![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 16 months ago
Closed 16 months ago
#15521 closed defect (duplicate)
Crash in Mac display reconfiguration
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Window Toolkit | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description (last modified by )
The following bug report has been submitted:
Platform: macOS-13.4.1-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 0x00000001f27bde00 (most recent call first):
File "/private/var/folders/xc/c7gm55q95yj8048w35kh7_p00000gn/T/AppTranslocation/60F6A285-2291-45F3-B232-4FE622BAE214/d/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 "/private/var/folders/xc/c7gm55q95yj8048w35kh7_p00000gn/T/AppTranslocation/60F6A285-2291-45F3-B232-4FE622BAE214/d/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 "/private/var/folders/xc/c7gm55q95yj8048w35kh7_p00000gn/T/AppTranslocation/60F6A285-2291-45F3-B232-4FE622BAE214/d/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, chimerax.pdb_lib._load_libs, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, 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, psutil._psutil_osx, psutil._psutil_posix, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw, PIL._imagingmath, 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 (total: 116)
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===== Log before crash start =====
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> /Users/matteogiono/Desktop/PhD/MT_Processing/MATCAP2/2024_MATCAP/run_class001.mrc
Opened run_class001.mrc as #1, grid size 600,600,600, pixel 1.06, shown at
level 0.0109, step 4, values float32
> volume #1 step 1
> volume #1 step 4
> volume #1 level 0.003309
> volume #1 step 2
> volume #1 level 0.002618
> volume #1 step 1
> ui windowfill toggle
> open
> /Users/matteogiono/Downloads/ChimeraX/AlphaFold/prediction_9/best_model.pdb
> format pdb
Chain information for best_model.pdb #2
---
Chain | Description
A | No description available
> select add #2
3530 atoms, 3621 bonds, 436 residues, 1 model selected
> select subtract #2
Nothing selected
> select add #2
3530 atoms, 3621 bonds, 436 residues, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models #2,1,0,0,120.53,0,1,0,394.37,0,0,1,427.05
> view matrix models #2,1,0,0,174.96,0,1,0,381.65,0,0,1,419.26
> view matrix models #2,1,0,0,188.03,0,1,0,403.7,0,0,1,407.67
> view matrix models #2,1,0,0,178.38,0,1,0,405.04,0,0,1,401.34
> ui tool show "Fit in Map"
> fitmap #2 inMap #1
Fit molecule best_model.pdb (#2) to map run_class001.mrc (#1) using 3530 atoms
average map value = 0.004756, steps = 296
shifted from previous position = 37.5
rotated from previous position = 11.7 degrees
atoms outside contour = 1675, contour level = 0.0026177
Position of best_model.pdb (#2) relative to run_class001.mrc (#1) coordinates:
Matrix rotation and translation
0.99074134 0.02673135 0.13310533 215.60687941
-0.00623194 0.98834519 -0.15210177 395.81719257
-0.13561990 0.14986401 0.97936103 404.98594309
Axis 0.74455538 0.66259434 -0.08127741
Axis point 0.00000000 -2760.19484561 1115.39531511
Rotation angle (degrees) 11.69972659
Shift along axis 389.88128506
> view matrix models
> #2,0.99074,0.026731,0.13311,177.66,-0.0062319,0.98835,-0.1521,390.04,-0.13562,0.14986,0.97936,396.86
> view matrix models
> #2,0.99074,0.026731,0.13311,171.93,-0.0062319,0.98835,-0.1521,406.84,-0.13562,0.14986,0.97936,400.01
> view matrix models
> #2,0.99074,0.026731,0.13311,159.83,-0.0062319,0.98835,-0.1521,405.01,-0.13562,0.14986,0.97936,399.72
> fitmap #2 inMap #1
Fit molecule best_model.pdb (#2) to map run_class001.mrc (#1) using 3530 atoms
average map value = 0.005393, steps = 332
shifted from previous position = 65.6
rotated from previous position = 23.4 degrees
atoms outside contour = 1435, contour level = 0.0026177
Position of best_model.pdb (#2) relative to run_class001.mrc (#1) coordinates:
Matrix rotation and translation
0.86946068 0.16883360 0.46425569 225.75097571
-0.02254401 0.95236634 -0.30412188 396.44865442
-0.49348748 0.25395584 0.83185127 413.07251972
Axis 0.49612336 0.85142040 -0.17013204
Axis point 908.36058118 0.00000000 174.45015774
Rotation angle (degrees) 34.22460214
Shift along axis 379.26793241
> view matrix models
> #2,0.86946,0.16883,0.46426,176.6,-0.022544,0.95237,-0.30412,406.89,-0.49349,0.25396,0.83185,414.43
> view matrix models
> #2,0.86946,0.16883,0.46426,211.52,-0.022544,0.95237,-0.30412,362.42,-0.49349,0.25396,0.83185,302.89
> view matrix models
> #2,0.86946,0.16883,0.46426,227.32,-0.022544,0.95237,-0.30412,388.96,-0.49349,0.25396,0.83185,339.98
> view matrix models
> #2,0.86946,0.16883,0.46426,146.99,-0.022544,0.95237,-0.30412,352.24,-0.49349,0.25396,0.83185,345.59
> view matrix models
> #2,0.86946,0.16883,0.46426,142.89,-0.022544,0.95237,-0.30412,329.11,-0.49349,0.25396,0.83185,336.3
> ui windowfill toggle
> open 7Z5G format mmcif fromDatabase pdbe_bio
Summary of feedback from opening 7Z5G fetched from pdbe_bio
---
warnings | Atom H is not in the residue template for LEU /A:140
Missing or incomplete sequence information. Inferred polymer connectivity.
Atom H is not in the residue template for LEU /B:140
Missing or incomplete sequence information. Inferred polymer connectivity.
Atom H is not in the residue template for VAL /C:141
Missing or incomplete sequence information. Inferred polymer connectivity.
Atom H is not in the residue template for VAL /D:141
Missing or incomplete sequence information. Inferred polymer connectivity.
7Z5G bioassembly 1 title:
human apo MATCAP [more info...]
Chain information for 7Z5G bioassembly 1 #3.1
---
Chain | Description
A | Uncharacterized protein KIAA0895-like
7Z5G bioassembly 1 mmCIF Assemblies
---
1| author_defined_assembly
2| author_defined_assembly
3| author_defined_assembly
4| author_defined_assembly
7Z5G bioassembly 2 title:
human apo MATCAP [more info...]
Chain information for 7Z5G bioassembly 2 #3.2
---
Chain | Description
B | Uncharacterized protein KIAA0895-like
7Z5G bioassembly 2 mmCIF Assemblies
---
1| author_defined_assembly
2| author_defined_assembly
3| author_defined_assembly
4| author_defined_assembly
7Z5G bioassembly 3 title:
human apo MATCAP [more info...]
Chain information for 7Z5G bioassembly 3 #3.3
---
Chain | Description
C | Uncharacterized protein KIAA0895-like
7Z5G bioassembly 3 mmCIF Assemblies
---
1| author_defined_assembly
2| author_defined_assembly
3| author_defined_assembly
4| author_defined_assembly
7Z5G bioassembly 4 title:
human apo MATCAP [more info...]
Chain information for 7Z5G bioassembly 4 #3.4
---
Chain | Description
D | Uncharacterized protein KIAA0895-like
7Z5G bioassembly 4 mmCIF Assemblies
---
1| author_defined_assembly
2| author_defined_assembly
3| author_defined_assembly
4| author_defined_assembly
Opened 4 biological assemblies for 7Z5G
> ui tool show Matchmaker
> matchmaker #3.1 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker best_model.pdb, chain A (#2) with 7Z5G bioassembly 1, chain A
(#3.1), sequence alignment score = 1260.7
RMSD between 314 pruned atom pairs is 0.729 angstroms; (across all 330 pairs:
0.959)
> ui windowfill toggle
> close #2
> select add #3.1
5490 atoms, 5473 bonds, 414 residues, 1 model selected
> view matrix models
> #3.1,-0.93394,0.00043864,0.35743,122.96,0.22599,-0.77403,0.59144,348.2,0.27692,0.63314,0.7228,382.58
> view matrix models
> #3.1,-0.93394,0.00043864,0.35743,139.13,0.22599,-0.77403,0.59144,347.53,0.27692,0.63314,0.7228,339.58
> ui tool show "Fit in Map"
> fitmap #3.1 inMap #1
Fit molecule 7Z5G bioassembly 1 (#3.1) to map run_class001.mrc (#1) using 5490
atoms
average map value = 0.00245, steps = 132
shifted from previous position = 7.61
rotated from previous position = 11 degrees
atoms outside contour = 3119, contour level = 0.0026177
Position of 7Z5G bioassembly 1 (#3.1) relative to run_class001.mrc (#1)
coordinates:
Matrix rotation and translation
-0.89712597 0.14097768 0.41867684 143.85213868
0.12121777 -0.83278725 0.54015890 349.77712788
0.42481908 0.53534165 0.73002607 339.35240903
Axis -0.22673830 -0.28910295 -0.93005872
Axis point 31.18867501 122.02593890 0.00000000
Rotation angle (degrees) 179.39133923
Shift along axis -449.35605787
> volume #1 step 2
> view matrix models
> #3.1,-0.89713,0.14098,0.41868,146.52,0.12122,-0.83279,0.54016,343.64,0.42482,0.53534,0.73003,339.64
> view matrix models
> #3.1,-0.89713,0.14098,0.41868,140.37,0.12122,-0.83279,0.54016,340.94,0.42482,0.53534,0.73003,338.33
> fitmap #3.1 inMap #1
Fit molecule 7Z5G bioassembly 1 (#3.1) to map run_class001.mrc (#1) using 5490
atoms
average map value = 0.002516, steps = 152
shifted from previous position = 9.87
rotated from previous position = 13.4 degrees
atoms outside contour = 3059, contour level = 0.0026177
Position of 7Z5G bioassembly 1 (#3.1) relative to run_class001.mrc (#1)
coordinates:
Matrix rotation and translation
-0.79599275 0.32863836 0.50832310 150.21048614
0.06131846 -0.79167923 0.60785199 349.39498420
0.60219232 0.51501537 0.61001933 340.57019723
Axis -0.31138157 -0.31484497 -0.89661261
Axis point 24.49001940 114.63825852 0.00000000
Rotation angle (degrees) 171.42684110
Shift along axis -462.13756224
> ui windowfill toggle
> open "/Users/matteogiono/Downloads/emd_14529 (1).map" format ccp4
Opened emd_14529 (1).map as #2, grid size 416,416,416, pixel 1.3, shown at
level 0.124, step 2, values float32
> ui windowfill toggle
> volume #2 step 1
> volume #2 level 0.1205
> volume #2 level 0.1175
> volume #2 level 0.09297
> volume #2 level 0.0654
> volume #2 level 0.05315
> volume #2 level 0.004151
> surface dust #2 size 13
> volume #2 level 0.02559
> ui windowfill toggle
> open 7Z6S format mmcif fromDatabase pdbe_bio
Summary of feedback from opening 7Z6S fetched from pdbe_bio
---
warning | Missing or incomplete sequence information. Inferred polymer connectivity.
7Z6S bioassembly 1 title:
MATCAP bound to a human 14 protofilament microtubule [more info...]
Chain information for 7Z6S bioassembly 1 #4
---
Chain | Description
A D | Tubulin alpha-1B chain
B C | Tubulin beta-3 chain
E F | Uncharacterized protein KIAA0895-like
Non-standard residues in 7Z6S bioassembly 1 #4
---
GDP — (GDP)
GTP — (GTP)
MG — (MG)
ZN — (ZN)
Opened 1 biological assemblies for 7Z6S
> color #2.1 #aaffc7ff
> color #2.1 #aaffc787
> color #2.1 #aaffc782
> select add #4
24624 atoms, 25049 bonds, 4 pseudobonds, 2814 residues, 3 models selected
> hide sel atoms
> show sel cartoons
> select clear
> volume #2 level 0.05009
Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps,
got 5 atomic models, 2 maps.
> hide #!4 models
> hide #!3 models
> show #!4 models
Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps,
got 1 atomic models, 2 maps.
> fitmap #2 inMap #1
Fit map emd_14529 (1).map in map run_class001.mrc using 4134776 points
correlation = 0.5976, correlation about mean = 0.07057, overlap = 2240
steps = 380, shift = 69.9, angle = 0.791 degrees
Position of emd_14529 (1).map (#2) relative to run_class001.mrc (#1)
coordinates:
Matrix rotation and translation
0.99990692 0.01305285 0.00397249 43.01706112
-0.01304426 0.99991255 -0.00217896 50.27401777
-0.00400058 0.00212694 0.99998974 -21.83928801
Axis 0.15586674 0.28861245 -0.94467371
Axis point 2946.85249751 -2774.90530904 0.00000000
Rotation angle (degrees) 0.79143831
Shift along axis 41.84563759
> fitmap #4 inMap #2
Fit molecule 7Z6S bioassembly 1 (#4) to map emd_14529 (1).map (#2) using 19134
atoms
average map value = 0.1185, steps = 596
shifted from previous position = 66.4
rotated from previous position = 1.43 degrees
atoms outside contour = 9942, contour level = 0.050091
Position of 7Z6S bioassembly 1 (#4) relative to emd_14529 (1).map (#2)
coordinates:
Matrix rotation and translation
0.99994059 0.00392717 0.01016779 -5.74650580
-0.00406745 0.99989633 0.01381286 -3.16948582
-0.01011249 -0.01385339 0.99985290 41.00392316
Axis -0.78547067 0.57577627 -0.22697471
Axis point 0.00000000 2851.68172514 -25.00468531
Rotation angle (degrees) 1.00910285
Shift along axis -6.61805667
> select add #4
19134 atoms, 19576 bonds, 4 pseudobonds, 2400 residues, 2 models selected
> view matrix models
> #4,0.99975,0.016923,0.014319,36.015,-0.017089,0.99979,0.0115,48.83,-0.014121,-0.011742,0.99983,62.494
> fitmap #4 inMap #2
Fit molecule 7Z6S bioassembly 1 (#4) to map emd_14529 (1).map (#2) using 19134
atoms
average map value = 0.2217, steps = 116
shifted from previous position = 3.35
rotated from previous position = 0.699 degrees
atoms outside contour = 4896, contour level = 0.050091
Position of 7Z6S bioassembly 1 (#4) relative to emd_14529 (1).map (#2)
coordinates:
Matrix rotation and translation
0.99999454 0.00325950 0.00055188 -2.19853874
-0.00326293 0.99997463 0.00633154 -0.62421843
-0.00053123 -0.00633331 0.99997980 83.26010038
Axis -0.88647011 0.07581135 -0.45653411
Axis point 0.00000000 10544.37436557 -291.52446511
Rotation angle (degrees) 0.40929119
Shift along axis -36.10945949
> view matrix models
> #4,0.99986,0.016287,0.0046069,38.273,-0.016306,0.99986,0.0041449,48.243,-0.0045387,-0.0042194,0.99998,-22.03
> fitmap #4 inMap #2
Fit molecule 7Z6S bioassembly 1 (#4) to map emd_14529 (1).map (#2) using 19134
atoms
average map value = 0.2626, steps = 60
shifted from previous position = 3.62
rotated from previous position = 0.191 degrees
atoms outside contour = 3993, contour level = 0.050091
Position of 7Z6S bioassembly 1 (#4) relative to emd_14529 (1).map (#2)
coordinates:
Matrix rotation and translation
0.99999989 -0.00008054 0.00046185 -0.71593925
0.00007760 0.99997975 0.00636318 -2.00985147
-0.00046236 -0.00636314 0.99997965 1.01023948
Axis -0.99729683 0.07242565 0.01239190
Axis point 0.00000000 156.59984855 322.96722296
Rotation angle (degrees) 0.36557300
Shift along axis 0.58095794
> fitmap #4 inMap #2
Fit molecule 7Z6S bioassembly 1 (#4) to map emd_14529 (1).map (#2) using 19134
atoms
average map value = 0.2627, steps = 44
shifted from previous position = 0.0287
rotated from previous position = 0.0159 degrees
atoms outside contour = 3996, contour level = 0.050091
Position of 7Z6S bioassembly 1 (#4) relative to emd_14529 (1).map (#2)
coordinates:
Matrix rotation and translation
0.99999988 -0.00031649 0.00037997 -0.62778669
0.00031411 0.99998046 0.00624331 -2.02218983
-0.00038194 -0.00624319 0.99998044 0.95569584
Axis -0.99687776 0.06082882 0.05034459
Axis point 0.00000000 147.60220020 329.72652117
Rotation angle (degrees) 0.35883485
Shift along axis 0.55093329
> select subtract #4
Nothing selected
> show #!3 models
> hide #!3 models
> close #3
> show #!1 models
> hide #!2 models
> hide #2.1 models
> hide #!4 models
> volume #1 step 1
> volume #1 level 0.007214
> volume #1 level 0.005737
> volume #1 level 0.004998
> volume #1 level 0.004588
> ui mousemode right "mark surface"
> marker #3 position 258.5,220.2,186.3 color yellow radius 1
> marker #3 position 258.7,221.1,186.3 color yellow radius 1
> marker change #3:2 radius 9
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> view matrix models #3,1,0,0,8.3886,0,1,0,-29.719,0,0,1,-17.244
