues, 3 models selected  

> select down

5060 atoms, 626 residues, 26 models selected  

> hide sel surfaces

> select #10/Q:700-2000

5289 atoms, 5408 bonds, 3 pseudobonds, 660 residues, 2 models selected  

> hide sel surfaces

> undo

[Repeated 3 time(s)]

> select #10/Q:700-2000

5289 atoms, 5408 bonds, 3 pseudobonds, 660 residues, 2 models selected  

> show sel cartoons

> select #10/Q:482, 483, 487, 490, 504, 505, 512, 515, 522, 545, 544, 537,
> 534, 533, 526, 523

160 atoms, 150 bonds, 16 residues, 1 model selected  

> show sel surfaces

> cartoon style (#!10 & sel) xsection oval modeHelix default

> select clear

> select #10/Q

6394 atoms, 6526 bonds, 4 pseudobonds, 790 residues, 2 models selected  

> ui tool show ""Color Actions""

> color sel fire brick

> transparency (#!10 & sel) 80

> select clear

> select #I,J,A-H

Expected an objects specifier or a keyword  

> select #10/I,J,A-H

12477 atoms, 13355 bonds, 1 pseudobond, 1067 residues, 2 models selected  

> hide sel surfaces

> nucleotides sel atoms

> style nucleic & sel stick

Changed 6601 atom styles  

> nucleotides sel fill

> style nucleic & sel stick

Changed 6601 atom styles  

> nucleotides sel fill

> style nucleic & sel stick

Changed 6601 atom styles  

> nucleotides sel ladder

> show sel atoms

> undo

> select #10/I,J

6601 atoms, 7404 bonds, 322 residues, 1 model selected  

> nucleotides sel ladder

> show sel atoms

> select clear

> preset cartoons/nucleotides cylinders/stubs

Using preset: Cartoons/Nucleotides / Cylinders/Stubs  
Changed 49041 atom styles  
Preset expands to these ChimeraX commands:

    
    
    show nucleic
    hide protein|solvent|H
    surf hide
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    ~worm
    cartoon
    cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    cartoon style ~(nucleic|strand) x round
    cartoon style (nucleic|strand) x rect
    cartoon style protein modeh tube rad 2 sides 24 thick 0.6
    cartoon style nucleic x round width 1.6 thick 1.6
    nucleotides stubs

  

> undo

> select #10/Q:482, 483, 487, 490, 504, 505, 512, 515, 522, 545, 544, 537,
> 534, 533, 526, 523

160 atoms, 150 bonds, 16 residues, 1 model selected  

> show sel surfaces

> select clear

> open ""/Users/upneet/Library/CloudStorage/Box-Box/INO-yeastNCP/Map and
> Model/WT-0N80Xe-ADPBeF/121124-0n80-xe-wt-adpbef-final-coot-0-pymol-
> shortdna.pdb""

Chain information for 121124-0n80-xe-wt-adpbef-final-coot-0-pymol-shortdna.pdb
#1  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
F | No description available  
G | No description available  
H | No description available  
I | No description available  
J | No description available  
K | No description available  
L | No description available  
M | No description available  
O | No description available  
Q | No description available  
R | No description available  
S | No description available  
T | No description available  
U | No description available  
V | No description available  
W | No description available  
X | No description available  
Y | No description available  
Z | No description available  
  

> hide #!10 models

> hide #!1 atoms

> show #!1 cartoons

Drag select of 104 residues  

> ui mousemode right select

> ui mousemode right ""translate selected models""

> select clear

> ui tool show ""Side View""

> show #!10 models

> select add #10

55996 atoms, 57633 bonds, 14 pseudobonds, 6600 residues, 3 models selected  

> ui mousemode right ""translate selected models""

> view matrix models #10,1,0,0,7.7309,0,1,0,-1.5622,0,0,1,28.761

> view matrix models #10,1,0,0,21.604,0,1,0,-1.7319,0,0,1,10.905

> select #1/T-Y,R,S,Z

26265 atoms, 26627 bonds, 8 pseudobonds, 3449 residues, 2 models selected  

> hide sel cartoons

> select add #10

82261 atoms, 84260 bonds, 22 pseudobonds, 10049 residues, 5 models selected  

> select add #1

114335 atoms, 117752 bonds, 34 pseudobonds, 13459 residues, 29 models selected  

> view matrix models
> #10,0.99854,0.0039952,-0.053886,36.374,-0.0072529,0.99815,-0.060394,16.722,0.053545,0.060697,0.99672,-6.6013,#1,0.99854,0.0039952,-0.053886,15.396,-0.0072529,0.99815,-0.060394,19.266,0.053545,0.060697,0.99672,-18.522

> view matrix models
> #10,0.99854,0.0039952,-0.053886,24.172,-0.0072529,0.99815,-0.060394,14.423,0.053545,0.060697,0.99672,-11.756,#1,0.99854,0.0039952,-0.053886,3.1942,-0.0072529,0.99815,-0.060394,16.967,0.053545,0.060697,0.99672,-23.676

> select subtract #1

55996 atoms, 57633 bonds, 14 pseudobonds, 6600 residues, 27 models selected  

> view matrix models
> #10,0.99854,0.0039952,-0.053886,19.269,-0.0072529,0.99815,-0.060394,13.67,0.053545,0.060697,0.99672,-14.121

> ui tool show Matchmaker

> matchmaker #10/A to #1/A pairing ss

Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 121124-0n80-xe-wt-adpbef-final-coot-0-pymol-shortdna.pdb, chain A
(#1) with 042624-x40-wt-adpbef-withadpbef-final.pdb, chain A (#10), sequence
alignment score = 464.5  
RMSD between 92 pruned atom pairs is 0.625 angstroms; (across all 94 pairs:
1.166)  
  

> select #1/Q:1022-1294

1922 atoms, 1967 bonds, 1 pseudobond, 241 residues, 2 models selected  

> hide sel cartoons

> select #10/Q:1022-1294

1916 atoms, 1961 bonds, 1 pseudobond, 241 residues, 2 models selected  

> hide sel cartoons

> select #10/I,J-A-H

3300 atoms, 3692 bonds, 161 residues, 1 model selected  

> color (#!10 & sel) light gray

> select #1/I,J-A-H

3873 atoms, 4329 bonds, 190 residues, 1 model selected  

> color sel light gray

> select #1/I,J-A-H

3873 atoms, 4329 bonds, 190 residues, 1 model selected  

> color sel light gray

> select #1/Q

6141 atoms, 6266 bonds, 8 pseudobonds, 758 residues, 2 models selected  

> ui tool show ""Color Actions""

> color sel fire brick

> view matrix models
> #1,0.99854,0.0039952,-0.053886,11.602,-0.0072529,0.99815,-0.060394,23.788,0.053545,0.060697,0.99672,-13.106

> undo

> ui mousemode right select

Drag select of 7 residues  

> select up

7787 atoms, 8735 bonds, 380 residues, 1 model selected  

> select up

58339 atoms, 60119 bonds, 6859 residues, 1 model selected  

> select down

7787 atoms, 8735 bonds, 380 residues, 1 model selected  

> color sel light gray

> nucleotides sel ladder

> show sel atoms

Drag select of 183 residues, 1 pseudobonds  

> select up

2840 atoms, 2860 bonds, 1 pseudobond, 364 residues, 8 models selected  

> select up

7567 atoms, 7659 bonds, 1 pseudobond, 956 residues, 8 models selected  

> color (#!1,10 & sel) light gray

> select up

114335 atoms, 117752 bonds, 12 pseudobonds, 13459 residues, 8 models selected  

> select down

7567 atoms, 7659 bonds, 1 pseudobond, 956 residues, 27 models selected  
Drag select of 56 residues  

> select up

2398 atoms, 2426 bonds, 304 residues, 6 models selected  

> color (#!1,10 & sel) light gray

Drag select of 12 residues  

> select up

170 atoms, 170 bonds, 21 residues, 3 models selected  

> select up

1286 atoms, 1300 bonds, 162 residues, 3 models selected  

> color (#!1,10 & sel) light gray

Drag select of 27 residues  

> select up

947 atoms, 963 bonds, 118 residues, 4 models selected  

> color (#!1,10 & sel) light gray

> select #1/K,L,M,O

12253 atoms, 12523 bonds, 3 pseudobonds, 1525 residues, 2 models selected  

> hide sel cartoons

[Repeated 1 time(s)]

> select #1/Q:482, 483, 487, 490, 504, 505, 512, 515, 522, 545, 544, 537, 534,
> 533, 526, 523

160 atoms, 150 bonds, 16 residues, 1 model selected  

> show sel atoms

> style sel stick

Changed 160 atom styles  

> show sel surfaces

> transparency (#!1 & sel) 90

> transparency (#!1 & sel) 80

> select clear

[Repeated 2 time(s)]Drag select of 4 residues, 5 shapes  

> select clear

> ui mousemode right ""translate selected models""

> ui mousemode right select

Drag select of 2 residues  

> select up

739 atoms, 750 bonds, 95 residues, 1 model selected  

> color sel light gray

> select clear

> save ""/Users/upneet/Desktop/Narlilkar Lab/Manuscript_INO80_AutoInib/Figures
> /Figure 1/Version 1/Chimera Session V2/HSa.cxs"" includeMaps true

Drag select of 4 residues, 2 shapes  

> select clear

> ui mousemode right ""translate selected models""

> hide #!10 models

> select #1/K,L,M,O

12253 atoms, 12523 bonds, 3 pseudobonds, 1525 residues, 2 models selected  

> show sel cartoons

> select #1/K

5614 atoms, 5735 bonds, 1 pseudobond, 692 residues, 2 models selected  

> color (#!1 & sel) medium blue

> select #1/L

2862 atoms, 2925 bonds, 1 pseudobond, 364 residues, 2 models selected  

> ui tool show ""Color Actions""

> color sel gold

> select #1/M

3430 atoms, 3507 bonds, 1 pseudobond, 429 residues, 2 models selected  

> color sel deep sky blue

> select #1/O

347 atoms, 356 bonds, 40 residues, 1 model selected  

> color sel cornflower blue

> select #1/K,L,M,O

12253 atoms, 12523 bonds, 3 pseudobonds, 1525 residues, 2 models selected  

> show sel surfaces

> transparency (#!1 & sel) 90

> hide sel cartoons

> hide sel surfaces

> view matrix models
> #1,0.99854,0.0039952,-0.053886,13.787,-0.0072529,0.99815,-0.060394,17.309,0.053545,0.060697,0.99672,-14.708

> select #1/K,L,M,O

12253 atoms, 12523 bonds, 3 pseudobonds, 1525 residues, 2 models selected  

> select #1/K,L,M,O

12253 atoms, 12523 bonds, 3 pseudobonds, 1525 residues, 2 models selected  

> show sel cartoons

> hide sel cartoons

> show sel surfaces

> color (#!1 & sel) light gray

> transparency (#!1 & sel) 90

> select clear

> hide #!1 surfaces

> undo

> select #1/Q:482, 483, 487, 490, 504, 505, 512, 515, 522, 545, 544, 537, 534,
> 533, 526, 523

160 atoms, 150 bonds, 16 residues, 1 model selected  

> show sel surfaces

> select clear

> cartoon style #1 xsection oval modeHelix default

> cartoon style #1 modeHelix tube sides 20

> cartoon style modeHelix tube radius 1.5

> select #1/I,J

7787 atoms, 8735 bonds, 380 residues, 1 model selected  

> color sel light slate gray

> select clear

> select #1/K,L,M,O

12253 atoms, 12523 bonds, 3 pseudobonds, 1525 residues, 2 models selected  

> show sel cartoons

> transparency #1/K,L,M,O 80 cartoons

> select clear

> graphics silhouettes true

> select #1/K,L,M,O 80 c

Expected a keyword  

> select #1/K,L,M,O

12253 atoms, 12523 bonds, 3 pseudobonds, 1525 residues, 2 models selected  

> color sel cornflower blue

> color sel blue

> color sel medium blue

> color sel cornflower blue

> color sel deep sky blue

> color sel cyan

> color sel cornflower blue

> select clear

> show #!10 models

> select add #10

55996 atoms, 57633 bonds, 14 pseudobonds, 6600 residues, 3 models selected  

> view matrix models
> #10,0.98483,-0.12885,-0.11623,65.285,0.11868,0.9888,-0.090544,-1.7103,0.1266,0.075375,0.98909,-24.897

> select subtract #10

24 models selected  

> select add #1

58339 atoms, 60119 bonds, 20 pseudobonds, 6859 residues, 6 models selected  

> select add #10

114335 atoms, 117752 bonds, 34 pseudobonds, 13459 residues, 14 models selected  

> select subtract #1

55996 atoms, 57633 bonds, 14 pseudobonds, 6600 residues, 32 models selected  

> select subtract #10

24 models selected  

> hide #!1 models

> show #!1 models

> select #10/K,L,M,O

6565 atoms, 6712 bonds, 4 pseudobonds, 829 residues, 3 models selected  

> show sel cartoons

> select #10/N

5060 atoms, 5173 bonds, 626 residues, 1 model selected  

> show sel cartoons

> select #10/N,K,L,M,O

11625 atoms, 11885 bonds, 4 pseudobonds, 1455 residues, 3 models selected  

> color sel cornflower blue

> transparency #10/N,K,L,M,O 90 cartoons

> select clear

> transparency #1/K,L,M,O 90 cartoons

> select clear

> select #1/ L

2862 atoms, 2925 bonds, 1 pseudobond, 364 residues, 2 models selected  

> color sel gold

> select #10/ L

2824 atoms, 2886 bonds, 1 pseudobond, 361 residues, 2 models selected  

> color sel gold

> select #10/ M

3422 atoms, 3498 bonds, 1 pseudobond, 431 residues, 2 models selected  

> color sel deep sky blue

> color sel cyan

> color sel deep sky blue

> select #1/ M

3430 atoms, 3507 bonds, 1 pseudobond, 429 residues, 2 models selected  

> color sel royal blue

> color sel deep sky blue

> select clear

> save ""/Users/upneet/Desktop/Narlilkar Lab/Manuscript_INO80_AutoInib/Figures
> /Figure 1/Version 1/Chimera Session V2/HSa.cxs"" includeMaps true

——— End of log from Sat Dec 21 18:53:40 2024 ———

opened ChimeraX session  

> select #10/I,J

6601 atoms, 7404 bonds, 322 residues, 1 model selected  

> select clear

> hide #!10 models

> SEL #1/K,L,M,O

Unknown command: SEL #1/K,L,M,O  

> select #1/K,L,M,O

12253 atoms, 12523 bonds, 3 pseudobonds, 1525 residues, 2 models selected  

> hide sel cartoons

> view matrix models
> #1,0.99854,0.0039952,-0.053886,26.023,-0.0072529,0.99815,-0.060394,15.967,0.053545,0.060697,0.99672,-3.2803

> view matrix models
> #1,0.99854,0.0039952,-0.053886,42.833,-0.0072529,0.99815,-0.060394,16.012,0.053545,0.060697,0.99672,14.844

> view matrix models
> #1,0.99854,0.0039952,-0.053886,42.856,-0.0072529,0.99815,-0.060394,15.964,0.053545,0.060697,0.99672,14.815

> view matrix models
> #1,0.99854,0.0039952,-0.053886,46.079,-0.0072529,0.99815,-0.060394,15.76,0.053545,0.060697,0.99672,17.042

> ui mousemode right ""rotate selected models""

> view matrix models
> #1,0.99848,0.002554,-0.055102,46.617,-0.005834,0.99821,-0.059446,15.308,0.054852,0.059677,0.99671,17.015

> ui mousemode right ""translate selected models""

> view matrix models
> #1,0.99848,0.002554,-0.055102,47.291,-0.005834,0.99821,-0.059446,15.318,0.054852,0.059677,0.99671,17.531

> save ""/Users/upneet/Desktop/Narlilkar Lab/Manuscript_INO80_AutoInib/Figures
> /Figure 1/Version 1/Chimera Session V2/0N80_HSA.png"" width 3600 height 2686
> supersample 3 transparentBackground true

> save ""/Users/upneet/Desktop/Narlilkar Lab/Manuscript_INO80_AutoInib/Figures
> /Figure 1/Version 1/Chimera Session V2/0N80_HSA.png"" width 3600 height 2686
> supersample 3

> hide #!1 models

> show #!10 models

> view matrix models
> #1,0.99848,0.002554,-0.055102,24.086,-0.005834,0.99821,-0.059446,21.606,0.054852,0.059677,0.99671,7.1292

> view matrix models
> #1,0.99848,0.002554,-0.055102,5.6807,-0.005834,0.99821,-0.059446,26.158,0.054852,0.059677,0.99671,-1.8649

> view matrix models
> #1,0.99848,0.002554,-0.055102,-32.619,-0.005834,0.99821,-0.059446,46.065,0.054852,0.059677,0.99671,-2.6764

> view matrix models
> #1,0.99848,0.002554,-0.055102,-67.761,-0.005834,0.99821,-0.059446,61.29,0.054852,0.059677,0.99671,-8.8338

> select add #10

68249 atoms, 70156 bonds, 17 pseudobonds, 8125 residues, 9 models selected  

> select add #1

114335 atoms, 117752 bonds, 34 pseudobonds, 13459 residues, 33 models selected  

> select subtract #1

55996 atoms, 57633 bonds, 14 pseudobonds, 6600 residues, 32 models selected  

> view matrix models
> #10,0.98483,-0.12885,-0.11623,37.367,0.11868,0.9888,-0.090544,10.581,0.1266,0.075375,0.98909,-29.439

> select clear

> select #10/K,L,M,O

6565 atoms, 6712 bonds, 4 pseudobonds, 829 residues, 3 models selected  

> hide sel cartoons

> select #10/N

5060 atoms, 5173 bonds, 626 residues, 1 model selected  

> hide sel cartoons

> view matrix models
> #10,0.98483,-0.12885,-0.11623,20.474,0.11868,0.9888,-0.090544,33.043,0.1266,0.075375,0.98909,-49.921

> save ""/Users/upneet/Desktop/Narlilkar Lab/Manuscript_INO80_AutoInib/Figures
> /Figure 1/Version 1/Chimera Session V2/0N40_HSA.png"" width 3600 height 2686
> supersample 3

> select #10/N,K,L,M,O

11625 atoms, 11885 bonds, 4 pseudobonds, 1455 residues, 3 models selected  

> show sel cartoons

> select clear

> select #10/N,K,L,M,O

11625 atoms, 11885 bonds, 4 pseudobonds, 1455 residues, 3 models selected  

> color (#!10 & sel) gray

> select clear

> show #!1 models

> select add #1

58339 atoms, 60119 bonds, 20 pseudobonds, 6859 residues, 2 models selected  

> view matrix models
> #1,0.99848,0.002554,-0.055102,-34.947,-0.005834,0.99821,-0.059446,32.857,0.054852,0.059677,0.99671,-30.505

> select subtract #1

5 models selected  

> select #1/A-H

5893 atoms, 5968 bonds, 1 pseudobond, 747 residues, 2 models selected  

> hide sel cartoons

> select #2/A-H

Nothing selected  

> select #10/A-H

5876 atoms, 5951 bonds, 1 pseudobond, 745 residues, 2 models selected  

> hide sel cartoons

> select #10/I,J

6601 atoms, 7404 bonds, 322 residues, 1 model selected  

> ui tool show ""Color Actions""

