![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 5 months ago
Closed 5 months ago
#17740 closed defect (duplicate)
Crash destroying OpenGL context on exit
| 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
The following bug report has been submitted:
Platform: macOS-15.4.1-arm64-arm-64bit
ChimeraX Version: 1.10.dev202502120650 (2025-02-12 06:50:33 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 0x00000001fd910c80 (most recent call first):
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 440 in quit
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 805 in closeEvent
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 302 in event
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 339 in event_loop
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1054 in init
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1217 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, psutil._psutil_osx, psutil._psutil_posix, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, charset_normalizer.md, requests.packages.charset_normalizer.md, requests.packages.chardet.md, PIL._imaging, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.pdb_lib._load_libs, chimerax.surface._surface, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, PIL._imagingmath, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif (total: 53)
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"codeSigningFlags" : 570491649,
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===== Log before crash start =====
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.10.dev202502120650 (2025-02-12)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> /Users/toni/Downloads/cryosparc_P89_J935_00279_volume_series/J935_class_00_00279_volume.mrc
Opened J935_class_00_00279_volume.mrc as #1, grid size 160,160,160, pixel
2.87, shown at level 0.252, step 1, values float32
> open
> /Users/toni/Downloads/cryosparc_P89_J935_00279_volume_series/J935_class_01_00279_volume.mrc
Opened J935_class_01_00279_volume.mrc as #2, grid size 160,160,160, pixel
2.87, shown at level 0.252, step 1, values float32
> open
> /Users/toni/Downloads/cryosparc_P89_J935_00279_volume_series/J935_class_02_00279_volume.mrc
Opened J935_class_02_00279_volume.mrc as #3, grid size 160,160,160, pixel
2.87, shown at level 0.26, step 1, values float32
> open
> /Users/toni/Downloads/cryosparc_P89_J935_00279_volume_series/J935_class_03_00279_volume.mrc
Opened J935_class_03_00279_volume.mrc as #4, grid size 160,160,160, pixel
2.87, shown at level 0.254, step 1, values float32
> open
> /Users/toni/Downloads/cryosparc_P89_J935_00279_volume_series/J935_class_04_00279_volume.mrc
Opened J935_class_04_00279_volume.mrc as #5, grid size 160,160,160, pixel
2.87, shown at level 0.253, step 1, values float32
> close
> open /Users/toni/Downloads/cryosparc_P89_J996_006_volume_map_sharp.mrc
Opened cryosparc_P89_J996_006_volume_map_sharp.mrc as #1, grid size
300,300,300, pixel 1.53, shown at level 0.149, step 2, values float32
> open /Users/toni/Downloads/cryosparc_P89_J997_007_volume_map_sharp.mrc
Opened cryosparc_P89_J997_007_volume_map_sharp.mrc as #2, grid size
300,300,300, pixel 1.53, shown at level 0.144, step 2, values float32
> surface dust #1 size 15.3
> surface dust #2 size 15.3
> hide #!1 models
> volume #2 step 1
> volume #1 step 1
> open /Users/toni/Downloads/cryosparc_P89_J998_005_volume_map_sharp.mrc
Opened cryosparc_P89_J998_005_volume_map_sharp.mrc as #3, grid size
300,300,300, pixel 1.53, shown at level 0.162, step 2, values float32
> hide #!1 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!1 models
> open /Users/toni/Downloads/cryosparc_P89_J999_005_volume_map_sharp.mrc
Opened cryosparc_P89_J999_005_volume_map_sharp.mrc as #4, grid size
300,300,300, pixel 1.53, shown at level 0.142, step 2, values float32
> open /Users/toni/Downloads/cryosparc_P89_J1000_005_volume_map_sharp.mrc
Opened cryosparc_P89_J1000_005_volume_map_sharp.mrc as #5, grid size
300,300,300, pixel 1.53, shown at level 0.149, step 2, values float32
> hide #!1 models
> volume #1-5
> volume #1-5 step 1 sdLevel 3