> view matrix models #3,1,0,0,6.3132,0,1,0,-37.372,0,0,1,-33.013
> view matrix models #3,1,0,0,6.7626,0,1,0,-40.476,0,0,1,-34.549
> view matrix models #3,1,0,0,-4.2977,0,1,0,-34.196,0,0,1,106.49
> ui mousemode right "mark surface"
> marker #3 position 208.3,347.6,297.9 color yellow radius 9
> show #!4 models
> select add #3
3 atoms, 3 residues, 1 model selected
> select subtract #3
Nothing selected
> select add #4
19134 atoms, 19576 bonds, 4 pseudobonds, 2400 residues, 2 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.99991,0.012711,0.0044338,73.483,-0.012729,0.99991,0.0040589,96.054,-0.0043819,-0.004115,0.99998,25.779
> view matrix models
> #4,0.99991,0.012711,0.0044338,75.261,-0.012729,0.99991,0.0040589,123.23,-0.0043819,-0.004115,0.99998,28.68
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.83151,0.55395,0.041751,-7.8003,-0.54919,0.83102,-0.088299,265.88,-0.083608,0.050492,0.99522,32.633
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.83151,0.55395,0.041751,-9.4995,-0.54919,0.83102,-0.088299,249.19,-0.083608,0.050492,0.99522,34.934
> view matrix models
> #4,0.83151,0.55395,0.041751,-31.394,-0.54919,0.83102,-0.088299,204.72,-0.083608,0.050492,0.99522,42.647
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.629,0.77045,-0.10373,-0.5376,-0.77444,0.63264,0.0028116,254.15,0.067793,0.078567,0.9946,13.044
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.629,0.77045,-0.10373,7.0637,-0.77444,0.63264,0.0028116,257.49,0.067793,0.078567,0.9946,11.885
> view matrix models
> #4,0.629,0.77045,-0.10373,-12.354,-0.77444,0.63264,0.0028116,191.68,0.067793,0.078567,0.9946,36.596
> view matrix models
> #4,0.629,0.77045,-0.10373,24.558,-0.77444,0.63264,0.0028116,330.37,0.067793,0.078567,0.9946,-27.996
> view matrix models
> #4,0.629,0.77045,-0.10373,25.38,-0.77444,0.63264,0.0028116,341.2,0.067793,0.078567,0.9946,-45.132
> open
> /Users/matteogiono/Desktop/PhD/MT_Processing/MATCAP2/2024_MATCAP/postprocess.mrc
Opened postprocess.mrc as #5, grid size 600,600,600, pixel 1.06, shown at
level 0.0141, step 4, values float32
> volume #5 step 1
> view matrix models
> #4,0.629,0.77045,-0.10373,9.1405,-0.77444,0.63264,0.0028116,366.33,0.067793,0.078567,0.9946,-25.047
> view matrix models
> #4,0.629,0.77045,-0.10373,2.8752,-0.77444,0.63264,0.0028116,373.79,0.067793,0.078567,0.9946,-17.603
> view matrix models
> #4,0.629,0.77045,-0.10373,-12.421,-0.77444,0.63264,0.0028116,341.39,0.067793,0.078567,0.9946,2.113
> fitmap #4 inMap #5
Fit molecule 7Z6S bioassembly 1 (#4) to map postprocess.mrc (#5) using 19134
atoms
average map value = 0.003513, steps = 168
shifted from previous position = 20.3
rotated from previous position = 9.84 degrees
atoms outside contour = 16952, contour level = 0.01406
Position of 7Z6S bioassembly 1 (#4) relative to postprocess.mrc (#5)
coordinates:
Matrix rotation and translation
0.53471663 0.84502295 0.00378630 -59.75185740
-0.84388317 0.53421818 -0.04972052 385.58459340
-0.04403769 0.02339120 0.99875599 30.41371836
Axis 0.04323159 0.02827874 -0.99866478
Axis point 321.53228652 246.62303014 0.00000000
Rotation angle (degrees) 57.73435658
Shift along axis -22.05243166
> view matrix models
> #4,0.53472,0.84502,0.0037863,-59.009,-0.84388,0.53422,-0.049721,397.26,-0.044038,0.023391,0.99876,35.755
> show #!1 models
> hide #!5 models
> hide #!4 models
> hide #3 models
> volume #1 level 0.002618
> volume #1 level 0.003028
> color #2.1 #aaffc7ff
> volume #2 level 0.1328
> volume #2 level 0.09909
> volume #2 level 0.1634
> volume #2 level 0.1818
> volume #2 level 0.06847
> volume #2 level 0.04397
> show #!4 models
> fitmap #4 inMap #2
Fit molecule 7Z6S bioassembly 1 (#4) to map emd_14529 (1).map (#2) using 19134
atoms
average map value = 0.08834, steps = 164
shifted from previous position = 5.45
rotated from previous position = 7.81 degrees
atoms outside contour = 6472, contour level = 0.043965
Position of 7Z6S bioassembly 1 (#4) relative to emd_14529 (1).map (#2)
coordinates:
Matrix rotation and translation
0.64757980 0.76199702 0.00097751 -111.04320011
-0.76199716 0.64757740 0.00195860 303.97117113
0.00085944 -0.00201321 0.99999760 58.56884237
Axis -0.00260618 0.00007747 -0.99999660
Axis point 273.02765857 272.19986899 0.00000000
Rotation angle (degrees) 49.64080358
Shift along axis -58.25569538
> show sel atoms
> style sel stick
Changed 19134 atom styles
> color sel byhetero
> open
> /Users/matteogiono/Downloads/ChimeraX/AlphaFold/prediction_9/best_model.pdb
> format pdb
Chain information for best_model.pdb #6
---
Chain | Description
A | No description available
> ui tool show Matchmaker
> matchmaker #6 to #4
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 7Z6S bioassembly 1, chain E (#4) with best_model.pdb, chain A (#6),
sequence alignment score = 1242.7
RMSD between 312 pruned atom pairs is 0.762 angstroms; (across all 330 pairs:
1.009)
> select add #6
22664 atoms, 23197 bonds, 4 pseudobonds, 2836 residues, 3 models selected
> style sel stick
Changed 22664 atom styles
> style sel stick
Changed 22664 atom styles
> color sel byhetero
> select clear
> select add #6
3530 atoms, 3621 bonds, 436 residues, 1 model selected
> style sel stick
Changed 3530 atom styles
> style sel stick
Changed 3530 atom styles
> show sel atoms
> select clear
> select #6/A:207
7 atoms, 6 bonds, 1 residue, 1 model selected
> cofr sel
> select clear
> select #4/E:259
11 atoms, 10 bonds, 1 residue, 1 model selected
> hide #!4 models
> hide #6 models
> volume #5 level 0.004278
> surface dust #5 size 10.6
> ui tool show "Side View"
> volume #5 step 2
> show #!4 models
> volume #5 level 0.009127
> volume #5 step 1
> hide #!4 models
> show #!4 models
> select add #4
19134 atoms, 19576 bonds, 4 pseudobonds, 2400 residues, 2 models selected
> view matrix models
> #4,0.63758,0.77037,0.0049755,-63.622,-0.77038,0.63759,-0.00023328,355.19,-0.003352,-0.0036843,0.99999,43.201
> view matrix models
> #4,0.63758,0.77037,0.0049755,-62.073,-0.77038,0.63759,-0.00023328,358.63,-0.003352,-0.0036843,0.99999,49.006
> hide #!5 models
> select clear
> show #!5 models
> select add #4
19134 atoms, 19576 bonds, 4 pseudobonds, 2400 residues, 2 models selected
> view matrix models
> #4,0.63758,0.77037,0.0049755,-62.576,-0.77038,0.63759,-0.00023328,357.15,-0.003352,-0.0036843,0.99999,50.878
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.43314,0.88502,-0.17068,-4.8543,-0.89104,0.44897,0.06685,394.23,0.1358,0.12313,0.98306,9.1842
> view matrix models
> #4,0.8732,0.4756,-0.10644,-16.339,0.48706,-0.85929,0.15614,392.52,-0.017198,-0.18818,-0.98198,607.9
> view matrix models
> #4,0.88065,0.40833,0.24024,-96.001,0.40972,-0.91102,0.046536,443.44,0.23786,0.057448,-0.9696,517.62
> fitmap #4 inMap #2
Fit molecule 7Z6S bioassembly 1 (#4) to map emd_14529 (1).map (#2) using 19134
atoms
average map value = 0.06576, steps = 180
shifted from previous position = 18.5
rotated from previous position = 16.9 degrees
atoms outside contour = 8665, contour level = 0.043965
Position of 7Z6S bioassembly 1 (#4) relative to emd_14529 (1).map (#2)
coordinates:
Matrix rotation and translation
0.96640176 0.25633581 0.01896294 -72.42593395
0.25625612 -0.96658665 0.00656070 437.44933693
0.02001107 -0.00148090 -0.99979866 577.40589150
Axis -0.99156483 -0.12923867 -0.00982638
Axis point 0.00000000 224.03502231 288.61330643
Rotation angle (degrees) 179.76766454
Shift along axis 9.60583066
> hide #!4 models
> show #3 models
> show #!4 models
> view matrix models
> #4,0.95688,0.25335,0.14211,-54.477,0.25935,-0.96546,-0.025094,492.83,0.13084,0.060867,-0.98953,523.43
> view matrix models
> #4,0.96145,0.27198,-0.040417,-10.774,0.27198,-0.96229,-0.0057175,485.11,-0.040448,-0.0054955,-0.99917,566
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.96145,0.27198,-0.040417,-14.418,0.27198,-0.96229,-0.0057175,489.07,-0.040448,-0.0054955,-0.99917,608.6
> hide sel atoms
> fitmap #4 inMap #2
Fit molecule 7Z6S bioassembly 1 (#4) to map emd_14529 (1).map (#2) using 19134
atoms
average map value = 0.06114, steps = 460
shifted from previous position = 6.72
rotated from previous position = 8.16 degrees
atoms outside contour = 8670, contour level = 0.043965
Position of 7Z6S bioassembly 1 (#4) relative to emd_14529 (1).map (#2)
coordinates:
Matrix rotation and translation
0.98225664 0.17951587 0.05427663 -68.77164132
0.17915480 -0.98375384 0.01148628 452.89480520
0.05545681 -0.00155855 -0.99845987 611.27179920
Axis -0.99555423 -0.09006906 -0.02755613
Axis point 0.00000000 230.56449754 305.84095588
Rotation angle (degrees) 179.62462161
Shift along axis 10.82980472
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.98612,0.16577,0.0095133,-6.7067,0.16584,-0.98058,-0.10471,532.68,-0.0080287,0.10483,-0.99446,578.99
> view matrix models
> #4,0.95025,0.2802,-0.13604,16.112,0.2756,-0.95987,-0.051933,497.16,-0.14513,0.011856,-0.98934,617.15
> fitmap #4 inMap #2
Fit molecule 7Z6S bioassembly 1 (#4) to map emd_14529 (1).map (#2) using 19134
atoms
average map value = 0.06114, steps = 608
shifted from previous position = 1.21
rotated from previous position = 13.1 degrees
atoms outside contour = 8670, contour level = 0.043965
Position of 7Z6S bioassembly 1 (#4) relative to emd_14529 (1).map (#2)
coordinates:
Matrix rotation and translation
0.98225397 0.17953208 0.05427118 -68.77278320
0.17917115 -0.98375089 0.01148433 452.89150210
0.05545112 -0.00155670 -0.99846019 611.27326858
Axis -0.99555356 -0.09007730 -0.02755335
Axis point 0.00000000 230.56289515 305.84183267
Rotation angle (degrees) 179.62473059
Shift along axis 10.82912132
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.98472,0.16667,0.05045,-24.581,0.16622,-0.986,0.012951,500.25,0.051902,-0.0043673,-0.99864,593.31
> fitmap #4 inMap #2
Fit molecule 7Z6S bioassembly 1 (#4) to map emd_14529 (1).map (#2) using 19134
atoms
average map value = 0.06114, steps = 336
shifted from previous position = 8.03
rotated from previous position = 0.0408 degrees
atoms outside contour = 8676, contour level = 0.043965
Position of 7Z6S bioassembly 1 (#4) relative to emd_14529 (1).map (#2)
coordinates:
Matrix rotation and translation
0.98237242 0.17886021 0.05434566 -68.68217553
0.17848948 -0.98387297 0.01164013 452.98332367
0.05555119 -0.00173481 -0.99845433 611.28279334
Axis -0.99558330 -0.08973477 -0.02759637
Axis point 0.00000000 230.61851126 305.82757514
Rotation angle (degrees) 179.61513336
Shift along axis 10.86128553
> view matrix models
> #4,0.98483,0.16599,0.050526,-25.003,0.16554,-0.98612,0.013106,500.79,0.052,-0.004543,-0.99864,597.24
> fitmap #4 inMap #2
Fit molecule 7Z6S bioassembly 1 (#4) to map emd_14529 (1).map (#2) using 19134
atoms
average map value = 0.06114, steps = 348
shifted from previous position = 10.2
rotated from previous position = 0.518 degrees
atoms outside contour = 8652, contour level = 0.043965
Position of 7Z6S bioassembly 1 (#4) relative to emd_14529 (1).map (#2)
coordinates:
Matrix rotation and translation
0.98084596 0.18723734 0.05369707 -69.90409746
0.18701855 -0.98231409 0.00911577 451.99571389
0.05445420 0.00110118 -0.99851566 610.99093307
Axis -0.99519995 -0.09401564 -0.02716828
Axis point 0.00000000 229.91805949 305.99143737
Rotation angle (degrees) 179.76929102
Shift along axis 10.47431380
> view matrix models
> #4,0.98341,0.1744,0.049844,-26.581,0.17409,-0.98467,0.01059,503.03,0.050927,-0.0017372,-0.9987,595.75
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.94367,0.20288,0.2614,-81.043,0.1621,-0.97214,0.16931,460.92,0.28847,-0.1174,-0.95027,565.99
> view matrix models
> #4,0.96685,0.19438,0.16559,-58.035,0.1707,-0.9743,0.14698,465.8,0.18991,-0.11384,-0.97518,587.86
> view matrix models
> #4,0.98157,0.18476,0.048877,-27.952,0.17792,-0.97678,0.11936,472.35,0.069795,-0.10846,-0.99165,610.67
> view matrix models
> #4,0.94135,0.33326,0.052787,-50.05,0.32745,-0.94004,0.095432,447.57,0.081425,-0.07255,-0.99404,602.74
> fitmap #4 inMap #2
Fit molecule 7Z6S bioassembly 1 (#4) to map emd_14529 (1).map (#2) using 19134
atoms
average map value = 0.06101, steps = 100
shifted from previous position = 9.66
rotated from previous position = 5.6 degrees
atoms outside contour = 8480, contour level = 0.043965
Position of 7Z6S bioassembly 1 (#4) relative to emd_14529 (1).map (#2)
coordinates:
Matrix rotation and translation
0.95337312 0.29919948 0.03948874 -83.74787378
0.29907217 -0.95418584 0.00923138 428.02965573
0.04044162 0.00300903 -0.99917737 611.88342463
Axis -0.98827451 -0.15134287 -0.02021966
Axis point 0.00000000 220.91471031 306.45689136
Rotation angle (degrees) 179.81962753
Shift along axis 5.61458007
> view matrix models
> #4,0.95872,0.25053,-0.13451,18.53,0.23928,-0.96635,-0.094354,514.9,-0.15363,0.058272,-0.98641,607.98
> view matrix models
> #4,0.96666,0.25591,-0.0089201,-16.776,0.25607,-0.96593,0.037548,477.43,0.00099299,-0.03858,-0.99926,604.28
> view matrix models
> #4,0.28906,0.899,-0.32901,57.764,0.95731,-0.27131,0.099712,218.33,0.00037541,-0.34379,-0.93905,645.26
> view matrix models
> #4,0.2802,0.9502,-0.13639,-0.95122,0.95955,-0.27319,0.068058,226.63,0.027409,-0.14994,-0.98831,617.81
> view matrix models
> #4,0.50894,0.82025,-0.2611,18.888,0.85316,-0.52098,0.026301,300.9,-0.11445,-0.23614,-0.96495,650.69
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.50894,0.82025,-0.2611,18.334,0.85316,-0.52098,0.026301,294.78,-0.11445,-0.23614,-0.96495,651.29
> view matrix models
> #4,0.50894,0.82025,-0.2611,18.041,0.85316,-0.52098,0.026301,294.38,-0.11445,-0.23614,-0.96495,652.5
> fitmap #4 inMap #2
Fit molecule 7Z6S bioassembly 1 (#4) to map emd_14529 (1).map (#2) using 19134
atoms
average map value = 0.09436, steps = 412
shifted from previous position = 24.6
rotated from previous position = 54.5 degrees
atoms outside contour = 4854, contour level = 0.043965
Position of 7Z6S bioassembly 1 (#4) relative to emd_14529 (1).map (#2)
coordinates:
Matrix rotation and translation
-0.38170726 0.92376446 -0.03096431 52.58503838
0.92379691 0.38020560 -0.04519931 64.95221814
-0.02998071 -0.04585763 -0.99849799 639.30327493
Axis -0.55600916 -0.83072433 0.02740262
Axis point 4.44182979 0.00000000 320.72577081
Rotation angle (degrees) 179.96608015
Shift along axis -65.67656468
> view matrix models
> #4,-0.36973,0.92846,-0.035518,97.629,0.92876,0.36822,-0.042616,112.23,-0.026488,-0.048744,-0.99846,616.82
> ui mousemode right "move picked models"
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.96357,0.25856,-0.068394,14.541,0.26745,-0.93323,0.2399,386.99,-0.0017975,-0.24946,-0.96838,642.2
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.96357,0.25856,-0.068394,16.228,0.26745,-0.93323,0.2399,402.87,-0.0017975,-0.24946,-0.96838,641.75
> view matrix models
> #4,0.96357,0.25856,-0.068394,-5.4054,0.26745,-0.93323,0.2399,408.04,-0.0017975,-0.24946,-0.96838,641.9
> view matrix models
> #4,0.96357,0.25856,-0.068394,-5.0072,0.26745,-0.93323,0.2399,408.33,-0.0017975,-0.24946,-0.96838,641.03
> view matrix models
> #4,0.96357,0.25856,-0.068394,-3.0847,0.26745,-0.93323,0.2399,410.32,-0.0017975,-0.24946,-0.96838,645.44
