id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
16079	Crash on Mac waking from sleep	milos.cvetkovic@…	Tom Goddard	"{{{
The following bug report has been submitted:
Platform:        macOS-14.6.1-x86_64-i386-64bit
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 0x00007ff848dd8dc0 (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.map._map, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, chimerax.surface._surface, 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, psutil._psutil_osx, psutil._psutil_posix, 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, PIL._imagingmath (total: 120)


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     ""treatmentId"" : ""c47ab4cc-c9c3-4b5d-a87c-e2433ce02597"",
     ""experimentId"" : ""6639bc6ba73d460582162323"",
     ""deploymentId"" : 400000006
   },
   {
     ""treatmentId"" : ""45f4e2a5-551b-4bc2-a2dc-19c244dda8f8"",
     ""experimentId"" : ""6643969b3099cf28e049862f"",
     ""deploymentId"" : 400000007
   }
 ]
}
}
===== 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/cvetkom/Documents/chimera_sessions/20241004_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_Jacob_Mrc1_AF3_modelling.cxs

Opened hetero_ref_good_nucleosome.mrc as #233, grid size 128,128,128, pixel
3.27, shown at level 2.79, step 1, values float32  
Opened consensus_extended.mrc as #8, grid size 588,588,588, pixel 0.95, shown
at level 0.155, step 1, values float32  
Opened deepEMhanced_nucleosome__cryosparc_P17_J1207_map_sharp.mrc z flip as
#13, grid size 440,440,440, pixel 0.95, shown at level 0.02, step 1, values
float32  
Opened sharpened_replisome.mrc copy as #42, grid size 588,588,588, pixel 0.95,
shown at level 0.3, step 1, values float32  
Opened cryosparc_P17_J1328_map_sharp_zflip.mrc as #46, grid size 440,440,440,
pixel 0.95, shown at level 0.27, step 1, values float32  
Opened cryosparc_P17_J1293_003_volume_map.mrc as #47, grid size 588,588,588,
pixel 0.95, shown at level 0.274, step 1, values float32  
Opened J842_005_volume_map_EMReady.mrc as #50, grid size 588,588,588, pixel
0.95, shown at level 2.1, step 1, values float32  
Opened leading_strand_vol_3p2 as #12, grid size 636,840,859, pixel 0.95, shown
at level 0.183, step 1, values float32  
Opened lagging_strand_vol_3p3 as #14, grid size 636,840,859, pixel 0.95, shown
at level 0.183, step 1, values float32  
Opened cryosparc_P17_J819_005_volume_map_sharp.mrc as #20, grid size
588,588,588, pixel 0.95, shown at level 0.45, step 1, values float32  
Opened cryosparc_P17_J819_005_volume_map.mrc as #21, grid size 588,588,588,
pixel 0.95, shown at level 0.16, step 1, values float32  
Opened cryosparc_P17_J842_005_volume_map.mrc as #23, grid size 588,588,588,
pixel 0.95, shown at level 0.18, step 1, values float32  
Log from Fri Oct 4 13:17:26 2024UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open
> /Users/cvetkom/Documents/chimera_sessions/20240913_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_density_comparison_Extended_struct_Mrc1.cxs

Opened hetero_ref_good_nucleosome.mrc as #233, grid size 128,128,128, pixel
3.27, shown at level 2.79, step 1, values float32  
Opened consensus_extended.mrc as #8, grid size 588,588,588, pixel 0.95, shown
at level 0.155, step 1, values float32  
Opened deepEMhanced_nucleosome__cryosparc_P17_J1207_map_sharp.mrc z flip as
#13, grid size 440,440,440, pixel 0.95, shown at level 0.02, step 1, values
float32  
Opened sharpened_replisome.mrc copy as #42, grid size 588,588,588, pixel 0.95,
shown at level 0.3, step 1, values float32  
Opened cryosparc_P17_J1328_map_sharp_zflip.mrc as #46, grid size 440,440,440,
pixel 0.95, shown at level 0.27, step 1, values float32  
Opened cryosparc_P17_J1293_003_volume_map.mrc as #47, grid size 588,588,588,
pixel 0.95, shown at level 0.274, step 1, values float32  
Opened J842_005_volume_map_EMReady.mrc as #50, grid size 588,588,588, pixel
0.95, shown at level 2.1, step 1, values float32  
Opened bad_nucleosome as #52, grid size 588,588,588, pixel 0.95, shown at
level 0.32, step 1, values float32  
Opened volume sum as #53, grid size 636,840,859, pixel 0.95, shown at level
0.255, step 1, values float32  
Opened volume sum as #2, grid size 636,840,859, pixel 0.95, shown at level
0.183, step 1, values float32  
Opened volume sum 0 as #9.1, grid size 636,840,859, pixel 0.95, shown at level
0.31, step 1, values float32  
Opened volume sum 0 as #3.1, grid size 636,840,859, pixel 0.95, shown at level
0.183, step 1, values float32  
Opened volume sum 1 as #3.2, grid size 636,840,859, pixel 0.95, shown at level
0.183, step 1, values float32  
Opened volume sum 2 as #3.3, grid size 636,840,859, pixel 0.95, shown at level
0.183, step 1, values float32  
Opened volume sum 3 as #3.4, grid size 636,840,859, pixel 0.95, shown at level
0.183, step 1, values float32  
Opened volume sum 4 as #3.5, grid size 636,840,859, pixel 0.95, shown at level
0.183, step 1, values float32  
Opened volume sum 5 as #3.6, grid size 636,840,859, pixel 0.95, shown at level
0.183, step 1, values float32  
Opened volume sum 6 as #3.7, grid size 636,840,859, pixel 0.95, shown at level
0.183, step 1, values float32  
Opened volume sum 7 as #3.8, grid size 636,840,859, pixel 0.95, shown at level
2.78, step 1, values float32  
Opened volume sum 8 as #3.9, grid size 636,840,859, pixel 0.95, shown at level
2.78, step 1, values float32  
Opened volume sum 9 as #3.10, grid size 636,840,859, pixel 0.95, shown at
level 2.78, step 1, values float32  
Opened volume sum 10 as #3.11, grid size 636,840,859, pixel 0.95, shown at
level 2.78, step 1, values float32  
Opened volume sum 11 as #3.12, grid size 636,840,859, pixel 0.95, shown at
level 2.78, step 1, values float32  
Opened volume sum 12 as #3.13, grid size 636,840,859, pixel 0.95, shown at
level 2.78, step 1, values float32  
Opened volume sum 13 as #3.14, grid size 636,840,859, pixel 0.95, shown at
level 2.78, step 1, values float32  
Opened volume sum 14 as #3.15, grid size 636,840,859, pixel 0.95, shown at
level 2.78, step 1, values float32  
Opened volume sum 15 as #3.16, grid size 636,840,859, pixel 0.95, shown at
level 2.78, step 1, values float32  
Opened volume sum 16 as #3.17, grid size 636,840,859, pixel 0.95, shown at
level 2.78, step 1, values float32  
Opened volume sum 17 as #3.18, grid size 636,840,859, pixel 0.95, shown at
level 2.78, step 1, values float32  
Opened Tof1_lower_level as #7, grid size 636,840,859, pixel 0.95, shown at
level 0.183, step 1, values float32  
Opened volume sum 7 copy 1 as #11.2, grid size 636,840,859, pixel 0.95, shown
at level 0.183, step 1, values float32  
Opened leading_strand_vol_3p2 as #12, grid size 636,840,859, pixel 0.95, shown
at level 0.183, step 1, values float32  
Opened lagging_strand_vol_3p3 as #14, grid size 636,840,859, pixel 0.95, shown
at level 0.183, step 1, values float32  
Opened cryosparc_P17_J819_005_volume_map_sharp.mrc as #20, grid size
588,588,588, pixel 0.95, shown at level 0.45, step 1, values float32  
Opened cryosparc_P17_J819_005_volume_map.mrc as #21, grid size 588,588,588,
pixel 0.95, shown at level 0.16, step 1, values float32  
Opened cryosparc_P17_J842_005_volume_map.mrc as #23, grid size 588,588,588,
pixel 0.95, shown at level 0.18, step 1, values float32  
Log from Wed Sep 25 19:02:23 2024UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open
> /Users/cvetkom/Documents/chimera_sessions/20240913_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_density_comparison_Extended_struct_Mrc1.cxs