> volume #1-5 step 1 sdLevel 5
> surface dust #3 size 15.3
> surface dust #4 size 15.3
> surface dust #5 size 15.3
> hide #!5 models
> show #!2 models
> hide #!4 models
> show #!1 models
> show #!4 models
> hide #!3 models
> hide #!2 models
> hide #!1 models
> show #!5 models
> hide #!4 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!4 models
> vop gaussian #1-5 sdlevel 3
> volume gaussian #1-5 sdlevel 3
Expected a keyword
> vop gaussian #1-5 sdlevel
> volume gaussian #1-5 sdlevel
Expected a keyword
> vop gaussian #1-5 sDlevel
> volume gaussian #1-5 sDlevel
Expected a keyword
> vop gaussian #1 sdlevel 3
> volume gaussian #1 sdlevel 3
Expected a keyword
> vop gaussian #1-5 sDev 3
Opened cryosparc_P89_J996_006_volume_map_sharp.mrc gaussian as #6, grid size
300,300,300, pixel 1.53, shown at step 1, values float32
Opened cryosparc_P89_J997_007_volume_map_sharp.mrc gaussian as #7, grid size
300,300,300, pixel 1.53, shown at step 1, values float32
Opened cryosparc_P89_J998_005_volume_map_sharp.mrc gaussian as #8, grid size
300,300,300, pixel 1.53, shown at step 1, values float32
Opened cryosparc_P89_J999_005_volume_map_sharp.mrc gaussian as #9, grid size
300,300,300, pixel 1.53, shown at step 1, values float32
Opened cryosparc_P89_J1000_005_volume_map_sharp.mrc gaussian as #10, grid size
300,300,300, pixel 1.53, shown at step 1, values float32
> hide #!6 models
> hide #!7 models
> hide #!8 models
> hide #!9 models
> hide #!10 models
> show #!10 models
> volume #1-5 step 1 sdLevel
Missing "sdLevel" keyword's argument
> volume #1-50 step 1 sdLevel 4
> hide #!10 models
> show #!9 models
> show #!10 models
> hide #!9 models
> hide #!10 models
> show #!6 models
> show #!7 models
> show #!8 models
> hide #!8 models
> hide #!7 models
> open /Users/toni/Library/CloudStorage/OneDrive-
> Personal/Desktop/cryoem/PDH/E3BP/biological_assembly_e3BP_A.pdb
Summary of feedback from opening /Users/toni/Library/CloudStorage/OneDrive-
Personal/Desktop/cryoem/PDH/E3BP/biological_assembly_e3BP_A.pdb
---
warnings | Ignored bad PDB record found on line 995
Duplicate atom serial number found: 1
Duplicate atom serial number found: 2
Duplicate atom serial number found: 3
Duplicate atom serial number found: 4
Duplicate atom serial number found: 5
987 messages similar to the above omitted
Ignored bad PDB record found on line 1989
Duplicate atom serial number found: 1
Duplicate atom serial number found: 2
Duplicate atom serial number found: 3
Duplicate atom serial number found: 4
Duplicate atom serial number found: 5
987 messages similar to the above omitted
Ignored bad PDB record found on line 2983
Duplicate atom serial number found: 1
Duplicate atom serial number found: 2
Duplicate atom serial number found: 3
Duplicate atom serial number found: 4
Duplicate atom serial number found: 5
987 messages similar to the above omitted
Ignored bad PDB record found on line 3977
Duplicate atom serial number found: 1
Duplicate atom serial number found: 2
Duplicate atom serial number found: 3
Duplicate atom serial number found: 4
Duplicate atom serial number found: 5
987 messages similar to the above omitted
Ignored bad PDB record found on line 4971
Duplicate atom serial number found: 1
Duplicate atom serial number found: 2
Duplicate atom serial number found: 3
Duplicate atom serial number found: 4
Duplicate atom serial number found: 5
987 messages similar to the above omitted
Ignored bad PDB record found on line 5965
Duplicate atom serial number found: 1
Duplicate atom serial number found: 2
Duplicate atom serial number found: 3
Duplicate atom serial number found: 4
Duplicate atom serial number found: 5
987 messages similar to the above omitted
Ignored bad PDB record found on line 6959
Duplicate atom serial number found: 1
Duplicate atom serial number found: 2
Duplicate atom serial number found: 3
Duplicate atom serial number found: 4
Duplicate atom serial number found: 5
987 messages similar to the above omitted
Ignored bad PDB record found on line 7953
Duplicate atom serial number found: 1
Duplicate atom serial number found: 2
Duplicate atom serial number found: 3
Duplicate atom serial number found: 4