> fitmap #4 inMap #2
Fit molecule 7Z6S bioassembly 1 (#4) to map emd_14529 (1).map (#2) using 19134
atoms
average map value = 0.06114, steps = 496
shifted from previous position = 9.68
rotated from previous position = 15.8 degrees
atoms outside contour = 8672, contour level = 0.043965
Position of 7Z6S bioassembly 1 (#4) relative to emd_14529 (1).map (#2)
coordinates:
Matrix rotation and translation
0.98217560 0.17997126 0.05423503 -68.83585876
0.17961720 -0.98367083 0.01137365 452.83556960
0.05539635 -0.00142938 -0.99846342 611.26255693
Axis -0.99553388 -0.09030135 -0.02753104
Axis point 0.00000000 230.52725201 305.85028210
Rotation angle (degrees) 179.63157234
Shift along axis 10.80807325
> view matrix models
> #4,0.98465,0.16711,0.050412,-24.368,0.16667,-0.98593,0.012841,500,0.051849,-0.0042416,-0.99865,597.14
> view matrix models
> #4,0.98465,0.16711,0.050412,-22.164,0.16667,-0.98593,0.012841,500.62,0.051849,-0.0042416,-0.99865,600.16
> view matrix models
> #4,0.98465,0.16711,0.050412,-22.355,0.16667,-0.98593,0.012841,500.62,0.051849,-0.0042416,-0.99865,599.95
> view matrix models
> #4,0.98465,0.16711,0.050412,-23.042,0.16667,-0.98593,0.012841,500.04,0.051849,-0.0042416,-0.99865,595.27
> fitmap #4 inMap #2
Fit molecule 7Z6S bioassembly 1 (#4) to map emd_14529 (1).map (#2) using 19134
atoms
average map value = 0.06114, steps = 220
shifted from previous position = 7.69
rotated from previous position = 0.0508 degrees
atoms outside contour = 8670, contour level = 0.043965
Position of 7Z6S bioassembly 1 (#4) relative to emd_14529 (1).map (#2)
coordinates:
Matrix rotation and translation
0.98232368 0.17913623 0.05431757 -68.72013540
0.17876958 -0.98382288 0.01157515 452.94621533
0.05551240 -0.00166022 -0.99845662 611.27760110
Axis -0.99557106 -0.08987550 -0.02757990
Axis point 0.00000000 230.59581358 305.83298153
Rotation angle (degrees) 179.61914487
Shift along axis 10.84803431
> select #5
2 models selected
> select #4/F:289
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #4/F:289
4 atoms, 3 bonds, 1 residue, 1 model selected
> select up
60 atoms, 61 bonds, 7 residues, 1 model selected
> select up
2722 atoms, 2787 bonds, 332 residues, 1 model selected
> select up
19134 atoms, 19576 bonds, 2400 residues, 1 model selected
> select down
2722 atoms, 2787 bonds, 332 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #4/E:320
6 atoms, 5 bonds, 1 residue, 1 model selected
> select up
72 atoms, 72 bonds, 10 residues, 1 model selected
> select up
2722 atoms, 2787 bonds, 332 residues, 1 model selected
> select up
16412 atoms, 16789 bonds, 2068 residues, 1 model selected
> select down
2722 atoms, 2787 bonds, 332 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select add #4
13690 atoms, 14002 bonds, 4 pseudobonds, 1736 residues, 2 models selected
> view matrix models
> #4,0.98479,0.16627,0.050497,-21.144,0.16582,-0.98607,0.013041,498.45,0.051962,-0.0044694,-0.99864,597.29
> fitmap #4 inMap #2
Fit molecule 7Z6S bioassembly 1 (#4) to map emd_14529 (1).map (#2) using 13690
atoms
average map value = 0.08595, steps = 132
shifted from previous position = 10.1
rotated from previous position = 11.6 degrees
atoms outside contour = 3108, contour level = 0.043965
Position of 7Z6S bioassembly 1 (#4) relative to emd_14529 (1).map (#2)
coordinates:
Matrix rotation and translation
0.92933803 0.36885734 0.01658562 -88.38315901
0.36890242 -0.92946806 0.00036574 412.37999121
0.01555071 0.00577858 -0.99986238 615.82947850
Axis 0.98217562 0.18778747 0.00818000
Axis point 0.00000000 214.20726243 308.57259506
Rotation angle (degrees) 179.84211907
Shift along axis -4.33050824
> view matrix models
> #4,0.93413,0.35671,0.012617,-40.202,0.35671,-0.93421,0.002328,464.06,0.012617,0.002326,-0.99992,559.44
> fitmap #4 inMap #2
Fit molecule 7Z6S bioassembly 1 (#4) to map emd_14529 (1).map (#2) using 13690
atoms
average map value = 0.09005, steps = 100
shifted from previous position = 6.2
rotated from previous position = 0.393 degrees
atoms outside contour = 3181, contour level = 0.043965
Position of 7Z6S bioassembly 1 (#4) relative to emd_14529 (1).map (#2)
coordinates:
Matrix rotation and translation
0.92874649 0.37057971 0.01003144 -86.89372353
0.37060299 -0.92879124 -0.00050324 411.57346932
0.00913062 0.00418506 -0.99994956 576.30879313
Axis 0.98202505 0.18868757 0.00487832
Axis point 0.00000000 213.78444008 288.62088974
Rotation angle (degrees) 179.86323143
Shift along axis -4.86159970
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.93317,0.35551,0.053004,-47.698,0.35431,-0.93462,0.03083,455.08,0.060499,-0.0099895,-0.99812,547.49
> view matrix models
> #4,0.80283,0.58827,0.097035,-81.782,0.59342,-0.80414,-0.034697,402.7,0.057619,0.085439,-0.99468,528.13
> fitmap #4 inMap #2
Fit molecule 7Z6S bioassembly 1 (#4) to map emd_14529 (1).map (#2) using 13690
atoms
average map value = 0.09084, steps = 96
shifted from previous position = 3.96
rotated from previous position = 6.97 degrees
atoms outside contour = 3153, contour level = 0.043965
Position of 7Z6S bioassembly 1 (#4) relative to emd_14529 (1).map (#2)
coordinates:
Matrix rotation and translation
0.81223568 0.58326550 -0.00863434 -102.92475167
0.58332729 -0.81218365 0.00932733 344.69607357
-0.00157236 -0.01261264 -0.99991922 584.16369701
Axis -0.95190058 -0.30639532 0.00268072
Axis point 0.00000000 190.68078403 290.89924320
Rotation angle (degrees) 179.33969187
Shift along axis -6.07315554
> view matrix models
> #4,0.96757,0.23627,0.089349,-39.269,0.22604,-0.96774,0.11127,461.56,0.11276,-0.087467,-0.98977,553.85
> fitmap #4 inMap #2
Fit molecule 7Z6S bioassembly 1 (#4) to map emd_14529 (1).map (#2) using 13690
atoms
average map value = 0.09005, steps = 152
shifted from previous position = 3.74
rotated from previous position = 10.9 degrees
atoms outside contour = 3179, contour level = 0.043965
Position of 7Z6S bioassembly 1 (#4) relative to emd_14529 (1).map (#2)
coordinates:
Matrix rotation and translation
0.92920342 0.36943218 0.01004270 -86.75438411
0.36945696 -0.92924760 -0.00066754 411.90911221
0.00908554 0.00433063 -0.99994935 576.28137392
Axis 0.98214137 0.18808144 0.00486912
Axis point 0.00000000 213.88807574 288.62313014
Rotation angle (degrees) 179.85420910
Shift along axis -4.92662488
> view matrix models
> #4,0.93471,0.35479,0.020866,-39.528,0.3547,-0.93495,0.0079621,460.98,0.022334,-4.1168e-05,-0.99975,552.85
> view matrix models
> #4,0.857,0.50386,-0.10803,-21.783,0.51419,-0.84998,0.11466,387.56,-0.034048,-0.15381,-0.98751,590.52
> fitmap #4 inMap #2
Fit molecule 7Z6S bioassembly 1 (#4) to map emd_14529 (1).map (#2) using 13690
atoms
average map value = 0.09085, steps = 144
shifted from previous position = 3.39
rotated from previous position = 8.97 degrees
atoms outside contour = 3148, contour level = 0.043965
Position of 7Z6S bioassembly 1 (#4) relative to emd_14529 (1).map (#2)
coordinates:
Matrix rotation and translation
0.81457154 0.57999717 -0.00874604 -102.66500325
0.58006046 -0.81452075 0.00926302 345.77041342
-0.00175131 -0.01261862 -0.99991885 584.20856620
Axis -0.95251389 -0.30448268 0.00275528
Axis point 0.00000000 191.05560010 290.91875957
Rotation angle (degrees) 179.34187139
Shift along axis -5.88160084
> fitmap #4 inMap #2
Fit molecule 7Z6S bioassembly 1 (#4) to map emd_14529 (1).map (#2) using 13690
atoms
average map value = 0.09085, steps = 48
shifted from previous position = 0.0361
rotated from previous position = 0.101 degrees
atoms outside contour = 3141, contour level = 0.043965
Position of 7Z6S bioassembly 1 (#4) relative to emd_14529 (1).map (#2)
coordinates:
Matrix rotation and translation
0.81354964 0.58143055 -0.00868830 -102.78690736
0.58149313 -0.81349789 0.00932285 345.26622075
-0.00164733 -0.01263679 -0.99991879 584.18021908
Axis -0.95224562 -0.30532101 0.00271360
Axis point 0.00000000 190.88004960 290.90394228
Rotation angle (degrees) 179.33933955
Shift along axis -5.95341772
> fitmap #4 inMap #2
Fit molecule 7Z6S bioassembly 1 (#4) to map emd_14529 (1).map (#2) using 13690
atoms
average map value = 0.09085, steps = 44
shifted from previous position = 0.0208
rotated from previous position = 0.0232 degrees
atoms outside contour = 3136, contour level = 0.043965
Position of 7Z6S bioassembly 1 (#4) relative to emd_14529 (1).map (#2)
coordinates:
Matrix rotation and translation
0.81377221 0.58111801 -0.00875485 -102.74321567
0.58118164 -0.81371914 0.00943730 345.34927781
-0.00163981 -0.01276797 -0.99991714 584.21878661
Axis -0.95230402 -0.30513868 0.00272893
Axis point 0.00000000 190.92341035 290.91070067
Rotation angle (degrees) 179.33199030
Shift along axis -5.94235425
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.82128,0.57039,-0.012603,-54.806,0.57052,-0.8212,0.011729,398.49,-0.0036592,-0.016823,-0.99985,562.34
> view matrix models
> #4,0.82128,0.57039,-0.012603,-56.015,0.57052,-0.8212,0.011729,399.22,-0.0036592,-0.016823,-0.99985,565.92
> fitmap #4 inMap #2
Fit molecule 7Z6S bioassembly 1 (#4) to map emd_14529 (1).map (#2) using 13690
atoms
average map value = 0.09085, steps = 64
shifted from previous position = 5.31
rotated from previous position = 0.0408 degrees
atoms outside contour = 3136, contour level = 0.043965
Position of 7Z6S bioassembly 1 (#4) relative to emd_14529 (1).map (#2)
coordinates:
Matrix rotation and translation
0.81336081 0.58169461 -0.00869330 -102.80052889
0.58175745 -0.81330731 0.00946008 345.16218159
-0.00156744 -0.01275185 -0.99991746 584.20130511
Axis -0.95219600 -0.30547588 0.00269408
Axis point 0.00000000 190.86000385 290.90380100
Rotation angle (degrees) 179.33171393
Shift along axis -5.97858415
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.76566,0.60591,-0.21594,2.7003,0.61077,-0.79013,-0.051435,398.52,-0.20178,-0.092506,-0.97505,608.09
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.76566,0.60591,-0.21594,-0.63322,0.61077,-0.79013,-0.051435,398.14,-0.20178,-0.092506,-0.97505,608.7
> view matrix models
> #4,0.76566,0.60591,-0.21594,-5.3475,0.61077,-0.79013,-0.051435,397.62,-0.20178,-0.092506,-0.97505,609.72
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.79149,0.61116,0.0050369,-68.213,0.61105,-0.79113,-0.027012,391.45,-0.012524,0.024458,-0.99962,558.48
> fitmap #4 inMap #2
Fit molecule 7Z6S bioassembly 1 (#4) to map emd_14529 (1).map (#2) using 13690
atoms
average map value = 0.09084, steps = 88
shifted from previous position = 8.39
rotated from previous position = 3.71 degrees
atoms outside contour = 3155, contour level = 0.043965
Position of 7Z6S bioassembly 1 (#4) relative to emd_14529 (1).map (#2)
coordinates:
Matrix rotation and translation
0.81290299 0.58233491 -0.00864730 -102.85545845
0.58239684 -0.81285168 0.00927734 345.01323240
-0.00162646 -0.01257774 -0.99991957 584.16868315
Axis -0.95207584 -0.30585014 0.00269783
Axis point 0.00000000 190.78824020 290.90431707
Rotation angle (degrees) 179.34236798
Shift along axis -6.02015930
> view matrix models
> #4,0.89965,0.43586,-0.025534,-36.975,0.43645,-0.89935,0.026124,431.82,-0.011578,-0.034647,-0.99933,568.36
> fitmap #4 inMap #2
Fit molecule 7Z6S bioassembly 1 (#4) to map emd_14529 (1).map (#2) using 13690
atoms
average map value = 0.09085, steps = 172
shifted from previous position = 0.705
rotated from previous position = 8.89 degrees
atoms outside contour = 3149, contour level = 0.043965
Position of 7Z6S bioassembly 1 (#4) relative to emd_14529 (1).map (#2)
coordinates:
Matrix rotation and translation
0.81475479 0.57973938 -0.00876802 -102.63983946
0.57980297 -0.81470405 0.00926429 345.85443442
-0.00177246 -0.01263185 -0.99991864 584.21540809
Axis -0.95256198 -0.30433208 0.00276646
Axis point 0.00000000 191.08565694 290.92077044
Rotation angle (degrees) 179.34146838
Shift along axis -5.86757993
> fitmap #4 inMap #2
Fit molecule 7Z6S bioassembly 1 (#4) to map emd_14529 (1).map (#2) using 13690
atoms
average map value = 0.09085, steps = 44
shifted from previous position = 0.0297
rotated from previous position = 0.158 degrees
atoms outside contour = 3144, contour level = 0.043965
Position of 7Z6S bioassembly 1 (#4) relative to emd_14529 (1).map (#2)
coordinates:
Matrix rotation and translation
0.81315541 0.58198098 -0.00874184 -102.80657074
0.58204448 -0.81310149 0.00949665 345.05115378
-0.00158113 -0.01281039 -0.99991669 584.21440639
Axis -0.95214206 -0.30564384 0.00271057
Axis point 0.00000000 190.82336685 290.90518020
Rotation angle (degrees) 179.32881413
Shift along axis -5.99274515
> fitmap #4 inMap #2
Fit molecule 7Z6S bioassembly 1 (#4) to map emd_14529 (1).map (#2) using 13690
atoms
average map value = 0.09084, steps = 56
shifted from previous position = 0.0323
rotated from previous position = 0.0588 degrees
atoms outside contour = 3147, contour level = 0.043965
Position of 7Z6S bioassembly 1 (#4) relative to emd_14529 (1).map (#2)
coordinates:
Matrix rotation and translation
0.81370132 0.58121937 -0.00861400 -102.78449723
0.58128066 -0.81365219 0.00910544 345.42674236
-0.00171654 -0.01241626 -0.99992144 584.15127392
Axis -0.95228551 -0.30519659 0.00271214
Axis point 0.00000000 190.91701758 290.90990506
Rotation angle (degrees) 179.35254241
Shift along axis -5.95857509
> view matrix models
> #4,0.82868,0.5594,-0.019251,-50.32,0.55879,-0.82481,0.086235,379.26,0.032361,-0.082218,-0.99609,569.02
> view matrix models
> #4,0.81285,0.58246,-0.0035285,-56.106,0.58066,-0.81078,-0.073938,413.92,-0.045926,0.058051,-0.99726,555.6
> view matrix models
> #4,0.81683,0.57683,-0.0079664,-54.558,0.57631,-0.81656,-0.033098,405.3,-0.025597,0.022444,-0.99942,559.56
> view matrix models
> #4,0.89661,0.43796,-0.065414,-26.528,0.43378,-0.89836,-0.069097,456.73,-0.089028,0.033578,-0.99546,567.82
> fitmap #4 inMap #2
Fit molecule 7Z6S bioassembly 1 (#4) to map emd_14529 (1).map (#2) using 13690
atoms
average map value = 0.09085, steps = 192
shifted from previous position = 0.684
rotated from previous position = 10.4 degrees
atoms outside contour = 3148, contour level = 0.043965
Position of 7Z6S bioassembly 1 (#4) relative to emd_14529 (1).map (#2)
coordinates:
Matrix rotation and translation
0.81479115 0.57968823 -0.00877164 -102.63523959
0.57975187 -0.81474044 0.00926168 345.87185062
-0.00177772 -0.01263171 -0.99991864 584.21662303
Axis -0.95257153 -0.30430219 0.00276876
Axis point 0.00000000 191.09160233 290.92135777
Rotation angle (degrees) 179.34155789
Shift along axis -5.86459711
> view matrix models
> #4,0.90814,0.41866,0.00029527,-41.766,0.41853,-0.90788,0.024333,437.23,0.010455,-0.021974,-0.9997,561.95
> view matrix models
> #4,0.90102,0.42495,0.087088,-64.17,0.42638,-0.90454,0.0024478,440.8,0.079815,0.034927,-0.9962,537.14
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.90102,0.42495,0.087088,-62.939,0.42638,-0.90454,0.0024478,444.1,0.079815,0.034927,-0.9962,540.01
> fitmap #4 inMap #2
Fit molecule 7Z6S bioassembly 1 (#4) to map emd_14529 (1).map (#2) using 13690
atoms
average map value = 0.09085, steps = 216
shifted from previous position = 4.94
rotated from previous position = 11 degrees