> color sel slate gray

> color sel light slate gray

> color sel light steel blue

[Repeated 1 time(s)]

> color sel light blue

> color sel light steel blue

> color sel light gray

> select clear

> ui mousemode right select

Drag select of 9 residues, 14 shapes  

> select up

6601 atoms, 7404 bonds, 322 residues, 3 models selected  

> select down

185 atoms, 9 residues, 3 models selected  

> hide sel atoms

> select #10/I,J

6601 atoms, 7404 bonds, 322 residues, 1 model selected  

> hide sel atoms

> hide sel cartoons

> select #1/K,L,M,O

12253 atoms, 12523 bonds, 3 pseudobonds, 1525 residues, 2 models selected  

> show sel cartoons

> select clear

> select #1/K,L,M,O

12253 atoms, 12523 bonds, 3 pseudobonds, 1525 residues, 2 models selected  

> hide sel cartoons

> show sel surfaces

> color (#!1 & sel) white

> transparency (#!1 & sel) 100

> select clear

> select #10/N,K,L,M,O

11625 atoms, 11885 bonds, 4 pseudobonds, 1455 residues, 3 models selected  

> hide sel cartoons

> show sel surfaces

> color (#!10 & sel) white

> transparency (#!10 & sel) 100

> select clear

> select #1/Q:482, 483, 487, 490, 504, 505, 512, 515, 522, 545, 544, 537, 534,
> 533, 526, 523

160 atoms, 150 bonds, 16 residues, 1 model selected  

> transparency (#!1 & sel) 50

> select clear

> select #2/Q:482, 483, 487, 490, 504, 505, 512, 515, 522, 545, 544, 537, 534,
> 533, 526, 523

Nothing selected  

> transparency 50

> select clear

> lighting soft

> lighting simple

> lighting soft

> lighting full

> lighting flat

> lighting shadows true intensity 0.5

> lighting shadows false

> lighting simple

> lighting soft

> save ""/Users/upneet/Desktop/Narlilkar Lab/Manuscript_INO80_AutoInib/Figures
> /Figure 1/Version 1/Chimera Session V2/HSa.cxs"" includeMaps true

——— End of log from Sat Dec 21 19:42:25 2024 ———

opened ChimeraX session  

> select #10/K,L,M,O

6565 atoms, 6712 bonds, 4 pseudobonds, 829 residues, 3 models selected  

> hide sel atoms

> hide sel cartoons

> hide sel surfaces

> select #10/K,L,M,O,N

11625 atoms, 11885 bonds, 4 pseudobonds, 1455 residues, 3 models selected  

> hide sel surfaces

> select #10/Q:0-700

1105 atoms, 1118 bonds, 130 residues, 1 model selected  

> coulombic sel

The following residues are missing heavy (non-hydrogen) atoms, which may
result in inaccurate electrostatics:  
042624-x40-wt-adpbef-withadpbef-final.pdb #10/Q LYS 707  
042624-x40-wt-adpbef-withadpbef-final.pdb #10/Q ARG 802  
042624-x40-wt-adpbef-withadpbef-final.pdb #10/Q ASN 804  
042624-x40-wt-adpbef-withadpbef-final.pdb #10/Q VAL 824  
042624-x40-wt-adpbef-withadpbef-final.pdb #10/Q ARG 863  
042624-x40-wt-adpbef-withadpbef-final.pdb #10/Q ARG 865  
042624-x40-wt-adpbef-withadpbef-final.pdb #10/Q ASP 896  
042624-x40-wt-adpbef-withadpbef-final.pdb #10/Q GLU 897  
042624-x40-wt-adpbef-withadpbef-final.pdb #10/Q LYS 947  
042624-x40-wt-adpbef-withadpbef-final.pdb #10/Q ARG 959  
042624-x40-wt-adpbef-withadpbef-final.pdb #10/Q ARG 1293  
042624-x40-wt-adpbef-withadpbef-final.pdb #10/Q LYS 1300  
042624-x40-wt-adpbef-withadpbef-final.pdb #10/Q ASP 1305  
042624-x40-wt-adpbef-withadpbef-final.pdb #10/Q ARG 1317  
042624-x40-wt-adpbef-withadpbef-final.pdb #10/Q LYS 1326  
042624-x40-wt-adpbef-withadpbef-final.pdb #10/Q MET 1327  
042624-x40-wt-adpbef-withadpbef-final.pdb #10/Q GLN 1403  
042624-x40-wt-adpbef-withadpbef-final.pdb #10/Q ARG 1407  
042624-x40-wt-adpbef-withadpbef-final.pdb #10/Q LEU 1423  
042624-x40-wt-adpbef-withadpbef-final.pdb #10/Q ILE 1428  
042624-x40-wt-adpbef-withadpbef-final.pdb #10/Q ARG 1431  
042624-x40-wt-adpbef-withadpbef-final.pdb #10/Q ARG 1433  
042624-x40-wt-adpbef-withadpbef-final.pdb #10/Q ARG 1435  
042624-x40-wt-adpbef-withadpbef-final.pdb #10/Q LYS 1437  
042624-x40-wt-adpbef-withadpbef-final.pdb #10/Q LYS 1439  

Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for 042624-x40-wt-adpbef-withadpbef-final.pdb_Q SES surface
#10.17: minimum, -21.85, mean -0.46, maximum 18.53  
To also show corresponding color key, enter the above coulombic command and
add key true  

> transparency (#!10 & sel) 50

> select clear

> select #10/K,L,M,O,N

11625 atoms, 11885 bonds, 4 pseudobonds, 1455 residues, 3 models selected  

> show sel cartoons

> select clear

> select #10/Q:0-700

1105 atoms, 1118 bonds, 130 residues, 1 model selected  

> hide sel cartoons

> select #10/Q:0-700

1105 atoms, 1118 bonds, 130 residues, 1 model selected  

> hide sel atoms

> select clear

> transparency 0

> ui tool show ""Side View""

> select #1/Q:0-700

957 atoms, 969 bonds, 118 residues, 1 model selected  

> coulombic sel

The following residues are missing heavy (non-hydrogen) atoms, which may
result in inaccurate electrostatics:  
121124-0n80-xe-wt-adpbef-final-coot-0-pymol-shortdna.pdb #1/Q LYS 707  
121124-0n80-xe-wt-adpbef-final-coot-0-pymol-shortdna.pdb #1/Q ARG 802  
121124-0n80-xe-wt-adpbef-final-coot-0-pymol-shortdna.pdb #1/Q ASN 804  
121124-0n80-xe-wt-adpbef-final-coot-0-pymol-shortdna.pdb #1/Q VAL 824  
121124-0n80-xe-wt-adpbef-final-coot-0-pymol-shortdna.pdb #1/Q ARG 863  
121124-0n80-xe-wt-adpbef-final-coot-0-pymol-shortdna.pdb #1/Q ARG 865  
121124-0n80-xe-wt-adpbef-final-coot-0-pymol-shortdna.pdb #1/Q ASP 896  
121124-0n80-xe-wt-adpbef-final-coot-0-pymol-shortdna.pdb #1/Q GLU 897  
121124-0n80-xe-wt-adpbef-final-coot-0-pymol-shortdna.pdb #1/Q ARG 1008  
121124-0n80-xe-wt-adpbef-final-coot-0-pymol-shortdna.pdb #1/Q LYS 1326  
121124-0n80-xe-wt-adpbef-final-coot-0-pymol-shortdna.pdb #1/Q TRP 1396  
121124-0n80-xe-wt-adpbef-final-coot-0-pymol-shortdna.pdb #1/Q ARG 1431  

Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for 121124-0n80-xe-wt-adpbef-final-coot-0-pymol-
shortdna.pdb_Q SES surface #1.2: minimum, -20.01, mean -0.29, maximum 21.82  
To also show corresponding color key, enter the above coulombic command and
add key true  

> select #1/K,L,M,O

12253 atoms, 12523 bonds, 3 pseudobonds, 1525 residues, 2 models selected  

> hide sel surfaces

> show sel cartoons

> select clear

> transparency 10

> transparency 0

> select #1/Q:0-700

957 atoms, 969 bonds, 118 residues, 1 model selected  

> hide sel cartoons

> transparency (#!1 & sel) 10

> hide sel atoms

> select clear

> select #1/K

5614 atoms, 5735 bonds, 1 pseudobond, 692 residues, 2 models selected  

> ui tool show ""Color Actions""

> color sel medium blue

> select #1/L

2862 atoms, 2925 bonds, 1 pseudobond, 364 residues, 2 models selected  

> color sel khaki

> select #1/M

3430 atoms, 3507 bonds, 1 pseudobond, 429 residues, 2 models selected  

> color sel deep sky blue

> select #1/O

347 atoms, 356 bonds, 40 residues, 1 model selected  

> color sel dark blue

> select clear

> transparency #1/K,L,M,O 30 cartoons

> transparency #1/K,L,M,O 70 cartoons

> transparency #1/K,L,M,O 80 cartoons

> select clear

> save ""/Users/upneet/Desktop/Narlilkar Lab/Manuscript_INO80_AutoInib/Figures
> /Figure 1/Version 2-resubmission/Chimera Session/HSA_0N80.png"" width 3600
> height 3544 supersample 3

No map chosen to save  

> save /Users/upneet/Desktop/test.jpg width 3600 height 3544 supersample 3

> save /Users/upneet/Desktop/test.tif width 3600 height 3544 supersample 3

> select #1/N

Nothing selected  

> color medium blue

> undo

> select #10/N

5060 atoms, 5173 bonds, 626 residues, 1 model selected  

> color sel medium blue

> select #10/L

2824 atoms, 2886 bonds, 1 pseudobond, 361 residues, 2 models selected  

> color sel khaki

> select #10/O

287 atoms, 296 bonds, 34 residues, 1 model selected  

> color sel deep sky blue

> select #10/M

3422 atoms, 3498 bonds, 1 pseudobond, 431 residues, 2 models selected  

> color sel deep sky blue

> select #10/O

287 atoms, 296 bonds, 34 residues, 1 model selected  

> color sel dark blue

> select clear

> transparency #10/N,L,M,O 80 cartoons

> select clear

> save ""/Users/upneet/Desktop/Narlilkar Lab/Manuscript_INO80_AutoInib/Figures
> /Figure 1/Version 2-resubmission/Chimera Session/HSA_0N40.png"" width 3600
> height 3544 supersample 3

> open ""/Users/upneet/Library/CloudStorage/Box-Box/INO-yeastNCP/Map and
> Model/mix-dataset/mix-global-refine.mrc""

Opened mix-global-refine.mrc as #2, grid size 448,448,448, pixel 0.835, shown
at level 0.00458, step 2, values float32  

> close #2

> open ""/Users/upneet/Desktop/Narlilkar Lab/Manuscript_INO80_AutoInib/Figures
> /Figure 2/Version 2- Resubmission/0_80_ApovsADPBeF_Maps.cxs""

Opened x0_80_ADPBeF_A8-Split.mrc as #1, grid size 480,480,480, pixel 0.835,
shown at level 0.00261, step 1, values float32  
Opened x0_80_ADPBeF_Ies2.mrc as #3, grid size 480,480,480, pixel 0.835, shown
at level 0.348, step 1, values float32  
Opened 041924-global-resampleonapo.mrc 0 as #5.1, grid size 480,480,480, pixel
0.835, shown at level 0.221, step 1, values float32  
Opened 041924-global-resampleonapo.mrc 1 as #5.2, grid size 480,480,480, pixel
0.835, shown at level 0.238, step 1, values float32  
Opened 041924-global-resampleonapo.mrc 2 as #5.3, grid size 480,480,480, pixel
0.835, shown at level 0.221, step 1, values float32  
Opened 041924-global-resampleonapo.mrc 3 as #5.4, grid size 480,480,480, pixel
0.835, shown at level 0.221, step 1, values float32  
Opened 041924-global-resampleonapo.mrc 4 as #5.5, grid size 480,480,480, pixel
0.835, shown at level 0.221, step 1, values float32  
Opened 041924-global-resampleonapo.mrc 5 as #5.6, grid size 480,480,480, pixel
0.835, shown at level 0.221, step 1, values float32  
Opened 041924-global-resampleonapo.mrc 6 as #5.7, grid size 480,480,480, pixel
0.835, shown at level 0.221, step 1, values float32  
Opened 041924-global-resampleonapo.mrc 7 as #5.8, grid size 480,480,480, pixel
0.835, shown at level 0.221, step 1, values float32  
Opened 041924-global-resampleonapo.mrc 8 as #5.9, grid size 480,480,480, pixel
0.835, shown at level 0.235, step 1, values float32  
Opened 041924-global-resampleonapo.mrc 9 as #5.10, grid size 480,480,480,
pixel 0.835, shown at level 0.174, step 1, values float32  
Opened x0_80_ADPBeF_nuc.mrc as #6, grid size 480,480,480, pixel 0.835, shown
at level 1.44, step 1, values float32  
Opened y0_80_ADPBeF_Core.mrc as #7, grid size 448,448,448, pixel 0.835, shown
at level 0.186, step 1, values float32  
Opened y0_80_ADPBeF_Core-filter.mrc as #8, grid size 256,256,256, pixel 1.67,
shown at level 0.0143, step 1, values float32  
Opened y0_80_Apo_A8-split.mrc as #10, grid size 512,512,512, pixel 0.819,
shown at level 0.0016, step 1, values float32  
Opened y0_80_Apo_core_nuc.mrc as #11, grid size 512,512,512, pixel 0.819,
shown at level 0.157, step 1, values float32  
Opened 122324-x80-apo-a8-split-resample.mrc as #12, grid size 480,480,480,
pixel 0.835, shown at level 0.00122, step 1, values float32  
Opened 122324-x80-apo-arp5-resample.mrc as #13, grid size 480,480,480, pixel
0.835, shown at level 0.0832, step 1, values float32  
Opened 122324-x80-apo-atpasehighres-resample.mrc as #14, grid size
480,480,480, pixel 0.835, shown at level 0.0212, step 1, values float32  
Opened 122324-x80-apo-dna-resample.mrc as #15, grid size 480,480,480, pixel
0.835, shown at level 0.847, step 1, values float32  
Opened 122324-x80-apo-grappler-resample.mrc as #16, grid size 480,480,480,
pixel 0.835, shown at level 0.11, step 1, values float32  
Opened 122324-x80-apo-histone-resample.mrc as #17, grid size 480,480,480,
pixel 0.835, shown at level 1.29, step 1, values float32  
Opened 122324-x80-apo-i2highres-resample.mrc as #18, grid size 480,480,480,
pixel 0.835, shown at level 0.104, step 1, values float32  
Opened 122324-x80-apo-rvb-resample.mrc as #20, grid size 480,480,480, pixel
0.835, shown at level 0.221, step 1, values float32  
Opened 122324-x80-ies2lowres-resample.mrc as #21, grid size 480,480,480, pixel
0.835, shown at level 0.00032, step 1, values float32  
opened ChimeraX session  

> open ""/Users/upneet/Desktop/Narlilkar Lab/Manuscript_INO80_AutoInib/Figures
> /Figure 2/Version 2- Resubmission/0_80_ApovsADPBeF_Maps.cxs""

Opened x0_80_ADPBeF_A8-Split.mrc as #1, grid size 480,480,480, pixel 0.835,
shown at level 0.00261, step 1, values float32  
Opened x0_80_ADPBeF_Ies2.mrc as #3, grid size 480,480,480, pixel 0.835, shown
at level 0.348, step 1, values float32  
Opened 041924-global-resampleonapo.mrc 0 as #5.1, grid size 480,480,480, pixel
0.835, shown at level 0.221, step 1, values float32  
Opened 041924-global-resampleonapo.mrc 1 as #5.2, grid size 480,480,480, pixel
0.835, shown at level 0.238, step 1, values float32  
Opened 041924-global-resampleonapo.mrc 2 as #5.3, grid size 480,480,480, pixel
0.835, shown at level 0.221, step 1, values float32  
Opened 041924-global-resampleonapo.mrc 3 as #5.4, grid size 480,480,480, pixel
0.835, shown at level 0.221, step 1, values float32  
Opened 041924-global-resampleonapo.mrc 4 as #5.5, grid size 480,480,480, pixel
0.835, shown at level 0.221, step 1, values float32  
Opened 041924-global-resampleonapo.mrc 5 as #5.6, grid size 480,480,480, pixel
0.835, shown at level 0.221, step 1, values float32  
Opened 041924-global-resampleonapo.mrc 6 as #5.7, grid size 480,480,480, pixel
0.835, shown at level 0.221, step 1, values float32  
Opened 041924-global-resampleonapo.mrc 7 as #5.8, grid size 480,480,480, pixel
0.835, shown at level 0.221, step 1, values float32  
Opened 041924-global-resampleonapo.mrc 8 as #5.9, grid size 480,480,480, pixel
0.835, shown at level 0.235, step 1, values float32  
Opened 041924-global-resampleonapo.mrc 9 as #5.10, grid size 480,480,480,
pixel 0.835, shown at level 0.174, step 1, values float32  
Opened x0_80_ADPBeF_nuc.mrc as #6, grid size 480,480,480, pixel 0.835, shown
at level 1.44, step 1, values float32  
Opened y0_80_ADPBeF_Core.mrc as #7, grid size 448,448,448, pixel 0.835, shown
at level 0.186, step 1, values float32  
Opened y0_80_ADPBeF_Core-filter.mrc as #8, grid size 256,256,256, pixel 1.67,
shown at level 0.0143, step 1, values float32  
Opened y0_80_Apo_A8-split.mrc as #10, grid size 512,512,512, pixel 0.819,
shown at level 0.0016, step 1, values float32  
Opened y0_80_Apo_core_nuc.mrc as #11, grid size 512,512,512, pixel 0.819,
shown at level 0.157, step 1, values float32  
Opened 122324-x80-apo-a8-split-resample.mrc as #12, grid size 480,480,480,
pixel 0.835, shown at level 0.00122, step 1, values float32  
Opened 122324-x80-apo-arp5-resample.mrc as #13, grid size 480,480,480, pixel
0.835, shown at level 0.0832, step 1, values float32  
Opened 122324-x80-apo-atpasehighres-resample.mrc as #14, grid size
480,480,480, pixel 0.835, shown at level 0.0212, step 1, values float32  
Opened 122324-x80-apo-dna-resample.mrc as #15, grid size 480,480,480, pixel
0.835, shown at level 0.847, step 1, values float32  
Opened 122324-x80-apo-grappler-resample.mrc as #16, grid size 480,480,480,
pixel 0.835, shown at level 0.11, step 1, values float32  
Opened 122324-x80-apo-histone-resample.mrc as #17, grid size 480,480,480,
pixel 0.835, shown at level 1.29, step 1, values float32  
Opened 122324-x80-apo-i2highres-resample.mrc as #18, grid size 480,480,480,
pixel 0.835, shown at level 0.104, step 1, values float32  
Opened 122324-x80-apo-rvb-resample.mrc as #20, grid size 480,480,480, pixel
0.835, shown at level 0.221, step 1, values float32  
Opened 122324-x80-ies2lowres-resample.mrc as #21, grid size 480,480,480, pixel
0.835, shown at level 0.00032, step 1, values float32  
opened ChimeraX session  