Opened hetero_ref_good_nucleosome.mrc as #233, grid size 128,128,128, pixel
3.27, shown at level 2.79, step 1, values float32  
Opened consensus_extended.mrc as #8, grid size 588,588,588, pixel 0.95, shown
at level 0.155, step 1, values float32  
Opened deepEMhanced_nucleosome__cryosparc_P17_J1207_map_sharp.mrc z flip as
#13, grid size 440,440,440, pixel 0.95, shown at level 0.02, step 1, values
float32  
Opened sharpened_replisome.mrc copy as #42, grid size 588,588,588, pixel 0.95,
shown at level 0.3, step 1, values float32  
Opened cryosparc_P17_J1328_map_sharp_zflip.mrc as #46, grid size 440,440,440,
pixel 0.95, shown at level 0.27, step 1, values float32  
Opened cryosparc_P17_J1293_003_volume_map.mrc as #47, grid size 588,588,588,
pixel 0.95, shown at level 0.274, step 1, values float32  
Opened J842_005_volume_map_EMReady.mrc as #50, grid size 588,588,588, pixel
0.95, shown at level 2.1, step 1, values float32  
Opened bad_nucleosome as #52, grid size 588,588,588, pixel 0.95, shown at
level 0.32, step 1, values float32  
Opened volume sum as #53, grid size 636,840,859, pixel 0.95, shown at level
0.255, step 1, values float32  
Opened volume sum as #2, grid size 636,840,859, pixel 0.95, shown at level
0.183, step 1, values float32  
Opened volume sum 0 as #9.1, grid size 636,840,859, pixel 0.95, shown at level
0.31, step 1, values float32  
Opened volume sum 0 as #3.1, grid size 636,840,859, pixel 0.95, shown at level
0.183, step 1, values float32  
Opened volume sum 1 as #3.2, grid size 636,840,859, pixel 0.95, shown at level
0.183, step 1, values float32  
Opened volume sum 2 as #3.3, grid size 636,840,859, pixel 0.95, shown at level
0.183, step 1, values float32  
Opened volume sum 3 as #3.4, grid size 636,840,859, pixel 0.95, shown at level
0.183, step 1, values float32  
Opened volume sum 4 as #3.5, grid size 636,840,859, pixel 0.95, shown at level
0.183, step 1, values float32  
Opened volume sum 5 as #3.6, grid size 636,840,859, pixel 0.95, shown at level
0.183, step 1, values float32  
Opened volume sum 6 as #3.7, grid size 636,840,859, pixel 0.95, shown at level
0.183, step 1, values float32  
Opened volume sum 7 as #3.8, grid size 636,840,859, pixel 0.95, shown at level
2.78, step 1, values float32  
Opened volume sum 8 as #3.9, grid size 636,840,859, pixel 0.95, shown at level
2.78, step 1, values float32  
Opened volume sum 9 as #3.10, grid size 636,840,859, pixel 0.95, shown at
level 2.78, step 1, values float32  
Opened volume sum 10 as #3.11, grid size 636,840,859, pixel 0.95, shown at
level 2.78, step 1, values float32  
Opened volume sum 11 as #3.12, grid size 636,840,859, pixel 0.95, shown at
level 2.78, step 1, values float32  
Opened volume sum 12 as #3.13, grid size 636,840,859, pixel 0.95, shown at
level 2.78, step 1, values float32  
Opened volume sum 13 as #3.14, grid size 636,840,859, pixel 0.95, shown at
level 2.78, step 1, values float32  
Opened volume sum 14 as #3.15, grid size 636,840,859, pixel 0.95, shown at
level 2.78, step 1, values float32  
Opened volume sum 15 as #3.16, grid size 636,840,859, pixel 0.95, shown at
level 2.78, step 1, values float32  
Opened volume sum 16 as #3.17, grid size 636,840,859, pixel 0.95, shown at
level 2.78, step 1, values float32  
Opened volume sum 17 as #3.18, grid size 636,840,859, pixel 0.95, shown at
level 2.78, step 1, values float32  
Opened Tof1_lower_level as #7, grid size 636,840,859, pixel 0.95, shown at
level 0.183, step 1, values float32  
Opened volume sum 7 copy 1 as #11.2, grid size 636,840,859, pixel 0.95, shown
at level 0.183, step 1, values float32  
Opened leading_strand_vol_3p2 as #12, grid size 636,840,859, pixel 0.95, shown
at level 0.183, step 1, values float32  
Opened lagging_strand_vol_3p3 as #14, grid size 636,840,859, pixel 0.95, shown
at level 0.183, step 1, values float32  
Opened cryosparc_P17_J819_005_volume_map_sharp.mrc as #20, grid size
588,588,588, pixel 0.95, shown at level 0.45, step 1, values float32  
Opened cryosparc_P17_J819_005_volume_map.mrc as #21, grid size 588,588,588,
pixel 0.95, shown at level 0.16, step 1, values float32  
Opened cryosparc_P17_J842_005_volume_map.mrc as #23, grid size 588,588,588,
pixel 0.95, shown at level 0.18, step 1, values float32  
Log from Tue Sep 24 13:00:23 2024UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open
> /Users/cvetkom/Documents/chimera_sessions/20240913_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_density_comparison_Extended_struct_Mrc1.cxs

Opened hetero_ref_good_nucleosome.mrc as #233, grid size 128,128,128, pixel
3.27, shown at level 2.79, step 1, values float32  
Opened consensus_extended.mrc as #8, grid size 588,588,588, pixel 0.95, shown
at level 0.155, step 1, values float32  
Opened deepEMhanced_nucleosome__cryosparc_P17_J1207_map_sharp.mrc z flip as
#13, grid size 440,440,440, pixel 0.95, shown at level 0.02, step 1, values
float32  
Opened sharpened_replisome.mrc copy as #42, grid size 588,588,588, pixel 0.95,
shown at level 0.3, step 1, values float32  
Opened cryosparc_P17_J1328_map_sharp_zflip.mrc as #46, grid size 440,440,440,
pixel 0.95, shown at level 0.27, step 1, values float32  
Opened cryosparc_P17_J1293_003_volume_map.mrc as #47, grid size 588,588,588,
pixel 0.95, shown at level 0.274, step 1, values float32  
Opened J842_005_volume_map_EMReady.mrc as #50, grid size 588,588,588, pixel
0.95, shown at level 2.1, step 1, values float32  
Opened bad_nucleosome as #52, grid size 588,588,588, pixel 0.95, shown at
level 0.32, step 1, values float32  
Opened volume sum as #53, grid size 636,840,859, pixel 0.95, shown at level
0.255, step 1, values float32  
Opened volume sum as #2, grid size 636,840,859, pixel 0.95, shown at level
0.183, step 1, values float32  
Opened volume sum 0 as #9.1, grid size 636,840,859, pixel 0.95, shown at level
0.31, step 1, values float32  
Opened volume sum 0 as #3.1, grid size 636,840,859, pixel 0.95, shown at level
0.183, step 1, values float32  
Opened volume sum 1 as #3.2, grid size 636,840,859, pixel 0.95, shown at level
0.183, step 1, values float32  
Opened volume sum 2 as #3.3, grid size 636,840,859, pixel 0.95, shown at level
0.183, step 1, values float32  
Opened volume sum 3 as #3.4, grid size 636,840,859, pixel 0.95, shown at level
0.183, step 1, values float32  
Opened volume sum 4 as #3.5, grid size 636,840,859, pixel 0.95, shown at level
0.183, step 1, values float32  
Opened volume sum 5 as #3.6, grid size 636,840,859, pixel 0.95, shown at level
0.183, step 1, values float32  
Opened volume sum 6 as #3.7, grid size 636,840,859, pixel 0.95, shown at level
0.183, step 1, values float32  
Opened volume sum 7 as #3.8, grid size 636,840,859, pixel 0.95, shown at level
2.78, step 1, values float32  
Opened volume sum 8 as #3.9, grid size 636,840,859, pixel 0.95, shown at level
2.78, step 1, values float32  
Opened volume sum 9 as #3.10, grid size 636,840,859, pixel 0.95, shown at
level 2.78, step 1, values float32  
Opened volume sum 10 as #3.11, grid size 636,840,859, pixel 0.95, shown at
level 2.78, step 1, values float32  
Opened volume sum 11 as #3.12, grid size 636,840,859, pixel 0.95, shown at
level 2.78, step 1, values float32  
Opened volume sum 12 as #3.13, grid size 636,840,859, pixel 0.95, shown at
level 2.78, step 1, values float32  
Opened volume sum 13 as #3.14, grid size 636,840,859, pixel 0.95, shown at
level 2.78, step 1, values float32  
Opened volume sum 14 as #3.15, grid size 636,840,859, pixel 0.95, shown at
level 2.78, step 1, values float32  
Opened volume sum 15 as #3.16, grid size 636,840,859, pixel 0.95, shown at
level 2.78, step 1, values float32  
Opened volume sum 16 as #3.17, grid size 636,840,859, pixel 0.95, shown at
level 2.78, step 1, values float32  
Opened volume sum 17 as #3.18, grid size 636,840,859, pixel 0.95, shown at
level 2.78, step 1, values float32  
Opened Tof1_lower_level as #7, grid size 636,840,859, pixel 0.95, shown at
level 0.183, step 1, values float32  
Opened volume sum 7 copy 1 as #11.2, grid size 636,840,859, pixel 0.95, shown
at level 0.183, step 1, values float32  
Opened leading_strand_vol_3p2 as #12, grid size 636,840,859, pixel 0.95, shown
at level 0.183, step 1, values float32  
Opened lagging_strand_vol_3p3 as #14, grid size 636,840,859, pixel 0.95, shown
at level 0.183, step 1, values float32  
Opened cryosparc_P17_J819_005_volume_map_sharp.mrc as #20, grid size
588,588,588, pixel 0.95, shown at level 0.45, step 1, values float32  
Opened cryosparc_P17_J819_005_volume_map.mrc as #21, grid size 588,588,588,
pixel 0.95, shown at level 0.16, step 1, values float32  
Opened cryosparc_P17_J842_005_volume_map.mrc as #23, grid size 588,588,588,
pixel 0.95, shown at level 0.18, step 1, values float32  
Log from Mon Sep 16 15:36:42 2024UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open
> /Users/cvetkom/Documents/chimera_sessions/20240908_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_density_comparison_Extended_struct.cxs