atoms outside contour = 3148, contour level = 0.043965
Position of 7Z6S bioassembly 1 (#4) relative to emd_14529 (1).map (#2)
coordinates:
Matrix rotation and translation
0.81454092 0.58004018 -0.00874451 -102.67050420
0.58010345 -0.81449014 0.00926209 345.75755277
-0.00174994 -0.01261707 -0.99991887 584.20800433
Axis -0.95250585 -0.30450782 0.00275454
Axis point 0.00000000 191.05137093 290.91864919
Rotation angle (degrees) 179.34194037
Shift along axis -5.88239656
> select #4/B:420
6 atoms, 5 bonds, 1 residue, 1 model selected
> select up
160 atoms, 162 bonds, 19 residues, 1 model selected
> select up
3367 atoms, 3442 bonds, 429 residues, 1 model selected
> select up
13690 atoms, 14002 bonds, 1736 residues, 1 model selected
> select down
3367 atoms, 3442 bonds, 429 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #4/D:426
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
174 atoms, 175 bonds, 22 residues, 1 model selected
> select up
3102 atoms, 3173 bonds, 395 residues, 1 model selected
> select up
3206 atoms, 3281 bonds, 408 residues, 1 model selected
> select up
3414 atoms, 3493 bonds, 435 residues, 1 model selected
> select up
10323 atoms, 10560 bonds, 1307 residues, 1 model selected
> select down
3414 atoms, 3493 bonds, 435 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select add #4
6909 atoms, 7067 bonds, 2 pseudobonds, 872 residues, 2 models selected
> fitmap #4 inMap #2
Fit molecule 7Z6S bioassembly 1 (#4) to map emd_14529 (1).map (#2) using 6909
atoms
average map value = 0.0895, steps = 104
shifted from previous position = 0.694
rotated from previous position = 6.35 degrees
atoms outside contour = 1496, contour level = 0.043965
Position of 7Z6S bioassembly 1 (#4) relative to emd_14529 (1).map (#2)
coordinates:
Matrix rotation and translation
0.75215516 0.65642841 -0.05800307 -95.87228185
0.65735367 -0.75357144 -0.00403006 322.28287762
-0.04635490 -0.03509730 -0.99830827 596.24172471
Axis -0.93598560 -0.35093290 0.02787575
Axis point 0.00000000 181.75834430 295.27500690
Rotation angle (degrees) 179.04907550
Shift along axis -6.74390646
> view matrix models
> #4,0.76048,0.64639,-0.062016,-45.503,0.64759,-0.76199,-0.0010978,377.42,-0.047965,-0.039326,-0.99807,570.17
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.67735,0.66199,0.32089,-116.88,0.69117,-0.72205,0.030628,354.64,0.25197,0.20105,-0.94662,456.59
> view matrix models
> #4,0.71307,0.70109,0.0015109,-61.605,0.70107,-0.71304,-0.0088887,359.65,-0.0051544,0.0073975,-0.99996,553.5
> view matrix models
> #4,0.67981,0.7218,0.12987,-87.633,0.72707,-0.68649,0.0095424,345.63,0.096043,0.087938,-0.99149,517.23
> fitmap #4 inMap #2
Fit molecule 7Z6S bioassembly 1 (#4) to map emd_14529 (1).map (#2) using 6909
atoms
average map value = 0.09138, steps = 148
shifted from previous position = 9.79
rotated from previous position = 15.1 degrees
atoms outside contour = 1339, contour level = 0.043965
Position of 7Z6S bioassembly 1 (#4) relative to emd_14529 (1).map (#2)
coordinates:
Matrix rotation and translation
0.54624094 0.83457496 -0.07145259 -89.86790678
0.83621280 -0.54828706 -0.01137788 252.82939223
-0.04867223 -0.05353450 -0.99737910 603.22685449
Axis -0.87925415 -0.47512653 0.03416023
Axis point 0.00000000 154.81298303 298.21048976
Rotation angle (degrees) 178.62631998
Shift along axis -20.50285272
> color #5 #b2ffff87 models
> select clear
> select add #4
6909 atoms, 7067 bonds, 2 pseudobonds, 872 residues, 2 models selected
> view matrix models
> #4,0.90419,0.42656,0.022177,-45.843,0.42695,-0.90103,-0.076565,459.01,-0.012678,0.078697,-0.99682,548.38
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.90419,0.42656,0.022177,-44.744,0.42695,-0.90103,-0.076565,459.77,-0.012678,0.078697,-0.99682,550.67
> view matrix models
> #4,0.90419,0.42656,0.022177,-44.734,0.42695,-0.90103,-0.076565,459.84,-0.012678,0.078697,-0.99682,550.42
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.94511,0.32577,0.025357,-32.806,0.32657,-0.93914,-0.10662,492.22,-0.01092,0.10905,-0.99398,543.45
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.94511,0.32577,0.025357,-32.751,0.32657,-0.93914,-0.10662,491.36,-0.01092,0.10905,-0.99398,543.04
> view matrix models
> #4,0.94511,0.32577,0.025357,-33.048,0.32657,-0.93914,-0.10662,492.84,-0.01092,0.10905,-0.99398,542.34
> view matrix models
> #4,0.94511,0.32577,0.025357,-33.899,0.32657,-0.93914,-0.10662,491.79,-0.01092,0.10905,-0.99398,542.93
> view matrix models
> #4,0.94511,0.32577,0.025357,-37.723,0.32657,-0.93914,-0.10662,492.44,-0.01092,0.10905,-0.99398,545.47
> view matrix models
> #4,0.94511,0.32577,0.025357,-38.191,0.32657,-0.93914,-0.10662,491.9,-0.01092,0.10905,-0.99398,541.63
> view matrix models
> #4,0.94511,0.32577,0.025357,-38.338,0.32657,-0.93914,-0.10662,491.97,-0.01092,0.10905,-0.99398,541.46
> fitmap #4 inMap #2
Fit molecule 7Z6S bioassembly 1 (#4) to map emd_14529 (1).map (#2) using 6909
atoms
average map value = 0.08926, steps = 196
shifted from previous position = 3.79
rotated from previous position = 12.1 degrees
atoms outside contour = 1448, contour level = 0.043965
Position of 7Z6S bioassembly 1 (#4) relative to emd_14529 (1).map (#2)
coordinates:
Matrix rotation and translation
0.91764483 0.39738106 -0.00403252 -87.25716070
0.39610075 -0.91377379 0.09012025 384.81966184
0.03212726 -0.08429567 -0.99592273 590.40257698
Axis -0.97915291 -0.20299732 -0.00718751
Axis point 0.00000000 214.90801141 286.73899672
Rotation angle (degrees) 174.89019798
Shift along axis 3.07722152
> view matrix models
> #4,0.92286,0.38508,-0.0068121,-38.789,0.38403,-0.91869,0.092335,431.92,0.029298,-0.087828,-0.9957,570.51
> fitmap #4 inMap #2
Fit molecule 7Z6S bioassembly 1 (#4) to map emd_14529 (1).map (#2) using 6909
atoms
average map value = 0.08924, steps = 136
shifted from previous position = 2.97
rotated from previous position = 3.83 degrees
atoms outside contour = 1422, contour level = 0.043965
Position of 7Z6S bioassembly 1 (#4) relative to emd_14529 (1).map (#2)
coordinates:
Matrix rotation and translation
0.89614627 0.44145700 -0.04513942 -83.70074501
0.44369675 -0.88967262 0.10777669 367.34435762
0.00741947 -0.11661190 -0.99314984 601.86901971
Axis -0.97360135 -0.22804817 0.00971805
Axis point 0.00000000 211.34279546 289.58648682
Rotation angle (degrees) 173.38274068
Shift along axis 3.56794349
> volume #5 level 0.007768
> view matrix models
> #4,0.90188,0.42934,-0.047674,-34.799,0.43195,-0.8951,0.11052,417.85,0.004778,-0.12027,-0.99273,583.12
> view matrix models
> #4,0.90188,0.42934,-0.047674,-34.24,0.43195,-0.8951,0.11052,418.01,0.004778,-0.12027,-0.99273,582.62
> fitmap #4 inMap #2
Fit molecule 7Z6S bioassembly 1 (#4) to map emd_14529 (1).map (#2) using 6909
atoms
average map value = 0.08924, steps = 88
shifted from previous position = 1.76
rotated from previous position = 0.14 degrees
atoms outside contour = 1423, contour level = 0.043965
Position of 7Z6S bioassembly 1 (#4) relative to emd_14529 (1).map (#2)
coordinates:
Matrix rotation and translation
0.89517148 0.44351065 -0.04434331 -84.11273897
0.44564052 -0.88866666 0.10805597 366.74825559
0.00851755 -0.11648980 -0.99315536 601.65716038
Axis -0.97335000 -0.22913868 0.00923248
Axis point 0.00000000 211.15832826 289.50481378
Rotation angle (degrees) 173.37636686
Shift along axis 3.38971133
> color #5 #b2ffffc9 models
> close #4
> open
> /Users/matteogiono/Desktop/PhD/MT_Processing/MT_structures/Tubulin_for_building.pdb
Chain information for Tubulin_for_building.pdb #4
---
Chain | Description
A E | No description available
B F G H | No description available
52 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> select #4/B:423@CD
1 atom, 1 residue, 1 model selected
> select up
17 atoms, 16 bonds, 1 residue, 1 model selected
> select up
311 atoms, 313 bonds, 20 residues, 1 model selected
> select up
6577 atoms, 6652 bonds, 426 residues, 1 model selected
> select up
39590 atoms, 40044 bonds, 2560 residues, 1 model selected
> select up
43123 atoms, 43665 bonds, 2999 residues, 9 models selected
> select down
39590 atoms, 40044 bonds, 2560 residues, 1 model selected
> hide sel atoms
> show sel cartoons
> view matrix models #4,1,0,0,135.07,0,1,0,106.64,0,0,1,128.51
> view matrix models #4,1,0,0,185.58,0,1,0,171.28,0,0,1,150.28
> view matrix models #4,1,0,0,199.12,0,1,0,232.59,0,0,1,175.17
> view matrix models #4,1,0,0,196.68,0,1,0,248.69,0,0,1,179.06
> view matrix models #4,1,0,0,120.33,0,1,0,219.04,0,0,1,188.96
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.86217,0.5066,-0.0039097,87.901,-0.49654,0.84347,-0.20494,294.2,-0.10052,0.17863,0.97877,183.8
> view matrix models
> #4,0.53835,0.83193,0.13447,76.456,-0.84102,0.54051,0.02305,333.09,-0.053509,-0.12551,0.99065,205.67
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.53835,0.83193,0.13447,76.194,-0.84102,0.54051,0.02305,341.71,-0.053509,-0.12551,0.99065,202.78
> fitmap #4 inMap #2
Fit molecule Tubulin_for_building.pdb (#4) to map emd_14529 (1).map (#2) using
39590 atoms
average map value = 0.1129, steps = 160
shifted from previous position = 7.44
rotated from previous position = 7.55 degrees
atoms outside contour = 10213, contour level = 0.043965
Position of Tubulin_for_building.pdb (#4) relative to emd_14529 (1).map (#2)
coordinates:
Matrix rotation and translation
0.51996603 0.85415569 0.00730671 36.98625183
-0.85418277 0.51997121 0.00132228 297.66395460
-0.00266984 -0.00692880 0.99997243 216.61490369
Axis -0.00482975 0.00583975 -0.99997129
Axis point 283.92701566 117.48091660 0.00000000
Rotation angle (degrees) 58.67077803
Shift along axis -215.04903634
> view matrix models
> #4,0.50876,0.86084,0.011296,87.827,-0.86088,0.5088,-0.00095205,349.63,-0.0065668,-0.0092399,0.99994,150.87
> fitmap #4 inMap #2
Fit molecule Tubulin_for_building.pdb (#4) to map emd_14529 (1).map (#2) using
39590 atoms
average map value = 0.1138, steps = 132
shifted from previous position = 5.27
rotated from previous position = 0.236 degrees
atoms outside contour = 10248, contour level = 0.043965
Position of Tubulin_for_building.pdb (#4) relative to emd_14529 (1).map (#2)
coordinates:
Matrix rotation and translation
0.51913451 0.85465842 0.00763866 37.08558640
-0.85466971 0.51916524 -0.00267111 297.73828258
-0.00624861 -0.00514186 0.99996726 175.40228863
Axis -0.00144540 0.00812412 -0.99996595
Axis point 284.27468490 116.84480860 0.00000000
Rotation angle (degrees) 58.72585341
Shift along axis -173.03105780
> fitmap #4 inMap #2
Fit molecule Tubulin_for_building.pdb (#4) to map emd_14529 (1).map (#2) using
39590 atoms
average map value = 0.1138, steps = 76
shifted from previous position = 0.00207
rotated from previous position = 0.00581 degrees
atoms outside contour = 10249, contour level = 0.043965
Position of Tubulin_for_building.pdb (#4) relative to emd_14529 (1).map (#2)
coordinates:
Matrix rotation and translation
0.51912908 0.85466080 0.00773989 37.07668941
-0.85467263 0.51916044 -0.00266940 297.74049010
-0.00629968 -0.00522931 0.99996648 175.41330696
Axis -0.00149755 0.00821319 -0.99996515
Axis point 284.27942529 116.86989784 0.00000000
Rotation angle (degrees) 58.72622200
Shift along axis -173.01731832
> hide #3 models
> show #3 models
> hide #3 models
> hide #!4 models
> show #!4 models
> show #!2 models
> hide #!2 models
> hide #!5 models
> select clear
> select #4/F:167
20 atoms, 20 bonds, 1 residue, 1 model selected
> select up
111 atoms, 111 bonds, 7 residues, 1 model selected
> select up
6588 atoms, 6663 bonds, 426 residues, 1 model selected
> select up
39590 atoms, 40044 bonds, 2560 residues, 1 model selected
> select down
6588 atoms, 6663 bonds, 426 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #4/E:228
14 atoms, 13 bonds, 1 residue, 1 model selected
> select up
248 atoms, 248 bonds, 15 residues, 1 model selected
> select up
6085 atoms, 6156 bonds, 391 residues, 1 model selected
> select up
6209 atoms, 6281 bonds, 400 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #4/H:399
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #4/E:20
11 atoms, 10 bonds, 1 residue, 1 model selected
> select up
276 atoms, 279 bonds, 19 residues, 1 model selected
> select up
427 atoms, 431 bonds, 28 residues, 1 model selected
> select up
26793 atoms, 27099 bonds, 1734 residues, 1 model selected
> select down
427 atoms, 431 bonds, 28 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #4/H:410
15 atoms, 14 bonds, 1 residue, 1 model selected
> select up
290 atoms, 291 bonds, 19 residues, 1 model selected
> select up
6588 atoms, 6663 bonds, 426 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> show #!5 models
> fitmap #4 inMap #2
Fit molecule Tubulin_for_building.pdb (#4) to map emd_14529 (1).map (#2) using
19778 atoms
average map value = 0.09395, steps = 88
shifted from previous position = 1.02
rotated from previous position = 7.78 degrees
atoms outside contour = 4439, contour level = 0.043965
Position of Tubulin_for_building.pdb (#4) relative to emd_14529 (1).map (#2)
coordinates:
Matrix rotation and translation
0.62989973 0.77667336 0.00219541 38.71628943
-0.77667474 0.62988985 0.00389030 280.56576325
0.00163863 -0.00415562 0.99999002 175.25905257
Axis -0.00517966 0.00035843 -0.99998652
Axis point 313.36092469 100.64328904 0.00000000
Rotation angle (degrees) 50.95800747
Shift along axis -175.35666313
> select #4/A:427
10 atoms, 9 bonds, 1 residue, 1 model selected
> select #4/A:426
10 atoms, 9 bonds, 1 residue, 1 model selected
> select add #4
19778 atoms, 20005 bonds, 1 pseudobond, 1280 residues, 2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.48534,0.87355,-0.036883,89.76,-0.87384,0.48604,0.012901,348.54,0.029196,0.025968,0.99924,148.55
> fitmap #4 inMap #2
Fit molecule Tubulin_for_building.pdb (#4) to map emd_14529 (1).map (#2) using
19778 atoms
average map value = 0.09395, steps = 112
shifted from previous position = 0.959
rotated from previous position = 9.58 degrees
atoms outside contour = 4437, contour level = 0.043965
Position of Tubulin_for_building.pdb (#4) relative to emd_14529 (1).map (#2)
coordinates:
Matrix rotation and translation
0.62995935 0.77662487 0.00224347 38.71259426
-0.77662646 0.62994943 0.00387991 280.55700199
0.00159996 -0.00418652 0.99998996 175.26640608
Axis -0.00519319 0.00041429 -0.99998643
Axis point 313.38806139 100.64620741 0.00000000
Rotation angle (degrees) 50.95361292
Shift along axis -175.34883711
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.61977,0.78476,0.0062664,84.602,-0.78478,0.61977,0.0016714,331.2,-0.0025721,-0.0059536,0.99998,150.58
> view matrix models
> #4,0.61977,0.78476,0.0062664,84.906,-0.78478,0.61977,0.0016714,329.84,-0.0025721,-0.0059536,0.99998,149.95
> view matrix models
> #4,0.61977,0.78476,0.0062664,83.379,-0.78478,0.61977,0.0016714,331.39,-0.0025721,-0.0059536,0.99998,153.42
> fitmap #4 inMap #2
Fit molecule Tubulin_for_building.pdb (#4) to map emd_14529 (1).map (#2) using
19778 atoms
average map value = 0.09394, steps = 56
shifted from previous position = 3.13
rotated from previous position = 0.249 degrees