> volume #10 level 0.002171

> volume #10 level 0.002364

> hide #!10 models

> hide #!11 models

> show #!20 models

> show #!21 models

> show #!19 models

> hide #!19 models

> show #!18 models

> show #!17 models

> show #!16 models

> show #!15 models

> show #!14 models

> show #!13 models

> show #!12 models

> hide #!12 models

> hide #!13 models

> hide #!14 models

> hide #!15 models

> hide #!16 models

> hide #!17 models

> hide #!18 models

> hide #!20 models

> hide #!21 models

> open ""/Users/upneet/Library/CloudStorage/Box-Box/INO-yeastNCP/Map and
> Model/mix-dataset/mix-global-refine.mrc""

Opened mix-global-refine.mrc as #22, grid size 448,448,448, pixel 0.835, shown
at level 0.00458, step 2, values float32  

> close #22


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

Log:
UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open ""/Users/upneet/Desktop/Narlilkar Lab/Manuscript_INO80_AutoInib/Figures
> /Figure 2/Version 2- Resubmission/0_80_ApovsADPBeF_Maps.cxs""

Opened x0_80_ADPBeF_A8-Split.mrc as #1, grid size 480,480,480, pixel 0.835,
shown at level 0.00261, step 1, values float32  
Opened x0_80_ADPBeF_Ies2.mrc as #3, grid size 480,480,480, pixel 0.835, shown
at level 0.348, step 1, values float32  
Opened 041924-global-resampleonapo.mrc 0 as #5.1, grid size 480,480,480, pixel
0.835, shown at level 0.221, step 1, values float32  
Opened 041924-global-resampleonapo.mrc 1 as #5.2, grid size 480,480,480, pixel
0.835, shown at level 0.238, step 1, values float32  
Opened 041924-global-resampleonapo.mrc 2 as #5.3, grid size 480,480,480, pixel
0.835, shown at level 0.221, step 1, values float32  
Opened 041924-global-resampleonapo.mrc 3 as #5.4, grid size 480,480,480, pixel
0.835, shown at level 0.221, step 1, values float32  
Opened 041924-global-resampleonapo.mrc 4 as #5.5, grid size 480,480,480, pixel
0.835, shown at level 0.221, step 1, values float32  
Opened 041924-global-resampleonapo.mrc 5 as #5.6, grid size 480,480,480, pixel
0.835, shown at level 0.221, step 1, values float32  
Opened 041924-global-resampleonapo.mrc 6 as #5.7, grid size 480,480,480, pixel
0.835, shown at level 0.221, step 1, values float32  
Opened 041924-global-resampleonapo.mrc 7 as #5.8, grid size 480,480,480, pixel
0.835, shown at level 0.221, step 1, values float32  
Opened 041924-global-resampleonapo.mrc 8 as #5.9, grid size 480,480,480, pixel
0.835, shown at level 0.235, step 1, values float32  
Opened 041924-global-resampleonapo.mrc 9 as #5.10, grid size 480,480,480,
pixel 0.835, shown at level 0.174, step 1, values float32  
Opened x0_80_ADPBeF_nuc.mrc as #6, grid size 480,480,480, pixel 0.835, shown
at level 1.44, step 1, values float32  
Opened y0_80_ADPBeF_Core.mrc as #7, grid size 448,448,448, pixel 0.835, shown
at level 0.186, step 1, values float32  
Opened y0_80_ADPBeF_Core-filter.mrc as #8, grid size 256,256,256, pixel 1.67,
shown at level 0.0143, step 1, values float32  
Opened y0_80_Apo_A8-split.mrc as #10, grid size 512,512,512, pixel 0.819,
shown at level 0.0016, step 1, values float32  
Opened y0_80_Apo_core_nuc.mrc as #11, grid size 512,512,512, pixel 0.819,
shown at level 0.157, step 1, values float32  
Opened 122324-x80-apo-a8-split-resample.mrc as #12, grid size 480,480,480,
pixel 0.835, shown at level 0.00122, step 1, values float32  
Opened 122324-x80-apo-arp5-resample.mrc as #13, grid size 480,480,480, pixel
0.835, shown at level 0.0832, step 1, values float32  
Opened 122324-x80-apo-atpasehighres-resample.mrc as #14, grid size
480,480,480, pixel 0.835, shown at level 0.0212, step 1, values float32  
Opened 122324-x80-apo-dna-resample.mrc as #15, grid size 480,480,480, pixel
0.835, shown at level 0.847, step 1, values float32  
Opened 122324-x80-apo-grappler-resample.mrc as #16, grid size 480,480,480,
pixel 0.835, shown at level 0.11, step 1, values float32  
Opened 122324-x80-apo-histone-resample.mrc as #17, grid size 480,480,480,
pixel 0.835, shown at level 1.29, step 1, values float32  
Opened 122324-x80-apo-i2highres-resample.mrc as #18, grid size 480,480,480,
pixel 0.835, shown at level 0.104, step 1, values float32  
Opened 122324-x80-apo-rvb-resample.mrc as #20, grid size 480,480,480, pixel
0.835, shown at level 0.221, step 1, values float32  
Opened 122324-x80-ies2lowres-resample.mrc as #21, grid size 480,480,480, pixel
0.835, shown at level 0.00032, step 1, values float32  
Log from Mon Dec 30 10:55:42 2024UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open ""/Users/upneet/Desktop/Narlilkar Lab/Manuscript_INO80_AutoInib/Figures
> /Figure 2/Version 2- Resubmission/0_80_ApovsADPBeF_Maps.cxs""

Opened x0_80_ADPBeF_A8-Split.mrc as #1, grid size 480,480,480, pixel 0.835,
shown at level 0.00261, step 1, values float32  
Opened x0_80_ADPBeF_Ies2.mrc as #3, grid size 480,480,480, pixel 0.835, shown
at level 0.348, step 1, values float32  
Opened 041924-global-resampleonapo.mrc 0 as #5.1, grid size 480,480,480, pixel
0.835, shown at level 0.221, step 1, values float32  
Opened 041924-global-resampleonapo.mrc 1 as #5.2, grid size 480,480,480, pixel
0.835, shown at level 0.238, step 1, values float32  
Opened 041924-global-resampleonapo.mrc 2 as #5.3, grid size 480,480,480, pixel
0.835, shown at level 0.221, step 1, values float32  
Opened 041924-global-resampleonapo.mrc 3 as #5.4, grid size 480,480,480, pixel
0.835, shown at level 0.221, step 1, values float32  
Opened 041924-global-resampleonapo.mrc 4 as #5.5, grid size 480,480,480, pixel
0.835, shown at level 0.221, step 1, values float32  
Opened 041924-global-resampleonapo.mrc 5 as #5.6, grid size 480,480,480, pixel
0.835, shown at level 0.221, step 1, values float32  
Opened 041924-global-resampleonapo.mrc 6 as #5.7, grid size 480,480,480, pixel
0.835, shown at level 0.221, step 1, values float32  
Opened 041924-global-resampleonapo.mrc 7 as #5.8, grid size 480,480,480, pixel
0.835, shown at level 0.221, step 1, values float32  
Opened 041924-global-resampleonapo.mrc 8 as #5.9, grid size 480,480,480, pixel
0.835, shown at level 0.235, step 1, values float32  
Opened 041924-global-resampleonapo.mrc 9 as #5.10, grid size 480,480,480,
pixel 0.835, shown at level 0.174, step 1, values float32  
Opened x0_80_ADPBeF_nuc.mrc as #6, grid size 480,480,480, pixel 0.835, shown
at level 1.44, step 1, values float32  
Opened y0_80_ADPBeF_Core.mrc as #7, grid size 448,448,448, pixel 0.835, shown
at level 0.167, step 2, values float32  
Opened y0_80_ADPBeF_Core-filter.mrc as #8, grid size 256,256,256, pixel 1.67,
shown at level 0.0143, step 1, values float32  
Opened y0_80_Apo_A8-split.mrc as #10, grid size 512,512,512, pixel 0.819,
shown at level 0.000899, step 1, values float32  
Opened y0_80_Apo_core_nuc.mrc as #11, grid size 512,512,512, pixel 0.819,
shown at level 0.147, step 1, values float32  
Opened 122324-x80-apo-a8-split-resample.mrc as #12, grid size 480,480,480,
pixel 0.835, shown at level 0.00122, step 1, values float32  
Opened 122324-x80-apo-arp5-resample.mrc as #13, grid size 480,480,480, pixel
0.835, shown at level 0.0832, step 1, values float32  
Opened 122324-x80-apo-atpasehighres-resample.mrc as #14, grid size
480,480,480, pixel 0.835, shown at level 0.0212, step 1, values float32  
Opened 122324-x80-apo-dna-resample.mrc as #15, grid size 480,480,480, pixel
0.835, shown at level 0.847, step 1, values float32  
Opened 122324-x80-apo-grappler-resample.mrc as #16, grid size 480,480,480,
pixel 0.835, shown at level 0.11, step 1, values float32  
Opened 122324-x80-apo-histone-resample.mrc as #17, grid size 480,480,480,
pixel 0.835, shown at level 1.29, step 1, values float32  
Opened 122324-x80-apo-i2highres-resample.mrc as #18, grid size 480,480,480,
pixel 0.835, shown at level 0.104, step 1, values float32  
Opened 122324-x80-apo-rvb-resample.mrc as #20, grid size 480,480,480, pixel
0.835, shown at level 0.221, step 1, values float32  
Opened 122324-x80-ies2lowres-resample.mrc as #21, grid size 480,480,480, pixel
0.835, shown at level 0.00032, step 1, values float32  
Log from Mon Dec 30 10:34:25 2024UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open ""/Users/upneet/Desktop/Narlilkar Lab/Manuscript_INO80_AutoInib/Figures
> /Figure 2/Version 2- Resubmission/0_80_ApovsADPBeF_Maps.cxs""

Opened x0_80_ADPBeF_A8-Split.mrc as #1, grid size 480,480,480, pixel 0.835,
shown at level 0.00375, step 1, values float32  
Opened x0_80_ADPBeF_Ies2.mrc as #3, grid size 480,480,480, pixel 0.835, shown
at level 0.348, step 1, values float32  
Opened 041924-global-resampleonapo.mrc 0 as #5.1, grid size 480,480,480, pixel
0.835, shown at level 0.221, step 1, values float32  
Opened 041924-global-resampleonapo.mrc 1 as #5.2, grid size 480,480,480, pixel
0.835, shown at level 0.238, step 1, values float32  
Opened 041924-global-resampleonapo.mrc 2 as #5.3, grid size 480,480,480, pixel
0.835, shown at level 0.221, step 1, values float32  
Opened 041924-global-resampleonapo.mrc 3 as #5.4, grid size 480,480,480, pixel
0.835, shown at level 0.221, step 1, values float32  
Opened 041924-global-resampleonapo.mrc 4 as #5.5, grid size 480,480,480, pixel
0.835, shown at level 0.221, step 1, values float32  
Opened 041924-global-resampleonapo.mrc 5 as #5.6, grid size 480,480,480, pixel
0.835, shown at level 0.221, step 1, values float32  
Opened 041924-global-resampleonapo.mrc 6 as #5.7, grid size 480,480,480, pixel
0.835, shown at level 0.221, step 1, values float32  
Opened 041924-global-resampleonapo.mrc 7 as #5.8, grid size 480,480,480, pixel
0.835, shown at level 0.221, step 1, values float32  
Opened 041924-global-resampleonapo.mrc 8 as #5.9, grid size 480,480,480, pixel
0.835, shown at level 0.235, step 1, values float32  
Opened 041924-global-resampleonapo.mrc 9 as #5.10, grid size 480,480,480,
pixel 0.835, shown at level 0.174, step 1, values float32  
Opened x0_80_ADPBeF_nuc.mrc as #6, grid size 480,480,480, pixel 0.835, shown
at level 1.44, step 1, values float32  
Opened y0_80_ADPBeF_Core.mrc as #7, grid size 448,448,448, pixel 0.835, shown
at level 0.167, step 2, values float32  
Opened y0_80_ADPBeF_Core-filter.mrc as #8, grid size 256,256,256, pixel 1.67,
shown at level 0.0143, step 1, values float32  
Opened y0_80_Apo_A8-split.mrc as #10, grid size 512,512,512, pixel 0.819,
shown at level 0.000444, step 2, values float32  
Opened y0_80_Apo_core_nuc.mrc as #11, grid size 512,512,512, pixel 0.819,
shown at level 0.0802, step 2, values float32  
Opened 122324-x80-apo-a8-split-resample.mrc as #12, grid size 480,480,480,
pixel 0.835, shown at level 0.000239, step 2, values float32  
Opened 122324-x80-apo-arp5-resample.mrc as #13, grid size 480,480,480, pixel
0.835, shown at level 0.000123, step 2, values float32  
Opened 122324-x80-apo-atpasehighres-resample.mrc as #14, grid size
480,480,480, pixel 0.835, shown at level 0.000139, step 2, values float32  
Opened 122324-x80-apo-dna-resample.mrc as #15, grid size 480,480,480, pixel
0.835, shown at level 0.000354, step 2, values float32  
Opened 122324-x80-apo-grappler-resample.mrc as #16, grid size 480,480,480,
pixel 0.835, shown at level 3.54e-05, step 2, values float32  
Opened 122324-x80-apo-histone-resample.mrc as #17, grid size 480,480,480,
pixel 0.835, shown at level 0.000232, step 2, values float32  
Opened 122324-x80-apo-i2highres-resample.mrc as #18, grid size 480,480,480,
pixel 0.835, shown at level 3.03e-06, step 2, values float32  
Opened 122324-x80-apo-rvb-resample.mrc as #20, grid size 480,480,480, pixel
0.835, shown at level 7.73e-05, step 2, values float32  
Opened 122324-x80-ies2lowres-resample.mrc as #21, grid size 480,480,480, pixel
0.835, shown at level 2.62e-07, step 2, values float32  
Log from Sun Dec 29 17:47:13 2024UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open ""/Users/upneet/Desktop/Narlilkar Lab/Manuscript_INO80_AutoInib/Figures
> /Figure 1/Version 2-resubmission/Chimera Session/Figure1.cxs""

Opened 121124-a8-split_xl080.mrc as #1, grid size 480,480,480, pixel 0.835,
shown at level 0.00375, step 1, values float32  
Opened ies2-x80-lowres.mrc as #3, grid size 480,480,480, pixel 0.835, shown at
level 0.348, step 1, values float32  
Opened 041924-global-resampleonapo.mrc 0 as #5.1, grid size 480,480,480, pixel
0.835, shown at level 0.221, step 1, values float32  
Opened 041924-global-resampleonapo.mrc 1 as #5.2, grid size 480,480,480, pixel
0.835, shown at level 0.238, step 1, values float32  
Opened 041924-global-resampleonapo.mrc 2 as #5.3, grid size 480,480,480, pixel
0.835, shown at level 0.221, step 1, values float32  
Opened 041924-global-resampleonapo.mrc 3 as #5.4, grid size 480,480,480, pixel
0.835, shown at level 0.221, step 1, values float32  
Opened 041924-global-resampleonapo.mrc 4 as #5.5, grid size 480,480,480, pixel
0.835, shown at level 0.221, step 1, values float32  
Opened 041924-global-resampleonapo.mrc 5 as #5.6, grid size 480,480,480, pixel
0.835, shown at level 0.221, step 1, values float32  
Opened 041924-global-resampleonapo.mrc 6 as #5.7, grid size 480,480,480, pixel
0.835, shown at level 0.221, step 1, values float32  
Opened 041924-global-resampleonapo.mrc 7 as #5.8, grid size 480,480,480, pixel
0.835, shown at level 0.221, step 1, values float32  
Opened 041924-global-resampleonapo.mrc 8 as #5.9, grid size 480,480,480, pixel
0.835, shown at level 0.235, step 1, values float32  
Opened 041924-global-resampleonapo.mrc 9 as #5.10, grid size 480,480,480,
pixel 0.835, shown at level 0.174, step 1, values float32  
Opened 041924-nuc-resampleonapo_xl080.mrc as #6, grid size 480,480,480, pixel
0.835, shown at level 1.44, step 1, values float32  
Opened 121124-a8-split_Xl040.mrc as #4, grid size 448,448,448, pixel 0.831,
shown at level 0.00268, step 1, values float32  
Opened onlyies2-lowres-Xl040.mrc as #7, grid size 448,448,448, pixel 0.831,
shown at level 0.0519, step 1, values float32  
Opened onlynuc_Xl040.mrc as #8, grid size 448,448,448, pixel 0.831, shown at
level 0.411, step 1, values float32  
Opened inocore_Xl040.mrc as #9, grid size 448,448,448, pixel 0.831, shown at
level 0.218, step 1, values float32  
Log from Sat Dec 28 15:21:23 2024UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open ""/Users/upneet/Desktop/Narlilkar Lab/Manuscript_INO80_AutoInib/Figures
> /Figure 1/Version 2-resubmission/Chimera Session/Figure1.cxs""

Opened 121124-a8-split_xl080.mrc as #1, grid size 480,480,480, pixel 0.835,
shown at level 0.00375, step 1, values float32  
Opened ies2-x80-lowres.mrc as #3, grid size 480,480,480, pixel 0.835, shown at
level 0.348, step 1, values float32  
Opened 041924-global-resampleonapo.mrc 0 as #5.1, grid size 480,480,480, pixel
0.835, shown at level 0.221, step 1, values float32  
Opened 041924-global-resampleonapo.mrc 1 as #5.2, grid size 480,480,480, pixel
0.835, shown at level 0.238, step 1, values float32  
Opened 041924-global-resampleonapo.mrc 2 as #5.3, grid size 480,480,480, pixel
0.835, shown at level 0.221, step 1, values float32  
Opened 041924-global-resampleonapo.mrc 3 as #5.4, grid size 480,480,480, pixel
0.835, shown at level 0.221, step 1, values float32  
Opened 041924-global-resampleonapo.mrc 4 as #5.5, grid size 480,480,480, pixel
0.835, shown at level 0.221, step 1, values float32  
Opened 041924-global-resampleonapo.mrc 5 as #5.6, grid size 480,480,480, pixel
0.835, shown at level 0.221, step 1, values float32  
Opened 041924-global-resampleonapo.mrc 6 as #5.7, grid size 480,480,480, pixel
0.835, shown at level 0.221, step 1, values float32  
Opened 041924-global-resampleonapo.mrc 7 as #5.8, grid size 480,480,480, pixel
0.835, shown at level 0.221, step 1, values float32  
Opened 041924-global-resampleonapo.mrc 8 as #5.9, grid size 480,480,480, pixel
0.835, shown at level 0.235, step 1, values float32  
Opened 041924-global-resampleonapo.mrc 9 as #5.10, grid size 480,480,480,
pixel 0.835, shown at level 0.174, step 1, values float32  
Opened 041924-nuc-resampleonapo_xl080.mrc as #6, grid size 480,480,480, pixel
0.835, shown at level 1.44, step 1, values float32  
Opened 121124-a8-split_Xl040.mrc as #4, grid size 448,448,448, pixel 0.831,
shown at level 0.0026, step 1, values float32  
Opened onlyies2-lowres-Xl040.mrc as #7, grid size 448,448,448, pixel 0.831,
shown at level 0.0519, step 1, values float32  
Opened onlynuc_Xl040.mrc as #8, grid size 448,448,448, pixel 0.831, shown at
level 0.411, step 1, values float32  
Opened inocore_Xl040.mrc as #9, grid size 448,448,448, pixel 0.831, shown at
level 0.218, step 1, values float32  
Log from Thu Dec 12 15:18:18 2024 Startup Messages  
---  
warnings | Replacing fetcher for 'ngff' and format OME-Zarr from OME-Zarr bundle with that from OME-Zarr bundle  
Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR bundle with
that from NMRSTAR bundle  
  