Duplicate atom serial number found: 5
987 messages similar to the above omitted
Ignored bad PDB record found on line 8947
Duplicate atom serial number found: 1
Duplicate atom serial number found: 2
Duplicate atom serial number found: 3
Duplicate atom serial number found: 4
Duplicate atom serial number found: 5
987 messages similar to the above omitted
Ignored bad PDB record found on line 9941
Duplicate atom serial number found: 1
Duplicate atom serial number found: 2
Duplicate atom serial number found: 3
Duplicate atom serial number found: 4
Duplicate atom serial number found: 5
987 messages similar to the above omitted
Ignored bad PDB record found on line 10935
Duplicate atom serial number found: 1
Duplicate atom serial number found: 2
Duplicate atom serial number found: 3
Duplicate atom serial number found: 4
Duplicate atom serial number found: 5
987 messages similar to the above omitted
Ignored bad PDB record found on line 11929
Ignored bad PDB record found on line 11930
Chain information for biological_assembly_e3BP_A.pdb #11
---
Chain | Description
A B C D E F G H I J K L | No description available
> select add #11
11904 atoms, 12096 bonds, 12 pseudobonds, 1512 residues, 2 models selected
> ui mousemode right "translate selected models"
> view matrix models #11,1,0,0,13.017,0,1,0,2.0623,0,0,1,45.548
> view matrix models #11,1,0,0,14.038,0,1,0,31.209,0,0,1,32.738
> ui tool show "Fit in Map"
> fitmap #11 inMap #6
Fit molecule biological_assembly_e3BP_A.pdb (#11) to map
cryosparc_P89_J996_006_volume_map_sharp.mrc gaussian (#6) using 11904 atoms
average map value = 0.1231, steps = 100
shifted from previous position = 14.8
rotated from previous position = 0.422 degrees
atoms outside contour = 3067, contour level = 0.088286
Position of biological_assembly_e3BP_A.pdb (#11) relative to
cryosparc_P89_J996_006_volume_map_sharp.mrc gaussian (#6) coordinates:
Matrix rotation and translation
0.99999184 0.00334560 -0.00226314 25.32757196
-0.00335949 0.99997535 -0.00616553 27.54298177
0.00224245 0.00617309 0.99997843 23.69083973
Axis 0.83663654 -0.30550765 -0.45464753
Axis point 0.00000000 -3969.37531503 4582.43915000
Rotation angle (degrees) 0.42249970
Shift along axis 2.00439896
> show #!7 models
> hide #!6 models
> fitmap #11 inMap #7
Fit molecule biological_assembly_e3BP_A.pdb (#11) to map
cryosparc_P89_J997_007_volume_map_sharp.mrc gaussian (#7) using 11904 atoms
average map value = 0.07373, steps = 48
shifted from previous position = 0.106
rotated from previous position = 1.31 degrees
atoms outside contour = 7000, contour level = 0.08561
Position of biological_assembly_e3BP_A.pdb (#11) relative to
cryosparc_P89_J997_007_volume_map_sharp.mrc gaussian (#7) coordinates:
Matrix rotation and translation
0.99982467 -0.01872422 -0.00016475 29.47648205
0.01872413 0.99982452 -0.00057362 22.02535374
0.00017547 0.00057044 0.99999982 25.24774376
Axis 0.03053484 -0.00908048 0.99949246
Axis point -1174.42621402 1542.94618641 0.00000000
Rotation angle (degrees) 1.07342380
Shift along axis 25.93498838
> show #!8 models
> hide #!7 models
> fitmap #11 inMap #8
Fit molecule biological_assembly_e3BP_A.pdb (#11) to map
cryosparc_P89_J998_005_volume_map_sharp.mrc gaussian (#8) using 11904 atoms
average map value = 0.1178, steps = 52
shifted from previous position = 0.254
rotated from previous position = 0.863 degrees
atoms outside contour = 3807, contour level = 0.093453
Position of biological_assembly_e3BP_A.pdb (#11) relative to
cryosparc_P89_J998_005_volume_map_sharp.mrc gaussian (#8) coordinates:
Matrix rotation and translation
0.99998600 -0.00455613 -0.00268979 27.19678492
0.00454270 0.99997729 -0.00497884 25.65353023
0.00271241 0.00496655 0.99998399 23.66181293
Axis 0.68485808 -0.37200560 0.62656305
Axis point 0.00000000 -1725.64990633 6946.75093443
Rotation angle (degrees) 0.41602320
Shift along axis 23.90829861
> show #!9 models
> hide #!8 models
> fitmap #11 inMap #8
Fit molecule biological_assembly_e3BP_A.pdb (#11) to map
cryosparc_P89_J998_005_volume_map_sharp.mrc gaussian (#8) using 11904 atoms
average map value = 0.1178, steps = 28