Opened hetero_ref_good_nucleosome.mrc as #233, grid size 128,128,128, pixel
3.27, shown at level 2.79, step 1, values float32  
Opened consensus_extended.mrc as #8, grid size 588,588,588, pixel 0.95, shown
at level 0.155, step 1, values float32  
Opened deepEMhanced_nucleosome__cryosparc_P17_J1207_map_sharp.mrc z flip as
#13, grid size 440,440,440, pixel 0.95, shown at level 0.02, step 1, values
float32  
Opened sharpened_replisome.mrc copy as #42, grid size 588,588,588, pixel 0.95,
shown at level 0.3, step 1, values float32  
Opened cryosparc_P17_J1328_map_sharp_zflip.mrc as #46, grid size 440,440,440,
pixel 0.95, shown at level 0.27, step 1, values float32  
Opened cryosparc_P17_J1293_003_volume_map.mrc as #47, grid size 588,588,588,
pixel 0.95, shown at level 0.274, step 1, values float32  
Opened J842_005_volume_map_EMReady.mrc as #50, grid size 588,588,588, pixel
0.95, shown at level 2.1, step 1, values float32  
Opened bad_nucleosome as #52, grid size 588,588,588, pixel 0.95, shown at
level 0.32, step 1, values float32  
Opened volume sum as #53, grid size 636,840,859, pixel 0.95, shown at level
0.255, step 1, values float32  
Opened volume sum as #2, grid size 636,840,859, pixel 0.95, shown at level
0.183, step 1, values float32  
Opened volume sum 0 as #9.1, grid size 636,840,859, pixel 0.95, shown at level
0.31, step 1, values float32  
Opened volume sum 0 as #3.1, grid size 636,840,859, pixel 0.95, shown at level
0.183, step 1, values float32  
Opened volume sum 1 as #3.2, grid size 636,840,859, pixel 0.95, shown at level
0.183, step 1, values float32  
Opened volume sum 2 as #3.3, grid size 636,840,859, pixel 0.95, shown at level
0.183, step 1, values float32  
Opened volume sum 3 as #3.4, grid size 636,840,859, pixel 0.95, shown at level
0.183, step 1, values float32  
Opened volume sum 4 as #3.5, grid size 636,840,859, pixel 0.95, shown at level
0.183, step 1, values float32  
Opened volume sum 5 as #3.6, grid size 636,840,859, pixel 0.95, shown at level
0.183, step 1, values float32  
Opened volume sum 6 as #3.7, grid size 636,840,859, pixel 0.95, shown at level
0.183, step 1, values float32  
Opened volume sum 7 as #3.8, grid size 636,840,859, pixel 0.95, shown at level
2.78, step 1, values float32  
Opened volume sum 8 as #3.9, grid size 636,840,859, pixel 0.95, shown at level
2.78, step 1, values float32  
Opened volume sum 9 as #3.10, grid size 636,840,859, pixel 0.95, shown at
level 2.78, step 1, values float32  
Opened volume sum 10 as #3.11, grid size 636,840,859, pixel 0.95, shown at
level 2.78, step 1, values float32  
Opened volume sum 11 as #3.12, grid size 636,840,859, pixel 0.95, shown at
level 2.78, step 1, values float32  
Opened volume sum 12 as #3.13, grid size 636,840,859, pixel 0.95, shown at
level 2.78, step 1, values float32  
Opened volume sum 13 as #3.14, grid size 636,840,859, pixel 0.95, shown at
level 2.78, step 1, values float32  
Opened volume sum 14 as #3.15, grid size 636,840,859, pixel 0.95, shown at
level 2.78, step 1, values float32  
Opened volume sum 15 as #3.16, grid size 636,840,859, pixel 0.95, shown at
level 2.78, step 1, values float32  
Opened volume sum 16 as #3.17, grid size 636,840,859, pixel 0.95, shown at
level 2.78, step 1, values float32  
Opened volume sum 17 as #3.18, grid size 636,840,859, pixel 0.95, shown at
level 2.78, step 1, values float32  
Opened Tof1_lower_level as #7, grid size 636,840,859, pixel 0.95, shown at
level 0.183, step 1, values float32  
Opened volume sum 7 copy 1 as #11.2, grid size 636,840,859, pixel 0.95, shown
at level 0.183, step 1, values float32  
Opened leading_strand_vol_3p2 as #12, grid size 636,840,859, pixel 0.95, shown
at level 0.183, step 1, values float32  
Opened lagging_strand_vol_3p3 as #14, grid size 636,840,859, pixel 0.95, shown
at level 0.183, step 1, values float32  
Log from Wed Sep 11 12:56:29 2024UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open
> /Users/cvetkom/Documents/chimera_sessions/20240908_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_density_comparison_Extended_struct.cxs

Opened hetero_ref_good_nucleosome.mrc as #233, grid size 128,128,128, pixel
3.27, shown at level 2.79, step 1, values float32  
Opened consensus_extended.mrc as #8, grid size 588,588,588, pixel 0.95, shown
at level 0.155, step 1, values float32  
Opened deepEMhanced_nucleosome__cryosparc_P17_J1207_map_sharp.mrc z flip as
#13, grid size 440,440,440, pixel 0.95, shown at level 0.02, step 1, values
float32  
Opened sharpened_replisome.mrc copy as #42, grid size 588,588,588, pixel 0.95,
shown at level 0.3, step 1, values float32  
Opened cryosparc_P17_J1328_map_sharp_zflip.mrc as #46, grid size 440,440,440,
pixel 0.95, shown at level 0.27, step 1, values float32  
Opened cryosparc_P17_J1293_003_volume_map.mrc as #47, grid size 588,588,588,
pixel 0.95, shown at level 0.274, step 1, values float32  
Opened J842_005_volume_map_EMReady.mrc as #50, grid size 588,588,588, pixel
0.95, shown at level 2.1, step 1, values float32  
Opened bad_nucleosome as #52, grid size 588,588,588, pixel 0.95, shown at
level 0.32, step 1, values float32  
Opened volume sum as #53, grid size 636,840,859, pixel 0.95, shown at level
0.255, step 1, values float32  
Opened volume sum as #2, grid size 636,840,859, pixel 0.95, shown at level
0.183, step 1, values float32  

[deleted to fit within ticket limits]

> color sel hot pink

> select #31/B #32/B #33/B

7806 atoms, 7926 bonds, 1002 residues, 3 models selected  

> color sel yellow

> select #31/C #32/C #33/C

23784 atoms, 24171 bonds, 3051 residues, 3 models selected  

> color sel orange

> select #31/D #32/D #33/D

15693 atoms, 15963 bonds, 1950 residues, 3 models selected  

> color sel light gray

> select #31/E #32/E #33/E

29835 atoms, 30399 bonds, 3714 residues, 3 models selected  

> ui tool show ""Color Actions""

> color sel slate blue

> select #31/F #32/F #33/F

14724 atoms, 14886 bonds, 1821 residues, 3 models selected  

> color sel red

> select add #31

47368 atoms, 48086 bonds, 5928 residues, 3 models selected  

> select add #32

80012 atoms, 81286 bonds, 10035 residues, 3 models selected  

> select subtract #31

42460 atoms, 43124 bonds, 5321 residues, 2 models selected  

> select subtract #32

4908 atoms, 4962 bonds, 607 residues, 1 model selected  

> select add #33

37552 atoms, 38162 bonds, 4714 residues, 1 model selected  

> select subtract #33

Nothing selected  

> select clear

> matchmaker #32/A to #10/2 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 extended_structure, chain 2 (#10) with
fold_2024_09_23_mcm256_c_cdc45_tof1_mrc1_321_927_model_1.cif, chain A (#32),
sequence alignment score = 3505.1  
RMSD between 253 pruned atom pairs is 0.693 angstroms; (across all 293 pairs:
1.550)  