UCSF ChimeraX version: 1.7.1 (2024-01-23)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open ""/Users/upneet/Library/CloudStorage/Box-Box/INO-yeastNCP/Map and
> Model/wtINO80-0N80-Yeast-Apo/121124-a8-split.mrc""

Opened 121124-a8-split.mrc as #1, grid size 512,512,512, pixel 0.819, shown at
level 0.000444, step 2, values float32  

> set bgColor white

> open ""/Users/upneet/Library/CloudStorage/Box-Box/INO-yeastNCP/Map and
> Model/wtINO80-0N80-Yeast-Apo/120524-inocore-nuc-3.16A.mrc""

Opened 120524-inocore-nuc-3.16A.mrc as #2, grid size 512,512,512, pixel 0.819,
shown at level 0.0802, step 2, values float32  

> volume #1 step 1

> volume #2 step 1

> volume #1 level 0.001846

> surface dust #1 size 8.19

> surface dust #2 size 8.19

> volume #2 level 0.1187

> volume #1 level 0.002828

> volume #2 level 0.1524

> volume #2 level 0.1596

> volume #2 level 0.1741

> color #2 silver models

> open ""/Users/upneet/Library/CloudStorage/Box-Box/INO-yeastNCP/Map and
> Model/wtINO80-0N80-Yeast-Apo/120524-final-ino80-0y80-apo-512box.pdb""

Chain information for 120524-final-ino80-0y80-apo-512box.pdb #3  
---  
Chain | Description  
A E | No description available  
B F | No description available  
C | No description available  
D H | No description available  
G | No description available  
I | No description available  
J | No description available  
K | No description available  
L | No description available  
M | No description available  
O | No description available  
Q | No description available  
R | No description available  
S | No description available  
T | No description available  
U | No description available  
V | No description available  
W | No description available  
X | No description available  
Y | No description available  
Z | No description available  
  

> volume #1 level 0.003126

> hide #!1 models

> hide #!2 models

> hide atoms

> show cartoons

> select #3/A-H,T-Y

26415 atoms, 26739 bonds, 2 pseudobonds, 3403 residues, 2 models selected  

> ui tool show ""Color Actions""

> color sel light gray

> select #3/I,J

7702 atoms, 8638 bonds, 1 pseudobond, 376 residues, 2 models selected  

> color sel slate gray

> show sel atoms

> hide sel atoms

> nucleotides sel atoms

> style nucleic & sel stick

Changed 7702 atom styles  

> nucleotides sel ladder

> show sel atoms

> select #3/Q

6141 atoms, 6266 bonds, 8 pseudobonds, 758 residues, 2 models selected  

> color sel fire brick

> select #3/Z

464 atoms, 469 bonds, 1 pseudobond, 72 residues, 2 models selected  

> color sel fire brick

> color sel orange

> select #3/R,S

4527 atoms, 4639 bonds, 2 pseudobonds, 570 residues, 2 models selected  

> color sel medium sea green

> select #3/K

5092 atoms, 5206 bonds, 628 residues, 1 model selected  

> color sel medium blue

> select #3/L

2856 atoms, 2919 bonds, 1 pseudobond, 363 residues, 2 models selected  

> color sel gold

> select #3/M

3454 atoms, 3531 bonds, 1 pseudobond, 433 residues, 2 models selected  

> color sel deep sky blue

> select #3/N

Nothing selected  

> color dim gray

> undo

> select #3/O

287 atoms, 296 bonds, 34 residues, 1 model selected  

> color sel dim gray

> select clear

> show #!2 models

> show #!1 models

> ui tool show ""Color Zone""

> color zone #1 near #3 distance 4.91

> color zone #1 near #3 distance 4.81

> color zone #1 near #3 distance 4.71

> color zone #1 near #3 distance 4.61

> color zone #1 near #3 distance 4.51

> color zone #1 near #3 distance 4.41

> color zone #1 near #3 distance 4.31

> color zone #1 near #3 distance 4.21

> color zone #1 near #3 distance 4.11

> color zone #1 near #3 distance 4.01

> color zone #1 near #3 distance 3.91

> color zone #1 near #3 distance 3.81

> color zone #1 near #3 distance 3.71

> color zone #1 near #3 distance 3.61

> color zone #1 near #3 distance 3.51

> color zone #1 near #3 distance 3.41

> color zone #1 near #3 distance 3.83

> color zone #1 near #3 distance 9.39

> color zone #1 near #3 distance 1

> color zone #1 near #3 distance 10

[Repeated 1 time(s)]

> volume #1 level 0.00344

> color zone #2 near #3 distance 4.91

> volume #1 level 0.003283

> lighting simple

> lighting soft

> lighting simple

> lighting soft

> ui tool show ""Side View""

> hide #!3 models

> color #1 #b2b2b224 models

> color #1 #b2b2b297 models

> color #1 #b2b2b296 models

> undo

[Repeated 4 time(s)]

> color zone #1 near #3 distance 10

> volume #2 level 0.1046

> volume #2 level 0.1313

> volume #2 level 0.1607

> volume #2 level 0.118

> volume #2 level 0.1287

> volume #2 level 0.15

> volume #2 level 0.1634

No map chosen to save  

> save /Users/upneet/Desktop/test.png width 3600 height 2697 supersample 3
> transparentBackground true

> hide #!2 models

> hide #!1 models

> show #!3 models

> hide #!3 models

> show #!1 models

> show #!3 models

> hide #!1 models

> show #!1 models

> open ""/Users/upneet/Library/CloudStorage/Box-Box/INO-yeastNCP/Map and
> Model/WT-0N80Xe-ADPBeF/121124-a8-split.mrc""

Opened 121124-a8-split.mrc as #4, grid size 480,480,480, pixel 0.835, shown at
level 0.000837, step 2, values float32  

> volume #4 level 0.003553

> volume #4 step 1

> hide #!3 models

> hide #!4 models

> hide #!1 models

> show #!4 models

> volume #4 level 0.003726

> volume #4 level 0.003661

> color #4 silver models

> open ""/Users/upneet/Library/CloudStorage/Box-Box/INO-yeastNCP/Map and
> Model/INO-40yeastnuc-ADPBeF/121124-a8-split.mrc""

Opened 121124-a8-split.mrc as #5, grid size 480,480,480, pixel 0.835, shown at
level 4.83e-07, step 2, values float32  

> volume #5 level 0.003775

> volume #5 level 0.003851

> hide #!4 models

> hide #!5 models

> show #!3 models

> select ::name=""ARG""

3893 atoms, 3559 bonds, 362 residues, 1 model selected  

> ui mousemode right select

> select clear

Drag select of 1 residues  

> show sel surfaces

> hide sel surfaces

> style sel stick

Changed 11 atom styles  

> show sel atoms

> color sel byhetero

> hide #!3 models

> show #!1 models

> show #!2 models

> close #1-5

> open ""/Users/upneet/Library/CloudStorage/Box-Box/INO-yeastNCP/Map and
> Model/WT-0N80Xe-ADPBeF/121124-a8-split.mrc""

Opened 121124-a8-split.mrc as #1, grid size 480,480,480, pixel 0.835, shown at
level 4.88e-06, step 2, values float32  

> open ""/Users/upneet/Library/CloudStorage/Box-Box/INO-yeastNCP/Map and
> Model/WT-0N80Xe-ADPBeF/121124-0n80-xe-wt-adpbef-final-coot-0-pymol-
> shortdna.pdb""

Chain information for 121124-0n80-xe-wt-adpbef-final-coot-0-pymol-shortdna.pdb
#2  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
F | No description available  
G | No description available  
H | No description available  
I | No description available  
J | No description available  
K | No description available  
L | No description available  
M | No description available  
O | No description available  
Q | No description available  
R | No description available  
S | No description available  
T | No description available  
U | No description available  
V | No description available  
W | No description available  
X | No description available  
Y | No description available  
Z | No description available  
  

> hide atoms

> show cartoons

> volume #1 step 1

> volume #1 level 0.004082

> hide #!2 models

> show #!2 models

> hide #!1 models

> color #2/Q firebrick

> color #2/Q firebrick, #2/R,S seagreen

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

> color #2/Q firebrick

> color #2/R,S medium seagreen

> color #2/T-Y, A-H grey

> color #2/T-Y, A-H lightr grey

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

> color #2/T-Y, A-H light grey

> color #2/Z orange

> color #2/k medium blue

> color #2/L gold

> color #2/N deep skyblue

> color #2/M deep skyblue

[Repeated 1 time(s)]

> color #2/O grey

> color #2/I,J slate blue

> color #2/I,J slate grey

> select #2/I,J

7787 atoms, 8735 bonds, 380 residues, 1 model selected  

> nucleotides sel ladder

> show sel atoms

> select clear

[Repeated 2 time(s)]

> show #!1 models

> ui tool show ""Color Zone""

> color zone #1 near #2 distance 5.01

> color zone #1 near #2 distance 5.19

> color zone #1 near #2 distance 11.56

> color zone #1 near #2 distance 11.7

[Repeated 1 time(s)]

> color zone #1 near #2 distance 1

> color zone #1 near #2 distance 10

[Repeated 1 time(s)]

> color zone #1 near #2 distance 1

> color zone #1 near #2 distance 15

[Repeated 1 time(s)]

> volume #1 level 0.004276

> volume #1 level 0.004216

> volume #1 level 0.003992

> open ""/Users/upneet/Library/CloudStorage/Box-Box/INO-yeastNCP/Map and
> Model/WT-0N80Xe-ADPBeF/ies2-x80-lowres.mrc""

Opened ies2-x80-lowres.mrc as #3, grid size 480,480,480, pixel 0.835, shown at
level 5.64e-05, step 2, values float32  

> volume #3 step 1

> volume #3 level 0.3484

> hide #!3 models

> volume #1 level 0.003664

> surface dust #1 size 8.35

> volume #1 level 0.003843

> volume #1 level 0.003873

> ui tool show ""Side View""

> volume #1 level 0.003754

> volume #1 level 0.003664

> surface dust #1 size 8.35

> volume #1 level 0.003754

> select #2/L

2862 atoms, 2925 bonds, 1 pseudobond, 364 residues, 2 models selected  

> ui tool show ""Color Actions""

> color sel sandy brown

> color zone #1 near #2 distance 15

> color sel navajo white

> color zone #1 near #2 distance 15

> hide #!1 models

> show #!1 models

> color sel goldenrod

> color zone #1 near #2 distance 15

> color sel orange

> color zone #1 near #2 distance 15

> color (#!2 & sel) #ffd479ff

> color zone #1 near #2 distance 15

> color (#!2 & sel) #ffd778ff

> color (#!2 & sel) #ffd87aff

> color (#!2 & sel) #ffdb82ff

> color (#!2 & sel) #ffdc89ff

> color (#!2 & sel) #ffe296ff

> color (#!2 & sel) #ffe396ff

> color (#!2 & sel) #ffea91ff

> color (#!2 & sel) #ffe482ff

> color (#!2 & sel) #ffe077ff

> color (#!2 & sel) #ffe370ff

> color (#!2 & sel) #ffea6cff

> color (#!2 & sel) #fff26aff

> color (#!2 & sel) #fff36aff

> color (#!2 & sel) #fff36dff

> color (#!2 & sel) #fff475ff

> color zone #1 near #2 distance 15

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> select #2/O

347 atoms, 356 bonds, 40 residues, 1 model selected  

> color sel #011993ff

> color zone #1 near #2 distance 15

> color sel #9437ffff

> color zone #1 near #2 distance 15

> color sel #76d6ffff

> color zone #1 near #2 distance 15

> color sel #79b8ffff

> color zone #1 near #2 distance 15

> color sel #00fdffff

> color sel #73fdffff

> color zone #1 near #2 distance 15

> color sel #ffd479ff

> color zone #1 near #2 distance 15

> color sel #011993ff

> color sel #005493ff

> color zone #1 near #2 distance 15

> select clear

> select #2/Z

467 atoms, 472 bonds, 1 pseudobond, 72 residues, 2 models selected  

> color (#!2 & sel) #ff2600ff

> color (#!2 & sel) #ff7e79ff

> select clear

> select #2/M

3430 atoms, 3507 bonds, 1 pseudobond, 429 residues, 2 models selected  

> select #2/L

2862 atoms, 2925 bonds, 1 pseudobond, 364 residues, 2 models selected  

> select #2/L

2862 atoms, 2925 bonds, 1 pseudobond, 364 residues, 2 models selected  

> select #2/K

5614 atoms, 5735 bonds, 1 pseudobond, 692 residues, 2 models selected  

> ui tool show ""Color Actions""

> color sel cornflower blue

> color zone #1 near #2 distance 15

> color sel royal blue

> color zone #1 near #2 distance 15

> select #2/M

3430 atoms, 3507 bonds, 1 pseudobond, 429 residues, 2 models selected  

> ui tool show ""Color Actions""

> color sel light pink

> color zone #1 near #2 distance 15

> color sel plum

> color zone #1 near #2 distance 15

> color sel pink

> color zone #1 near #2 distance 15

> color sel light pink

> color zone #1 near #2 distance 15

> hide #!1 models

> cartoon style (#!2 & sel) modeHelix tube sides 20

> cartoon style modeHelix tube radius 1.5

> select clear

> show #!1 models

> select #2/L

2862 atoms, 2925 bonds, 1 pseudobond, 364 residues, 2 models selected  

> select #2/K

5614 atoms, 5735 bonds, 1 pseudobond, 692 residues, 2 models selected  

> ui tool show ""Color Actions""

> color sel cornflower blue

> color sel blue

> color zone #1 near #2 distance 15

> color sel medium blue

> color zone #1 near #2 distance 15

> select #2/M

3430 atoms, 3507 bonds, 1 pseudobond, 429 residues, 2 models selected  

> ui tool show ""Color Actions""

> color sel deep sky blue

> color zone #1 near #2 distance 15

> select clear

> hide #!1 models

> show #!1 models

> open ""/Users/upneet/Library/CloudStorage/Box-Box/INO-yeastNCP/Map and
> Model/WT-0N80Xe-ADPBeF/041924-global-resampleonapo.mrc""

Opened 041924-global-resampleonapo.mrc as #4, grid size 480,480,480, pixel
0.835, shown at level 0.105, step 2, values float32  

> volume #4 step 1

> volume #4 level 0.1559

> volume #4 level 0.2387

> volume #4 level 0.3295

> volume #4 level 0.2569

> volume #4 level 0.2205

> color zone #4 near #2 distance 5.01

> hide #!2 models

> lighting soft

> lighting simple

> lighting soft

> volume splitbyzone #4

Opened 041924-global-resampleonapo.mrc 0 as #5.1, grid size 480,480,480, pixel
0.835, shown at level 0.221, step 1, values float32  
Opened 041924-global-resampleonapo.mrc 1 as #5.2, grid size 480,480,480, pixel
0.835, shown at level 0.221, step 1, values float32  
Opened 041924-global-resampleonapo.mrc 2 as #5.3, grid size 480,480,480, pixel
0.835, shown at level 0.221, step 1, values float32  
Opened 041924-global-resampleonapo.mrc 3 as #5.4, grid size 480,480,480, pixel
0.835, shown at level 0.221, step 1, values float32  
Opened 041924-global-resampleonapo.mrc 4 as #5.5, grid size 480,480,480, pixel
0.835, shown at level 0.221, step 1, values float32  
Opened 041924-global-resampleonapo.mrc 5 as #5.6, grid size 480,480,480, pixel
0.835, shown at level 0.221, step 1, values float32  
Opened 041924-global-resampleonapo.mrc 6 as #5.7, grid size 480,480,480, pixel
0.835, shown at level 0.221, step 1, values float32  
Opened 041924-global-resampleonapo.mrc 7 as #5.8, grid size 480,480,480, pixel
0.835, shown at level 0.221, step 1, values float32  
Opened 041924-global-resampleonapo.mrc 8 as #5.9, grid size 480,480,480, pixel
0.835, shown at level 0.221, step 1, values float32  
Opened 041924-global-resampleonapo.mrc 9 as #5.10, grid size 480,480,480,
pixel 0.835, shown at level 0.221, step 1, values float32  

> hide #!5 models

> show #!5 models

> hide #!5.2 models

> show #!5.2 models

> hide #!5.3 models

> hide #5.2.1 models

> show #5.2.1 models

> volume #5.2 level 0.2383

> volume #5.8 level 0.2205

> volume #5.9 level 0.2241

> volume #5.10 level 0.164

> volume #5.10 level 0.174

> surface dust #1 size 8.35

> surface dust #5.1 size 8.35

> surface dust #5.2 size 8.35

> surface dust #5.4 size 8.35

> surface dust #5.5 size 8.35

> surface dust #5.6 size 8.35

> surface dust #5.7 size 8.35

> surface dust #5.8 size 8.35

> surface dust #5.9 size 8.35

> surface dust #5.10 size 8.35

> open ""/Users/upneet/Library/CloudStorage/Box-Box/INO-yeastNCP/Map and
> Model/WT-0N80Xe-ADPBeF/041924-nuc-resampleonapo.mrc""

Opened 041924-nuc-resampleonapo.mrc as #6, grid size 480,480,480, pixel 0.835,
shown at level 0.188, step 2, values float32  

> color zone #6 near #2 distance 5.01

> surface dust #1 size 8.35

> surface dust #5.1 size 8.35

> surface dust #5.2 size 8.35

> surface dust #5.4 size 8.35

> surface dust #5.5 size 8.35

> surface dust #5.6 size 8.35

> surface dust #5.7 size 8.35

> surface dust #5.8 size 8.35

> surface dust #5.9 size 8.35

> surface dust #5.10 size 8.35

> surface dust #6 size 8.35

> volume #6 step 1

> volume #6 level 0.7474

> volume #6 level 0.9057

> color zone #6 near #2 distance 5.01

[Repeated 1 time(s)]

> volume #6 level 1.127

> volume #6 level 1.233

> color zone #6 near #2 distance 5.11

> color zone #6 near #2 distance 5.21

> color zone #6 near #2 distance 5.31

> color zone #6 near #2 distance 5.41

> color zone #6 near #2 distance 5.51

> color zone #6 near #2 distance 5.61

> color zone #6 near #2 distance 5.71

> color zone #6 near #2 distance 5.81

> color zone #6 near #2 distance 5.91

> color zone #6 near #2 distance 6.01

> color zone #6 near #2 distance 6.11

> color zone #6 near #2 distance 6.21

> volume #6 level 1.444

> volume #5.9 level 0.2348

> show #!3 models

> color zone #3 near #2 distance 5.01

> select clear

> save /Users/upneet/Desktop/test.png width 3600 height 2671 supersample 3
> transparentBackground true

> close #4

> rename #5 ""041924-global-resampleonapo_xl080.mrc split""