shifted from previous position = 0.0182
rotated from previous position = 0.00833 degrees
atoms outside contour = 3803, contour level = 0.093453
Position of biological_assembly_e3BP_A.pdb (#11) relative to
cryosparc_P89_J998_005_volume_map_sharp.mrc gaussian (#8) coordinates:
Matrix rotation and translation
0.99998538 -0.00469848 -0.00267582 27.23274020
0.00468519 0.99997676 -0.00495308 25.61342002
0.00269903 0.00494047 0.99998415 23.68413135
Axis 0.67500972 -0.36671089 0.64022262
Axis point -0.00000000 -1641.66283141 6967.11501166
Rotation angle (degrees) 0.41989279
Shift along axis 24.15276096
> fitmap #11 inMap #9
Fit molecule biological_assembly_e3BP_A.pdb (#11) to map
cryosparc_P89_J999_005_volume_map_sharp.mrc gaussian (#9) using 11904 atoms
average map value = 0.07397, steps = 2000
shifted from previous position = 0.459
rotated from previous position = 3.99 degrees
atoms outside contour = 6668, contour level = 0.086114
Position of biological_assembly_e3BP_A.pdb (#11) relative to
cryosparc_P89_J999_005_volume_map_sharp.mrc gaussian (#9) coordinates:
Matrix rotation and translation
0.99883925 -0.03813402 0.02942714 27.86300108
0.03974892 0.99761678 -0.05639844 29.01802933
-0.02720631 0.05750267 0.99797458 19.61146856
Axis 0.76365377 0.37970086 0.52216873
Axis point 0.00000000 53.16658883 225.89690202
Rotation angle (degrees) 4.27688395
Shift along axis 42.53635207
> show #!10 models
> hide #!9 models
> select subtract #11
Nothing selected
> hide #!11 models
> show #!9 models
> fitmap #9 inMap #10
Fit map cryosparc_P89_J999_005_volume_map_sharp.mrc gaussian in map
cryosparc_P89_J1000_005_volume_map_sharp.mrc gaussian using 436516 points
correlation = 0.969, correlation about mean = 0.6195, overlap = 6695
steps = 48, shift = 0.0813, angle = 0.182 degrees
Position of cryosparc_P89_J999_005_volume_map_sharp.mrc gaussian (#9) relative
to cryosparc_P89_J1000_005_volume_map_sharp.mrc gaussian (#10) coordinates:
Matrix rotation and translation
0.99999516 -0.00078211 0.00301125 -0.55059297
0.00078025 0.99999951 0.00061733 -0.26306370
-0.00301174 -0.00061498 0.99999528 0.79046249
Axis -0.19427246 0.94952193 0.24630532
Axis point 257.93610444 0.00000000 179.91285577
Rotation angle (degrees) 0.18171906
Shift along axis 0.05187542
> select add #10
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #10,0.78611,0.49308,-0.37269,21.419,-0.46658,0.86888,0.1654,99.287,0.40537,0.043868,0.9131,-83.21
> view matrix models
> #10,0.68932,0.66307,0.29183,-148.34,-0.70669,0.5268,0.4723,162.54,0.15943,-0.5318,0.83173,124.45
> view matrix models
> #10,0.54594,0.8177,0.18251,-125.84,-0.73106,0.35852,0.58053,181.95,0.40927,-0.45036,0.79352,57.119
> fitmap #9 inMap #10
Fit map cryosparc_P89_J999_005_volume_map_sharp.mrc gaussian in map
cryosparc_P89_J1000_005_volume_map_sharp.mrc gaussian using 436516 points
correlation = 0.9644, correlation about mean = 0.513, overlap = 6581
steps = 76, shift = 0.477, angle = 5.48 degrees
Position of cryosparc_P89_J999_005_volume_map_sharp.mrc gaussian (#9) relative
to cryosparc_P89_J1000_005_volume_map_sharp.mrc gaussian (#10) coordinates:
Matrix rotation and translation
0.55885039 -0.71956560 0.41220333 171.83919178
0.79085423 0.31292324 -0.52595498 97.09428588
0.24947110 0.61992289 0.74394877 -140.95108443
Axis 0.60218635 0.08551970 0.79376191
Axis point 55.30522761 204.98600276 0.00000000
Rotation angle (degrees) 72.06961606
Shift along axis -0.09891203
> fitmap #9 inMap #10
Fit map cryosparc_P89_J999_005_volume_map_sharp.mrc gaussian in map
cryosparc_P89_J1000_005_volume_map_sharp.mrc gaussian using 436516 points
correlation = 0.9644, correlation about mean = 0.513, overlap = 6581
steps = 28, shift = 0.0342, angle = 0.0163 degrees
Position of cryosparc_P89_J999_005_volume_map_sharp.mrc gaussian (#9) relative
to cryosparc_P89_J1000_005_volume_map_sharp.mrc gaussian (#10) coordinates:
Matrix rotation and translation
0.55908073 -0.71945589 0.41208247 171.81762357
0.79068794 0.31310053 -0.52609946 97.14411975
0.24948211 0.61996071 0.74391357 -140.95545735
Axis 0.60232031 0.08545581 0.79366715
Axis point 55.24521293 205.02674211 0.00000000