> matchmaker #33/A to #10/2 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 extended_structure, chain 2 (#10) with
fold_2024_09_23_mcm256_c_cdc45_tof1_mrc1_321_927_model_2.cif, chain A (#33),
sequence alignment score = 3502.1  
RMSD between 258 pruned atom pairs is 0.659 angstroms; (across all 293 pairs:
1.500)  


> lighting simple

> hide #32 models

> hide #33 models

> show #33 models

> hide #33 models

> show #33 models

> hide #33 models

> show #33 models

> hide #33 models

> show #32 models

> hide #32 models

> show #32 models

> hide #31 models

> show #31 models

> hide #31 models

> show #31 models

> hide #31 models

> show #31 models

> hide #32 models

> show #32 models

> hide #32 models

> show #32 models

> hide #32 models

> show #32 models

> hide #32 models

> show #32 models

> hide #32 models

> show #32 models

> hide #32 models

> hide #!10 models

> show #!50 models

> hide #!50 models

> show #!23 models

> hide #!23 models

> show #!23 models

> hide #!23 models

> show #!23 models

> hide #!23 models

> show #!23 models

> hide #!23 models

> show #!23 models

> hide #!23 models

> show #!23 models

> hide #!23 models

> show #!23 models

> hide #!23 models

> show #!23 models

> hide #!23 models

> show #!23 models

> hide #!23 models

> show #!23 models

> hide #!23 models

> show #!23 models

> hide #!23 models

> show #!23 models

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

> save
> /Users/cvetkom/Documents/chimera_sessions/20240913_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_density_comparison_Extended_struct_Mrc1.cxs

\u2014\u2014\u2014 End of log from Tue Sep 24 13:00:23 2024 \u2014\u2014\u2014

opened ChimeraX session  

> lighting simple

> open /Users/cvetkom/Documents/pdb/4c95_Ctf4_Sld5.pdb

4c95_Ctf4_Sld5.pdb title:  
Crystal structure of the carboxy-terminal domain of yeast CTF4 bound to SLD5
[more info...]  

Chain information for 4c95_Ctf4_Sld5.pdb #34  
---  
Chain | Description  
A B C | No description available  
D E | No description available  

24 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  

> select add #34

9660 atoms, 9722 bonds, 4 pseudobonds, 1360 residues, 2 models selected  

> hide sel atoms

> show sel cartoons

> select subtract #34

Nothing selected  

> select #34/A

3494 atoms, 3493 bonds, 2 pseudobonds, 510 residues, 2 models selected  

> select #34/B

3531 atoms, 3550 bonds, 1 pseudobond, 498 residues, 2 models selected  

> select #34/C

2427 atoms, 2473 bonds, 1 pseudobond, 326 residues, 2 models selected  

> select #34/D

104 atoms, 103 bonds, 13 residues, 1 model selected  

> select #34/E

104 atoms, 103 bonds, 13 residues, 1 model selected  

> select #34/D,E

208 atoms, 206 bonds, 26 residues, 1 model selected  

> color sel red

> hide #31 models

> open
> /Users/cvetkom/Documents/AlphaFold/fold_2024_09_23_3c_ctf4_mrc1_1081_1096/fold_2024_09_23_3c_ctf4_mrc1_1081_1096_model_0.cif

Chain information for fold_2024_09_23_3c_ctf4_mrc1_1081_1096_model_0.cif #35  
---  
Chain | Description  
A B C | .  
D | .  


> show #!10 models

> hide #!23 models

> select clear

> ui tool show Matchmaker

> matchmaker #34/B to #10/S 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 extended_structure, chain S (#10) with 4c95_Ctf4_Sld5.pdb, chain B
(#34), sequence alignment score = 2232.7  
RMSD between 391 pruned atom pairs is 0.878 angstroms; (across all 424 pairs:
1.248)  


> matchmaker #35/A to #10/S 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 extended_structure, chain S (#10) with
fold_2024_09_23_3c_ctf4_mrc1_1081_1096_model_0.cif, chain A (#35), sequence
alignment score = 2301.6  
RMSD between 411 pruned atom pairs is 0.645 angstroms; (across all 425 pairs:
0.817)  


> hide #!10 models

> show #!10 models

> show #!23 models

> hide #!23 models

> show #!42 models

> color #42 #b2b2ffeb models

> color #42 #b2b2ffff models

> color #42 #b2b2ffb7 models

> color #42 #b2b2ff95 models

> color #42 #b2b2ff84 models

> hide #!10 models

> lighting soft

> lighting full

> lighting simple

> ui tool show ""Side View""

> hide #!42 models

> show #!42 models

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

> hide #35 models

> show #35 models

> hide #!42 models

> show #!42 models

> hide #35 models

> show #35 models

> select #35/D

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

> color sel orange

> color sel orange red

> color sel orange

> select clear

> hide #!34 models

> show #!34 models

> ui tool show ""Fit in Map""

> hide #!42 models

> show #!42 models

> fitmap #34 inMap #42

Fit molecule 4c95_Ctf4_Sld5.pdb (#34) to map sharpened_replisome.mrc copy
(#42) using 9660 atoms  
average map value = 0.381, steps = 128  
shifted from previous position = 2.63  
rotated from previous position = 6.17 degrees  
atoms outside contour = 4354, contour level = 0.3  

Position of 4c95_Ctf4_Sld5.pdb (#34) relative to sharpened_replisome.mrc copy
(#42) coordinates:  
Matrix rotation and translation  
0.28572805 -0.31647925 0.90454429 338.42345045  
-0.43402411 -0.88427381 -0.17228725 294.11719747  
0.85439016 -0.34336673 -0.39002146 373.35631167  
Axis -0.80114939 0.23486712 -0.55045172  
Axis point 0.00000000 201.64420355 57.39058667  
Rotation angle (degrees) 173.87077288  
Shift along axis -407.56390486  


> fitmap #35 inMap #42

Fit molecule fold_2024_09_23_3c_ctf4_mrc1_1081_1096_model_0.cif (#35) to map
sharpened_replisome.mrc copy (#42) using 11336 atoms  
average map value = 0.4111, steps = 68  
shifted from previous position = 0.628  
rotated from previous position = 1.83 degrees  
atoms outside contour = 4371, contour level = 0.3  

Position of fold_2024_09_23_3c_ctf4_mrc1_1081_1096_model_0.cif (#35) relative
to sharpened_replisome.mrc copy (#42) coordinates:  
Matrix rotation and translation  
-0.98706242 -0.07882972 0.13961966 285.86123137  
0.08488406 0.48183004 0.87214363 299.11678968  
-0.13602378 0.87271169 -0.46890494 372.10103280  
Axis 0.00177188 0.85978425 0.51065438  
Axis point 149.35362784 0.00000000 83.84935178  
Rotation angle (degrees) 170.77580491  
Shift along axis 447.69744149  


> hide #35 models

> hide #!42 models

> show #!42 models

> hide #!34 models

> show #!50 models

> hide #!50 models

> show #!50 models

> hide #!50 models

> show #!50 models

> hide #!50 models

> hide #!42 models

> show #!42 models

> color #42 #b2b2ffff models

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

> ui tool show ""Side View""

> show #!233 models

> hide #!233 models

> show #!233 models

> hide #!233 models

> show #!47 models

> show #!46 models

> hide #!47 models

> show #!47 models

> hide #!47 models

> hide #!42 models

> hide #!46 models

> show #!43 models

> hide #!43 models

> show #!34 models

> show #33 models

> hide #33 models

> show #35 models

> hide #!34 models

> show #!34 models

> hide #35 models

> show #35 models

> show #!2 models

> hide #!2 models

> save
> /Users/cvetkom/Documents/chimera_sessions/20240913_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_density_comparison_Extended_struct_Mrc1.cxs

\u2014\u2014\u2014 End of log from Wed Sep 25 19:02:23 2024 \u2014\u2014\u2014

opened ChimeraX session  

> hide #!34 models

> hide #35 models

> show #35 models

> hide #35 models

> close #2-3

> close #7

> close #11

> close #9

> show #!50 models

> hide #!50 models

> show #!53 models

> close #53

> show #!52 models

> close #52

> show #!16 models

> hide #!16 models

> show #!17 models

> hide #!17 models

> show #!18 models

> hide #!18 models

> show #!19 models

> hide #!19 models

> show #!10 models

> save
> /Users/cvetkom/Documents/chimera_sessions/20241004_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_Jacob_Mrc1_AF3_modelling.cxs

\u2014\u2014\u2014 End of log from Fri Oct 4 13:17:26 2024 \u2014\u2014\u2014

opened ChimeraX session  

> hide #!10 models

> open
> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J819_005_volume_map_EMready.mrc

Opened cryosparc_P17_J819_005_volume_map_EMready.mrc as #2, grid size
588,588,588, pixel 0.95, shown at level 0.0383, step 4, values float32  