> rename #6 041924-nuc-resampleonapo_xl080.mrc

> rename #1 121124-a8-split_xl080.mrc

> open ""/Users/upneet/Library/CloudStorage/Box-Box/INO-yeastNCP/Map and
> Model/INO-40Xenuc-ADPBe/121124-a8-split.mrc""

Opened 121124-a8-split.mrc as #4, grid size 448,448,448, pixel 0.831, shown at
level 0.0002, step 2, values float32  

> open ""/Users/upneet/Library/CloudStorage/Box-Box/INO-yeastNCP/Map and
> Model/INO-40Xenuc-ADPBe/onlyies2-lowres.mrc""

Opened onlyies2-lowres.mrc as #7, grid size 448,448,448, pixel 0.831, shown at
level 2.07e-05, step 2, values float32  

> open ""/Users/upneet/Library/CloudStorage/Box-Box/INO-yeastNCP/Map and
> Model/INO-40Xenuc-ADPBe/onlynuc.mrc""

Opened onlynuc.mrc as #8, grid size 448,448,448, pixel 0.831, shown at level
9.79e-05, step 2, values float32  

> open ""/Users/upneet/Library/CloudStorage/Box-Box/INO-yeastNCP/Map and
> Model/INO-40Xenuc-ADPBe/inocore.mrc""

Opened inocore.mrc as #9, grid size 448,448,448, pixel 0.831, shown at level
3.68e-05, step 2, values float32  

> open ""/Users/upneet/Library/CloudStorage/Box-Box/INO-yeastNCP/Map and
> Model/INO-40Xenuc-ADPBe/nuc-resample.mrc""

Opened nuc-resample.mrc as #10, grid size 448,448,448, pixel 0.831, shown at
level 0.326, step 2, values float32  

> surface dust #1 size 8.35

> surface dust #3 size 8.35

> surface dust #5.1 size 8.35

> surface dust #5.2 size 8.35

> surface dust #5.4 size 8.35

> surface dust #5.5 size 8.35

> surface dust #5.6 size 8.35

> surface dust #5.7 size 8.35

> surface dust #5.8 size 8.35

> surface dust #5.9 size 8.35

> surface dust #5.10 size 8.35

> surface dust #6 size 8.35

> surface dust #4 size 8.31

> surface dust #7 size 8.31

> surface dust #8 size 8.31

> surface dust #9 size 8.31

> surface dust #10 size 8.31

> hide #!7 models

> hide #!8 models

> hide #!9 models

> hide #!10 models

> rename #7 onlyies2-lowres-Xl040.mrc

> rename #8 onlynuc_Xl040.mrc

> rename #9 inocore_Xl040.mrc

> rename #10 nuc-resample_Xl040.mrc

> surface dust #1 size 8.35

> surface dust #3 size 8.35

> surface dust #5.1 size 8.35

> surface dust #5.2 size 8.35

> surface dust #5.4 size 8.35

> surface dust #5.5 size 8.35

> surface dust #5.6 size 8.35

> surface dust #5.7 size 8.35

> surface dust #5.8 size 8.35

> surface dust #5.9 size 8.35

> surface dust #5.10 size 8.35

> surface dust #6 size 8.35

> surface dust #4 size 8.31

> surface dust #10 size 8.31

> volume #7 step 1

> volume #8 step 1

> volume #9 step 1

> volume #10 step 1

> volume #7 level 0.00766

> volume #7 level 0.04253

> volume #8 level 0.1849

> volume #9 level 0.1834

> hide #!1 models

> hide #!3 models

> hide #!4 models

> hide #!5 models

> hide #!6 models

> show #!4 models

> hide #!4 models

> volume #10 level 0.6999

> volume #8 level 0.4115

> volume #7 level 0.05194

> volume #9 level 0.2181

> surface dust #7 size 8.31

> surface dust #8 size 8.31

> surface dust #9 size 8.31

> show #!4 models

> volume #4 step 1

> volume #4 level 0.002465

> lighting simple

> lighting soft

> volume #4 level 0.0026

> close #10

> rename #4 121124-a8-split_Xl040.mrc

> open ""/Users/upneet/Library/CloudStorage/Box-Box/INO-yeastNCP/Map and
> Model/Final-withADPBeF/042624-x40-wt-adpbef-withadpbef-final.pdb""

Chain information for 042624-x40-wt-adpbef-withadpbef-final.pdb #10  
---  
Chain | Description  
A | No description available  
B | No description available  
C G | No description available  
D | No description available  
E | No description available  
F | No description available  
H | No description available  
I | No description available  
J | No description available  
L | No description available  
M | No description available  
N | No description available  
O | No description available  
Q | No description available  
R | No description available  
S | No description available  
T | No description available  
U | No description available  
V | No description available  
W | No description available  
X | No description available  
Y | No description available  
Z | No description available  
  

> hide #!10 cartoons

> hide #!10 atoms

> show #!10 cartoons

> hide #!7 models

> hide #!8 models

> hide #!9 models

> hide #!10 models

> hide #!4 models

> show #!10 models

> color #10/Q firebrick

Drag select of 808 residues  

> color #10/R,S medium seagreen

> color #10/T-Y,A-H medium seagreen

> color #10/T-Y,A-H light gray

> select clear

> color #10/T-Y,I,J light slate gray

> color #10/I,J light slate gray

> nucleotides #!10 ladder

> show #!10 atoms

> undo

> select #10/I,J

6601 atoms, 7404 bonds, 322 residues, 1 model selected  

> show sel atoms

> select clear

> select #10/K

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

> color #10/N medium blue

[Repeated 1 time(s)]

> select #10/L

2824 atoms, 2886 bonds, 1 pseudobond, 361 residues, 2 models selected  

> ui tool show ""Color Actions""

> color sel sandy brown

> color sel goldenrod

[Repeated 1 time(s)]

> show #!2 models

> cartoon style (#!10 & sel) modeHelix tube sides 20

> select up

55996 atoms, 57633 bonds, 12 pseudobonds, 6600 residues, 2 models selected  

> select up

55996 atoms, 57633 bonds, 14 pseudobonds, 6600 residues, 3 models selected  

> select up

55996 atoms, 57633 bonds, 14 pseudobonds, 6600 residues, 3 models selected  

> select up

114335 atoms, 117752 bonds, 14 pseudobonds, 13459 residues, 19 models selected  

> select down

55996 atoms, 57633 bonds, 14 pseudobonds, 6600 residues, 3 models selected  

> select down

14 pseudobonds, 2 models selected  

> cartoon style modeHelix tube radius 1.5

> select #10/Z

467 atoms, 472 bonds, 1 pseudobond, 72 residues, 2 models selected  

> color sel salmon

[Repeated 1 time(s)]

> color sel dark salmon

> color sel salmon

> select #10/L

2824 atoms, 2886 bonds, 1 pseudobond, 361 residues, 2 models selected  

> color (#!10 & sel) #ffd479ff

> color (#!10 & sel) #feff80ff

[Repeated 1 time(s)]

> select clear

> select #10/M

3422 atoms, 3498 bonds, 1 pseudobond, 431 residues, 2 models selected  

> color sel deep sky blue

> select #10/O\

Nothing selected  

> select #10/O

287 atoms, 296 bonds, 34 residues, 1 model selected  

> color sel royal blue

> color sel #2163a6ff

[Repeated 1 time(s)]

> select clear

> hide #!2 models

> show #!9 models

> show #!8 models

> show #!4 models

> show #!7 models

> ui tool show ""Color Zone""

> color zone #4 near #10 distance 4.99

> color zone #4 near #10 distance 1

> color zone #4 near #10 distance 10

> color zone #7 near #10 distance 4.99

> color zone #8 near #10 distance 4.99

> color zone #9 near #10 distance 4.99

> hide #!4 models

> show #!4 models

> hide #!10 models

> ui tool show ""Side View""

> show #!2 models

> hide #!2 models

> show #!1 models

> hide #!1 models

> show #!6 models

> hide #!6 models

> show #!5 models

> hide #!5 models

> show #!1 models

> hide #!7 models

> hide #!8 models

> hide #!9 models

> hide #!4 models

> show #!3 models

> show #!4 models

> hide #!4 models

> show #!5 models

> show #!6 models

> save ""/Users/upneet/Desktop/Narlilkar Lab/Manuscript_INO80_AutoInib/Figures
> /Figure 1/Version 2/xl_080_map.png"" width 3600 height 2934 supersample 3
> transparentBackground true

> hide #!1 models

> hide #!3 models

> hide #!5 models

> hide #!6 models

> show #!8 models

> show #!9 models

> show #!7 models

> show #!4 models

> save ""/Users/upneet/Desktop/Narlilkar Lab/Manuscript_INO80_AutoInib/Figures
> /Figure 1/Version 2/xl_040_map.png"" width 3600 height 2934 supersample 3
> transparentBackground true

> save ""/Users/upneet/Desktop/Narlilkar Lab/Manuscript_INO80_AutoInib/Figures
> /Figure 1/Version 2-resubmission/Chimera Session/Figure1.cxs"" includeMaps
> true

> show #!10 models

> select #10/L

2824 atoms, 2886 bonds, 1 pseudobond, 361 residues, 2 models selected  

> ui tool show ""Color Actions""

> color sel gold

[Repeated 1 time(s)]

> color zone #9 near #10 distance 4.99

> color zone #4 near #10 distance 10

> select clear

> hide #!10 models

> save ""/Users/upneet/Desktop/Narlilkar Lab/Manuscript_INO80_AutoInib/Figures
> /Figure 1/Version 2-resubmission/Chimera Session/Xl_0N40_map.png"" width 3600
> height 2700 supersample 3 transparentBackground true

> save ""/Users/upneet/Desktop/Narlilkar Lab/Manuscript_INO80_AutoInib/Figures
> /Figure 1/Version 2-resubmission/Chimera Session/Xl_0N40_map.png"" width 3600
> height 2700 supersample 4 transparentBackground true

> select clear

> save ""/Users/upneet/Desktop/Narlilkar Lab/Manuscript_INO80_AutoInib/Figures
> /Figure 1/Version 2-resubmission/Chimera Session/Xl_0N40_map.png"" width 3600
> height 2700 supersample 1 transparentBackground true

> graphics silhouettes true

> save ""/Users/upneet/Desktop/Narlilkar Lab/Manuscript_INO80_AutoInib/Figures
> /Figure 1/Version 2-resubmission/Chimera Session/Xl_0N40_map.png"" width 3600
> height 2700 supersample 3 transparentBackground true

> graphics silhouettes false

> save ""/Users/upneet/Desktop/Narlilkar Lab/Manuscript_INO80_AutoInib/Figures
> /Figure 1/Version 2-resubmission/Chimera Session/Xl_0N40_map.png"" width 3600
> height 2700 supersample 3 transparentBackground true

> hide #!4 models

> hide #!7 models

> hide #!8 models

> hide #!9 models

> show #!1 models

> show #!3 models

> show #!5 models

> show #!6 models

> save ""/Users/upneet/Desktop/Narlilkar Lab/Manuscript_INO80_AutoInib/Figures
> /Figure 1/Version 2-resubmission/Chimera Session/Xl_0N80_map.png"" width 3600
> height 2700 supersample 3 transparentBackground true

> save ""/Users/upneet/Desktop/Narlilkar Lab/Manuscript_INO80_AutoInib/Figures
> /Figure 1/Version 2-resubmission/Chimera Session/Figure1.cxs"" includeMaps
> true

——— End of log from Thu Dec 12 15:18:18 2024 ———

opened ChimeraX session  

Cell requested for row 0 is out of bounds for table with 20 rows! Resizing
table model.  

> hide #!1 models

> hide #!3 models

> hide #!5 models

> hide #!6 models

> show #!7 models

> show #!8 models

> show #!9 models

> show #!10 models

> show #!4 models

> surface dust #4 size 8.31

> surface dust #7 size 8.31

> surface dust #8 size 8.31

> surface dust #9 size 8.31

> volume #4 level 0.002924

> volume #4 level 0.002769

> volume #4 level 0.00284

> volume #4 level 0.002896

> volume #4 level 0.002685

> select #10/L

2824 atoms, 2886 bonds, 1 pseudobond, 361 residues, 2 models selected  

> ui tool show ""Color Actions""

> color sel khaki

> ui tool show ""Color Zone""

> color zone #4 near #10 distance 10

> show #!1 models

> color (#!10 & sel) #ffff86ff

> select #10/L

2824 atoms, 2886 bonds, 1 pseudobond, 361 residues, 2 models selected  

> color zone #4 near #10 distance 10

> select clear

> hide #!1 models

> hide #!7 models

> show #!7 models

> hide #!7 models

> show #!7 models

> hide #!10 models

> save ""/Users/upneet/Desktop/Narlilkar Lab/Manuscript_INO80_AutoInib/Figures
> /Figure 1/Version 2-resubmission/Chimera Session/Xl_0N40_map.png"" width 3600
> height 3398 supersample 3 transparentBackground true

> save ""/Users/upneet/Desktop/Narlilkar Lab/Manuscript_INO80_AutoInib/Figures
> /Figure 1/Version 2-resubmission/Chimera Session/Figure1.cxs"" includeMaps
> true

——— End of log from Sat Dec 28 15:21:23 2024 ———

opened ChimeraX session  

> show #!1 models

> show #!2 models

> show #!3 models

> show #!5 models

> hide #!5 models

> show #!6 models

> hide #!6 models

> hide #!1 models

> hide #!2 models

> hide #!3 models

> hide #!4 models

> hide #!7 models

> hide #!8 models

> hide #!9 models

> close #4,7-10

> open ""/Users/upneet/Library/CloudStorage/Box-Box/INO-yeastNCP/Map and
> Model/INO-80Yeastnuc-ADPBeF/20231226-wt-y80nuc-adpbef-inocore-
> nuc_real_space_refined_009-coot-1.pdb""

Chain information for 20231226-wt-y80nuc-adpbef-inocore-
nuc_real_space_refined_009-coot-1.pdb #4  
---  
Chain | Description  
C | No description available  
D | No description available  
E h | No description available  
F j | No description available  
G | No description available  
H | No description available  
K | No description available  
L | No description available  
Q | No description available  
R | No description available  
S | No description available  
T | No description available  
U | No description available  
V | No description available  
W | No description available  
X | No description available  
Y | No description available  
Z | No description available  
  

> open ""/Users/upneet/Library/CloudStorage/Box-Box/INO-yeastNCP/Map and
> Model/INO-80Yeastnuc-ADPBeF/1x448-global-cryosparc-refine-unsharp-
> align-2.91A.mrc""

Opened 1x448-global-cryosparc-refine-unsharp-align-2.91A.mrc as #7, grid size
448,448,448, pixel 0.835, shown at level 0.167, step 2, values float32  

> open ""/Users/upneet/Library/CloudStorage/Box-Box/INO-yeastNCP/Map and
> Model/INO-80Yeastnuc-ADPBeF/filter.mrc""

Opened filter.mrc as #8, grid size 256,256,256, pixel 1.67, shown at level
0.0143, step 1, values float32  

> open ""/Users/upneet/Library/CloudStorage/Box-Box/INO-yeastNCP/Map and
> Model/wtINO80-0N80-Yeast-Apo/121124-0n80-ye-wt-apo-final-coot-0-pymol.pdb""

Chain information for 121124-0n80-ye-wt-apo-final-coot-0-pymol.pdb #9  
---  
Chain | Description  
A E | No description available  
B F | No description available  
C | No description available  
D H | No description available  
G | No description available  
I | No description available  
J | No description available  
K | No description available  
L | No description available  
M | No description available  
O | No description available  
Q | No description available  
R | No description available  
S | No description available  
T | No description available  
U | No description available  
V | No description available  
W | No description available  
X | No description available  
Y | No description available  
Z | No description available  
  

> open ""/Users/upneet/Library/CloudStorage/Box-Box/INO-yeastNCP/Map and
> Model/wtINO80-0N80-Yeast-Apo/121124-a8-split.mrc""

Opened 121124-a8-split.mrc as #10, grid size 512,512,512, pixel 0.819, shown
at level 0.000444, step 2, values float32  

> open ""/Users/upneet/Library/CloudStorage/Box-Box/INO-yeastNCP/Map and
> Model/wtINO80-0N80-Yeast-Apo/120524-inocore-nuc-3.16A.mrc""

Opened 120524-inocore-nuc-3.16A.mrc as #11, grid size 512,512,512, pixel
0.819, shown at level 0.0802, step 2, values float32  

> open ""/Users/upneet/Library/CloudStorage/Box-Box/INO-yeastNCP/Map and
> Model/wtINO80-0N80-Xe-Apo/122324-x80-apo-a8-split-resample.mrc""

Opened 122324-x80-apo-a8-split-resample.mrc as #12, grid size 480,480,480,
pixel 0.835, shown at level 0.000239, step 2, values float32  

> open ""/Users/upneet/Library/CloudStorage/Box-Box/INO-yeastNCP/Map and
> Model/wtINO80-0N80-Xe-Apo/122324-x80-apo-arp5-resample.mrc""

Opened 122324-x80-apo-arp5-resample.mrc as #13, grid size 480,480,480, pixel
0.835, shown at level 0.000123, step 2, values float32  

> open ""/Users/upneet/Library/CloudStorage/Box-Box/INO-yeastNCP/Map and
> Model/wtINO80-0N80-Xe-Apo/122324-x80-apo-atpasehighres-resample.mrc""

Opened 122324-x80-apo-atpasehighres-resample.mrc as #14, grid size
480,480,480, pixel 0.835, shown at level 0.000139, step 2, values float32  

> open ""/Users/upneet/Library/CloudStorage/Box-Box/INO-yeastNCP/Map and
> Model/wtINO80-0N80-Xe-Apo/122324-x80-apo-dna-resample.mrc""

Opened 122324-x80-apo-dna-resample.mrc as #15, grid size 480,480,480, pixel
0.835, shown at level 0.000354, step 2, values float32  

> open ""/Users/upneet/Library/CloudStorage/Box-Box/INO-yeastNCP/Map and
> Model/wtINO80-0N80-Xe-Apo/122324-x80-apo-grappler-resample.mrc""

Opened 122324-x80-apo-grappler-resample.mrc as #16, grid size 480,480,480,
pixel 0.835, shown at level 3.54e-05, step 2, values float32  

> open ""/Users/upneet/Library/CloudStorage/Box-Box/INO-yeastNCP/Map and
> Model/wtINO80-0N80-Xe-Apo/122324-x80-apo-histone-resample.mrc""

Opened 122324-x80-apo-histone-resample.mrc as #17, grid size 480,480,480,
pixel 0.835, shown at level 0.000232, step 2, values float32  

> open ""/Users/upneet/Library/CloudStorage/Box-Box/INO-yeastNCP/Map and
> Model/wtINO80-0N80-Xe-Apo/122324-x80-apo-i2highres-resample.mrc""

Opened 122324-x80-apo-i2highres-resample.mrc as #18, grid size 480,480,480,
pixel 0.835, shown at level 3.03e-06, step 2, values float32  

> open ""/Users/upneet/Library/CloudStorage/Box-Box/INO-yeastNCP/Map and
> Model/wtINO80-0N80-Xe-Apo/122324-x80-apo-resample.pdb""