Rotation angle (degrees) 72.05840218
Shift along axis -0.08094137
> close #7-11
> close #6
> close #4-5
> open /Users/toni/Downloads/cryosparc_P89_J1024_006_volume_map_sharp.mrc
Opened cryosparc_P89_J1024_006_volume_map_sharp.mrc as #4, grid size
300,300,300, pixel 1.53, shown at level 0.154, step 2, values float32
> open /Users/toni/Downloads/cryosparc_P89_J1025_009_volume_map_sharp.mrc
Opened cryosparc_P89_J1025_009_volume_map_sharp.mrc as #5, grid size
300,300,300, pixel 1.53, shown at level 0.157, step 2, values float32
> select add #5
2 models selected
> view matrix models
> #5,0.88194,0.22402,-0.41472,72.157,-0.30249,0.94376,-0.13349,114.75,0.36149,0.24317,0.90011,-117.55
> view matrix models
> #5,0.5114,-0.70734,-0.48799,393.32,0.34881,0.68985,-0.63439,139.97,0.78537,0.15421,0.59951,-124.93
> view matrix models
> #5,0.48196,-0.70241,-0.52377,407.39,0.3334,0.69982,-0.63174,140.6,0.81029,0.12985,0.57147,-118.46
> view matrix models
> #5,0.86888,0.14802,-0.47238,106.47,-0.23737,0.96197,-0.13518,95.742,0.43441,0.22958,0.87097,-124.5
> view matrix models
> #5,0.91252,0.12209,-0.3904,83.194,-0.21356,0.95621,-0.20014,106.77,0.34886,0.26601,0.89863,-119.61
> ui mousemode right "translate selected models"
> view matrix models
> #5,0.91252,0.12209,-0.3904,83.236,-0.21356,0.95621,-0.20014,109.16,0.34886,0.26601,0.89863,-118.15
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.68391,0.72544,-0.077413,-78.012,-0.72777,0.68582,-0.0026576,245.73,0.051163,0.058156,0.997,-23.341
> fitmap #4 inMap #5
Fit map cryosparc_P89_J1024_006_volume_map_sharp.mrc in map
cryosparc_P89_J1025_009_volume_map_sharp.mrc using 33730 points
correlation = 0.9534, correlation about mean = 0.8017, overlap = 3176
steps = 108, shift = 6.36, angle = 4.95 degrees
Position of cryosparc_P89_J1024_006_volume_map_sharp.mrc (#4) relative to
cryosparc_P89_J1025_009_volume_map_sharp.mrc (#5) coordinates:
Matrix rotation and translation
0.71349516 -0.70066012 0.00022501 226.50878547
0.70066013 0.71349518 0.00001571 -95.05114281
-0.00017155 0.00014645 0.99999997 0.01819651
Axis 0.00009330 0.00028299 0.99999996
Axis point 229.48027169 229.44302407 0.00000000
Rotation angle (degrees) 44.47999254
Shift along axis 0.01243091
> select subtract #5
Nothing selected
> hide #!5 models
> show #!5 models
> hide #!5 models
> volume #5 step 1
> volume #4 step 1
> surface dust #4 size 15.3
> show #!5 models
> select add #5
2 models selected
> surface dust #5 size 15.3
> select subtract #5
Nothing selected
> select add #5
2 models selected
> view matrix models
> #5,0.53513,0.81805,0.21078,-131.18,-0.6753,0.56416,-0.47508,369.93,-0.50755,0.11189,0.85433,125.34
> undo
> select add #4
4 models selected
> select subtract #5
2 models selected
> view matrix models
> #4,0.99516,0.08185,-0.054337,-7.0502,-0.083506,0.99609,-0.028921,32.691,0.051757,0.033319,0.9981,-18.033
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.99516,0.08185,-0.054337,-8.634,-0.083506,0.99609,-0.028921,59.369,0.051757,0.033319,0.9981,27.739
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.99498,0.081588,-0.058003,-7.6905,-0.083138,0.99623,-0.024829,58.313,0.055758,0.029526,0.99801,27.715
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.99498,0.081588,-0.058003,4.11,-0.083138,0.99623,-0.024829,43.267,0.055758,0.029526,0.99801,-18.62
> view matrix models
> #4,0.99498,0.081588,-0.058003,-1.465,-0.083138,0.99623,-0.024829,37.762,0.055758,0.029526,0.99801,-17.989
> fitmap #4 inMap #5
Fit map cryosparc_P89_J1024_006_volume_map_sharp.mrc in map
cryosparc_P89_J1025_009_volume_map_sharp.mrc using 269003 points
correlation = 0.9537, correlation about mean = 0.8017, overlap = 2.544e+04
steps = 80, shift = 7.68, angle = 3.07 degrees
Position of cryosparc_P89_J1024_006_volume_map_sharp.mrc (#4) relative to
cryosparc_P89_J1025_009_volume_map_sharp.mrc (#5) coordinates:
Matrix rotation and translation
0.71356884 -0.70058511 0.00002445 226.52748083
0.70058511 0.71356884 0.00001489 -95.05882293
-0.00002788 0.00000650 1.00000000 0.01344891
Axis -0.00000599 0.00003735 1.00000000
Axis point 229.51645154 229.50361780 0.00000000
Rotation angle (degrees) 44.47396677