> volume #2 step 1

> volume #2 level 0.9283

> volume #2 level 1.647

> ui tool show ""Side View""

> hide #!2 models

> show #!21 models

> show #!2 models

> select add #2

2 models selected  

> lighting simple

> ui mousemode right ""rotate selected models""

> view matrix models
> #2,0.21372,0.65189,-0.72758,228.01,-0.15215,0.75791,0.63437,-52.313,0.96497,-0.024879,0.26116,-76.828

> view matrix models
> #2,-0.22904,0.42092,-0.8777,455.06,-0.48229,0.73415,0.47793,87.401,0.84554,0.53277,0.034859,-139.12

> view matrix models
> #2,-0.30253,0.24312,-0.92161,536.06,-0.68897,0.61238,0.38771,202.38,0.65863,0.75225,-0.017761,-133.46

> view matrix models
> #2,-0.17917,0.019523,-0.98362,578.75,-0.64564,0.75206,0.13253,216.8,0.74233,0.65881,-0.12214,-104.65

> view matrix models
> #2,-0.39996,0.21624,-0.89066,563.08,-0.18128,0.93391,0.30815,-9.3049,0.89843,0.28471,-0.33432,8.6733

> view matrix models
> #2,-0.45252,0.485,-0.74833,467.43,0.38691,0.86285,0.32525,-154.48,0.80345,-0.14235,-0.57811,215.56

> view matrix models
> #2,-0.19899,0.25008,-0.94756,511.54,0.14679,0.96359,0.22349,-88.484,0.96895,-0.094621,-0.22845,66.354

> view matrix models
> #2,-0.40366,0.20697,-0.89119,566.81,-0.0090314,0.97313,0.23009,-48.812,0.91486,0.10093,-0.39095,69.189

> view matrix models
> #2,-0.42359,0.12332,-0.89742,597.11,0.0008642,0.99074,0.13574,-32.363,0.90585,0.056721,-0.41978,91.291

> ui mousemode right ""translate selected models""

> view matrix models
> #2,-0.42359,0.12332,-0.89742,572.5,0.0008642,0.99074,0.13574,-244.94,0.90585,0.056721,-0.41978,20.155

> ui mousemode right ""rotate selected models""

> view matrix models
> #2,-0.42268,0.11844,-0.8985,573.87,0.0011522,0.99149,0.13015,-243.8,0.90628,0.053978,-0.41923,20.651

> view matrix models
> #2,-0.54332,-0.16268,-0.82361,666.33,-0.42868,0.89727,0.10557,-90.185,0.72182,0.41043,-0.55725,9.6598

> view matrix models
> #2,-0.59204,-0.092954,-0.80053,654.96,-0.41205,0.88859,0.20156,-117.01,0.6926,0.44919,-0.56439,9.0402

> ui mousemode right ""translate selected models""

> view matrix models
> #2,-0.59204,-0.092954,-0.80053,657.43,-0.41205,0.88859,0.20156,-126.64,0.6926,0.44919,-0.56439,12.296

> view matrix models
> #2,-0.59204,-0.092954,-0.80053,663.52,-0.41205,0.88859,0.20156,-124.44,0.6926,0.44919,-0.56439,2.3033

> ui mousemode right zoom

> ui tool show ""Fit in Map""

> fitmap #2 inMap #21

Fit map cryosparc_P17_J819_005_volume_map_EMready.mrc in map
cryosparc_P17_J819_005_volume_map.mrc using 740829 points  
correlation = 0.938, correlation about mean = 0.7691, overlap = 1.576e+06  
steps = 160, shift = 3.85, angle = 10.8 degrees  

Position of cryosparc_P17_J819_005_volume_map_EMready.mrc (#2) relative to
cryosparc_P17_J819_005_volume_map.mrc (#21) coordinates:  
Matrix rotation and translation  
0.99999999 0.00005310 -0.00009395 0.01216343  
-0.00005312 0.99999998 -0.00020453 0.08100750  
0.00009394 0.00020453 0.99999998 -0.07859161  
Axis 0.88443714 -0.40622568 -0.22967726  
Axis point 0.00000000 388.90207101 387.88928499  
Rotation angle (degrees) 0.01324986  
Shift along axis -0.00409883  


> select subtract #2

Nothing selected  

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!20 models

> hide #!21 models

> show #!21 models

> hide #!21 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> hide #!20 models

> show #!42 models

> open
> /Users/cvetkom/Documents/cryoSPARC/cryosparc_P17_J842_005_volume_map_sharp.mrc

Opened cryosparc_P17_J842_005_volume_map_sharp.mrc as #3, grid size
588,588,588, pixel 0.95, shown at level 0.15, step 4, values float32  

> volume #3 step 1

> volume #3 level 0.2175

> volume #3 level 0.4032

> select add #3

3 models selected  

> ui mousemode right ""rotate selected models""

> view matrix models
> #3,0.96087,0.15628,0.2287,-100.29,-0.086083,0.95323,-0.28971,123.99,-0.26328,0.25869,0.92939,24.765

> view matrix models
> #3,0.94784,0.022072,0.31799,-87.222,0.026112,0.98887,-0.14647,39.853,-0.31769,0.14713,0.93671,67.954

> ui mousemode right ""translate selected models""

> view matrix models
> #3,0.94784,0.022072,0.31799,-188.13,0.026112,0.98887,-0.14647,-129.94,-0.31769,0.14713,0.93671,62.858

> view matrix models
> #3,0.94784,0.022072,0.31799,-118.63,0.026112,0.98887,-0.14647,-168.34,-0.31769,0.14713,0.93671,-44.135

> ui mousemode right ""rotate selected models""

> view matrix models
> #3,0.79338,0.092061,0.60172,-179.94,0.1255,0.94252,-0.30967,-134.37,-0.59565,0.32121,0.73623,46.771

> ui mousemode right ""translate selected models""

> view matrix models
> #3,0.79338,0.092061,0.60172,-166.19,0.1255,0.94252,-0.30967,-142.23,-0.59565,0.32121,0.73623,35.37

> view matrix models
> #3,0.79338,0.092061,0.60172,-165.26,0.1255,0.94252,-0.30967,-141.13,-0.59565,0.32121,0.73623,35.671

> select subtract #3

Nothing selected  

> fitmap #3 inMap #42

Fit map cryosparc_P17_J842_005_volume_map_sharp.mrc in map
sharpened_replisome.mrc copy using 329084 points  
correlation = 1, correlation about mean = 0.9999, overlap = 1.568e+05  
steps = 236, shift = 0.4, angle = 16.9 degrees  

Position of cryosparc_P17_J842_005_volume_map_sharp.mrc (#3) relative to
sharpened_replisome.mrc copy (#42) coordinates:  
Matrix rotation and translation  
1.00000000 -0.00001351 0.00004557 -0.02152036  
0.00001352 1.00000000 -0.00003397 0.01017840  
-0.00004557 0.00003397 1.00000000 0.00711885  
Axis 0.58150158 0.77996616 0.23131947  
Axis point 171.08172050 0.00000000 434.91154679  
Rotation angle (degrees) 0.00334730  
Shift along axis -0.00292859  


> hide #!42 models

> show #!42 models

> volume #3 level 0.3

> hide #!42 models

> show #!42 models

> hide #!42 models

> show #!42 models

> ui mousemode right zoom

> ui tool show ""Hide Dust""

> surface undust #42

> fitmap #3 inMap #42

Fit map cryosparc_P17_J842_005_volume_map_sharp.mrc in map
sharpened_replisome.mrc copy using 586182 points  
correlation = 1, correlation about mean = 0.9999, overlap = 1.874e+05  
steps = 28, shift = 0.0238, angle = 0.00733 degrees  

Position of cryosparc_P17_J842_005_volume_map_sharp.mrc (#3) relative to
sharpened_replisome.mrc copy (#42) coordinates:  
Matrix rotation and translation  
1.00000000 0.00000906 -0.00005933 0.02130757  
-0.00000906 1.00000000 0.00003559 -0.01782195  
0.00005933 -0.00003559 1.00000000 0.00029158  
Axis -0.51008916 -0.85026779 -0.12982191  
Axis point -14.19118466 0.00000000 395.65343560  
Rotation angle (degrees) 0.00399795  
Shift along axis 0.00424682  


> hide #!42 models

> show #!42 models

> hide #!42 models

> show #!42 models

> hide #!42 models

> show #!42 models

> hide #!42 models

> show #!42 models

> hide #!42 models

> open
> /Users/cvetkom/Documents/cryoSPARC/Jacob_cryosparc_P5_J117_006_volume_map.mrc

Opened Jacob_cryosparc_P5_J117_006_volume_map.mrc as #7, grid size
480,480,480, pixel 0.95, shown at level 0.152, step 2, values float32  