Chain information for 122324-x80-apo-resample.pdb #19  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
F | No description available  
H | No description available  
I | No description available  
J | No description available  
K | No description available  
L | No description available  
M | No description available  
O | No description available  
Q | No description available  
R | No description available  
S | No description available  
T | No description available  
U | No description available  
V | No description available  
W | No description available  
X | No description available  
Y | No description available  
Z | No description available  
a | No description available  
b | No description available  
f | No description available  
h | No description available  
k | No description available  
  

> open ""/Users/upneet/Library/CloudStorage/Box-Box/INO-yeastNCP/Map and
> Model/wtINO80-0N80-Xe-Apo/122324-x80-apo-rvb-resample.mrc""

Opened 122324-x80-apo-rvb-resample.mrc as #20, grid size 480,480,480, pixel
0.835, shown at level 7.73e-05, step 2, values float32  

> open ""/Users/upneet/Library/CloudStorage/Box-Box/INO-yeastNCP/Map and
> Model/wtINO80-0N80-Xe-Apo/122324-x80-ies2lowres-resample.mrc""

Opened 122324-x80-ies2lowres-resample.mrc as #21, grid size 480,480,480, pixel
0.835, shown at level 2.62e-07, step 2, values float32  

> save ""/Users/upneet/Desktop/Narlilkar Lab/Manuscript_INO80_AutoInib/Figures
> /Figure 2/Version 2- Resubmission/0_80_ApovsADPBeF_Maps.cxs"" includeMaps
> true

> hide #!11 models

> hide #!12 models

> hide #!13 models

> hide #!14 models

> hide #!15 models

> hide #!16 models

> hide #!17 models

> hide #!18 models

> hide #!19 models

> hide #!20 models

> hide #!21 models

> hide #!4 models

> hide #!7 models

> hide #!8 models

> hide #!9 models

> show #!9 models

> show #!8 models

> hide #!8 models

> hide #!9 atoms

> show #!9 atoms

> hide #!9 atoms

> show #!9 cartoons

> show #!2 models

> ui tool show Matchmaker

> matchmaker #9/A to #2/A pairing ss

Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 121124-0n80-xe-wt-adpbef-final-coot-0-pymol-shortdna.pdb, chain A
(#2) with 121124-0n80-ye-wt-apo-final-coot-0-pymol.pdb, chain A (#9), sequence
alignment score = 421.7  
RMSD between 90 pruned atom pairs is 0.778 angstroms; (across all 94 pairs:
1.004)  
  

> ui tool show ""Fit in Map""

> hide #!10 models

> hide #!2 models

> hide #!9 models

> show #!2 models

> show #!11 models

> hide #!11 models

> show #!11 models

> hide #!11 models

> show #!11 models

> ui mousemode right ""translate selected models""

> ui mousemode right ""rotate selected models""

> select add #11

3 models selected  

> view matrix models
> #11,0.46801,-0.5411,-0.6987,391.67,0.76816,0.63998,0.018915,-119.95,0.43692,-0.54557,0.71516,64.823

> view matrix models
> #11,-0.46811,-0.17111,-0.86695,584.39,0.81301,0.30101,-0.4984,53.015,0.34624,-0.93814,-0.0017941,326.48

> ui mousemode right ""translate selected models""

> view matrix models
> #11,-0.46811,-0.17111,-0.86695,548.45,0.81301,0.30101,-0.4984,96.499,0.34624,-0.93814,-0.0017941,342.22

> hide #!2 models

> show #!9 models

> view matrix models
> #11,-0.46811,-0.17111,-0.86695,569.09,0.81301,0.30101,-0.4984,71.249,0.34624,-0.93814,-0.0017941,328.15

> fitmap #2 inMap #11

Fit molecule 121124-0n80-xe-wt-adpbef-final-coot-0-pymol-shortdna.pdb (#2) to
map 120524-inocore-nuc-3.16A.mrc (#11) using 58339 atoms  
average map value = 0.04758, steps = 196  
shifted from previous position = 14.4  
rotated from previous position = 7.46 degrees  
atoms outside contour = 42985, contour level = 0.080218  
  
Position of 121124-0n80-xe-wt-adpbef-final-coot-0-pymol-shortdna.pdb (#2)
relative to 120524-inocore-nuc-3.16A.mrc (#11) coordinates:  
Matrix rotation and translation  
-0.45865907 0.76124611 0.45840617 66.04130277  
-0.26224952 0.37693123 -0.88834004 373.23224661  
-0.84903300 -0.52766202 0.02675350 515.57895222  
Axis 0.21227268 0.76947747 -0.60236595  
Axis point 165.83506426 0.00000000 379.29198569  
Rotation angle (degrees) 121.83582990  
Shift along axis -9.35463366  
  

> fitmap #9 inMap #11

Fit molecule 121124-0n80-ye-wt-apo-final-coot-0-pymol.pdb (#9) to map
120524-inocore-nuc-3.16A.mrc (#11) using 57717 atoms  
average map value = 0.2017, steps = 1708  
shifted from previous position = 35.3  
rotated from previous position = 75 degrees  
atoms outside contour = 17523, contour level = 0.080218  
  
Position of 121124-0n80-ye-wt-apo-final-coot-0-pymol.pdb (#9) relative to
120524-inocore-nuc-3.16A.mrc (#11) coordinates:  
Matrix rotation and translation  
1.00000000 -0.00006074 0.00005427 0.01055650  
0.00006074 1.00000000 0.00000568 -0.02064744  
-0.00005427 -0.00000568 1.00000000 0.01686760  
Axis -0.06958774 0.66463915 0.74391689  
Axis point 319.03804700 171.59046789 0.00000000  
Rotation angle (degrees) 0.00467819  
Shift along axis -0.00190961  
  

> ui tool show ""Side View""

> show #!5 models

> select subtract #11

Nothing selected  

> hide #!5 models

> show #!5 models

> hide #!5 models

> show #!7 models

> hide #!9 models

> hide #!11 models

> show #!2 models

> hide #!2 models

> show #!5 models

> hide #!5 models

> show #!6 models

> hide #!6 models

> show #!9 models

> hide #!9 models

> show #!10 models

> hide #!10 models

> show #!11 models

> hide #!11 models

> show #!11 models

> surface dust #7 size 8.35

> surface dust #11 size 8.19

> select add #11

2 models selected  

> view matrix models
> #11,-0.46811,-0.17111,-0.86695,549.14,0.81301,0.30101,-0.4984,69.47,0.34624,-0.93814,-0.0017941,317.54

> ui mousemode right rotate

> ui mousemode right ""rotate selected models""

> view matrix models
> #11,-0.8341,0.48974,-0.25383,367.01,0.26446,-0.048787,-0.96316,370.59,-0.48408,-0.8705,-0.088827,517.57

> ui mousemode right ""translate selected models""

> view matrix models
> #11,-0.8341,0.48974,-0.25383,360.21,0.26446,-0.048787,-0.96316,375.41,-0.48408,-0.8705,-0.088827,530.18

> view matrix models
> #11,-0.8341,0.48974,-0.25383,358.84,0.26446,-0.048787,-0.96316,383.34,-0.48408,-0.8705,-0.088827,519.86

> ui mousemode right ""rotate selected models""

> view matrix models
> #11,-0.82246,0.54164,-0.17371,327.61,0.20486,-0.0028233,-0.97879,392.41,-0.53064,-0.8406,-0.10864,529.86

> view matrix models
> #11,-0.69285,0.68006,0.23976,174.05,-0.18361,0.15515,-0.97068,451.29,-0.69732,-0.71655,0.01737,515.69

> ui mousemode right ""translate selected models""

> view matrix models
> #11,-0.69285,0.68006,0.23976,166.8,-0.18361,0.15515,-0.97068,441.71,-0.69732,-0.71655,0.01737,521.17

> view matrix models
> #11,-0.69285,0.68006,0.23976,174.07,-0.18361,0.15515,-0.97068,439.89,-0.69732,-0.71655,0.01737,504.12

> view matrix models
> #11,-0.69285,0.68006,0.23976,169.03,-0.18361,0.15515,-0.97068,443.43,-0.69732,-0.71655,0.01737,503.91

> ui mousemode right ""rotate selected models""

> view matrix models
> #11,-0.72409,0.58246,0.36937,163.26,-0.37781,0.11308,-0.91895,483.65,-0.57702,-0.80496,0.13818,463.57

> view matrix models
> #11,-0.90807,0.26406,0.32508,274.47,-0.3083,0.10391,-0.9456,475.62,-0.28348,-0.95889,-0.012948,459.88

> view matrix models
> #11,-0.93735,0.33746,0.086626,324.52,-0.03972,0.14351,-0.98885,416.66,-0.34613,-0.93034,-0.12112,494.85

> ui mousemode right ""translate selected models""

> view matrix models
> #11,-0.93735,0.33746,0.086626,330.67,-0.03972,0.14351,-0.98885,410.13,-0.34613,-0.93034,-0.12112,506.84

> ui tool show ""Fit in Map""

> fitmap #11 inMap #5.8

Fit map 120524-inocore-nuc-3.16A.mrc in map 041924-global-resampleonapo.mrc 7
using 167598 points  
correlation = 0.2717, correlation about mean = 0.05944, overlap = 682.8  
steps = 236, shift = 3.15, angle = 11.2 degrees  
  
Position of 120524-inocore-nuc-3.16A.mrc (#11) relative to 041924-global-
resampleonapo.mrc 7 (#5.8) coordinates:  
Matrix rotation and translation  
-0.88632457 0.45950295 -0.05732199 331.62490500  
0.11024555 0.08916261 -0.98989694 386.02823887  
-0.44974958 -0.88368947 -0.12968517 520.47184865  
Axis 0.19816062 0.73218669 -0.65164025  
Axis point 162.64429754 0.00000000 401.27755246  
Rotation angle (degrees) 164.45570404  
Shift along axis 9.19933237  
  

> show #!10 models

> hide #!10 models

> show #!9 models

> fitmap #9 inMap #11

Fit molecule 121124-0n80-ye-wt-apo-final-coot-0-pymol.pdb (#9) to map
120524-inocore-nuc-3.16A.mrc (#11) using 57717 atoms  
average map value = 0.06358, steps = 524  
shifted from previous position = 21.4  
rotated from previous position = 23.6 degrees  
atoms outside contour = 39139, contour level = 0.080218  
  
Position of 121124-0n80-ye-wt-apo-final-coot-0-pymol.pdb (#9) relative to
120524-inocore-nuc-3.16A.mrc (#11) coordinates:  
Matrix rotation and translation  
0.60709616 0.65538577 0.44933700 -150.63587196  
-0.57100015 0.75305562 -0.32690373 245.95812177  
-0.55262381 -0.05810950 0.83140255 171.50849007  
Axis 0.16733755 0.62376959 -0.76348520  
Axis point 265.73463114 388.45394890 0.00000000  
Rotation angle (degrees) 53.43194556  
Shift along axis -2.73003438  
  

> show #!10 models

> select subtract #11

Nothing selected  

> select add #10

3 models selected  

> view matrix models #10,1,0,0,-42.69,0,1,0,28.059,0,0,1,10.168

> ui mousemode right ""rotate selected models""

> view matrix models
> #10,-0.62,0.55054,-0.55902,487.63,0.71305,0.69264,-0.10869,-115.76,0.32736,-0.466,-0.822,391.76

> ui mousemode right ""translate selected models""

> view matrix models
> #10,-0.62,0.55054,-0.55902,412.65,0.71305,0.69264,-0.10869,-19.792,0.32736,-0.466,-0.822,461.07

> ui mousemode right ""rotate selected models""

> view matrix models
> #10,-0.80313,0.46625,-0.37093,434.96,0.55878,0.80549,-0.19737,30.687,0.20676,-0.36578,-0.90744,502.6

> view matrix models
> #10,-0.73853,-0.32286,-0.59189,572.19,0.51443,0.2976,-0.80423,250.23,0.43581,-0.89844,-0.053698,312

> ui mousemode right ""translate selected models""

> view matrix models
> #10,-0.73853,-0.32286,-0.59189,575.43,0.51443,0.2976,-0.80423,233.34,0.43581,-0.89844,-0.053698,323.6

> view matrix models
> #10,-0.73853,-0.32286,-0.59189,576.08,0.51443,0.2976,-0.80423,235.18,0.43581,-0.89844,-0.053698,321.07

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!10 models

> hide #!9 models

> show #!10 models

> view matrix models
> #10,-0.73853,-0.32286,-0.59189,525.98,0.51443,0.2976,-0.80423,242.04,0.43581,-0.89844,-0.053698,302.07

> ui mousemode right ""rotate selected models""

> view matrix models
> #10,-0.96781,-0.019089,0.25096,360.53,-0.18592,0.72632,-0.66174,358.14,-0.16964,-0.6871,-0.70648,600.72

> ui mousemode right ""translate selected models""

> view matrix models
> #10,-0.96781,-0.019089,0.25096,334.89,-0.18592,0.72632,-0.66174,295.54,-0.16964,-0.6871,-0.70648,587.83

> ui mousemode right ""rotate selected models""

> view matrix models
> #10,-0.99457,0.10342,-0.011745,386.22,0.021508,0.093791,-0.99536,395.41,-0.10184,-0.99021,-0.095506,469.24

> view matrix models
> #10,-0.99331,0.099471,-0.058607,397.07,0.057616,-0.012807,-0.99826,399.75,-0.10005,-0.99496,0.0069906,445.98

> ui mousemode right ""translate selected models""

> view matrix models
> #10,-0.99331,0.099471,-0.058607,405.04,0.057616,-0.012807,-0.99826,411.07,-0.10005,-0.99496,0.0069906,440.48

> fitmap #10 inMap #1

Fit map 121124-a8-split.mrc in map 121124-a8-split_xl080.mrc using 167748
points  
correlation = 0.9841, correlation about mean = 0.987, overlap = 2.479  
steps = 264, shift = 35.9, angle = 17.3 degrees  
  
Position of 121124-a8-split.mrc (#10) relative to 121124-a8-split_xl080.mrc
(#1) coordinates:  
Matrix rotation and translation  
-0.93714444 0.33750899 0.08858891 329.85593650  
-0.05354817 0.11177048 -0.99229026 416.63699329  
-0.34480851 -0.93466307 -0.08667210 498.17344367  
Axis 0.09824214 0.73885064 -0.66666949  
Axis point 188.32785546 0.00000000 403.66415364  
Rotation angle (degrees) 162.94487597  
Shift along axis 8.12122851  
  

> show #!9 models

> rename #7 y0_80_ADPBeF_Core.mrc

> rename #8 y0_80_ADPBeF_Core-filter.mrc

> select add #9

57717 atoms, 59577 bonds, 15 pseudobonds, 6675 residues, 4 models selected  

> select add #10

57717 atoms, 59577 bonds, 15 pseudobonds, 6675 residues, 5 models selected  

> view matrix models
> #9,-0.76878,-0.23152,-0.59613,525.04,0.56306,0.19692,-0.80261,228,0.30321,-0.95269,-0.021028,338.17,#10,-0.93714,0.33751,0.088589,286.57,-0.053548,0.11177,-0.99229,423.06,-0.34481,-0.93466,-0.086672,487.71

> undo

> select subtract #10

57717 atoms, 59577 bonds, 15 pseudobonds, 6675 residues, 2 models selected  

> ui mousemode right ""rotate selected models""

> view matrix models
> #9,-0.94202,0.26393,0.20722,343.39,-0.02008,0.57211,-0.81993,335.43,-0.33496,-0.77656,-0.53363,631.23

> ui mousemode right ""translate selected models""

> view matrix models
> #9,-0.94202,0.26393,0.20722,313.8,-0.02008,0.57211,-0.81993,324.18,-0.33496,-0.77656,-0.53363,633.54

> show #!2 models

> fitmap #9 inMap #11

Fit molecule 121124-0n80-ye-wt-apo-final-coot-0-pymol.pdb (#9) to map
120524-inocore-nuc-3.16A.mrc (#11) using 57717 atoms  
average map value = 0.2017, steps = 772  
shifted from previous position = 72  
rotated from previous position = 31.2 degrees  
atoms outside contour = 17524, contour level = 0.080218  
  
Position of 121124-0n80-ye-wt-apo-final-coot-0-pymol.pdb (#9) relative to
120524-inocore-nuc-3.16A.mrc (#11) coordinates:  
Matrix rotation and translation  
1.00000000 -0.00006501 0.00004475 0.00518918  
0.00006501 1.00000000 0.00002173 -0.01831902  
-0.00004475 -0.00002172 1.00000000 0.01687531  
Axis -0.26537272 0.54669131 0.79416997  
Axis point 298.68209806 88.00700545 0.00000000  
Rotation angle (degrees) 0.00469039  
Shift along axis 0.00200995  
  

> hide #!1 models

> hide #!2 models

> hide #!7 models

> fitmap #9 inMap #10

Fit molecule 121124-0n80-ye-wt-apo-final-coot-0-pymol.pdb (#9) to map
121124-a8-split.mrc (#10) using 57717 atoms  
average map value = 0.001464, steps = 376  
shifted from previous position = 6.79  
rotated from previous position = 11.8 degrees  
atoms outside contour = 40556, contour level = 0.00044382  
  
Position of 121124-0n80-ye-wt-apo-final-coot-0-pymol.pdb (#9) relative to
121124-a8-split.mrc (#10) coordinates:  
Matrix rotation and translation  
0.99996889 0.00779041 0.00123500 -0.92235426  
-0.00779156 0.99996921 0.00092843 2.92489776  
-0.00122773 -0.00093803 0.99999880 0.56357269  
Axis -0.11749503 0.15503124 -0.98089767  
Axis point 374.74059597 119.75654981 0.00000000  
Rotation angle (degrees) 0.45508845  
Shift along axis 0.00901544  
  

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!10 models

> show #!10 models

> save ""/Users/upneet/Desktop/Narlilkar Lab/Manuscript_INO80_AutoInib/Figures
> /Figure 2/Version 2- Resubmission/0_80_ApovsADPBeF_Maps.cxs"" includeMaps
> true

> hide #!9 models

> select subtract #9

Nothing selected  

> hide #!10 models

> hide #!11 models

> rename #1 x0_80_ADPBeF_A8-Split.mrc

> rename #2 x0_80_ADPBeF.pdb

> rename #3 x0_80_ADPBeF_Ies21.mrc

> rename #3 x0_80_ADPBeF_Ies2.mrc

> rename #4 y0_80_ADPBeF

> show #!4 models

> hide #!4 models

> show #!5 models

> hide #!5 models

> rename #5 ""x0_80_ADPBeF_core.mrc split""

> rename #6 x0_80_ADPBeF_nuc.mrc

> rename #9 y0_80_Apo.pdb

> show #!10 models

> hide #!10 models

> rename #10 x0_80_Apo_A8-split.mrc

> rename #11 x0_80_Apo_core_nuc.mrc

> rename #10 y0_80_Apo_A8-split.mrc

> rename #11 y0_80_Apo_core_nuc.mrc

> show #!4 models

> show #!8 models

> show #!7 models

> hide #!7 models

> rename #4 y0_80_ADPBeF.pdb

> hide #!1 models

> hide #!4 models

> hide #!8 models

> ui favorite true ""Model Panel""