Shift along axis 0.00854215
> view matrix models
> #4,0.99626,0.038512,-0.077385,8.2149,-0.038835,0.99924,-0.0026652,15.004,0.077224,0.0056605,0.997,-17.232
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.96702,0.013469,-0.25435,61.27,0.097074,0.90374,0.41692,-90.443,0.23548,-0.42786,0.87263,74.696
> view matrix models
> #4,0.95215,0.088024,-0.29268,56.319,0.043762,0.90849,0.4156,-78.996,0.30248,-0.40853,0.86117,57.498
> undo
> view matrix models
> #4,0.1139,0.13661,-0.98406,396.1,-0.54012,0.83985,0.054072,153.73,0.83384,0.52535,0.16945,-120.69
> fitmap #4 inMap #5
Fit map cryosparc_P89_J1024_006_volume_map_sharp.mrc in map
cryosparc_P89_J1025_009_volume_map_sharp.mrc using 269003 points
correlation = 0.2265, correlation about mean = 0.03602, overlap = 2715
steps = 104, shift = 0.606, angle = 4.96 degrees
Position of cryosparc_P89_J1024_006_volume_map_sharp.mrc (#4) relative to
cryosparc_P89_J1025_009_volume_map_sharp.mrc (#5) coordinates:
Matrix rotation and translation
0.46910610 -0.50234789 -0.72635120 404.06939087
-0.30656844 0.67869035 -0.66737935 297.17688095
0.82822416 0.53574808 0.16437377 -121.18401198
Axis 0.60902820 -0.78693263 0.09910439
Axis point 407.16804487 0.00000000 258.51323205
Rotation angle (degrees) 81.02026571
Shift along axis 0.22160299
> fitmap #4 inMap #5
Fit map cryosparc_P89_J1024_006_volume_map_sharp.mrc in map
cryosparc_P89_J1025_009_volume_map_sharp.mrc using 269003 points
correlation = 0.2265, correlation about mean = 0.03604, overlap = 2715
steps = 28, shift = 0.0336, angle = 0.00872 degrees
Position of cryosparc_P89_J1024_006_volume_map_sharp.mrc (#4) relative to
cryosparc_P89_J1025_009_volume_map_sharp.mrc (#5) coordinates:
Matrix rotation and translation
0.46922285 -0.50234384 -0.72627859 404.00627956
-0.30658423 0.67861445 -0.66744927 297.19405691
0.82815217 0.53584801 0.16441071 -121.21846022
Axis 0.60911798 -0.78686433 0.09909496
Axis point 407.20728121 -0.00000000 258.48696922
Rotation angle (degrees) 81.01800926
Shift along axis 0.22394546
> fitmap #4 inMap #5
Fit map cryosparc_P89_J1024_006_volume_map_sharp.mrc in map
cryosparc_P89_J1025_009_volume_map_sharp.mrc using 269003 points
correlation = 0.2265, correlation about mean = 0.03603, overlap = 2715
steps = 36, shift = 0.00883, angle = 0.00471 degrees
Position of cryosparc_P89_J1024_006_volume_map_sharp.mrc (#4) relative to
cryosparc_P89_J1025_009_volume_map_sharp.mrc (#5) coordinates:
Matrix rotation and translation
0.46918078 -0.50240920 -0.72626055 404.03134786
-0.30654745 0.67860320 -0.66747761 297.19843690
0.82818962 0.53580098 0.16437532 -121.20156407
Axis 0.60910419 -0.78686858 0.09914596
Axis point 407.20117868 0.00000000 258.50837340
Rotation angle (degrees) 81.02058226
Shift along axis 0.22442988
> fitmap #4 inMap #5
Fit map cryosparc_P89_J1024_006_volume_map_sharp.mrc in map
cryosparc_P89_J1025_009_volume_map_sharp.mrc using 269003 points
correlation = 0.2265, correlation about mean = 0.03603, overlap = 2715
steps = 40, shift = 0.00466, angle = 0.00225 degrees
Position of cryosparc_P89_J1024_006_volume_map_sharp.mrc (#4) relative to
cryosparc_P89_J1025_009_volume_map_sharp.mrc (#5) coordinates:
Matrix rotation and translation
0.46920504 -0.50239001 -0.72625815 404.01841108
-0.30656937 0.67859222 -0.66747870 297.20389845
0.82816777 0.53583288 0.16438150 -121.20850433
Axis 0.60912183 -0.78685752 0.09912531
Axis point 407.20910017 0.00000000 258.49917684
Rotation angle (degrees) 81.02001800
Shift along axis 0.22448202
> fitmap #4 inMap #5
Fit map cryosparc_P89_J1024_006_volume_map_sharp.mrc in map
cryosparc_P89_J1025_009_volume_map_sharp.mrc using 269003 points
correlation = 0.2265, correlation about mean = 0.03602, overlap = 2715
steps = 28, shift = 0.0209, angle = 0.00521 degrees
Position of cryosparc_P89_J1024_006_volume_map_sharp.mrc (#4) relative to
cryosparc_P89_J1025_009_volume_map_sharp.mrc (#5) coordinates:
Matrix rotation and translation
0.46915424 -0.50236111 -0.72631096 404.04699215
-0.30656486 0.67865191 -0.66742009 297.18851608
0.82819822 0.53578438 0.16438616 -121.19359359
Axis 0.60906827 -0.78690053 0.09911307