atoms outside contour = 4410, contour level = 0.043965
Position of Tubulin_for_building.pdb (#4) relative to emd_14529 (1).map (#2)
coordinates:
Matrix rotation and translation
0.63325575 0.77393622 0.00314536 38.70874647
-0.77394190 0.63324442 0.00392976 280.03866051
0.00104960 -0.00492287 0.99998733 175.38060404
Axis -0.00571911 0.00135393 -0.99998273
Axis point 314.58599547 100.35188802 0.00000000
Rotation angle (degrees) 50.71015185
Shift along axis -175.21980151
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.54651,0.83745,0.00070151,86.104,-0.83744,0.5465,-0.0049246,341.49,-0.0045075,0.0021038,0.99999,153.18
> view matrix models
> #4,0.48765,0.87261,-0.027205,88.878,-0.87277,0.48804,0.009479,348.56,0.021549,0.019121,0.99958,149.73
> fitmap #4 inMap #2
Fit molecule Tubulin_for_building.pdb (#4) to map emd_14529 (1).map (#2) using
19778 atoms
average map value = 0.09395, steps = 100
shifted from previous position = 0.931
rotated from previous position = 9.24 degrees
atoms outside contour = 4445, contour level = 0.043965
Position of Tubulin_for_building.pdb (#4) relative to emd_14529 (1).map (#2)
coordinates:
Matrix rotation and translation
0.62911204 0.77731196 0.00203683 38.71343547
-0.77731271 0.62910249 0.00387375 280.69150586
0.00172974 -0.00402028 0.99999042 175.24110348
Axis -0.00507771 0.00019753 -0.99998709
Axis point 313.08676952 100.72816218 0.00000000
Rotation angle (degrees) 51.01606396
Shift along axis -175.37997072
> view matrix models
> #4,0.49343,0.86859,-0.045615,90.483,-0.86978,0.49296,-0.021832,350.59,0.003523,0.050448,0.99872,147.81
> view matrix models
> #4,0.49041,0.87131,0.01773,84.887,-0.87145,0.49048,0.00053409,349,-0.0082307,-0.015713,0.99984,155.25
> view matrix models
> #4,0.39952,0.91642,-0.023523,89.947,-0.91494,0.39701,-0.07259,367.82,-0.057184,0.050524,0.99708,152
> fitmap #4 inMap #2
Fit molecule Tubulin_for_building.pdb (#4) to map emd_14529 (1).map (#2) using
19778 atoms
average map value = 0.09395, steps = 208
shifted from previous position = 1.48
rotated from previous position = 15.5 degrees
atoms outside contour = 4422, contour level = 0.043965
Position of Tubulin_for_building.pdb (#4) relative to emd_14529 (1).map (#2)
coordinates:
Matrix rotation and translation
0.63043635 0.77623770 0.00224587 38.72609930
-0.77623903 0.63042572 0.00404783 280.47845230
0.00172622 -0.00429523 0.99998929 175.26226065
Axis -0.00537396 0.00033472 -0.99998550
Axis point 313.51487745 100.58781584 0.00000000
Rotation angle (degrees) 50.91846467
Shift along axis -175.37395163
> view matrix models
> #4,0.34788,0.92194,0.17033,75.95,-0.9318,0.36006,-0.045783,370.39,-0.10354,-0.14279,0.98432,175.93
> view matrix models
> #4,0.43782,0.89829,0.03728,83.952,-0.89896,0.43801,0.0034254,355.95,-0.013252,-0.035013,0.9993,157.6
> fitmap #4 inMap #2
Fit molecule Tubulin_for_building.pdb (#4) to map emd_14529 (1).map (#2) using
19778 atoms
average map value = 0.09395, steps = 128
shifted from previous position = 1.25
rotated from previous position = 12.5 degrees
atoms outside contour = 4436, contour level = 0.043965
Position of Tubulin_for_building.pdb (#4) relative to emd_14529 (1).map (#2)
coordinates:
Matrix rotation and translation
0.63018119 0.77644473 0.00229188 38.71254806
-0.77644652 0.63017118 0.00388402 280.52112826
0.00157145 -0.00422716 0.99998983 175.27289101
Axis -0.00522321 0.00046392 -0.99998625
Axis point 313.46522044 100.62356512 0.00000000
Rotation angle (degrees) 50.93725276
Shift along axis -175.34254516
> view matrix models
> #4,0.49507,0.86864,0.019074,84.735,-0.86874,0.49455,0.026638,346.13,0.013706,-0.029758,0.99946,155.25
> view matrix models
> #4,0.45062,0.89268,-0.0074947,87.565,-0.89178,0.45052,0.041931,350.83,0.040808,-0.012211,0.99909,151.69
> view matrix models
> #4,0.4834,0.87496,0.027802,84.109,-0.87533,0.4827,0.028399,347.62,0.011428,-0.038064,0.99921,156.28
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.4834,0.87496,0.027802,84.593,-0.87533,0.4827,0.028399,349.11,0.011428,-0.038064,0.99921,156.97
> fitmap #4 inMap #2
Fit molecule Tubulin_for_building.pdb (#4) to map emd_14529 (1).map (#2) using
19778 atoms
average map value = 0.09395, steps = 112
shifted from previous position = 2.61
rotated from previous position = 9.62 degrees
atoms outside contour = 4437, contour level = 0.043965
Position of Tubulin_for_building.pdb (#4) relative to emd_14529 (1).map (#2)
coordinates:
Matrix rotation and translation
0.63005537 0.77654701 0.00222991 38.71513640
-0.77654852 0.63004541 0.00389511 280.54000566
0.00161979 -0.00418577 0.99998993 175.26529217
Axis -0.00520301 0.00039284 -0.99998639
Axis point 313.41357393 100.62868200 0.00000000
Rotation angle (degrees) 50.94653137
Shift along axis -175.35413527
> view matrix models
> #4,0.61987,0.78468,0.006253,86.969,-0.7847,0.61987,0.0016867,332.73,-0.0025525,-0.0059523,0.99998,151.9
> fitmap #4 inMap #2
Fit molecule Tubulin_for_building.pdb (#4) to map emd_14529 (1).map (#2) using
19778 atoms
average map value = 0.09394, steps = 56
shifted from previous position = 3.58
rotated from previous position = 0.1 degrees
atoms outside contour = 4431, contour level = 0.043965
Position of Tubulin_for_building.pdb (#4) relative to emd_14529 (1).map (#2)
coordinates:
Matrix rotation and translation
0.63135866 0.77548625 0.00270404 38.69719256
-0.77548993 0.63134828 0.00383624 280.32622985
0.00126776 -0.00451900 0.99998899 175.33164416
Axis -0.00538700 0.00092604 -0.99998506
Axis point 313.89982979 100.53496436 0.00000000
Rotation angle (degrees) 50.85035679
Shift along axis -175.27789397
> view matrix models
> #4,0.62118,0.78364,0.0067263,87.73,-0.78366,0.62119,0.0016217,334.01,-0.0029075,-0.0062785,0.99998,150.44
> view matrix models
> #4,0.62118,0.78364,0.0067263,87.075,-0.78366,0.62119,0.0016217,333.68,-0.0029075,-0.0062785,0.99998,152.57
> fitmap #4 inMap #2
Fit molecule Tubulin_for_building.pdb (#4) to map emd_14529 (1).map (#2) using
19778 atoms
average map value = 0.09393, steps = 96
shifted from previous position = 4.36
rotated from previous position = 0.275 degrees
atoms outside contour = 4415, contour level = 0.043965
Position of Tubulin_for_building.pdb (#4) relative to emd_14529 (1).map (#2)
coordinates:
Matrix rotation and translation
0.63494781 0.77254510 0.00391730 38.67901949
-0.77255495 0.63493720 0.00368902 279.78033016
0.00036270 -0.00536867 0.99998552 175.48252700
Axis -0.00586209 0.00230052 -0.99998017
Axis point 315.29862308 100.25002021 0.00000000
Rotation angle (degrees) 50.58481641
Shift along axis -175.06214804
> fitmap #4 inMap #2
Fit molecule Tubulin_for_building.pdb (#4) to map emd_14529 (1).map (#2) using
19778 atoms
average map value = 0.09393, steps = 44
shifted from previous position = 0.0173
rotated from previous position = 0.153 degrees
atoms outside contour = 4413, contour level = 0.043965
Position of Tubulin_for_building.pdb (#4) relative to emd_14529 (1).map (#2)
coordinates:
Matrix rotation and translation
0.63296747 0.77417185 0.00318399 38.69106867
-0.77417789 0.63295698 0.00374966 280.07860495
0.00088755 -0.00483839 0.99998790 175.39261792
Axis -0.00554649 0.00148313 -0.99998352
Axis point 314.51607906 100.38888525 0.00000000
Rotation angle (degrees) 50.73143795
Shift along axis -175.18893434
> volume #5 step 2
> view matrix models
> #4,0.62281,0.78234,0.0072051,87.347,-0.78237,0.62281,0.0015289,332.25,-0.0032913,-0.0065892,0.99997,152.84
> view matrix models
> #4,0.62281,0.78234,0.0072051,87.286,-0.78237,0.62281,0.0015289,333.76,-0.0032913,-0.0065892,0.99997,151.44
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.56768,0.82244,0.036527,84.32,-0.82302,0.56801,0.0017339,342.04,-0.019321,-0.031047,0.99933,155.07
> view matrix models
> #4,0.42828,0.90286,0.037581,85.329,-0.90335,0.42883,-0.0075612,362.42,-0.022942,-0.03071,0.99926,155.28
> fitmap #4 inMap #2
Fit molecule Tubulin_for_building.pdb (#4) to map emd_14529 (1).map (#2) using
19778 atoms
average map value = 0.09395, steps = 172
shifted from previous position = 6.23
rotated from previous position = 13.1 degrees
atoms outside contour = 4440, contour level = 0.043965
Position of Tubulin_for_building.pdb (#4) relative to emd_14529 (1).map (#2)
coordinates:
Matrix rotation and translation
0.63022818 0.77640670 0.00225224 38.71424381
-0.77640829 0.63021814 0.00390726 280.50823223
0.00161422 -0.00421113 0.99998983 175.26655697
Axis -0.00522810 0.00041087 -0.99998625
Axis point 313.46531029 100.60854403 0.00000000
Rotation angle (degrees) 50.93378625
Shift along axis -175.35129573
> view matrix models
> #4,0.50649,0.86136,-0.03915,89.787,-0.86186,0.5071,0.007067,346.09,0.025941,0.030163,0.99921,148.34
> view matrix models
> #4,0.51523,0.85562,-0.049536,90.694,-0.85633,0.51631,0.011269,344.42,0.035218,0.036613,0.99871,147.11
> fitmap #4 inMap #2
Fit molecule Tubulin_for_building.pdb (#4) to map emd_14529 (1).map (#2) using
19778 atoms
average map value = 0.09395, steps = 100
shifted from previous position = 0.763
rotated from previous position = 7.9 degrees
atoms outside contour = 4440, contour level = 0.043965
Position of Tubulin_for_building.pdb (#4) relative to emd_14529 (1).map (#2)
coordinates:
Matrix rotation and translation
0.62960818 0.77691032 0.00197429 38.73525791
-0.77691039 0.62959779 0.00410723 280.61289241
0.00194794 -0.00411979 0.99998962 175.22918259
Axis -0.00529463 0.00001696 -0.99998598
Axis point 313.20474131 100.65774278 0.00000000
Rotation angle (degrees) 50.97954533
Shift along axis -175.42705750
> fitmap #4 inMap #2
Fit molecule Tubulin_for_building.pdb (#4) to map emd_14529 (1).map (#2) using
19778 atoms
average map value = 0.09394, steps = 44
shifted from previous position = 0.0427
rotated from previous position = 0.232 degrees
atoms outside contour = 4416, contour level = 0.043965
Position of Tubulin_for_building.pdb (#4) relative to emd_14529 (1).map (#2)
coordinates:
Matrix rotation and translation
0.63265640 0.77442704 0.00293997 38.71313840
-0.77443166 0.63264510 0.00397254 280.13002046
0.00121648 -0.00479006 0.99998779 175.35370345
Axis -0.00565736 0.00111273 -0.99998338
Axis point 314.34983660 100.40036911 0.00000000
Rotation angle (degrees) 50.75448999
Shift along axis -175.25809471
> fitmap #4 inMap #2
Fit molecule Tubulin_for_building.pdb (#4) to map emd_14529 (1).map (#2) using
19778 atoms
average map value = 0.09393, steps = 48
shifted from previous position = 0.029
rotated from previous position = 0.046 degrees
atoms outside contour = 4414, contour level = 0.043965
Position of Tubulin_for_building.pdb (#4) relative to emd_14529 (1).map (#2)
coordinates:
Matrix rotation and translation
0.63319904 0.77398224 0.00323578 38.69193381
-0.77398856 0.63318865 0.00372199 280.04572505
0.00083190 -0.00486122 0.99998784 175.39835626
Axis -0.00554473 0.00155290 -0.99998342
Axis point 314.60915026 100.36186769 0.00000000
Rotation angle (degrees) 50.71429672
Shift along axis -175.17510096
> fitmap #4 inMap #2
Fit molecule Tubulin_for_building.pdb (#4) to map emd_14529 (1).map (#2) using
19778 atoms
average map value = 0.09394, steps = 44
shifted from previous position = 0.02
rotated from previous position = 0.112 degrees
atoms outside contour = 4426, contour level = 0.043965
Position of Tubulin_for_building.pdb (#4) relative to emd_14529 (1).map (#2)
coordinates:
Matrix rotation and translation
0.63173171 0.77518226 0.00273984 38.70273118
-0.77518611 0.63172130 0.00383273 280.27282463
0.00124025 -0.00454514 0.99998890 175.33414358
Axis -0.00540371 0.00096723 -0.99998493
Axis point 314.03564997 100.48442949 0.00000000
Rotation angle (degrees) 50.82279420
Shift along axis -175.26955188
> fitmap #4 inMap #2
Fit molecule Tubulin_for_building.pdb (#4) to map emd_14529 (1).map (#2) using
19778 atoms
average map value = 0.09394, steps = 44
shifted from previous position = 0.00272
rotated from previous position = 0.019 degrees
atoms outside contour = 4428, contour level = 0.043965
Position of Tubulin_for_building.pdb (#4) relative to emd_14529 (1).map (#2)
coordinates:
Matrix rotation and translation
0.63148050 0.77538716 0.00266843 38.70340159
-0.77539068 0.63147014 0.00384230 280.31185555
0.00129424 -0.00449541 0.99998906 175.32505518
Axis -0.00537639 0.00088612 -0.99998515
Axis point 313.94118033 100.50776405 0.00000000
Rotation angle (degrees) 50.84135123
Shift along axis -175.28214714
> fitmap #4 inMap #2
Fit molecule Tubulin_for_building.pdb (#4) to map emd_14529 (1).map (#2) using
19778 atoms
average map value = 0.09394, steps = 48
shifted from previous position = 0.00733
rotated from previous position = 0.0155 degrees
atoms outside contour = 4424, contour level = 0.043965
Position of Tubulin_for_building.pdb (#4) relative to emd_14529 (1).map (#2)
coordinates:
Matrix rotation and translation
0.63167508 0.77522833 0.00276164 38.69749893
-0.77523230 0.63166475 0.00381066 280.27928451
0.00120970 -0.00454801 0.99998893 175.33903143
Axis -0.00539101 0.00100094 -0.99998497
Axis point 314.01935042 100.49749407 0.00000000
Rotation angle (degrees) 50.82697562
Shift along axis -175.26447018
> fitmap #4 inMap #2
Fit molecule Tubulin_for_building.pdb (#4) to map emd_14529 (1).map (#2) using
19778 atoms
average map value = 0.09394, steps = 44
shifted from previous position = 0.00811
rotated from previous position = 0.0032 degrees
atoms outside contour = 4424, contour level = 0.043965
Position of Tubulin_for_building.pdb (#4) relative to emd_14529 (1).map (#2)
coordinates:
Matrix rotation and translation
0.63166154 0.77523953 0.00271440 38.70196411
-0.77524326 0.63165116 0.00383457 280.28659029
0.00125815 -0.00452647 0.99998896 175.33054480
Axis -0.00539246 0.00093921 -0.99998502
Axis point 314.01112091 100.49224760 0.00000000
Rotation angle (degrees) 50.82797690
Shift along axis -175.27336921
> fitmap #4 inMap #2
Fit molecule Tubulin_for_building.pdb (#4) to map emd_14529 (1).map (#2) using
19778 atoms
average map value = 0.09395, steps = 36
shifted from previous position = 0.0088
rotated from previous position = 0.044 degrees
atoms outside contour = 4420, contour level = 0.043965
Position of Tubulin_for_building.pdb (#4) relative to emd_14529 (1).map (#2)
coordinates:
Matrix rotation and translation
0.63108989 0.77570561 0.00252059 38.70944027
-0.77570835 0.63107939 0.00391801 280.37191248
0.00144853 -0.00442786 0.99998915 175.30413781
Axis -0.00537945 0.00069101 -0.99998529
Axis point 313.77959554 100.54088397 0.00000000
Rotation angle (degrees) 50.87020991
Shift along axis -175.31605521
> fitmap #4 inMap #2
Fit molecule Tubulin_for_building.pdb (#4) to map emd_14529 (1).map (#2) using
19778 atoms
average map value = 0.09394, steps = 44
shifted from previous position = 0.00899
rotated from previous position = 0.0277 degrees
atoms outside contour = 4427, contour level = 0.043965
Position of Tubulin_for_building.pdb (#4) relative to emd_14529 (1).map (#2)
coordinates:
Matrix rotation and translation
0.63144623 0.77541514 0.00265077 38.70414656
-0.77541856 0.63143586 0.00384896 280.31691477