> open
> /Users/cvetkom/Documents/cryoSPARC/Jacob_cryosparc_P5_J117_006_volume_map_sharp.mrc

Opened Jacob_cryosparc_P5_J117_006_volume_map_sharp.mrc as #9, grid size
480,480,480, pixel 0.95, shown at level 0.28, step 2, values float32  

> open
> /Users/cvetkom/Documents/cryoSPARC/Jacob_cryosparc_P5_J117_006_volume_map_EMReady.mrc

Opened Jacob_cryosparc_P5_J117_006_volume_map_EMReady.mrc as #11, grid size
480,480,480, pixel 0.95, shown at level 0.569, step 2, values float32  

> volume #11 level 2.423

> volume #9 level 0.9574

> volume #11 step 1

> volume #9 step 1

> volume #7 step 1

> volume #7 level 0.2399

> select add #7

2 models selected  

> select add #9

4 models selected  

> select add #11

6 models selected  

> ui mousemode right ""rotate selected models""

> view matrix models
> #7,-0.31536,0.44395,0.83873,0.5068,-0.77807,0.38503,-0.49635,422.96,-0.54329,-0.80911,0.224,478.2,#9,-0.31536,0.44395,0.83873,0.5068,-0.77807,0.38503,-0.49635,422.96,-0.54329,-0.80911,0.224,478.2,#11,-0.31536,0.44395,0.83873,0.5068,-0.77807,0.38503,-0.49635,422.96,-0.54329,-0.80911,0.224,478.2

> view matrix models
> #7,-0.73321,-0.54683,0.4042,411.11,0.31221,-0.79877,-0.51428,443.38,0.60409,-0.25088,0.7564,-22.885,#9,-0.73321,-0.54683,0.4042,411.11,0.31221,-0.79877,-0.51428,443.38,0.60409,-0.25088,0.7564,-22.885,#11,-0.73321,-0.54683,0.4042,411.11,0.31221,-0.79877,-0.51428,443.38,0.60409,-0.25088,0.7564,-22.885

> view matrix models
> #7,-0.27775,-0.26716,0.92276,128.06,0.32065,-0.93125,-0.1731,391.13,0.90556,0.2478,0.34432,-103.14,#9,-0.27775,-0.26716,0.92276,128.06,0.32065,-0.93125,-0.1731,391.13,0.90556,0.2478,0.34432,-103.14,#11,-0.27775,-0.26716,0.92276,128.06,0.32065,-0.93125,-0.1731,391.13,0.90556,0.2478,0.34432,-103.14

> view matrix models
> #7,0.8345,-0.016866,0.55076,-87.575,-0.27678,-0.87711,0.39251,380.66,0.47645,-0.47999,-0.73662,402.79,#9,0.8345,-0.016866,0.55076,-87.575,-0.27678,-0.87711,0.39251,380.66,0.47645,-0.47999,-0.73662,402.79,#11,0.8345,-0.016866,0.55076,-87.575,-0.27678,-0.87711,0.39251,380.66,0.47645,-0.47999,-0.73662,402.79

> view matrix models
> #7,0.93667,-0.11461,-0.33094,116.1,-0.073314,-0.98817,0.13471,419.63,-0.34246,-0.10191,-0.93399,548.21,#9,0.93667,-0.11461,-0.33094,116.1,-0.073314,-0.98817,0.13471,419.63,-0.34246,-0.10191,-0.93399,548.21,#11,0.93667,-0.11461,-0.33094,116.1,-0.073314,-0.98817,0.13471,419.63,-0.34246,-0.10191,-0.93399,548.21

> view matrix models
> #7,0.73012,-0.060917,-0.6806,231.63,-0.11744,-0.99238,-0.03716,470.33,-0.67315,0.10706,-0.73172,529.05,#9,0.73012,-0.060917,-0.6806,231.63,-0.11744,-0.99238,-0.03716,470.33,-0.67315,0.10706,-0.73172,529.05,#11,0.73012,-0.060917,-0.6806,231.63,-0.11744,-0.99238,-0.03716,470.33,-0.67315,0.10706,-0.73172,529.05

> view matrix models
> #7,-0.001777,-0.5744,-0.81857,538.78,-0.99932,-0.029179,0.022644,442.03,-0.036892,0.81806,-0.57396,195.39,#9,-0.001777,-0.5744,-0.81857,538.78,-0.99932,-0.029179,0.022644,442.03,-0.036892,0.81806,-0.57396,195.39,#11,-0.001777,-0.5744,-0.81857,538.78,-0.99932,-0.029179,0.022644,442.03,-0.036892,0.81806,-0.57396,195.39

> view matrix models
> #7,-0.19049,-0.64648,-0.73876,577.96,-0.97965,0.17364,0.10066,375.18,0.063205,0.74291,-0.66641,211.06,#9,-0.19049,-0.64648,-0.73876,577.96,-0.97965,0.17364,0.10066,375.18,0.063205,0.74291,-0.66641,211.06,#11,-0.19049,-0.64648,-0.73876,577.96,-0.97965,0.17364,0.10066,375.18,0.063205,0.74291,-0.66641,211.06

> view matrix models
> #7,0.12078,-0.88633,-0.44703,493.31,-0.85691,-0.32042,0.40377,385.39,-0.50111,0.33429,-0.79821,456.57,#9,0.12078,-0.88633,-0.44703,493.31,-0.85691,-0.32042,0.40377,385.39,-0.50111,0.33429,-0.79821,456.57,#11,0.12078,-0.88633,-0.44703,493.31,-0.85691,-0.32042,0.40377,385.39,-0.50111,0.33429,-0.79821,456.57

> view matrix models
> #7,0.37394,-0.74381,-0.554,430.71,-0.52804,-0.66181,0.53214,357.01,-0.76246,0.093543,-0.64024,530.6,#9,0.37394,-0.74381,-0.554,430.71,-0.52804,-0.66181,0.53214,357.01,-0.76246,0.093543,-0.64024,530.6,#11,0.37394,-0.74381,-0.554,430.71,-0.52804,-0.66181,0.53214,357.01,-0.76246,0.093543,-0.64024,530.6

> view matrix models
> #7,0.094335,-0.81529,-0.57132,512.56,-0.75251,-0.43412,0.49525,365.75,-0.65179,0.38321,-0.65446,445.97,#9,0.094335,-0.81529,-0.57132,512.56,-0.75251,-0.43412,0.49525,365.75,-0.65179,0.38321,-0.65446,445.97,#11,0.094335,-0.81529,-0.57132,512.56,-0.75251,-0.43412,0.49525,365.75,-0.65179,0.38321,-0.65446,445.97

> ui mousemode right ""translate selected models""

> view matrix models
> #7,0.094335,-0.81529,-0.57132,537.82,-0.75251,-0.43412,0.49525,374.18,-0.65179,0.38321,-0.65446,478.27,#9,0.094335,-0.81529,-0.57132,537.82,-0.75251,-0.43412,0.49525,374.18,-0.65179,0.38321,-0.65446,478.27,#11,0.094335,-0.81529,-0.57132,537.82,-0.75251,-0.43412,0.49525,374.18,-0.65179,0.38321,-0.65446,478.27

> ui mousemode right ""rotate selected models""

> view matrix models
> #7,0.11661,-0.85928,-0.49804,525.44,-0.7549,-0.40255,0.51777,362.57,-0.64539,0.31559,-0.69561,501.2,#9,0.11661,-0.85928,-0.49804,525.44,-0.7549,-0.40255,0.51777,362.57,-0.64539,0.31559,-0.69561,501.2,#11,0.11661,-0.85928,-0.49804,525.44,-0.7549,-0.40255,0.51777,362.57,-0.64539,0.31559,-0.69561,501.2

> view matrix models
> #7,0.042668,-0.87433,-0.48344,541.79,-0.70941,-0.36724,0.60156,325.24,-0.70351,0.31729,-0.63593,499.88,#9,0.042668,-0.87433,-0.48344,541.79,-0.70941,-0.36724,0.60156,325.24,-0.70351,0.31729,-0.63593,499.88,#11,0.042668,-0.87433,-0.48344,541.79,-0.70941,-0.36724,0.60156,325.24,-0.70351,0.31729,-0.63593,499.88

> ui mousemode right ""translate selected models""

> view matrix models
> #7,0.042668,-0.87433,-0.48344,547.1,-0.70941,-0.36724,0.60156,161.23,-0.70351,0.31729,-0.63593,420.52,#9,0.042668,-0.87433,-0.48344,547.1,-0.70941,-0.36724,0.60156,161.23,-0.70351,0.31729,-0.63593,420.52,#11,0.042668,-0.87433,-0.48344,547.1,-0.70941,-0.36724,0.60156,161.23,-0.70351,0.31729,-0.63593,420.52