> log metadata #4

No models had metadata

> log chains #4

Chain information for y0_80_ADPBeF.pdb #4  
---  
Chain | Description  
C | No description available  
D | No description available  
E h | No description available  
F j | No description available  
G | No description available  
H | No description available  
K | No description available  
L | No description available  
Q | No description available  
R | No description available  
S | No description available  
T | No description available  
U | No description available  
V | No description available  
W | No description available  
X | No description available  
Y | No description available  
Z | No description available  
  

> hide #!5.2,4-10 target m

> show #!1 models

> show #!2 models

> show #!3 models

> show #!5 models

> show #!6 models

> hide #!5 models

> hide #!3 models

> hide #!2 models

> show #!2 models

> hide #!1 models

> hide #!2 models

> hide #!6 models

> show #!7 models

> show #!4 models

> show #!8 models

> hide #!4 atoms

> show #!4 cartoons

> select #4/A-H,T-Y

24941 atoms, 25248 bonds, 3218 residues, 1 model selected  

> color sel light gray

> select #4/Q

5289 atoms, 5407 bonds, 3 pseudobonds, 660 residues, 2 models selected  

> ui tool show ""Color Actions""

> color sel fire brick

> select #4/R,S

4562 atoms, 4675 bonds, 2 pseudobonds, 567 residues, 2 models selected  

> color sel sea green

> select #4/Z

248 atoms, 254 bonds, 28 residues, 1 model selected  

> color sel indian red

> hide #!7 models

> hide #!8 models

> select #4/I,J

Nothing selected  

> ui tool show ""Color Actions""

> color light slate gray

> nucleotides #!4 ladder

> show #!4 atoms

> undo

[Repeated 3 time(s)]

> select #4/I,J

Nothing selected  

> ui mousemode right select

Drag select of 2 residues  

> select up

2969 atoms, 3334 bonds, 144 residues, 1 model selected  

> select up

42356 atoms, 43634 bonds, 4935 residues, 1 model selected  

> select down

2969 atoms, 3334 bonds, 144 residues, 1 model selected  

> select #4/K,L

5904 atoms, 6622 bonds, 288 residues, 1 model selected  

> color sel light slate gray

> nucleotides sel ladder

> show sel atoms

Drag select of 5 residues  

> select up

194 atoms, 197 bonds, 22 residues, 1 model selected  

> select up

785 atoms, 794 bonds, 95 residues, 1 model selected  

> color sel light gray

> select clear

> show #!7 models

> ui tool show ""Color Zone""

> color zone #7 near #4 distance 5.01

> hide #!7 models

Drag select of 17 residues  

> select up

733 atoms, 737 bonds, 91 residues, 1 model selected  

> color sel light gray

> select clear

Drag select of 22 residues  
Drag select of 21 residues  

> select up

580 atoms, 586 bonds, 68 residues, 1 model selected  

> select up

3578 atoms, 3635 bonds, 449 residues, 1 model selected  

> select down

580 atoms, 586 bonds, 68 residues, 1 model selected  
Drag select of 63 residues  

> select up

1514 atoms, 1521 bonds, 196 residues, 1 model selected  

> color sel light gray

Drag select of 82 residues  

> select up

1870 atoms, 1889 bonds, 232 residues, 1 model selected  

> select down

673 atoms, 82 residues, 1 model selected  

> color sel light gray

Drag select of 291 residues  

> color sel light gray

Drag select of 20 residues  

> color sel light gray

> select clear

> show #!7 models

> color zone #7 near #4 distance 5.01

[Repeated 2 time(s)]

> color zone #7 near #4 distance 8

[Repeated 1 time(s)]

> show #!8 models

> hide #!8 models

> save ""/Users/upneet/Desktop/Narlilkar Lab/Manuscript_INO80_AutoInib/Figures
> /Figure 2/Version 2- Resubmission/0_80_ApovsADPBeF_Maps.cxs"" includeMaps
> true

> hide #!4 models

> hide #!7 models

> show #!9 models

> select #9/A-H,T-Y

26415 atoms, 26739 bonds, 2 pseudobonds, 3403 residues, 2 models selected  

> color (#!9 & sel) light gray

> select #9/Q

6141 atoms, 6266 bonds, 8 pseudobonds, 758 residues, 2 models selected  

> ui tool show ""Color Actions""

> color sel fire brick

> save ""/Users/upneet/Desktop/Narlilkar Lab/Manuscript_INO80_AutoInib/Figures
> /Figure 2/Version 2- Resubmission/0_80_ApovsADPBeF_Maps.cxs"" includeMaps
> true

——— End of log from Sun Dec 29 17:47:13 2024 ———

opened ChimeraX session  

> select #9/I,K

9286 atoms, 9879 bonds, 835 residues, 1 model selected  

> select #9/I,J

8481 atoms, 9512 bonds, 414 residues, 1 model selected  

> ui tool show ""Color Actions""

> color sel light slate gray

> nucleotides sel atoms

> style nucleic & sel stick

Changed 8481 atom styles  

> nucleotides sel atoms

> style nucleic & sel stick

Changed 8481 atom styles  

> nucleotides sel ladder

> show sel atoms

> select #9/K

5092 atoms, 5206 bonds, 628 residues, 1 model selected  

> color sel medium blue

> select #9/L

2856 atoms, 2919 bonds, 1 pseudobond, 363 residues, 2 models selected  

> color sel khaki

> select #9/M

3454 atoms, 3531 bonds, 1 pseudobond, 433 residues, 2 models selected  

> color sel royal blue

> color sel deep sky blue

> select #9/O

287 atoms, 296 bonds, 34 residues, 1 model selected  

> color sel dark blue

> select #9/Z

464 atoms, 469 bonds, 1 pseudobond, 72 residues, 2 models selected  

> color sel indian red

> select clear

> show #!10 models

> show #!11 models

> volume #10 level 0.00122

> volume #10 step 1

> volume #10 level 0.0006063

> volume #11 level 0.08901

> volume #11 step 1

> volume #11 level 0.1187

> ui tool show ""Fit in Map""

> fitmap #9 inMap #11

Fit molecule y0_80_Apo.pdb (#9) to map y0_80_Apo_core_nuc.mrc (#11) using
57717 atoms  
average map value = 0.2017, steps = 312  
shifted from previous position = 6.79  
rotated from previous position = 11.8 degrees  
atoms outside contour = 20896, contour level = 0.11874  
  
Position of y0_80_Apo.pdb (#9) relative to y0_80_Apo_core_nuc.mrc (#11)
coordinates:  
Matrix rotation and translation  
1.00000000 -0.00003537 -0.00001420 0.01261198  
0.00003537 1.00000000 0.00006454 -0.02167371  
0.00001419 -0.00006454 1.00000000 0.01098547  
Axis -0.86107623 -0.18938758 0.47188990  
Axis point 0.00000000 181.69642546 340.45423658  
Rotation angle (degrees) 0.00429427  
Shift along axis -0.00157121  
  

> fitmap #9 inMap #10

Fit molecule y0_80_Apo.pdb (#9) to map y0_80_Apo_A8-split.mrc (#10) using
57717 atoms  
average map value = 0.001464, steps = 340  
shifted from previous position = 6.79  
rotated from previous position = 11.8 degrees  
atoms outside contour = 40619, contour level = 0.00060625  
  
Position of y0_80_Apo.pdb (#9) relative to y0_80_Apo_A8-split.mrc (#10)
coordinates:  
Matrix rotation and translation  
0.99996906 0.00776652 0.00124346 -0.90713737  
-0.00776759 0.99996946 0.00085491 2.93731787  
-0.00123678 -0.00086454 0.99999886 0.55705285  
Axis -0.10865733 0.15673404 -0.98164557  
Axis point 377.44174395 118.13477585 0.00000000  
Rotation angle (degrees) 0.45334497  
Shift along axis 0.01211637  
  

> fitmap #9 inMap #11

Fit molecule y0_80_Apo.pdb (#9) to map y0_80_Apo_core_nuc.mrc (#11) using
57717 atoms  
average map value = 0.2017, steps = 332  
shifted from previous position = 6.78  
rotated from previous position = 11.8 degrees  
atoms outside contour = 20891, contour level = 0.11874  
  
Position of y0_80_Apo.pdb (#9) relative to y0_80_Apo_core_nuc.mrc (#11)
coordinates:  
Matrix rotation and translation  
1.00000000 -0.00003686 0.00002583 0.00303389  
0.00003686 1.00000000 0.00002713 -0.01803754  
-0.00002583 -0.00002713 1.00000000 0.01936458  
Axis -0.51626765 0.49144166 0.70139348  
Axis point 531.38843357 126.43530707 0.00000000  
Rotation angle (degrees) 0.00301099  
Shift along axis 0.00315149  
  

> select add #10

2 models selected  

> ui mousemode right ""rotate selected models""

> view matrix models
> #10,-0.90529,0.42058,0.059653,315.92,-0.07551,-0.021135,-0.99692,442,-0.41803,-0.90701,0.050891,484.68

> view matrix models
> #10,-0.92895,0.36988,-0.015398,346.82,-0.038145,-0.137,-0.98984,444.9,-0.36823,-0.91892,0.14138,450.95

> view matrix models
> #10,-0.90265,0.42501,0.067688,312.71,-0.067158,0.01625,-0.99761,434.68,-0.4251,-0.90504,0.013875,494.95

> ui mousemode right ""translate selected models""

> view matrix models
> #10,-0.90265,0.42501,0.067688,326.32,-0.067158,0.01625,-0.99761,446.02,-0.4251,-0.90504,0.013875,489.37

> view matrix models
> #10,-0.90265,0.42501,0.067688,307.93,-0.067158,0.01625,-0.99761,452.76,-0.4251,-0.90504,0.013875,484.21

> select clear

> select add #10

2 models selected  

> select subtract #10

Nothing selected  

> ui tool show ""Color Zone""

> color zone #10 near #9 distance 4.91

> color zone #10 near #9 distance 1

> color zone #10 near #9 distance 15

> color zone #10 near #9 distance 2

> color zone #10 near #9 distance 20

> color zone #10 near #9 distance 3

> color zone #10 near #9 distance 30

> color zone #11 near #9 distance 4.91

> color zone #11 near #9 distance 7

> color zone #11 near #9 distance 9

> surface dust #10 size 8.19

> surface dust #11 size 8.19

> select #9/R,S

4527 atoms, 4639 bonds, 2 pseudobonds, 570 residues, 2 models selected  

> color sel medium sea green

> color zone #11 near #9 distance 9

[Repeated 1 time(s)]

> volume #11 level 0.1329

> volume #10 level 0.000744

> volume #10 level 0.0008301

> volume #10 level 0.000899

> volume #11 level 0.1471

> save ""/Users/upneet/Desktop/Narlilkar Lab/Manuscript_INO80_AutoInib/Figures
> /Figure 2/Version 2- Resubmission/0_80_ApovsADPBeF_Maps.cxs"" includeMaps
> true

> hide #!9 models

> hide #!10 models

> hide #!11 models

> select add #19

62823 atoms, 64722 bonds, 17 pseudobonds, 7408 residues, 4 models selected  

> select subtract #19

4527 atoms, 4639 bonds, 2 pseudobonds, 570 residues, 2 models selected  

> show #!19 models

> show #!18 models

> hide #!18 models

> hide #!19 cartoons

> hide #!19 atoms

> show #!19 cartoons

> select #19/A-H,T-Y

32178 atoms, 32645 bonds, 6 pseudobonds, 4174 residues, 2 models selected  

> select #19/A-H,T-Y

32178 atoms, 32645 bonds, 6 pseudobonds, 4174 residues, 2 models selected  

> select

216708 atoms, 223413 bonds, 55 pseudobonds, 25307 residues, 61 models selected  

> color sel light gray

> select clear

> ui mousemode right select

Drag select of 6 residues  

> select up

209 atoms, 208 bonds, 42 residues, 1 model selected  

> select up

219 atoms, 218 bonds, 44 residues, 1 model selected  

> select up

58296 atoms, 60083 bonds, 6838 residues, 1 model selected  

> select up

216708 atoms, 223413 bonds, 25307 residues, 37 models selected  

> select down

58296 atoms, 60083 bonds, 6838 residues, 1 model selected  

> select down

219 atoms, 218 bonds, 44 residues, 1 model selected  

> select #19/F

219 atoms, 218 bonds, 44 residues, 1 model selected  

> color sel indian red

Drag select of 5 residues  

> select up

412 atoms, 416 bonds, 52 residues, 1 model selected  

> select up

957 atoms, 969 bonds, 118 residues, 1 model selected  

> select up

58296 atoms, 60083 bonds, 6838 residues, 1 model selected  

> select down

957 atoms, 969 bonds, 118 residues, 1 model selected  

> color sel fire brick

Drag select of 9 residues  

> select up

228 atoms, 231 bonds, 29 residues, 1 model selected  

> select up

2056 atoms, 2112 bonds, 247 residues, 1 model selected  

> select up

58296 atoms, 60083 bonds, 6838 residues, 1 model selected  

> select down

2056 atoms, 2112 bonds, 247 residues, 1 model selected  

> select #19/K

2056 atoms, 2112 bonds, 247 residues, 1 model selected  

> color sel fire brick

> select #19/Q

3409 atoms, 3474 bonds, 5 pseudobonds, 421 residues, 2 models selected  

> color sel fire brick

Drag select of 14 residues  

> select up

235 atoms, 234 bonds, 47 residues, 1 model selected  

> select up

404 atoms, 403 bonds, 81 residues, 1 model selected  

> select up

412 atoms, 410 bonds, 82 residues, 1 model selected  

> select up

651 atoms, 649 bonds, 130 residues, 1 model selected  

> select up

771 atoms, 768 bonds, 154 residues, 1 model selected  

> select up

58296 atoms, 60083 bonds, 6838 residues, 1 model selected  

> select down

771 atoms, 768 bonds, 154 residues, 1 model selected  

> color sel medium sea green

Drag select of 21 residues  

> select up

643 atoms, 663 bonds, 79 residues, 1 model selected  

> select up

2626 atoms, 2693 bonds, 327 residues, 1 model selected  

> select up

3029 atoms, 3109 bonds, 376 residues, 1 model selected  

> select up

4561 atoms, 4674 bonds, 570 residues, 1 model selected  

> color sel medium sea green

Drag select of 25 residues  

> select up

690 atoms, 696 bonds, 82 residues, 1 model selected  

> select up

5060 atoms, 5173 bonds, 626 residues, 1 model selected  

> color sel medium blue

Drag select of 7 residues  

> select up

195 atoms, 201 bonds, 22 residues, 1 model selected  

> select up

2570 atoms, 2628 bonds, 325 residues, 1 model selected  

> color sel khaki

Drag select of 13 residues  

> select up

381 atoms, 388 bonds, 47 residues, 1 model selected  

> select up

2540 atoms, 2602 bonds, 318 residues, 1 model selected  

> color sel deep sky blue

Drag select of 8 residues  

> select up

235 atoms, 241 bonds, 27 residues, 1 model selected  

> select up

1205 atoms, 1228 bonds, 149 residues, 1 model selected  

> color sel dark blue

> undo

> select #19/C

347 atoms, 356 bonds, 40 residues, 1 model selected  

> color sel dark blue

> select #19/B

3430 atoms, 3507 bonds, 1 pseudobond, 429 residues, 2 models selected  

> color sel deep sky blue

Drag select of 6 residues  

> select up

7828 atoms, 8781 bonds, 382 residues, 1 model selected  

> color sel light slate gray

> nucleotides sel ladder

> show sel cartoons

> show sel atoms

> select clear

> show #!12 models

> show #!13 models

> show #!14 models

> show #!15 models

> show #!16 models

> show #!17 models

> show #!18 models

> show #!20 models

> show #!21 models

> volume #21 step 1

> volume #21 level 0.0003197

> volume #20 step 1

> volume #20 level 0.241

> volume #20 level 0.2214

> volume #18 step 1

> volume #18 level 0.1038

> volume #17 step 1

> volume #17 level 0.4374

> volume #17 level 1.484

> volume #17 level 1.289

> volume #16 step 1

> volume #16 level 0.06124

> volume #16 level 0.1099

> volume #15 step 1

> volume #15 level 0.6283

> volume #15 level 0.8467

> volume #14 step 1

> volume #14 level 0.02117

> volume #13 step 1

> volume #13 level 0.04944

> volume #13 level 0.08318

> volume #12 step 1

> volume #12 level 0.001063

> color zone #12 near #19 distance 5.01

> color zone #12 near #19 distance 5.1

> color zone #12 near #19 distance 40.94

> color zone #12 near #19 distance 2

> color zone #12 near #19 distance 25

> color zone #12 near #19 distance 3

> color zone #12 near #19 distance 30

> volume #12 level 0.001206

> volume #12 level 0.001414

> volume #12 level 0.001297

> volume #12 level 0.001219

> color zone #13 near #19 distance 5.01

> color zone #14 near #19 distance 5.01

> color zone #15 near #19 distance 5.01

> color zone #16 near #19 distance 5.01

> color zone #17 near #19 distance 5.01

> color zone #18 near #19 distance 5.01

> color zone #21 near #19 distance 5.01

> surface dust #12 size 8.35

> surface dust #13 size 8.35

> surface dust #14 size 8.35

> surface dust #15 size 8.35

> surface dust #16 size 8.35

> surface dust #17 size 8.35

> surface dust #18 size 8.35

> surface dust #20 size 8.35

> surface dust #21 size 8.35

> save ""/Users/upneet/Desktop/Narlilkar Lab/Manuscript_INO80_AutoInib/Figures
> /Figure 2/Version 2- Resubmission/0_80_ApovsADPBeF_Maps.cxs"" includeMaps
> true

> show #!1 models

> show #!2 models

> show #!3 models

> show #!4 models

> hide #!4 models

> show #!5 models

> show #!6 models

> color zone #1 near #19 distance 5.01

> color zone #1 near #19 distance 2

> color zone #1 near #19 distance 20

> hide #!12 models

> hide #!2 models

> volume #1 level 0.003197

> volume #1 level 0.002949

> volume #1 level 0.002501

> volume #1 level 0.002609

> hide #!21 models

> hide #!20 models

> hide #!19 models

> hide #!18 models

> hide #!17 models

> hide #!16 models

> hide #!15 models

> hide #!14 models

> hide #!13 models

> show #!2 models

> hide #!6 models

> hide #!5 models

> hide #!2 models

> hide #!1 models

> hide #!3 models

> show #!2 models

> select #2/Q

6141 atoms, 6266 bonds, 8 pseudobonds, 758 residues, 2 models selected  

> color sel fire brick

> select #2/R,S

5315 atoms, 5425 bonds, 5 pseudobonds, 726 residues, 2 models selected  

> color sel medium sea green

> select #2/z

467 atoms, 472 bonds, 1 pseudobond, 72 residues, 2 models selected  

> color sel indian red

> select #2/K

5614 atoms, 5735 bonds, 1 pseudobond, 692 residues, 2 models selected  

> color sel medium blue

> select #2/l

2862 atoms, 2925 bonds, 1 pseudobond, 364 residues, 2 models selected  

> color sel deep sky blue

> color sel khaki

> select #2/m

3430 atoms, 3507 bonds, 1 pseudobond, 429 residues, 2 models selected  

> color sel deep sky blue

[Repeated 1 time(s)]