Axis point 407.18550124 0.00000000 258.51014715
Rotation angle (degrees) 81.01962501
Shift along axis 0.22253602
> fitmap #4 inMap #5
Fit map cryosparc_P89_J1024_006_volume_map_sharp.mrc in map
cryosparc_P89_J1025_009_volume_map_sharp.mrc using 269003 points
correlation = 0.2265, correlation about mean = 0.03603, overlap = 2715
steps = 28, shift = 0.0238, angle = 0.00428 degrees
Position of cryosparc_P89_J1024_006_volume_map_sharp.mrc (#4) relative to
cryosparc_P89_J1025_009_volume_map_sharp.mrc (#5) coordinates:
Matrix rotation and translation
0.46920618 -0.50234859 -0.72628606 404.01279300
-0.30659147 0.67861531 -0.66744508 297.19507315
0.82815894 0.53584247 0.16439471 -121.21371388
Axis 0.60911149 -0.78686954 0.09909345
Axis point 407.20332297 0.00000000 258.48711411
Rotation angle (degrees) 81.01893209
Shift along axis 0.22359975
> fitmap #4 inMap #5
Fit map cryosparc_P89_J1024_006_volume_map_sharp.mrc in map
cryosparc_P89_J1025_009_volume_map_sharp.mrc using 269003 points
correlation = 0.2265, correlation about mean = 0.03603, overlap = 2715
steps = 40, shift = 0.00387, angle = 0.00484 degrees
Position of cryosparc_P89_J1024_006_volume_map_sharp.mrc (#4) relative to
cryosparc_P89_J1025_009_volume_map_sharp.mrc (#5) coordinates:
Matrix rotation and translation
0.46919264 -0.50241766 -0.72624703 404.02547405
-0.30653776 0.67859463 -0.66749077 297.19943029
0.82818649 0.53580390 0.16438162 -121.20581101
Axis 0.60911280 -0.78686075 0.09915522
Axis point 407.20588933 0.00000000 258.50838860
Rotation angle (degrees) 81.02030407
Shift along axis 0.22433087
> view matrix models
> #4,0.18721,-0.17448,-0.9667,446.84,-0.66178,0.70486,-0.25538,284,0.72595,0.68755,0.016484,-97.648
> fitmap #4 inMap #5
Fit map cryosparc_P89_J1024_006_volume_map_sharp.mrc in map
cryosparc_P89_J1025_009_volume_map_sharp.mrc using 269003 points
correlation = 0.2534, correlation about mean = 0.02864, overlap = 3128
steps = 120, shift = 2.53, angle = 7.74 degrees
Position of cryosparc_P89_J1024_006_volume_map_sharp.mrc (#4) relative to
cryosparc_P89_J1025_009_volume_map_sharp.mrc (#5) coordinates:
Matrix rotation and translation
0.62201886 -0.68445581 -0.38027988 331.78991508
-0.18038784 0.34733971 -0.92022570 404.73524920
0.76194013 0.64099561 0.09258435 -114.62169703
Axis 0.78098532 -0.57138412 0.25215495
Axis point 0.00000000 399.25849403 156.00695193
Rotation angle (degrees) 88.22518230
Shift along axis -1.03866855
> view matrix models
> #4,0.20308,-0.32042,-0.92525,469.23,-0.52147,0.7644,-0.37917,267.86,0.82875,0.55949,-0.011855,-86.019
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.20308,-0.32042,-0.92525,465.56,-0.52147,0.7644,-0.37917,258.22,0.82875,0.55949,-0.011855,-81.989
> fitmap #4 inMap #5
Fit map cryosparc_P89_J1024_006_volume_map_sharp.mrc in map
cryosparc_P89_J1025_009_volume_map_sharp.mrc using 269003 points
correlation = 0.9771, correlation about mean = 0.8599, overlap = 2.584e+04
steps = 324, shift = 9.27, angle = 27.8 degrees
Position of cryosparc_P89_J1024_006_volume_map_sharp.mrc (#4) relative to
cryosparc_P89_J1025_009_volume_map_sharp.mrc (#5) coordinates:
Matrix rotation and translation
0.50002418 -0.86601144 -0.00000887 313.49107673
0.28867002 0.16668412 -0.94280752 341.36539270
0.81648358 0.47142400 0.33333763 -142.56599548
Axis 0.70711576 -0.40824623 0.57734073
Axis point 0.00000000 361.99029665 42.12401708
Rotation angle (degrees) 89.99868439
Shift along axis 0.00419116
> select subtract #4
Nothing selected
> hide #!4 models
> show #!4 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> hide #!4 models
> show #!4 models
> show #!5 models
> close #5
> close
> open "/Users/toni/Downloads/cryosparc_P89_J1471_02315_volume_series
> 2/J1471_class_00_02315_volume.mrc"
Opened J1471_class_00_02315_volume.mrc as #1, grid size 240,240,240, pixel
1.91, shown at level 0.0875, step 1, values float32
> open "/Users/toni/Downloads/cryosparc_P89_J1471_02315_volume_series
> 2/J1471_class_01_02315_volume.mrc"
Opened J1471_class_01_02315_volume.mrc as #2, grid size 240,240,240, pixel
1.91, shown at level 0.0877, step 1, values float32