> view matrix models
> #7,0.042668,-0.87433,-0.48344,536.67,-0.70941,-0.36724,0.60156,152.08,-0.70351,0.31729,-0.63593,408.34,#9,0.042668,-0.87433,-0.48344,536.67,-0.70941,-0.36724,0.60156,152.08,-0.70351,0.31729,-0.63593,408.34,#11,0.042668,-0.87433,-0.48344,536.67,-0.70941,-0.36724,0.60156,152.08,-0.70351,0.31729,-0.63593,408.34

> ui mousemode right ""rotate selected models""

> view matrix models
> #7,0.3552,-0.77911,-0.51654,454.02,-0.53271,-0.62278,0.57303,175.27,-0.76815,0.071622,-0.63625,476.51,#9,0.3552,-0.77911,-0.51654,454.02,-0.53271,-0.62278,0.57303,175.27,-0.76815,0.071622,-0.63625,476.51,#11,0.3552,-0.77911,-0.51654,454.02,-0.53271,-0.62278,0.57303,175.27,-0.76815,0.071622,-0.63625,476.51

> view matrix models
> #7,0.055668,-0.8551,-0.51546,537.02,-0.55774,-0.45484,0.6943,115.93,-0.82815,0.24884,-0.50224,419.95,#9,0.055668,-0.8551,-0.51546,537.02,-0.55774,-0.45484,0.6943,115.93,-0.82815,0.24884,-0.50224,419.95,#11,0.055668,-0.8551,-0.51546,537.02,-0.55774,-0.45484,0.6943,115.93,-0.82815,0.24884,-0.50224,419.95

> view matrix models
> #7,0.050991,-0.93462,-0.35197,517.42,-0.719,-0.27895,0.63657,126.78,-0.69313,0.2206,-0.68622,438.87,#9,0.050991,-0.93462,-0.35197,517.42,-0.719,-0.27895,0.63657,126.78,-0.69313,0.2206,-0.68622,438.87,#11,0.050991,-0.93462,-0.35197,517.42,-0.719,-0.27895,0.63657,126.78,-0.69313,0.2206,-0.68622,438.87

> view matrix models
> #7,-0.032857,-0.97559,-0.21713,513.67,-0.62463,-0.14955,0.76647,47.285,-0.78023,0.16081,-0.60447,452.3,#9,-0.032857,-0.97559,-0.21713,513.67,-0.62463,-0.14955,0.76647,47.285,-0.78023,0.16081,-0.60447,452.3,#11,-0.032857,-0.97559,-0.21713,513.67,-0.62463,-0.14955,0.76647,47.285,-0.78023,0.16081,-0.60447,452.3

> view matrix models
> #7,0.47176,-0.82185,-0.3194,391.59,-0.27024,-0.47958,0.83485,24.697,-0.8393,-0.30753,-0.44834,531.52,#9,0.47176,-0.82185,-0.3194,391.59,-0.27024,-0.47958,0.83485,24.697,-0.8393,-0.30753,-0.44834,531.52,#11,0.47176,-0.82185,-0.3194,391.59,-0.27024,-0.47958,0.83485,24.697,-0.8393,-0.30753,-0.44834,531.52

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!23 models

> hide #!23 models

> show #!23 models

> fitmap #7 inMap #23

Fit map Jacob_cryosparc_P5_J117_006_volume_map.mrc in map
cryosparc_P17_J842_005_volume_map.mrc using 611645 points  
correlation = 0.8586, correlation about mean = 0.4556, overlap = 8.71e+04  
steps = 244, shift = 17, angle = 22.5 degrees  

Position of Jacob_cryosparc_P5_J117_006_volume_map.mrc (#7) relative to
cryosparc_P17_J842_005_volume_map.mrc (#23) coordinates:  
Matrix rotation and translation  
0.55644781 -0.77930109 0.28819374 245.87868586  
-0.75685869 -0.33229301 0.56280215 362.24414012  
-0.34282757 -0.53129197 -0.77472452 653.58997201  
Axis -0.86611289 0.49953261 0.01776598  
Axis point 0.00000000 386.34237031 252.82329186  
Rotation angle (degrees) 140.83086649  
Shift along axis -20.39427278  


> hide #!7 models

> show #!7 models

> fitmap #9 inMap #23

Fit map Jacob_cryosparc_P5_J117_006_volume_map_sharp.mrc in map
cryosparc_P17_J842_005_volume_map.mrc using 166113 points  
correlation = 0.8354, correlation about mean = 0.2023, overlap = 1.093e+05  
steps = 240, shift = 17.3, angle = 22.5 degrees  

Position of Jacob_cryosparc_P5_J117_006_volume_map_sharp.mrc (#9) relative to
cryosparc_P17_J842_005_volume_map.mrc (#23) coordinates:  
Matrix rotation and translation  
0.55535502 -0.78023657 0.28777020 246.41094031  
-0.75768547 -0.33209636 0.56180488 362.67622759  
-0.34277328 -0.53004046 -0.77560530 653.54700022  
Axis -0.86582981 0.50001893 0.01788295  
Axis point 0.00000000 386.54023823 252.88749245  
Rotation angle (degrees) 140.91153143  
Shift along axis -20.31760982  


> fitmap #11 inMap #23

Fit map Jacob_cryosparc_P5_J117_006_volume_map_EMReady.mrc in map
cryosparc_P17_J842_005_volume_map.mrc using 547647 points  
correlation = 0.755, correlation about mean = 0.2272, overlap = 1.157e+06  
steps = 244, shift = 16, angle = 22.6 degrees  

Position of Jacob_cryosparc_P5_J117_006_volume_map_EMReady.mrc (#11) relative
to cryosparc_P17_J842_005_volume_map.mrc (#23) coordinates:  
Matrix rotation and translation  
0.55439930 -0.78039733 0.28917368 246.34842101  
-0.75807382 -0.33013049 0.56243927 362.20292573  
-0.34346106 -0.53103093 -0.77462290 653.67877730  
Axis -0.86543769 0.50070495 0.01766816  
Axis point 0.00000000 386.83809960 252.79416826  
Rotation angle (degrees) 140.82108735  
Shift along axis -20.29310612  


> ui mousemode right zoom

> select subtract #7

4 models selected  

> select subtract #9

2 models selected  

> select subtract #11

Nothing selected  

> hide #!7 models

> show #!7 models

> hide #!23 models

> show #!23 models

> hide #!23 models

> hide #!11 models

> hide #!7 models

> show #!7 models

> hide #!7 models

> show #!7 models

> hide #!7 models

> show #!7 models

> hide #!7 models

> show #!11 models

> hide #!11 models

> show #!11 models

> hide #!11 models

> volume #9 level 0.7158

> volume #9 level 0.7

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> volume #3 level 0.4

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!9 models

> show #!9 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> save
> /Users/cvetkom/Documents/chimera_sessions/20241004_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_Jacob_Mrc1_AF3_modelling.cxs

> hide #!9 models

> show #!9 models

> hide #!9 models

> show #!9 models

> hide #!9 models

> show #!9 models

> hide #!9 models

> show #!9 models

> hide #!9 models

> show #!9 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!20 models

> hide #!9 models

> show #!9 models

> hide #!20 models

> show #!20 models

> hide #!20 models

> show #!20 models

> hide #!20 models

> show #!20 models

> hide #!20 models

> show #!20 models

> hide #!20 models

> show #!20 models

> hide #!20 models

> show #!20 models

> hide #!20 models

> show #!20 models

> hide #!20 models

> show #!20 models

> hide #!20 models

> show #!20 models

> hide #!20 models

> show #!20 models

> hide #!20 models

> show #!20 models

> show #26 models

> hide #26 models

> hide #!20 models

> show #!20 models

> hide #!20 models

> show #!20 models

> hide #!20 models

> show #!20 models

> show #26 models

> hide #!20 models

> show #!23 models

> hide #!23 models

> show #!23 models

> hide #!23 models

> show #!50 models

> hide #!9 models

> hide #!50 models

> show #!50 models

> color #50 #b2b2b29c models

> volume #50 level 3

> volume #50 level 3.5

> volume #50 level 3.6

> volume #50 level 3.8

> volume #50 level 4.5

> show #!42 models

> hide #!50 models

> hide #!42 models

> show #!3 models

> select add #3

2 models selected  

> color #3.1 gray

> ui tool show ""Color Actions""

> color sel light blue

> color sel light sky blue

[Repeated 4 time(s)]

> color sel aquamarine

> color sel light sky blue

> select subtract #3

Nothing selected  

> color #3 #87cefaa8 models

> color #3 #87cefa98 models

> color #3 #87cefaa7 models

> color #3 #87cefa99 models

> color #3 #87cefaa4 models

> color #3 #87cefaa3 models

> volume #3 level 0.35

> fitmap #26 inMap #3

Fit molecule fold_mrc1_323_337_tof1_model_0.cif (#26) to map
cryosparc_P17_J842_005_volume_map_sharp.mrc (#3) using 10075 atoms  
average map value = 0.2438, steps = 52  
shifted from previous position = 0.293  
rotated from previous position = 0.36 degrees  
atoms outside contour = 7077, contour level = 0.35  