> select #2/o

347 atoms, 356 bonds, 40 residues, 1 model selected  

> color sel dark blue

> select #2/i,j

7787 atoms, 8735 bonds, 380 residues, 1 model selected  

> color sel light slate gray

> select clear

> show #!1 models

> color zone #1 near #2 distance 20

> ui tool show ""Fit in Map""

> fitmap #2 inMap #1

Fit molecule x0_80_ADPBeF.pdb (#2) to map x0_80_ADPBeF_A8-Split.mrc (#1) using
58339 atoms  
average map value = 0.001452, steps = 1000  
shifted from previous position = 15.1  
rotated from previous position = 7.37 degrees  
atoms outside contour = 42857, contour level = 0.0026092  
  
Position of x0_80_ADPBeF.pdb (#2) relative to x0_80_ADPBeF_A8-Split.mrc (#1)
coordinates:  
Matrix rotation and translation  
0.99994014 0.00694600 -0.00845407 0.33822171  
-0.00700867 0.99994801 -0.00740623 3.05230247  
0.00840219 0.00746504 0.99993684 -1.18934593  
Axis 0.56207240 -0.63709731 -0.52742927  
Axis point 213.16300362 0.00000000 113.44077700  
Rotation angle (degrees) 0.75798549  
Shift along axis -1.12721276  
  

> color zone #1 near #2 distance 20

> show #!3 models

> color zone #1 near #2 distance 20

> color zone #3 near #2 distance 5.01

> show #!4 models

> hide #!4 models

> show #!5 models

> select add #5

21 models selected  

> select subtract #5

Nothing selected  

> color zone #5.1 near #2 distance 5.01

[Repeated 1 time(s)]

> color zone #5.2 near #2 distance 5.01

> color zone #5.3 near #2 distance 5.01

> color zone #5.4 near #2 distance 5.01

> color zone #5.5 near #2 distance 5.01

> color zone #5.6 near #2 distance 5.01

> color zone #5.7 near #2 distance 5.01

> color zone #5.8 near #2 distance 5.01

> color zone #5.9 near #2 distance 5.01

> color zone #5.10 near #2 distance 5.01

> color zone #6 near #2 distance 5.01

> surface dust #1 size 8.35

> surface dust #3 size 8.35

> surface dust #5.1 size 8.35

> surface dust #5.2 size 8.35

> surface dust #5.3 size 8.35

> surface dust #5.4 size 8.35

> surface dust #5.5 size 8.35

> surface dust #5.6 size 8.35

> surface dust #5.7 size 8.35

> surface dust #5.8 size 8.35

> surface dust #5.9 size 8.35

> surface dust #5.10 size 8.35

> surface dust #6 size 8.35

> show #!12 models

> show #!13 models

> show #!14 models

> show #!15 models

> show #!16 models

> show #!18 models

> show #!17 models

> show #!19 models

> show #!20 models

> show #!21 models

> save ""/Users/upneet/Desktop/Narlilkar Lab/Manuscript_INO80_AutoInib/Figures
> /Figure 2/Version 2- Resubmission/0_80_ApovsADPBeF_Maps.cxs"" includeMaps
> true

——— End of log from Mon Dec 30 10:34:25 2024 ———

opened ChimeraX session  

Cell requested for row 0 is out of bounds for table with 31 rows! Resizing
table model.  

> hide #!1 models

> hide #!2 models

> hide #!3 models

> hide #!5 models

> hide #!6 models

> hide #!12 models

> hide #!13 models

> hide #!14 models

> hide #!15 models

> hide #!16 models

> hide #!17 models

> hide #!18 models

> hide #!19 models

> hide #!20 models

> hide #!21 models

> show #!4 models

> select #4/Q

5289 atoms, 5407 bonds, 3 pseudobonds, 660 residues, 2 models selected  

> show #!9 models

> select #4,9/Q

11430 atoms, 11673 bonds, 11 pseudobonds, 1418 residues, 4 models selected  

> ui tool show ""Color Actions""

> color sel fire brick

> select #4,9/Z

712 atoms, 723 bonds, 1 pseudobond, 100 residues, 3 models selected  

> color sel indian red

> select #4,9/R,S

9089 atoms, 9314 bonds, 4 pseudobonds, 1137 residues, 4 models selected  

> color sel medium sea green

> select #4,9/I,J

8481 atoms, 9512 bonds, 414 residues, 1 model selected  

> select #9/I,J

8481 atoms, 9512 bonds, 414 residues, 1 model selected  

> color sel light slate gray

> ui mousemode right select

Drag select of 5 residues, 14 shapes  

> select up

5904 atoms, 6622 bonds, 288 residues, 1 model selected  

> color sel light slate gray

> select #9/K

5092 atoms, 5206 bonds, 628 residues, 1 model selected  

> color sel medium blue

> select #9/L

2856 atoms, 2919 bonds, 1 pseudobond, 363 residues, 2 models selected  

> color sel khaki

> select #9/M

3454 atoms, 3531 bonds, 1 pseudobond, 433 residues, 2 models selected  

> color sel royal blue

> color sel deep sky blue

> select #9/O

287 atoms, 296 bonds, 34 residues, 1 model selected  

> color sel dark blue

> select clear

> hide #!9 models

> show #!7 models

> ui tool show ""Color Zone""

> color zone #7 near #4 distance 5.01

> color zone #7 near #4 distance 9

> color zone #7 near #4 distance 9.1

> color zone #7 near #4 distance 9.2

> color zone #7 near #4 distance 9.3

> color zone #7 near #4 distance 9.4

> color zone #7 near #4 distance 9.5

> color zone #7 near #4 distance 9.6

> color zone #7 near #4 distance 9.7

> color zone #7 near #4 distance 9.8

> color zone #7 near #4 distance 9.9

> color zone #7 near #4 distance 10

> color zone #7 near #4 distance 11

> color zone #7 near #4 distance 12

> color zone #7 near #4 distance 13

> color zone #7 near #4 distance 14

> color zone #7 near #4 distance 15

> color zone #7 near #4 distance 16

> color zone #7 near #4 distance 17

> color zone #7 near #4 distance 18

> color zone #7 near #4 distance 19

> color zone #7 near #4 distance 20

> color zone #7 near #4 distance 21

> color zone #7 near #4 distance 1

> color zone #7 near #4 distance 15

[Repeated 1 time(s)]

> volume #7 step 1

> volume #7 level 0.2222

> volume #7 level 0.2028

> volume #7 level 0.1861

> surface dust #7 size 8.35

> coulombic #!4

The following residues are missing heavy (non-hydrogen) atoms, which may
result in inaccurate electrostatics:  
y0_80_ADPBeF.pdb #4/G ILE 63  
y0_80_ADPBeF.pdb #4/G ILE 88  
y0_80_ADPBeF.pdb #4/Q LYS 707  
y0_80_ADPBeF.pdb #4/Q ARG 802  
y0_80_ADPBeF.pdb #4/Q ASN 804  
y0_80_ADPBeF.pdb #4/Q VAL 824  
y0_80_ADPBeF.pdb #4/Q ARG 863  
y0_80_ADPBeF.pdb #4/Q ARG 865  
y0_80_ADPBeF.pdb #4/Q ASP 896  
y0_80_ADPBeF.pdb #4/Q GLU 897  
y0_80_ADPBeF.pdb #4/Q LYS 947  
y0_80_ADPBeF.pdb #4/Q ARG 959  
y0_80_ADPBeF.pdb #4/Q ARG 1293  
y0_80_ADPBeF.pdb #4/Q LYS 1300  
y0_80_ADPBeF.pdb #4/Q ASP 1305  
y0_80_ADPBeF.pdb #4/Q ARG 1317  
y0_80_ADPBeF.pdb #4/Q LYS 1326  
y0_80_ADPBeF.pdb #4/Q MET 1327  
y0_80_ADPBeF.pdb #4/Q GLN 1403  
y0_80_ADPBeF.pdb #4/Q ARG 1407  
y0_80_ADPBeF.pdb #4/Q LEU 1423  
y0_80_ADPBeF.pdb #4/Q ILE 1428  
y0_80_ADPBeF.pdb #4/Q ARG 1431  
y0_80_ADPBeF.pdb #4/Q ARG 1433  
y0_80_ADPBeF.pdb #4/Q ARG 1435  
y0_80_ADPBeF.pdb #4/Q LYS 1437  
y0_80_ADPBeF.pdb #4/Q LYS 1439  
y0_80_ADPBeF.pdb #4/T LYS 161  
y0_80_ADPBeF.pdb #4/T THR 162  
y0_80_ADPBeF.pdb #4/T ILE 163  
y0_80_ADPBeF.pdb #4/U GLU 137  
y0_80_ADPBeF.pdb #4/U GLU 182  
y0_80_ADPBeF.pdb #4/W GLU 137  
y0_80_ADPBeF.pdb #4/Y GLU 137  

Using Amber 20 recommended default charges and atom types for standard
residues  
Hydrogen copy of y0_80_ADPBeF.pdb #/Q PRO 1289 H bonded to atom that should
not have hydrogens (copy of y0_80_ADPBeF.pdb #/Q PRO 1289 C)  

> save ""/Users/upneet/Desktop/Narlilkar Lab/Manuscript_INO80_AutoInib/Figures
> /Figure 2/Version 2- Resubmission/0_80_ApovsADPBeF_Maps.cxs"" includeMaps
> true

Cell requested for row 3 is out of bounds for table with 22 rows! Resizing
table model.  

> hide #!4 models

> save ""/Users/upneet/Desktop/Narlilkar Lab/Manuscript_INO80_AutoInib/Figures
> /Figure 2/Version 2- Resubmission/Sc_0N80_ADP.png"" width 3600 height 3121
> supersample 3 transparentBackground true

> hide #!7 models

> show #!8 models

> hide #!8 models

> show #!9 models

> show #!10 models

> show #!11 models

> show #!12 models

> show #!13 models

> hide #!12 models

> hide #!13 models

> ui tool show ""Fit in Map""

> fitmap #9 inMap #10

Fit molecule y0_80_Apo.pdb (#9) to map y0_80_Apo_A8-split.mrc (#10) using
57717 atoms  
average map value = 0.001464, steps = 336  
shifted from previous position = 10.2  
rotated from previous position = 11.2 degrees  
atoms outside contour = 40732, contour level = 0.000899  
  
Position of y0_80_Apo.pdb (#9) relative to y0_80_Apo_A8-split.mrc (#10)
coordinates:  
Matrix rotation and translation  
0.99996930 0.00773960 0.00121901 -0.89960346  
-0.00774083 0.99996953 0.00100630 2.88667355  
-0.00121118 -0.00101571 0.99999875 0.56591299  
Axis -0.12797580 0.15381035 -0.97977782  
Axis point 372.35967518 117.63351086 0.00000000  
Rotation angle (degrees) 0.45263969  
Shift along axis 0.00465875  
  

> fitmap #9 inMap #7

Fit molecule y0_80_Apo.pdb (#9) to map y0_80_ADPBeF_Core.mrc (#7) using 57717
atoms  
average map value = 0.2218, steps = 356  
shifted from previous position = 14.9  
rotated from previous position = 9.23 degrees  
atoms outside contour = 28944, contour level = 0.18614  
  
Position of y0_80_Apo.pdb (#9) relative to y0_80_ADPBeF_Core.mrc (#7)
coordinates:  
Matrix rotation and translation  
-0.94309943 0.33155029 0.02525599 343.62268043  
0.01465608 0.11733048 -0.99298477 400.56032429  
-0.33218769 -0.93611322 -0.11551354 502.14203310  
Axis 0.11822041 0.74302773 -0.65873647  
Axis point 181.59334510 0.00000000 400.47979006  
Rotation angle (degrees) 166.08206693  
Shift along axis 7.47137295  
  

> select add #10

2 models selected  
Drag select of 31 residues, 6 shapes, 10 y0_80_Apo_A8-split.mrc  

> ui mousemode right ""translate selected models""

> view matrix models
> #9,-0.9431,0.33155,0.025256,343.47,0.014656,0.11733,-0.99298,395.9,-0.33219,-0.93611,-0.11551,507.18,#10,-0.90265,0.42501,0.067688,307.78,-0.067158,0.01625,-0.99761,448.1,-0.4251,-0.90504,0.013875,489.25

> undo

> select add #9

57717 atoms, 59577 bonds, 15 pseudobonds, 6675 residues, 4 models selected  

> select subtract #9

2 models selected  

> view matrix models
> #10,-0.90265,0.42501,0.067688,305.68,-0.067158,0.01625,-0.99761,444.26,-0.4251,-0.90504,0.013875,492.99

> view matrix models
> #10,-0.90265,0.42501,0.067688,305.86,-0.067158,0.01625,-0.99761,442.74,-0.4251,-0.90504,0.013875,492.92

> select subtract #10

Nothing selected  

> color zone #10 near #9 distance 4.91

> color zone #10 near #9 distance 1

> color zone #10 near #9 distance 15

> color zone #10 near #9 distance 3

> color zone #10 near #9 distance 30

> select add #9

57717 atoms, 59577 bonds, 15 pseudobonds, 6675 residues, 2 models selected  

> select subtract #9

Nothing selected  

> select add #10

2 models selected  

> view matrix models
> #10,-0.90265,0.42501,0.067688,309.18,-0.067158,0.01625,-0.99761,438.01,-0.4251,-0.90504,0.013875,493.14

> color zone #10 near #9 distance 30

> volume #10 level 0.001061

> volume #10 level 0.001224

> volume #10 level 0.001477

> volume #10 level 0.001603

> surface dust #10 size 8.19

> color zone #11 near #9 distance 4.91

> color zone #11 near #9 distance 1

> color zone #11 near #9 distance 10

> select clear

> hide #!9 models

> volume #11 level 0.1719

> volume #11 level 0.1669

> volume #11 level 0.1644

> volume #11 level 0.157

> save ""/Users/upneet/Desktop/Narlilkar Lab/Manuscript_INO80_AutoInib/Figures
> /Figure 2/Version 2- Resubmission/Sc_0N80_Apo.png"" width 3600 height 3121
> supersample 3 transparentBackground true

> save ""/Users/upneet/Desktop/Narlilkar Lab/Manuscript_INO80_AutoInib/Figures
> /Figure 2/Version 2- Resubmission/0_80_ApovsADPBeF_Maps.cxs"" includeMaps
> true

——— End of log from Mon Dec 30 10:55:42 2024 ———

opened ChimeraX session  




OpenGL version: 4.1 Metal - 88
OpenGL renderer: Apple M3 Max
OpenGL vendor: Apple

Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: Mac15,9
      Model Number: Z1CM000M6LL/A
      Chip: Apple M3 Max
      Total Number of Cores: 16 (12 performance and 4 efficiency)
      Memory: 64 GB
      System Firmware Version: 10151.101.3
      OS Loader Version: 10151.101.3

Software:

    System Software Overview:

      System Version: macOS 14.4.1 (23E224)
      Kernel Version: Darwin 23.4.0
      Time since boot: 2 days, 23 hours, 34 minutes

Graphics/Displays:

    Apple M3 Max:

      Chipset Model: Apple M3 Max
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 40
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-in Liquid Retina XDR Display
          Resolution: 3456 x 2234 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal


Installed Packages:
    alabaster: 0.7.16
    appdirs: 1.4.4
    appnope: 0.1.4
    asttokens: 2.4.1
    Babel: 2.15.0
    beautifulsoup4: 4.12.3
    blockdiag: 3.0.0
    blosc2: 2.0.0
    build: 1.2.1
    certifi: 2023.11.17
    cftime: 1.6.4
    charset-normalizer: 3.3.2
    ChimeraX-AddCharge: 1.5.17
    ChimeraX-AddH: 2.2.6
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.5
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.12.7
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.57.1
    ChimeraX-AtomicLibrary: 14.0.6
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.4.6
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.12.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.7
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.4
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.6
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.8
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.3
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2.4
    ChimeraX-DiffPlot: 1.0
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.3
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-Label: 1.1.10
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.1.6
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.2
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.1.3
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.7.1
    ChimeraX-MedicalToolbar: 1.0.3
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.14.1
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.17
    ChimeraX-ModelPanel: 1.5
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.2
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.2
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.13.5
    ChimeraX-PDB: 2.7.5
    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: 1.1.1
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.4.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.2
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.2
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.0.15
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.11.2
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.16.5
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.2.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.5
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.39.1
    ChimeraX-uniprot: 2.3
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.3
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.4
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    contourpy: 1.2.1
    cxservices: 1.2.2
    cycler: 0.12.1
    Cython: 3.0.10
    debugpy: 1.8.1
    decorator: 5.1.1
    docutils: 0.20.1
    executing: 2.0.1
    filelock: 3.13.4
    fonttools: 4.53.0
    funcparserlib: 2.0.0a0
    glfw: 2.7.0
    grako: 3.16.5
    h5py: 3.11.0
    html2text: 2024.2.26
    idna: 3.7
    ihm: 1.0
    imagecodecs: 2024.1.1
    imagesize: 1.4.1
    ipykernel: 6.29.2
    ipython: 8.21.0
    ipywidgets: 8.1.3
    jedi: 0.19.1
    jinja2: 3.1.4
    jupyter-client: 8.6.0
    jupyter-core: 5.7.2
    jupyterlab-widgets: 3.0.11
    kiwisolver: 1.4.5
    line-profiler: 4.1.2
    lxml: 5.2.1
    lz4: 4.3.3
    MarkupSafe: 2.1.5
    matplotlib: 3.8.4
    matplotlib-inline: 0.1.7
    msgpack: 1.0.8
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.10.0
    numpy: 1.26.4
    openvr: 1.26.701
    packaging: 23.2
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pexpect: 4.9.0
    pillow: 10.3.0
    pip: 24.0
    pkginfo: 1.10.0
    platformdirs: 4.2.2
    prompt-toolkit: 3.0.47
    psutil: 5.9.8
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    pygments: 2.17.2
    pynmrstar: 3.3.4
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.3401
    pyparsing: 3.1.2
    pyproject-hooks: 1.1.0
    PyQt6-commercial: 6.6.1
    PyQt6-Qt6: 6.6.3
    PyQt6-sip: 13.6.0
    PyQt6-WebEngine-commercial: 6.6.0
    PyQt6-WebEngine-Qt6: 6.6.3
    python-dateutil: 2.9.0.post0
    pytz: 2024.1
    pyzmq: 26.0.3
    qtconsole: 5.5.1
    QtPy: 2.4.1
    RandomWords: 0.4.0
    requests: 2.31.0
    scipy: 1.13.0
    setuptools: 69.5.1
    setuptools-scm: 8.0.4
    sfftk-rw: 0.8.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.5
    sphinx: 7.2.6
    sphinx-autodoc-typehints: 2.0.1
    sphinxcontrib-applehelp: 1.0.8
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.6
    sphinxcontrib-htmlhelp: 2.0.5
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.7
    sphinxcontrib-serializinghtml: 1.1.10
    stack-data: 0.6.3
    superqt: 0.6.3
    tables: 3.8.0
    tcia-utils: 1.5.1
    tifffile: 2024.1.30
    tinyarray: 1.2.4
    tornado: 6.4.1
    traitlets: 5.14.2
    typing-extensions: 4.12.2
    tzdata: 2024.1
    urllib3: 2.2.1
    wcwidth: 0.2.13
    webcolors: 1.13
    wheel: 0.43.0
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.11
}}}
"	defect	new	normal		Unassigned