0.00131075 -0.00448586 0.99998908 175.32281542
Axis -0.00537433 0.00086405 -0.99998518
Axis point 313.92617074 100.50948153 0.00000000
Rotation angle (degrees) 50.84388329
Shift along axis -175.28601921
> fitmap #4 inMap #2
Fit molecule Tubulin_for_building.pdb (#4) to map emd_14529 (1).map (#2) using
19778 atoms
average map value = 0.09394, steps = 48
shifted from previous position = 0.00782
rotated from previous position = 0.0184 degrees
atoms outside contour = 4424, contour level = 0.043965
Position of Tubulin_for_building.pdb (#4) relative to emd_14529 (1).map (#2)
coordinates:
Matrix rotation and translation
0.63167762 0.77522626 0.00276252 38.69750012
-0.77523024 0.63166729 0.00380980 280.27903163
0.00120847 -0.00454816 0.99998893 175.33909924
Axis -0.00539057 0.00100231 -0.99998497
Axis point 314.02062224 100.49723415 0.00000000
Rotation angle (degrees) 50.82678775
Shift along axis -175.26413987
> fitmap #4 inMap #2
Fit molecule Tubulin_for_building.pdb (#4) to map emd_14529 (1).map (#2) using
19778 atoms
average map value = 0.09394, steps = 48
shifted from previous position = 0.0285
rotated from previous position = 0.0178 degrees
atoms outside contour = 4413, contour level = 0.043965
Position of Tubulin_for_building.pdb (#4) relative to emd_14529 (1).map (#2)
coordinates:
Matrix rotation and translation
0.63170048 0.77520823 0.00259146 38.72281016
-0.77521107 0.63168920 0.00406846 280.27564198
0.00151691 -0.00457898 0.99998837 175.30865285
Axis -0.00557740 0.00069306 -0.99998421
Axis point 313.96749818 100.47512323 0.00000000
Rotation angle (degrees) 50.82515455
Shift along axis -175.32760825
> fitmap #4 inMap #2
Fit molecule Tubulin_for_building.pdb (#4) to map emd_14529 (1).map (#2) using
19778 atoms
average map value = 0.09394, steps = 36
shifted from previous position = 0.018
rotated from previous position = 0.104 degrees
atoms outside contour = 4412, contour level = 0.043965
Position of Tubulin_for_building.pdb (#4) relative to emd_14529 (1).map (#2)
coordinates:
Matrix rotation and translation
0.63305995 0.77409672 0.00306158 38.71097061
-0.77410199 0.63304873 0.00392602 280.06934408
0.00110099 -0.00485538 0.99998761 175.36959027
Axis -0.00567191 0.00126635 -0.99998311
Axis point 314.51081873 100.36154690 0.00000000
Rotation angle (degrees) 50.72463145
Shift along axis -175.23152842
> fitmap #4 inMap #2
Fit molecule Tubulin_for_building.pdb (#4) to map emd_14529 (1).map (#2) using
19778 atoms
average map value = 0.09393, steps = 40
shifted from previous position = 0.00957
rotated from previous position = 0.0525 degrees
atoms outside contour = 4409, contour level = 0.043965
Position of Tubulin_for_building.pdb (#4) relative to emd_14529 (1).map (#2)
coordinates:
Matrix rotation and translation
0.63373639 0.77354192 0.00332978 38.70312669
-0.77354858 0.63372520 0.00386861 279.96570494
0.00088237 -0.00502743 0.99998697 175.40529943
Axis -0.00575007 0.00158192 -0.99998222
Axis point 314.78308881 100.31488958 0.00000000
Rotation angle (degrees) 50.67456925
Shift along axis -175.18184243
> fitmap #4 inMap #2
Fit molecule Tubulin_for_building.pdb (#4) to map emd_14529 (1).map (#2) using
19778 atoms
average map value = 0.09393, steps = 48
shifted from previous position = 0.021
rotated from previous position = 0.0276 degrees
atoms outside contour = 4414, contour level = 0.043965
Position of Tubulin_for_building.pdb (#4) relative to emd_14529 (1).map (#2)
coordinates:
Matrix rotation and translation
0.63338329 0.77383109 0.00332519 38.68922992
-0.77383785 0.63337287 0.00371313 280.01422944
0.00076725 -0.00492499 0.99998758 175.41042367
Axis -0.00558128 0.00165275 -0.99998306
Axis point 314.68078271 100.35216323 0.00000000
Rotation angle (degrees) 50.70066647
Shift along axis -175.16059509
> fitmap #4 inMap #2
Fit molecule Tubulin_for_building.pdb (#4) to map emd_14529 (1).map (#2) using
19778 atoms
average map value = 0.09394, steps = 40
shifted from previous position = 0.0377
rotated from previous position = 0.115 degrees
atoms outside contour = 4413, contour level = 0.043965
Position of Tubulin_for_building.pdb (#4) relative to emd_14529 (1).map (#2)
coordinates:
Matrix rotation and translation
0.63191858 0.77502994 0.00273838 38.71319779
-0.77503360 0.63190750 0.00397913 280.24361694
0.00135354 -0.00463682 0.99998833 175.32862340
Axis -0.00555836 0.00089339 -0.99998415
Axis point 314.07472833 100.46863927 0.00000000
Rotation angle (degrees) 50.80902687
Shift along axis -175.29065927
> fitmap #4 inMap #2
Fit molecule Tubulin_for_building.pdb (#4) to map emd_14529 (1).map (#2) using
19778 atoms
average map value = 0.09394, steps = 36
shifted from previous position = 0.0111
rotated from previous position = 0.0941 degrees
atoms outside contour = 4407, contour level = 0.043965
Position of Tubulin_for_building.pdb (#4) relative to emd_14529 (1).map (#2)
coordinates:
Matrix rotation and translation
0.63315759 0.77401671 0.00309739 38.71013562
-0.77402218 0.63314642 0.00390892 280.05579284
0.00106447 -0.00487241 0.99998756 175.37350298
Axis -0.00567246 0.00131320 -0.99998305
Axis point 314.55289695 100.35332198 0.00000000
Rotation angle (degrees) 50.71740386
Shift along axis -175.22234362
> fitmap #4 inMap #2
Fit molecule Tubulin_for_building.pdb (#4) to map emd_14529 (1).map (#2) using
19778 atoms
average map value = 0.09393, steps = 48
shifted from previous position = 0.0361
rotated from previous position = 0.0327 degrees
atoms outside contour = 4418, contour level = 0.043965
Position of Tubulin_for_building.pdb (#4) relative to emd_14529 (1).map (#2)
coordinates:
Matrix rotation and translation
0.63340879 0.77380960 0.00346560 38.68567653
-0.77381712 0.63339874 0.00361870 280.00977338
0.00060508 -0.00497386 0.99998745 175.42486320
Axis -0.00555199 0.00184829 -0.99998288
Axis point 314.72560914 100.36348181 0.00000000
Rotation angle (degrees) 50.69876973
Shift along axis -175.11910322
> fitmap #4 inMap #2
Fit molecule Tubulin_for_building.pdb (#4) to map emd_14529 (1).map (#2) using
19778 atoms
average map value = 0.09394, steps = 40
shifted from previous position = 0.0452
rotated from previous position = 0.0891 degrees
atoms outside contour = 4421, contour level = 0.043965
Position of Tubulin_for_building.pdb (#4) relative to emd_14529 (1).map (#2)
coordinates:
Matrix rotation and translation
0.63234922 0.77467832 0.00282298 38.71713173
-0.77468238 0.63233805 0.00397406 280.17890572
0.00129354 -0.00469990 0.99998812 175.33813695
Axis -0.00559833 0.00098712 -0.99998384
Axis point 314.23410581 100.41914270 0.00000000
Rotation angle (degrees) 50.77719533
Shift along axis -175.27548461
> fitmap #4 inMap #2
Fit molecule Tubulin_for_building.pdb (#4) to map emd_14529 (1).map (#2) using
19778 atoms
average map value = 0.09393, steps = 36
shifted from previous position = 0.0183
rotated from previous position = 0.0937 degrees
atoms outside contour = 4409, contour level = 0.043965
Position of Tubulin_for_building.pdb (#4) relative to emd_14529 (1).map (#2)
coordinates:
Matrix rotation and translation
0.63355765 0.77368848 0.00329289 38.70179142
-0.77369496 0.63354655 0.00385676 279.99310112
0.00089773 -0.00499118 0.99998714 175.40072870
Axis -0.00571790 0.00154785 -0.99998245
Axis point 314.71951089 100.33296548 0.00000000
Rotation angle (degrees) 50.68779722
Shift along axis -175.18555674
> fitmap #4 inMap #2
Fit molecule Tubulin_for_building.pdb (#4) to map emd_14529 (1).map (#2) using
19778 atoms
average map value = 0.09393, steps = 36
shifted from previous position = 0.00991
rotated from previous position = 0.0482 degrees
atoms outside contour = 4413, contour level = 0.043965
Position of Tubulin_for_building.pdb (#4) relative to emd_14529 (1).map (#2)
coordinates:
Matrix rotation and translation
0.63416824 0.77318688 0.00356306 38.69277993
-0.77319481 0.63415742 0.00376042 279.90243009
0.00064796 -0.00513968 0.99998658 175.43631190
Axis -0.00575533 0.00188508 -0.99998166
Axis point 314.98042131 100.29267680 0.00000000
Rotation angle (degrees) 50.64257622
Shift along axis -175.12814712
> fitmap #4 inMap #2
Fit molecule Tubulin_for_building.pdb (#4) to map emd_14529 (1).map (#2) using
19778 atoms
average map value = 0.09394, steps = 48
shifted from previous position = 0.0146
rotated from previous position = 0.0418 degrees
atoms outside contour = 4410, contour level = 0.043965
Position of Tubulin_for_building.pdb (#4) relative to emd_14529 (1).map (#2)
coordinates:
Matrix rotation and translation
0.63364760 0.77361472 0.00331490 38.70427504
-0.77362128 0.63363630 0.00389134 279.98133804
0.00090996 -0.00503022 0.99998693 175.40152002
Axis -0.00576603 0.00155432 -0.99998217
Axis point 314.74975869 100.32795674 0.00000000
Rotation angle (degrees) 50.68115068
Shift along axis -175.18638147
> fitmap #4 inMap #2
Fit molecule Tubulin_for_building.pdb (#4) to map emd_14529 (1).map (#2) using
19778 atoms
average map value = 0.09394, steps = 44
shifted from previous position = 0.00271
rotated from previous position = 0.00361 degrees
atoms outside contour = 4409, contour level = 0.043965
Position of Tubulin_for_building.pdb (#4) relative to emd_14529 (1).map (#2)
coordinates:
Matrix rotation and translation
0.63360113 0.77365280 0.00330836 38.70276601
-0.77365935 0.63358993 0.00387319 279.98767128
0.00090036 -0.00501360 0.99998703 175.40151111
Axis -0.00574327 0.00155622 -0.99998230
Axis point 314.73507218 100.33175423 0.00000000
Rotation angle (degrees) 50.68458497
Shift along axis -175.18496477
> fitmap #4 inMap #5
Fit molecule Tubulin_for_building.pdb (#4) to map postprocess.mrc (#5) using
19778 atoms
average map value = 0.01377, steps = 80
shifted from previous position = 1.8
rotated from previous position = 8.96 degrees
atoms outside contour = 7528, contour level = 0.007768
Position of Tubulin_for_building.pdb (#4) relative to postprocess.mrc (#5)
coordinates:
Matrix rotation and translation
0.49435244 0.86926045 -0.00139201 86.35315847
-0.86922797 0.49434678 0.00800006 348.52937692
0.00764227 -0.00274488 0.99996703 152.04875048
Axis -0.00618042 -0.00519646 -0.99996740
Axis point 341.59861391 100.46417431 0.00000000
Rotation angle (degrees) 60.37421449
Shift along axis -154.38861260
> fitmap #4 inMap #5
Fit molecule Tubulin_for_building.pdb (#4) to map postprocess.mrc (#5) using
19778 atoms
average map value = 0.01377, steps = 44
shifted from previous position = 0.00482
rotated from previous position = 0.0142 degrees
atoms outside contour = 7511, contour level = 0.007768
Position of Tubulin_for_building.pdb (#4) relative to postprocess.mrc (#5)
coordinates:
Matrix rotation and translation
0.49434456 0.86926504 -0.00131948 86.34801641
-0.86923094 0.49433767 0.00823722 348.51409998
0.00781260 -0.00292509 0.99996520 152.05411531
Axis -0.00642045 -0.00525268 -0.99996559
Axis point 341.55379715 100.48955216 0.00000000
Rotation angle (degrees) 60.37483474
Shift along axis -154.43391060
> fitmap #4 inMap #5
Fit molecule Tubulin_for_building.pdb (#4) to map postprocess.mrc (#5) using
19778 atoms
average map value = 0.01377, steps = 44
shifted from previous position = 0.0096
rotated from previous position = 0.00571 degrees
atoms outside contour = 7515, contour level = 0.007768
Position of Tubulin_for_building.pdb (#4) relative to postprocess.mrc (#5)
coordinates:
Matrix rotation and translation
0.49437074 0.86925021 -0.00128117 86.34193380
-0.86921554 0.49436329 0.00832406 348.49444305
0.00786905 -0.00300156 0.99996453 152.05485508
Axis -0.00651450 -0.00526320 -0.99996493
Axis point 341.53556420 100.49417155 0.00000000
Rotation angle (degrees) 60.37314965
Shift along axis -154.44619409
> volume #5 step 1
> fitmap #4 inMap #5
Fit molecule Tubulin_for_building.pdb (#4) to map postprocess.mrc (#5) using
19778 atoms
average map value = 0.01377, steps = 28
shifted from previous position = 0.0157
rotated from previous position = 0.0254 degrees
atoms outside contour = 6547, contour level = 0.007768
Position of Tubulin_for_building.pdb (#4) relative to postprocess.mrc (#5)
coordinates:
Matrix rotation and translation
0.49437259 0.86924899 -0.00139392 86.35526580
-0.86921730 0.49436723 0.00789462 348.54530494
0.00755150 -0.00269126 0.99996787 152.03708337
Axis -0.00608901 -0.00514542 -0.99996822
Axis point 341.63523061 100.45996112 0.00000000
Rotation angle (degrees) 60.37284908
Shift along axis -154.35148159
> select clear
> volume #5 level 0.01049
> fitmap #4 inMap #5
Fit molecule Tubulin_for_building.pdb (#4) to map postprocess.mrc (#5) using
19778 atoms
average map value = 0.01377, steps = 48
shifted from previous position = 0.0217
rotated from previous position = 0.00843 degrees
atoms outside contour = 8528, contour level = 0.010485
Position of Tubulin_for_building.pdb (#4) relative to postprocess.mrc (#5)
coordinates:
Matrix rotation and translation
0.49429127 0.86929530 -0.00134775 86.35291390
-0.86926295 0.49428528 0.00799853 348.54986508
0.00761926 -0.00278206 0.99996710 152.06340424
Axis -0.00620068 -0.00515756 -0.99996748
Axis point 341.59539825 100.48621214 0.00000000
Rotation angle (degrees) 60.37825459
Shift along axis -154.39157146
> ui windowfill toggle
> open 7Z6S format mmcif fromDatabase pdbe_bio
Summary of feedback from opening 7Z6S fetched from pdbe_bio
---
warning | Missing or incomplete sequence information. Inferred polymer connectivity.
7Z6S bioassembly 1 title:
MATCAP bound to a human 14 protofilament microtubule [more info...]
Chain information for 7Z6S bioassembly 1 #7
---
Chain | Description
A D | Tubulin alpha-1B chain
B C | Tubulin beta-3 chain
E F | Uncharacterized protein KIAA0895-like
Non-standard residues in 7Z6S bioassembly 1 #7
---
GDP — (GDP)
GTP — (GTP)
MG — (MG)
ZN — (ZN)
Opened 1 biological assemblies for 7Z6S
> ui tool show Matchmaker
> matchmaker #!7 to #4
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Tubulin_for_building.pdb, chain A (#4) with 7Z6S bioassembly 1,
chain A (#7), sequence alignment score = 2138.5
RMSD between 424 pruned atom pairs is 0.732 angstroms; (across all 428 pairs:
0.762)
> select add #7
19134 atoms, 19576 bonds, 4 pseudobonds, 2400 residues, 2 models selected
> hide sel atoms
> show sel cartoons
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> select #7/F:285
10 atoms, 10 bonds, 1 residue, 1 model selected
> select #7/F:371
6 atoms, 5 bonds, 1 residue, 1 model selected
> select up
95 atoms, 97 bonds, 11 residues, 1 model selected
> select up
2722 atoms, 2787 bonds, 332 residues, 1 model selected
> select up
19134 atoms, 19576 bonds, 2400 residues, 1 model selected
> select down
2722 atoms, 2787 bonds, 332 residues, 1 model selected
> select ~sel & ##selected
16412 atoms, 16789 bonds, 4 pseudobonds, 2068 residues, 2 models selected
> delete atoms (#!7 & sel)
> delete bonds (#!7 & sel)
> open 7Z6S format mmcif fromDatabase pdbe_bio
Summary of feedback from opening 7Z6S fetched from pdbe_bio
---
warning | Missing or incomplete sequence information. Inferred polymer connectivity.
7Z6S bioassembly 1 title:
MATCAP bound to a human 14 protofilament microtubule [more info...]
