id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 16542 Crash on Mac waking from sleep chimerax-bug-report@… Tom Goddard "{{{ 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, 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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 [deleted to fit within ticket limits] > 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 closed normal Window Toolkit duplicate all ChimeraX