Position of fold_mrc1_323_337_tof1_model_0.cif (#26) relative to
cryosparc_P17_J842_005_volume_map_sharp.mrc (#3) coordinates:  
Matrix rotation and translation  
0.84462737 0.15456521 -0.51255653 282.60576624  
0.06681694 0.91949322 0.38738573 335.32756599  
0.53116861 -0.36144406 0.76630157 241.89923621  
Axis -0.58158875 -0.81062320 -0.06815088  
Axis point -335.92841792 0.00000000 139.55904352  
Rotation angle (degrees) 40.07422511  
Shift along axis -452.67028623  


> volume #3 level 0.34

> lighting soft

> lighting full

> lighting simple

> lighting soft

> lighting simple

> lighting full

> lighting simple

> save
> /Users/cvetkom/Documents/Replication_meeting_Cambridge_2024/CMGC4MCT_J842_sharp_Mrc1_323-337_overview.png
> supersample 6 width 1800 transparentBackground true

> ui tool show ""Side View""

> rock y 20 136

[Repeated 1 time(s)]

> volume #3 level 0.32

> volume #3 level 0.33

> rock y 20 136

> movie record supersample 3 size 1800, 2000

> rock y 20 136

> wait

> movie encode quality highest framerate 30 output
> /Users/cvetkom/Documents/Replication_meeting_Cambridge_2024/CMGC4MTC_J842_sharp_Mrc1_323-337_zoomed.mp4

Movie saved to
/Users/cvetkom/.../Replication_meeting_Cambridge_2024/CMGC4MTC_J842_sharp_Mrc1_323-337_zoomed.mp4  


> hide #!3 models

> show #!50 models

> volume #50 level 5

> volume #50 level 4.6

> movie encode quality highest framerate 30 output
> /Users/cvetkom/Documents/Replication_meeting_Cambridge_2024/CMGC4MTC_J842_EMReady_Mrc1_323-337_zoomed.mp4

No frames have been recorded  

> movie record supersample 3 size 1800, 2000

> rock y 20 136

> wait

> movie encode quality highest framerate 30 output
> /Users/cvetkom/Documents/Replication_meeting_Cambridge_2024/CMGC4MTC_J842_EMReady_Mrc1_323-337_zoomed.mp4

Movie saved to
/Users/cvetkom/.../Replication_meeting_Cambridge_2024/CMGC4MTC_J842_EMReady_Mrc1_323-337_zoomed.mp4  


> fitmap #26 inMap #50

Fit molecule fold_mrc1_323_337_tof1_model_0.cif (#26) to map
J842_005_volume_map_EMReady.mrc (#50) using 10075 atoms  
average map value = 2.525, steps = 52  
shifted from previous position = 0.107  
rotated from previous position = 0.359 degrees  
atoms outside contour = 7517, contour level = 4.6  

Position of fold_mrc1_323_337_tof1_model_0.cif (#26) relative to
J842_005_volume_map_EMReady.mrc (#50) coordinates:  
Matrix rotation and translation  
0.84685173 0.15716115 -0.50807727 282.58642125  
0.06188411 0.91973007 0.38764280 335.21799844  
0.52821633 -0.35971789 0.76914923 241.85487927  
Axis -0.58331859 -0.80883211 -0.07436418  
Axis point -334.58664400 0.00000000 135.85619956  
Rotation angle (degrees) 39.83740038  
Shift along axis -453.95833613  


> save
> /Users/cvetkom/Documents/Replication_meeting_Cambridge_2024/CMGC4MCT_J842_EMReady_Mrc1_323-337_overview.png
> supersample 6 width 1800 transparentBackground true

> save
> /Users/cvetkom/Documents/chimera_sessions/20241004_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_Jacob_Mrc1_AF3_modelling.cxs

> select add #26

10075 atoms, 10266 bonds, 1253 residues, 1 model selected  

> cartoon hide sel

> show sel target ab

> style sel ball

Changed 10075 atom styles  

> color sel byhetero

> select clear

> cartoon #26,50

> hide #26,50 target a

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> hide #26 models

> show #26 models

> hide #!50 models

> show #!11 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!9 models

> hide #!9 models

> show #!9 models

> hide #!11 models

> show #!11 models

> hide #!11 models

> show #!11 models

> hide #!9 models

> show #!7 models

> hide #!11 models

> hide #!7 models

> show #!2 models

> hide #!2 models

> show #!3 models

> hide #!3 models

> show #!7 models

> hide #!7 models

> show #!7 models

> select add #7

2 models selected  

> ui tool show ""Color Actions""

> color sel turquoise

> color sel light sea green

[Repeated 1 time(s)]

> color #7 #b2ffff9d models

> color #7 #b2ffffd9 models

> color #7 #b2ffffb7 models

> color #7 #b2ffffa7 models

> color #7 #b2ffffa6 models

> select clear

> save
> /Users/cvetkom/Documents/Replication_meeting_Cambridge_2024/Jacob_J117_Mrc1_323-337_overview.png
> supersample 6 width 1800 transparentBackground true

> volume #7 level 0.22

> volume #7 level 0.2

> volume #7 level 0.18

> volume #7 level 0.16

> volume #7 level 0.18

> volume #7 level 0.2

> volume #7 level 0.18

> rock y 20 136

> movie record supersample 3 size 1800, 2000

> rock y 20 136

> wait

> movie encode quality highest framerate 30 output
> /Users/cvetkom/Documents/Replication_meeting_Cambridge_2024/Jacob_J117_Mrc1_323-337_zoomed.mp4

Movie saved to
/Users/cvetkom/.../Replication_meeting_Cambridge_2024/Jacob_J117_Mrc1_323-337_zoomed.mp4  


> save
> /Users/cvetkom/Documents/chimera_sessions/20241004_CMGC4MCT_Fpl20MN_krios_II_merged_NCP_Tof1HTH_Jacob_Mrc1_AF3_modelling.cxs

\u2014\u2014\u2014 End of log from Mon Oct 7 10:20:32 2024 \u2014\u2014\u2014

opened ChimeraX session  




OpenGL version: 4.1 ATI-5.5.17
OpenGL renderer: AMD Radeon Pro 5500M OpenGL Engine
OpenGL vendor: ATI Technologies Inc.

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: MacBookPro16,1
     Processor Name: 8-Core Intel Core i9
     Processor Speed: 2.3 GHz
     Number of Processors: 1
     Total Number of Cores: 8
     L2 Cache (per Core): 256 KB
     L3 Cache: 16 MB
     Hyper-Threading Technology: Enabled
     Memory: 16 GB
     System Firmware Version: 2022.140.5.0.0 (iBridge: 21.16.6074.0.0,0)
     OS Loader Version: 580.140.1~8

Software:

   System Software Overview:

     System Version: macOS 14.6.1 (23G93)
     Kernel Version: Darwin 23.6.0
     Time since boot: 11 days, 12 hours, 23 minutes

Graphics/Displays:

   Intel UHD Graphics 630:

     Chipset Model: Intel UHD Graphics 630
     Type: GPU
     Bus: Built-In
     VRAM (Dynamic, Max): 1536 MB
     Vendor: Intel
     Device ID: 0x3e9b
     Revision ID: 0x0002
     Automatic Graphics Switching: Supported
     gMux Version: 5.0.0
     Metal Support: Metal 3

   AMD Radeon Pro 5500M:

     Chipset Model: AMD Radeon Pro 5500M
     Type: GPU
     Bus: PCIe
     PCIe Lane Width: x16
     VRAM (Total): 8 GB
     Vendor: AMD (0x1002)
     Device ID: 0x7340
     Revision ID: 0x0040
     ROM Revision: 113-D3220E-190
     VBIOS Version: 113-D32206U1-019
     Option ROM Version: 113-D32206U1-019
     EFI Driver Version: 01.A1.190
     Automatic Graphics Switching: Supported
     gMux Version: 5.0.0
     Metal Support: Metal 3
     Displays:
       Color LCD:
         Display Type: Built-In Retina LCD
         Resolution: 3072 x 1920 Retina
         Framebuffer Depth: 30-Bit Color (ARGB2101010)
         Main Display: Yes
         Mirror: Off
         Online: Yes
         Automatically Adjust Brightness: Yes
         Connection Type: Internal
       DELL U2415:
         Resolution: 1920 x 1200 (WUXGA - Widescreen Ultra eXtended Graphics Array)
         UI Looks like: 1920 x 1200 @ 60.00Hz
         Framebuffer Depth: 30-Bit Color (ARGB2101010)
         Display Serial Number: 7MT016923MAL
         Mirror: Off
         Online: Yes
         Rotation: Supported
         Adapter Type: DVI or HDMI


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