Chain information for 7Z6S bioassembly 1 #8
---
Chain | Description
A D | Tubulin alpha-1B chain
B C | Tubulin beta-3 chain
E F | Uncharacterized protein KIAA0895-like
Non-standard residues in 7Z6S bioassembly 1 #8
---
GDP — (GDP)
GTP — (GTP)
MG — (MG)
ZN — (ZN)
Opened 1 biological assemblies for 7Z6S
> ui tool show Matchmaker
> matchmaker #!8 to #4
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Tubulin_for_building.pdb, chain A (#4) with 7Z6S bioassembly 1,
chain A (#8), sequence alignment score = 2138.5
RMSD between 424 pruned atom pairs is 0.732 angstroms; (across all 428 pairs:
0.762)
> hide #!4,7-8 atoms
> show #!4,7-8 cartoons
> select add #8
19134 atoms, 19576 bonds, 4 pseudobonds, 2400 residues, 2 models selected
> view matrix models
> #8,0.88368,0.46807,0.0041067,-48.988,0.46804,-0.88368,0.0070131,429.58,0.0069117,-0.0042752,-0.99997,477.37
> ui mousemode right "translate selected models"
> view matrix models
> #8,0.88368,0.46807,0.0041067,-49.233,0.46804,-0.88368,0.0070131,429,0.0069117,-0.0042752,-0.99997,476.84
> view matrix models
> #8,0.88368,0.46807,0.0041067,-46.709,0.46804,-0.88368,0.0070131,430.53,0.0069117,-0.0042752,-0.99997,515.79
> fitmap #8 inMap #5
Fit molecule 7Z6S bioassembly 1 (#8) to map postprocess.mrc (#5) using 19134
atoms
average map value = 0.01067, steps = 60
shifted from previous position = 4.07
rotated from previous position = 0.509 degrees
atoms outside contour = 11362, contour level = 0.010485
Position of 7Z6S bioassembly 1 (#8) relative to postprocess.mrc (#5)
coordinates:
Matrix rotation and translation
0.88457681 0.46637608 0.00415060 -48.88875758
0.46638555 -0.88457999 -0.00165978 432.47247442
0.00289746 0.00340399 -0.99999001 518.24216805
Axis 0.97071536 0.24022573 0.00181517
Axis point 0.00000000 221.93750444 259.44804366
Rotation angle (degrees) 179.85055719
Shift along axis 57.37464684
> select #8/F:189
10 atoms, 10 bonds, 1 residue, 1 model selected
> select up
117 atoms, 118 bonds, 15 residues, 1 model selected
> select up
2722 atoms, 2787 bonds, 332 residues, 1 model selected
> select up
19134 atoms, 19576 bonds, 2400 residues, 1 model selected
> select down
2722 atoms, 2787 bonds, 332 residues, 1 model selected
> select ~sel & ##selected
16412 atoms, 16789 bonds, 4 pseudobonds, 2068 residues, 2 models selected
> delete atoms (#!8 & sel)
> delete bonds (#!8 & sel)
> hide #!4 models
> show #!4 models
> vop gaussian #5 sdev 3.18
Opened postprocess.mrc gaussian as #9, grid size 600,600,600, pixel 1.06,
shown at step 1, values float32
> volume #9 level 0.002472
> volume #9 level 0.001989
> select #8/F:195
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
117 atoms, 118 bonds, 15 residues, 1 model selected
> select up
2722 atoms, 2787 bonds, 332 residues, 1 model selected
> view matrix models
> #8,0.88458,0.46638,0.0041506,-51.459,0.46639,-0.88458,-0.0016598,416.89,0.0028975,0.003404,-0.99999,540.99
> view matrix models
> #8,0.88458,0.46638,0.0041506,-47.321,0.46639,-0.88458,-0.0016598,423.78,0.0028975,0.003404,-0.99999,537.01
> fitmap #8 inMap #9
Fit molecule 7Z6S bioassembly 1 (#8) to map postprocess.mrc gaussian (#9)
using 2722 atoms
average map value = 0.005941, steps = 536
shifted from previous position = 53.4
rotated from previous position = 78.9 degrees
atoms outside contour = 70, contour level = 0.0019895
Position of 7Z6S bioassembly 1 (#8) relative to postprocess.mrc gaussian (#9)
coordinates:
Matrix rotation and translation
0.58398751 0.31660069 -0.74747748 248.79176440
0.80022072 -0.06980165 0.59562952 102.32194136
0.13640156 -0.94598717 -0.29411373 537.26198043
Axis -0.83707985 -0.47993599 0.26260002
Axis point 0.00000000 204.52338028 289.24893940
Rotation angle (degrees) 112.95225525
Shift along axis -116.28154581
> view matrix models
> #8,0.88458,0.46638,0.0041506,-52.079,0.46639,-0.88458,-0.0016598,417.56,0.0028975,0.003404,-0.99999,543.99
> view matrix models
> #8,0.88458,0.46638,0.0041506,-51.943,0.46639,-0.88458,-0.0016598,418.63,0.0028975,0.003404,-0.99999,542.58
> view matrix models
> #8,0.88458,0.46638,0.0041506,-52.124,0.46639,-0.88458,-0.0016598,419.93,0.0028975,0.003404,-0.99999,541.76
> fitmap #8 inMap #9
Fit molecule 7Z6S bioassembly 1 (#8) to map postprocess.mrc gaussian (#9)
using 2722 atoms
average map value = 0.005941, steps = 336
shifted from previous position = 56.4
rotated from previous position = 78.9 degrees
atoms outside contour = 70, contour level = 0.0019895
Position of 7Z6S bioassembly 1 (#8) relative to postprocess.mrc gaussian (#9)
coordinates:
Matrix rotation and translation
0.58402055 0.31656526 -0.74746667 248.79082970
0.80020501 -0.06984708 0.59564530 102.32881744
0.13635225 -0.94599568 -0.29410924 537.26907704
Axis -0.83709456 -0.47990422 0.26261121
Axis point 0.00000000 204.53087550 289.24860419
Rotation angle (degrees) 112.95250100
Shift along axis -116.27659911
> view matrix models
> #8,0.58402,0.31657,-0.74747,240.94,0.80021,-0.069847,0.59565,68.612,0.13635,-0.946,-0.29411,518.33
> view matrix models
> #8,0.58402,0.31657,-0.74747,217.54,0.80021,-0.069847,0.59565,89.594,0.13635,-0.946,-0.29411,500.85
> view matrix models
> #8,0.58402,0.31657,-0.74747,201.3,0.80021,-0.069847,0.59565,79.87,0.13635,-0.946,-0.29411,502.66
> view matrix models
> #8,0.58402,0.31657,-0.74747,203.3,0.80021,-0.069847,0.59565,83.998,0.13635,-0.946,-0.29411,516.57
> view matrix models
> #8,0.58402,0.31657,-0.74747,201.04,0.80021,-0.069847,0.59565,85.801,0.13635,-0.946,-0.29411,520.35
> fitmap #8 inMap #9
Fit molecule 7Z6S bioassembly 1 (#8) to map postprocess.mrc gaussian (#9)
using 2722 atoms
average map value = 0.005941, steps = 312
shifted from previous position = 53.3
rotated from previous position = 0.0212 degrees
atoms outside contour = 70, contour level = 0.0019895
Position of 7Z6S bioassembly 1 (#8) relative to postprocess.mrc gaussian (#9)
coordinates:
Matrix rotation and translation
0.58397044 0.31659997 -0.74749113 248.79503605
0.80028792 -0.07017325 0.59549555 102.43088973
0.13608000 -0.94595992 -0.29435024 537.35843486
Axis -0.83711271 -0.47983781 0.26267468
Axis point 0.00000000 204.54297173 289.26480453
Rotation angle (degrees) 112.97170648
Shift along axis -116.26924320
> view matrix models
> #8,0.58397,0.3166,-0.74749,209.38,0.80029,-0.070173,0.5955,78.934,0.13608,-0.94596,-0.29435,512.52
> view matrix models
> #8,0.58397,0.3166,-0.74749,201.52,0.80029,-0.070173,0.5955,88.526,0.13608,-0.94596,-0.29435,512.74
> view matrix models
> #8,0.58397,0.3166,-0.74749,201.74,0.80029,-0.070173,0.5955,88.597,0.13608,-0.94596,-0.29435,513.06
> volume #5 step 2
> volume #5 level 0.0004013
> surface dust #5 size 10.6
> volume #5 level 0.001662
> volume #5 step 4
> volume #5 level 0.002133
> volume #5 level 0.002604
> volume #5 level 0.00331
> view matrix models
> #8,0.58397,0.3166,-0.74749,201.48,0.80029,-0.070173,0.5955,87.12,0.13608,-0.94596,-0.29435,513.82
> view matrix models
> #8,0.58397,0.3166,-0.74749,201.82,0.80029,-0.070173,0.5955,87.327,0.13608,-0.94596,-0.29435,512.93
> ui mousemode right "rotate selected models"
> view matrix models
> #8,0.68,0.55546,-0.4786,80.851,0.63104,-0.111,0.76776,74.353,0.37334,-0.8241,-0.426,492.67
> view matrix models
> #8,0.30064,0.43984,-0.84626,242.8,0.92896,-0.33599,0.15539,225.36,-0.21599,-0.83286,-0.50961,593.74
> view matrix models
> #8,0.55266,-0.23977,-0.79817,315.17,0.7555,-0.2602,0.60127,124.88,-0.35185,-0.93531,0.037347,494.12
> view matrix models
> #8,0.31929,0.021829,-0.94741,337.95,0.91355,-0.2729,0.30159,180.23,-0.25196,-0.96179,-0.10707,521.16
> ui mousemode right "translate selected models"
> view matrix models
> #8,0.31929,0.021829,-0.94741,339.4,0.91355,-0.2729,0.30159,177.49,-0.25196,-0.96179,-0.10707,520.05
> view matrix models
> #8,0.31929,0.021829,-0.94741,339.89,0.91355,-0.2729,0.30159,177.62,-0.25196,-0.96179,-0.10707,517.72
> fitmap #8 inMap #5
Fit molecule 7Z6S bioassembly 1 (#8) to map postprocess.mrc (#5) using 2722
atoms
average map value = 0.002256, steps = 108
shifted from previous position = 4.94
rotated from previous position = 4.92 degrees
atoms outside contour = 2260, contour level = 0.0033101
Position of 7Z6S bioassembly 1 (#8) relative to postprocess.mrc (#5)
coordinates:
Matrix rotation and translation
0.36185121 0.06563505 -0.92992244 325.32695691
0.88762882 -0.32912865 0.32216364 187.28033569
-0.28491889 -0.94200126 -0.17735516 532.47475446
Axis -0.77080127 -0.39327904 0.50119557
Axis point 0.00000000 200.54595079 316.30213300
Rotation angle (degrees) 124.91190653
Shift along axis -57.54187367
> volume #5 step 2
> select #7/F:467
11 atoms, 10 bonds, 1 residue, 1 model selected
> select up
54 atoms, 53 bonds, 7 residues, 1 model selected
> select up
2722 atoms, 2787 bonds, 332 residues, 1 model selected
> view matrix models
> #7,0.88507,0.46529,0.012891,-54.134,0.46528,-0.88516,0.0037492,419.54,0.013155,0.0026795,-0.99991,478.9
> view matrix models
> #7,0.88507,0.46529,0.012891,-53.053,0.46528,-0.88516,0.0037492,416.45,0.013155,0.0026795,-0.99991,484.87
> view matrix models
> #7,0.88507,0.46529,0.012891,-52.855,0.46528,-0.88516,0.0037492,415.61,0.013155,0.0026795,-0.99991,484.45
> ui mousemode right "rotate selected models"
> view matrix models
> #7,-0.80146,-0.052899,0.59571,118.23,-0.35027,-0.76585,-0.53925,638.57,0.48475,-0.64084,0.59526,137.71
> fitmap #7 inMap #5
Fit molecule 7Z6S bioassembly 1 (#7) to map postprocess.mrc (#5) using 2722
atoms
average map value = 0.002129, steps = 96
shifted from previous position = 7.63
rotated from previous position = 3.69 degrees
atoms outside contour = 2282, contour level = 0.0033101
Position of 7Z6S bioassembly 1 (#7) relative to postprocess.mrc (#5)
coordinates:
Matrix rotation and translation
-0.79670809 -0.11600943 0.59312565 135.43533693
-0.30572821 -0.76920777 -0.56111466 638.78407461
0.52133146 -0.62837983 0.57736670 130.59297741
Axis -0.31474887 0.33594118 -0.88773683
Axis point 63.27610146 339.48234455 0.00000000
Rotation angle (degrees) 173.86593080
Shift along axis 56.03356403
> hide #!5 models
> show #!5 models
> hide #!7 models
> select subtract #7
Nothing selected
> show #!7 models
> select add #8
2722 atoms, 2787 bonds, 332 residues, 1 model selected
> view matrix models
> #8,0.075127,-0.75461,-0.65186,437.17,0.96878,0.21012,-0.13159,195.27,0.23627,-0.62162,0.74684,178.06
> fitmap #8 inMap #5
Fit molecule 7Z6S bioassembly 1 (#8) to map postprocess.mrc (#5) using 2722
atoms
average map value = 0.002256, steps = 116
shifted from previous position = 6.12
rotated from previous position = 19 degrees
atoms outside contour = 2286, contour level = 0.0033101
Position of 7Z6S bioassembly 1 (#8) relative to postprocess.mrc (#5)
coordinates:
Matrix rotation and translation
0.12283799 -0.73551521 -0.66627938 435.36384052
0.98874923 0.03295854 0.14590646 158.02331055
-0.08535683 -0.67670608 0.73128865 238.27662859
Axis -0.41196335 -0.29092530 0.86350951
Axis point 191.16376380 352.97567697 0.00000000
Rotation angle (degrees) 93.23649211
Shift along axis -19.57278943
> view matrix models
> #8,0.053165,-0.81446,-0.57777,436.45,0.99747,0.070703,-0.0078826,188.42,0.04727,-0.57589,0.81616,182
> ui mousemode right "translate selected models"
> view matrix models
> #8,0.053165,-0.81446,-0.57777,432.1,0.99747,0.070703,-0.0078826,183.84,0.04727,-0.57589,0.81616,181.99
> view matrix models
> #8,0.053165,-0.81446,-0.57777,431.56,0.99747,0.070703,-0.0078826,182.69,0.04727,-0.57589,0.81616,181
> ui mousemode right "rotate selected models"
> view matrix models
> #8,-0.67843,0.3386,-0.65199,347.61,0.54473,-0.36365,-0.75567,504.01,-0.49296,-0.86782,0.062268,490.81
> view matrix models
> #8,0.16076,-0.94308,0.29114,224.13,0.052533,-0.28638,-0.95668,606.25,0.98559,0.16909,0.0035053,127.59
> view matrix models
> #8,0.59299,0.16142,0.78886,-148.82,0.526,-0.81943,-0.22772,454.79,0.60966,0.54998,-0.57082,254.1
> view matrix models
> #8,0.63148,0.13745,0.76311,-143.43,0.56542,-0.75508,-0.33189,464.16,0.53059,0.64106,-0.55454,244.82
> fitmap #8 inMap #5
Fit molecule 7Z6S bioassembly 1 (#8) to map postprocess.mrc (#5) using 2722
atoms
average map value = 0.002076, steps = 56
shifted from previous position = 1.71
rotated from previous position = 5.39 degrees
atoms outside contour = 2337, contour level = 0.0033101
Position of 7Z6S bioassembly 1 (#8) relative to postprocess.mrc (#5)
coordinates:
Matrix rotation and translation
0.58772331 0.17163648 0.79064672 -150.70832119
0.63858977 -0.69844697 -0.32307111 442.22527192
0.49677402 0.69477532 -0.52009887 233.24810626
Axis 0.87914832 0.25382777 0.40332331
Axis point 0.00000000 205.96890773 227.99403186
Rotation angle (degrees) 144.62804718
Shift along axis 73.82848699
> ui tool show Matchmaker
> matchmaker #!8 to #7
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 7Z6S bioassembly 1, chain F (#7) with 7Z6S bioassembly 1, chain F
(#8), sequence alignment score = 1753.4
RMSD between 332 pruned atom pairs is 0.000 angstroms; (across all 332 pairs:
0.000)
> view matrix models
> #8,-0.80826,-0.1028,0.57979,137.99,-0.30863,-0.76459,-0.56581,639.54,0.50147,-0.63626,0.58626,132.41
> ui mousemode right "translate selected models"
> view matrix models
> #8,-0.80826,-0.1028,0.57979,106.06,-0.30863,-0.76459,-0.56581,633.81,0.50147,-0.63626,0.58626,170.16
> view matrix models
> #8,-0.80826,-0.1028,0.57979,130.7,-0.30863,-0.76459,-0.56581,638.44,0.50147,-0.63626,0.58626,191.82
> view matrix models
> #8,-0.80826,-0.1028,0.57979,138.95,-0.30863,-0.76459,-0.56581,643.83,0.50147,-0.63626,0.58626,193.27
> fitmap #8 inMap #5
Fit molecule 7Z6S bioassembly 1 (#8) to map postprocess.mrc (#5) using 2722
atoms
average map value = 0.002169, steps = 100
shifted from previous position = 3.46
rotated from previous position = 5.69 degrees
atoms outside contour = 2282, contour level = 0.0033101
Position of 7Z6S bioassembly 1 (#8) relative to postprocess.mrc (#5)
coordinates:
Matrix rotation and translation
-0.84758716 -0.10318636 0.52052721 159.79126396
-0.30152247 -0.71353052 -0.63242264 648.71119596
0.43666944 -0.69298396 0.57366631 212.11164891
Axis -0.27073828 0.37488461 -0.88665794
Axis point 67.89296798 364.04014512 0.00000000
Rotation angle (degrees) 173.57833064
Shift along axis 11.85975661
> view matrix models
> #8,-0.84759,-0.10319,0.52053,161.02,-0.30152,-0.71353,-0.63242,649.81,0.43667,-0.69298,0.57367,214.52
> fitmap #8 inMap #5
Fit molecule 7Z6S bioassembly 1 (#8) to map postprocess.mrc (#5) using 2722
atoms
average map value = 0.002177, steps = 92
shifted from previous position = 1.84
rotated from previous position = 10.6 degrees
atoms outside contour = 2315, contour level = 0.0033101
Position of 7Z6S bioassembly 1 (#8) relative to postprocess.mrc (#5)
coordinates:
Matrix rotation and translation
-0.87017440 -0.17430328 0.46088488 191.05638240
-0.28662161 -0.58177029 -0.76117763 657.86864985
0.40080489 -0.79445685 0.45628253 267.09059619
Axis -0.25277981 0.45635101 -0.85313898
Axis point 68.45126975 396.56197484 0.00000000
Rotation angle (degrees) 176.22568945
Shift along axis 24.05842369
> view matrix models
> #8,-0.87017,-0.1743,0.46088,188.64,-0.28662,-0.58177,-0.76118,656.67,0.4008,-0.79446,0.45628,271.15
> fitmap #8 inMap #5
Fit molecule 7Z6S bioassembly 1 (#8) to map postprocess.mrc (#5) using 2722
atoms
average map value = 0.00217, steps = 80
shifted from previous position = 1.52
rotated from previous position = 6.7 degrees
atoms outside contour = 2287, contour level = 0.0033101
Position of 7Z6S bioassembly 1 (#8) relative to postprocess.mrc (#5)
coordinates:
Matrix rotation and translation
-0.85379484 -0.07788747 0.51475035 157.81001258
-0.38684938 -0.56676613 -0.72740890 659.51383976
0.34839910 -0.82018882 0.45377128 282.77133460
Axis -0.25562182 0.45832127 -0.85123387
Axis point 71.37024554 397.10868421 0.00000000
Rotation angle (degrees) 169.54408897
Shift along axis 21.22499837
> select add #9
2722 atoms, 2787 bonds, 332 residues, 3 models selected
> select subtract #9
2722 atoms, 2787 bonds, 332 residues, 1 model selected
> select subtract #8
Nothing selected
> select add #7
2722 atoms, 2787 bonds, 332 residues, 1 model selected
> view matrix models
> #7,-0.79671,-0.11601,0.59313,137.88,-0.30573,-0.76921,-0.56111,641.55,0.52133,-0.62838,0.57737,131.55
> fitmap #8 inMap #5
Fit molecule 7Z6S bioassembly 1 (#8) to map postprocess.mrc (#5) using 2722
atoms
average map value = 0.00217, steps = 48
shifted from previous position = 0.0243
rotated from previous position = 0.0445 degrees
atoms outside contour = 2290, contour level = 0.0033101
Position of 7Z6S bioassembly 1 (#8) relative to postprocess.mrc (#5)
coordinates:
Matrix rotation and translation
-0.85349902 -0.07755939 0.51529017 157.58966470
-0.38732243 -0.56709899 -0.72689756 659.49859459
0.34859826 -0.81998980 0.45397795 282.63989969
Axis -0.25583530 0.45810127 -0.85128816
Axis point 71.33490223 397.01438222 0.00000000
Rotation angle (degrees) 169.51734650
Shift along axis 21.19214434
> fitmap #8 inMap #5
Fit molecule 7Z6S bioassembly 1 (#8) to map postprocess.mrc (#5) using 2722
atoms
average map value = 0.00217, steps = 40
shifted from previous position = 0.00669
rotated from previous position = 0.0191 degrees
atoms outside contour = 2287, contour level = 0.0033101
Position of 7Z6S bioassembly 1 (#8) relative to postprocess.mrc (#5)
coordinates:
Matrix rotation and translation
-0.85357027 -0.07784246 0.51512945 157.68823268
-0.38706856 -0.56706022 -0.72706302 659.50252698
0.34870579 -0.81998980 0.45389537 282.65047862
Axis -0.25581807 0.45814762 -0.85126839
Axis point 71.32439315 397.03835591 0.00000000
Rotation angle (degrees) 169.53547626
Shift along axis 21.19859326
> fitmap #7 inMap #5
Fit molecule 7Z6S bioassembly 1 (#7) to map postprocess.mrc (#5) using 2722
atoms
average map value = 0.002256, steps = 68
shifted from previous position = 1.31
rotated from previous position = 9.71 degrees
atoms outside contour = 2214, contour level = 0.0033101
Position of 7Z6S bioassembly 1 (#7) relative to postprocess.mrc (#5)
coordinates:
Matrix rotation and translation
-0.72999146 -0.12125154 0.67261470 110.31750947
-0.42741103 -0.68696284 -0.58770900 651.61560639
0.53332192 -0.71650549 0.44965276 176.68513494
Axis -0.35759612 0.38673843 -0.85003435
Axis point 51.50333886 358.91881197 0.00000000
Rotation angle (degrees) 169.62519947
Shift along axis 62.36724954
> select subtract #7
Nothing selected
> hide #!5 models
> molmap #5:.A,.B,.F 11 modelId 101
Missing or invalid "atoms" argument: only initial part "#5" of atom specifier
valid
> molmap #4,7,8:.A,.B,.F 11 modelId 101
Missing or invalid "atoms" argument: only initial part "#4,7,8" of atom
specifier valid
> select #4/G:111
15 atoms, 14 bonds, 1 residue, 1 model selected
> select up
66 atoms, 65 bonds, 5 residues, 1 model selected
> select up
6577 atoms, 6652 bonds, 426 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> molmap #4:.A,.B,.F 11 modelId 101
Missing or invalid "atoms" argument: only initial part "#4" of atom specifier
valid
> molmap #4:A 11 modelId 101
Expected a keyword
> molmap #4:A 11 modelId 101
Expected a keyword
> molmap #4:A 11 modelId 101
Expected a keyword
> molmap #4:A 11 modelId 101
Expected a keyword
> molmap #4:.A 11 modelId 101
Missing or invalid "atoms" argument: only initial part "#4" of atom specifier
valid
> molmap #4: .A 11 modelId 101
Missing or invalid "atoms" argument: only initial part "#4" of atom specifier
valid
> molmap #4, #7, #8 11 modelId 101
Missing or invalid "atoms" argument: only initial part "#4" of atom specifier
valid
> molmap #4/B, #4/A #7, #8 11 modelId 101
Missing or invalid "atoms" argument: only initial part "#4/B" of atom
specifier valid
> molmap #4.B, #4/A #7, #8 11 modelId 101
Missing or invalid "atoms" argument: only initial part "#4" of atom specifier
valid
> molmap #4
Missing or invalid "resolution" argument: Expected a number
> molmap #4, #7, #8
Missing or invalid "atoms" argument: only initial part "#4" of atom specifier
valid
> molmap #4,7,8
Missing or invalid "resolution" argument: Expected a number
> molmap #4,7,8 11 modelId 101
Expected a keyword
> molmap #4,7,8 11
Opened map 11 as #10, grid size 38,49,51, pixel 3.67, shown at level 0.0715,
step 1, values float32
> vop resample #10 onGrid #5
Opened map 11 resampled as #11, grid size 600,600,600, pixel 1.06, shown at
step 1, values float32
> show #!5 models
> save
> /Users/matteogiono/Desktop/PhD/MT_Processing/MATCAP2/MT_REF_MAPS/molmap11_MATCAP2_alphabeta_MATCAP2_box600_pix1.06.mrc
> models #11
> volume #11 level 0.203
> ui tool show "Show Sequence Viewer"
> sequence chain #6/A
Alignment identifier is 6/A
> sequence chain #7/F
Alignment identifier is 7/F
> select #6/A:1
10 atoms, 10 bonds, 1 residue, 1 model selected
> select #6/A
3530 atoms, 3621 bonds, 436 residues, 1 model selected
> select #7/F:140
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #7/F
2722 atoms, 2787 bonds, 332 residues, 1 model selected
> select #6/A
3530 atoms, 3621 bonds, 436 residues, 1 model selected
> select #7/F:140
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #7/F
2722 atoms, 2787 bonds, 332 residues, 1 model selected
> open
> /Users/matteogiono/Desktop/PhD/MT_Processing/MATCAP2/Val_run_class001.mrc
Opened Val_run_class001.mrc as #12, grid size 600,600,600, pixel 1.06, shown
at level 0.0095, step 4, values float32
> volume #12 step 1
> volume #12 level 0.006464
> volume #12 level 0.003905
> volume #12 step 4
> volume #12 level 0.001029
> surface dust #12 size 10.6
> volume #12 level 0.0007233
> close #12
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #2.1 models
> hide #!4 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> open
> /Users/matteogiono/Downloads/ChimeraX/AlphaFold/prediction_9/best_model.pdb
> format pdb
Chain information for best_model.pdb #12
---
Chain | Description
A | No description available
> ui tool show Matchmaker
> matchmaker #6 to #8
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 7Z6S bioassembly 1, chain F (#8) with best_model.pdb, chain A (#6),
sequence alignment score = 1242.7
RMSD between 312 pruned atom pairs is 0.762 angstroms; (across all 330 pairs:
1.009)
> hide #12 models
> show #12 models
> hide #12 models
> show #12 models
> hide #12 models
> show #12 models
> hide #12 models
> show #12 models
> hide #12 models
> show #!7 models
> hide #!7 models
> show #!7 models
> show #12 models
> hide #12 models
> show #12 models
> hide #12 models
> show #12 models
> hide #12 models
> show #12 models
> hide #12 models
> show #12 models
> hide #12 models
> show #12 models
> hide #12 models
> show #12 models
> hide #12 models
> show #12 models
> hide #12 models
> show #12 models
> hide #12 models
> show #12 models
> hide #!8 models
> show #!8 models
> hide #!7 models
> show #!7 models
> select add #12
6252 atoms, 6408 bonds, 768 residues, 2 models selected
> select subtract #12
2722 atoms, 2787 bonds, 332 residues, 1 model selected
> select subtract #7
Nothing selected
> select add #12
3530 atoms, 3621 bonds, 436 residues, 1 model selected
> ui tool show Matchmaker
> matchmaker #6 to #7
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 7Z6S bioassembly 1, chain F (#7) with best_model.pdb, chain A (#6),
sequence alignment score = 1242.7
RMSD between 312 pruned atom pairs is 0.762 angstroms; (across all 330 pairs:
1.009)
> ui tool show Matchmaker
> show #6 models
> hide #!8 models
> set bgColor white
> set bgColor #ffffff00
> select #6/A:1
10 atoms, 10 bonds, 1 residue, 1 model selected
> select #6/A:1-71
532 atoms, 545 bonds, 71 residues, 1 model selected
> select #6/A:84
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #6/A:1-84
641 atoms, 659 bonds, 84 residues, 1 model selected
> select #6/A:105
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #6/A:1-105
809 atoms, 832 bonds, 105 residues, 1 model selected
> view matrix models
> #6,-0.13383,-0.96822,0.21127,154.76,-0.080523,0.22311,0.97146,329.99,-0.98773,0.11299,-0.10782,233.53
> undo
> delete atoms sel
> delete bonds sel
> ui tool show Matchmaker
> matchmaker #6 to #7
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 7Z6S bioassembly 1, chain F (#7) with best_model.pdb, chain A (#6),
sequence alignment score = 1251.7
RMSD between 312 pruned atom pairs is 0.762 angstroms; (across all 330 pairs:
1.009)
> select add #6
2721 atoms, 2788 bonds, 331 residues, 1 model selected
> color sel cornflower blue
> color sel byhetero
> select clear
> select #7/F:154
9 atoms, 8 bonds, 1 residue, 1 model selected
> select clear
> select add #6
2721 atoms, 2788 bonds, 331 residues, 1 model selected
> hide sel atoms
> preset cartoons/nucleotides cylinders/stubs
Using preset: Cartoons/Nucleotides / Cylinders/Stubs
Changed 18645 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
~worm
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
cartoon style protein modeh tube rad 2 sides 24 thick 0.6
cartoon style nucleic x round width 1.6 thick 1.6
nucleotides stubs
> select clear
> open 7Z6S format mmcif fromDatabase pdbe_bio
Summary of feedback from opening 7Z6S fetched from pdbe_bio
---
warning | Missing or incomplete sequence information. Inferred polymer connectivity.
7Z6S bioassembly 1 title:
MATCAP bound to a human 14 protofilament microtubule [more info...]
Chain information for 7Z6S bioassembly 1 #13
---
Chain | Description
A D | Tubulin alpha-1B chain
B C | Tubulin beta-3 chain
E F | Uncharacterized protein KIAA0895-like
Non-standard residues in 7Z6S bioassembly 1 #13
---
GDP — (GDP)
GTP — (GTP)
MG — (MG)
ZN — (ZN)
Opened 1 biological assemblies for 7Z6S
> ui tool show Matchmaker
> matchmaker #12 to #13
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 7Z6S bioassembly 1, chain E (#13) with best_model.pdb, chain A
(#12), sequence alignment score = 1242.7
RMSD between 312 pruned atom pairs is 0.762 angstroms; (across all 330 pairs:
1.009)
> select add #12
3530 atoms, 3621 bonds, 436 residues, 1 model selected
> select add #13
22664 atoms, 23197 bonds, 4 pseudobonds, 2836 residues, 3 models selected
> hide sel atoms
> show sel cartoons
> select clear
> ui tool show "Show Sequence Viewer"
> sequence chain #12/A
Alignment identifier is 12/A
> select #12/A:105
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #12/A:1-105
809 atoms, 832 bonds, 105 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select add #13
19134 atoms, 19576 bonds, 4 pseudobonds, 2400 residues, 2 models selected
> preset cartoons/nucleotides cylinders/stubs
Using preset: Cartoons/Nucleotides / Cylinders/Stubs
Changed 19010 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
~worm
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
cartoon style protein modeh tube rad 2 sides 24 thick 0.6
cartoon style nucleic x round width 1.6 thick 1.6
nucleotides stubs
> select clear
Drag select of 2631 residues, 3 pseudobonds
> preset cartoons/nucleotides ribbons/slabs
Using preset: Cartoons/Nucleotides / Ribbons/Slabs
Changed 0 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
~worm
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
nucleotides tube/slab shape box
> select #13/E:198
7 atoms, 6 bonds, 1 residue, 1 model selected
Drag select of 516 residues
> select up
4925 atoms, 5040 bonds, 600 residues, 2 models selected
> select up
5443 atoms, 5575 bonds, 663 residues, 2 models selected
> preset cartoons/nucleotides cylinders/stubs
Using preset: Cartoons/Nucleotides / Cylinders/Stubs
Changed 0 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
~worm
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
cartoon style protein modeh tube rad 2 sides 24 thick 0.6
cartoon style nucleic x round width 1.6 thick 1.6
nucleotides stubs
> show sel atoms
> select #13/D:430
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
174 atoms, 175 bonds, 22 residues, 1 model selected
> select up
3102 atoms, 3173 bonds, 395 residues, 1 model selected
> show sel atoms
> color sel byhetero
> undo
> select clear
Drag select of 282 atoms, 98 residues, 237 bonds
Drag select of 1191 atoms, 335 residues, 1001 bonds
> show sel atoms
> color sel byhetero
> select clear
> select #12/A:210
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
39 atoms, 39 bonds, 5 residues, 1 model selected
> select up
2721 atoms, 2788 bonds, 331 residues, 1 model selected
> color sel cornflower blue
> color sel byhetero
> select clear
> ui mousemode right rotate
> save /Users/matteogiono/Desktop/image4.png supersample 3
> open
> /Users/matteogiono/Desktop/PhD/MT_Processing/MATCAP2/2024_MATCAP/postprocess.mrc
Opened postprocess.mrc as #14, grid size 600,600,600, pixel 1.06, shown at
level 0.0141, step 4, values float32
> hide #!7 models
> hide #6 models
> hide #!13 models
> hide #12 models
> volume #14 step 1
> volume #14 level 0.006386
> volume #14 level 0.003362
> surface dust #14 size 10.6
> lighting full
> volume #14 step 2
> close #14
> show #12 models
> show #!8 models
> hide #!8 models
> show #!7 models
> hide #!7 models
> show #!13 models
> hide #!13 models
> hide #12 models
> show #6 models
> show #!7 models
> ui tool show Matchmaker
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> preset cartoons/nucleotides ribbons/slabs
Using preset: Cartoons/Nucleotides / Ribbons/Slabs
Changed 0 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
~worm
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
nucleotides tube/slab shape box
> show #12 models
> show #!13 models
> ui tool show Matchmaker
> matchmaker #!13 to #7
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 7Z6S bioassembly 1, chain F (#7) with 7Z6S bioassembly 1, chain E
(#13), sequence alignment score = 1753.4
RMSD between 332 pruned atom pairs is 0.001 angstroms; (across all 332 pairs:
0.001)
> select clear
> hide #!13 models
> show #!13 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> save /Users/matteogiono/Desktop/image5.png supersample 3
> show #!13 models
> select #7/F:276
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #7/F:276-317
340 atoms, 349 bonds, 42 residues, 1 model selected
> show sel atoms
> select clear
> hide #!13 models
> show #!13 models
> open
> /Users/matteogiono/Desktop/PhD/MT_Processing/MATCAP2/2024_MATCAP/particles_star.mrc
Opened particles_star.mrc as #14, grid size 160,160,160, pixel 1.06, shown at
level 0.0116, step 1, values float32
> volume #14 level 0.007614
> volume #14 level 0.003804
> volume #14 level 0.001675
> surface dust #14 size 10.6
> view orient
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!1 models
> hide #!14 models
> hide #!13 models
> show #!13 models
> hide #12 models
> hide #!5 models
> hide #!13 models
> volume #5 step 1
> volume #5 level 0.0008073
> volume #5 step 2
> surface dust #5 size 10.6
> volume #5 step 1
> volume #5 level 0.00254
> open
> /Users/matteogiono/Desktop/PhD/MT_Processing/MATCAP2/2024_MATCAP/postprocess_FinalSymm.mrc
Opened postprocess_FinalSymm.mrc as #15, grid size 600,600,600, pixel 1.06,
shown at level 0.0141, step 4, values float32
> close #5
> volume #15 step 2
> lighting simple
> volume #15 level 0.006229
> volume #15 level 0.003402
> surface dust #15 size 10.6
> lighting full
> open
> /Users/matteogiono/Desktop/PhD/MT_Processing/MATCAP2/2024_MATCAP/postprocess_Final_C1.mrc
Opened postprocess_Final_C1.mrc as #5, grid size 600,600,600, pixel 1.06,
shown at level 0.0157, step 4, values float32
> volume #5 step 1
> show #!13 models
> hide #!13 models
> hide #2.1 models
> hide #!4 models
> hide #6 models
> hide #!7 models
> hide #!15 models
> show #6 models
> hide #6 models
> show #!7 models
> show #!8 models
> hide #!8 models
> hide #!7 models
> show #!13 models
> select add #13
19134 atoms, 19576 bonds, 4 pseudobonds, 2400 residues, 2 models selected
> ui tool show Clashes
> clashes interModel false intraMol false ignoreHiddenModels true
192 clashes
> show sel atoms
> select clear
> color #16 #d62a3dff models
> select add #16
192 pseudobonds, 1 model selected
> close #16
> open 7Z6S fromDatabase pdbe_bio format mmcif
Summary of feedback from opening 7Z6S fetched from pdbe_bio
---
warning | Missing or incomplete sequence information. Inferred polymer connectivity.
7Z6S bioassembly 1 title:
MATCAP bound to a human 14 protofilament microtubule [more info...]
Chain information for 7Z6S bioassembly 1 #16
---
Chain | Description
A D | Tubulin alpha-1B chain
B C | Tubulin beta-3 chain
E F | Uncharacterized protein KIAA0895-like
Non-standard residues in 7Z6S bioassembly 1 #16
---
GDP — (GDP)
GTP — (GTP)
MG — (MG)
ZN — (ZN)
Opened 1 biological assemblies for 7Z6S
> hide #!13 models
> show #!13 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> select add #16
19134 atoms, 19576 bonds, 4 pseudobonds, 2400 residues, 2 models selected
> ui tool show Clashes
> clashes interModel false intraMol false ignoreHiddenModels true color
> #d6282b
192 clashes
> show sel atoms
> show sel cartoons
> hide sel atoms
> style sel stick
Changed 19134 atom styles
> show sel atoms
> select clear
Drag select of 8953 atoms, 1829 residues, 193 pseudobonds, 7614 bonds
> color sel byhetero
> select clear
> open
> /Users/matteogiono/Downloads/ChimeraX/AlphaFold/prediction_9/best_model.pdb
> format pdb
Chain information for best_model.pdb #18
---
Chain | Description
A | No description available
> ui tool show Matchmaker
> matchmaker #18 to #16
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 7Z6S bioassembly 1, chain E (#16) with best_model.pdb, chain A
(#18), sequence alignment score = 1242.7
RMSD between 312 pruned atom pairs is 0.762 angstroms; (across all 330 pairs:
1.009)
> ui tool show "Show Sequence Viewer"
> sequence chain #18/A
Alignment identifier is 18/A
> select #18/A:1
10 atoms, 10 bonds, 1 residue, 1 model selected
> select #18/A:1-39
299 atoms, 305 bonds, 39 residues, 1 model selected
> select #18/A:1
10 atoms, 10 bonds, 1 residue, 1 model selected
> select #18/A:1-62
466 atoms, 476 bonds, 62 residues, 1 model selected
> select #18/A:105
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #18/A:1-105
809 atoms, 832 bonds, 105 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select add #18
2721 atoms, 2788 bonds, 331 residues, 1 model selected
> show sel atoms
> select clear
> select #18/A:209
10 atoms, 10 bonds, 1 residue, 1 model selected
> select #18/A:209
10 atoms, 10 bonds, 1 residue, 1 model selected
> select #18/A:226
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #18/A:226
6 atoms, 5 bonds, 1 residue, 1 model selected
===== Log before crash end =====
Log:
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 Metal - 83.1
OpenGL renderer: Apple M1 Pro
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: MacBookPro18,3
Model Number: Z15H000GAT/A
Chip: Apple M1 Pro
Total Number of Cores: 10 (8 performance and 2 efficiency)
Memory: 32 GB
System Firmware Version: 8422.121.1
OS Loader Version: 8422.121.1
Software:
System Software Overview:
System Version: macOS 13.4.1 (22F82)
Kernel Version: Darwin 22.5.0
Time since boot: 6 giorni, 20 ore e 2 minuti
Graphics/Displays:
Apple M1 Pro:
Chipset Model: Apple M1 Pro
Type: GPU
Bus: Built-In
Total Number of Cores: 16
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
SAMSUNG:
Resolution: 1600 x 900
UI Looks like: 1600 x 900 @ 60.00Hz
Main Display: Yes
Mirror: On
Mirror Status: Master Mirror
Online: Yes
Rotation: Supported
Television: Yes
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3024 x 1964 Retina
Mirror: On
Mirror Status: Hardware Mirror
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-clix: 0.1.6
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.6
ChimeraX-command-palette: 0.1.2
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-PDBImages: 1.2
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PhenixUI: 1.3.2
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.1
ChimeraX-PubChem: 2.2
ChimeraX-QScore: 1.1
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-StarMap: 1.2.15
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
MolecularDynamicsViewer: 1.4
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
pyqtgraph: 0.13.7
python-dateutil: 2.9.0.post0
pytz: 2024.1
pyzmq: 26.0.3
qt-command-palette: 0.0.10
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
Change History (2)
comment:1 by , 16 months ago
| Component: | Unassigned → Window Toolkit |
|---|---|
| Description: | modified (diff) |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash changing Mac display configuration |
comment:2 by , 16 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
| Summary: | Crash changing Mac display configuration → Crash in Mac display reconfiguration |
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Duplicate of #15413.
This ticket is the same as a crash I had on my Mac Studio waking from sleep with a single display. So I suspect this crash is not related to having two displays or connecting or disconnecting displays.
Eric if the crash is in _NSCGSDisplayConfigurationDidReconfigureNotificationHandler() but is not in "displayConfigFinalizedProc" then it would help to say "reconfigure" in the ticket title since it seems to be a different crash scenario.