> open "/Users/toni/Downloads/cryosparc_P89_J1471_02315_volume_series
> 2/J1471_class_02_02315_volume.mrc"
Opened J1471_class_02_02315_volume.mrc as #3, grid size 240,240,240, pixel
1.91, shown at level 0.0897, step 1, values float32
> open "/Users/toni/Downloads/cryosparc_P89_J1471_02315_volume_series
> 2/J1471_class_03_02315_volume.mrc"
Opened J1471_class_03_02315_volume.mrc as #4, grid size 240,240,240, pixel
1.91, shown at level 0.0894, step 1, values float32
> open "/Users/toni/Downloads/cryosparc_P89_J1471_02315_volume_series
> 2/J1471_class_04_02315_volume.mrc"
Opened J1471_class_04_02315_volume.mrc as #5, grid size 240,240,240, pixel
1.91, shown at level 0.0894, step 1, values float32
> open /Users/toni/Downloads/cryosparc_P89_J1471__mask_focus.mrc
Opened cryosparc_P89_J1471__mask_focus.mrc as #6, grid size 240,240,240, pixel
1.91, shown at level 5e-05, step 1, values float32
> hide #!6 models
> hide #!5 models
> hide #!4 models
> hide #!3 models
> show #!3 models
> hide #!2 models
> hide #!3 models
> hide #!1 models
> show #!1 models
> volume #1-50 step 1 sdLevel 4
> volume #1-50 step 1 sdLevel 3
> show #!2 models
> hide #!1 models
> show #!3 models
> hide #!2 models
> show #!4 models
> hide #!3 models
> show #!5 models
> hide #!4 models
> show #!6 models
> hide #!5 models
> hide #!6 models
> show #!5 models
> show #!4 models
> show #!3 models
> show #!2 models
> show #!1 models
> hide #!5 models
> hide #!4 models
> hide #!3 models
> hide #!2 models
> hide #!1 models
> show #!4 models
> volume #1-50 step 1 sdLevel 4
> volume #1-50 step 1 sdLevel 5
> show #!3 models
> hide #!4 models
> show #!2 models
> hide #!3 models
> show #!1 models
> hide #!2 models
> surface dust #1 size 19.1
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> close #6
> hide #!1 models
> show #!1 models
> volume #1-50 step 1 sdLevel 4
> volume #1-50 step 1 sdLevel 3
> show #!2 models
> hide #!1 models
> show #!3 models
> hide #!2 models
> volume #1-50 step 1 sdLevel 4
> volume #1-50 step 1 sdLevel 5
> volume #1-50 step 1 sdLevel 6
> show #!4 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> open /Users/toni/Downloads/cryosparc_P89_J1471__mask_focus.mrc
Opened cryosparc_P89_J1471__mask_focus.mrc as #6, grid size 240,240,240, pixel
1.91, shown at level 5e-05, step 1, values float32
> hide #!6 models
> show #!5 models
> hide #!4 models
> view #5 clip false
> show #!6 models
> hide #!6 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!2 models
> volume #2 level 0.07446
> hide #!2 models
> show #!1 models
> volume #1 level 0.0805
> close #5
> close
> open
> /Users/toni/Downloads/cryosparc_P89_J1473_01013_volume_series/J1473_class_00_01013_volume.mrc
Opened J1473_class_00_01013_volume.mrc as #1, grid size 240,240,240, pixel
1.91, shown at level 0.0891, step 1, values float32
> open
> /Users/toni/Downloads/cryosparc_P89_J1473_01013_volume_series/J1473_class_01_01013_volume.mrc
Opened J1473_class_01_01013_volume.mrc as #2, grid size 240,240,240, pixel
1.91, shown at level 0.0819, step 1, values float32
> open
> /Users/toni/Downloads/cryosparc_P89_J1473_01013_volume_series/J1473_class_02_01013_volume.mrc
Opened J1473_class_02_01013_volume.mrc as #3, grid size 240,240,240, pixel
1.91, shown at level 0.0888, step 1, values float32
> open
> /Users/toni/Downloads/cryosparc_P89_J1473_01013_volume_series/J1473_class_03_01013_volume.mrc
Opened J1473_class_03_01013_volume.mrc as #4, grid size 240,240,240, pixel
1.91, shown at level 0.0899, step 1, values float32
> open
> /Users/toni/Downloads/cryosparc_P89_J1473_01013_volume_series/J1473_class_04_01013_volume.mrc
Opened J1473_class_04_01013_volume.mrc as #5, grid size 240,240,240, pixel
1.91, shown at level 0.09, step 1, values float32
> open /Users/toni/Downloads/cryosparc_P89_J1473__mask_focus.mrc
Opened cryosparc_P89_J1473__mask_focus.mrc as #6, grid size 240,240,240, pixel
1.91, shown at level 5e-05, step 1, values float32
> volume #6 level 0.8163
> hide #!6 models
> volume #1-50 step 1 sdLevel 6
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> open /Users/toni/Downloads/cryosparc_P89_J1470_mask.mrc
Opened cryosparc_P89_J1470_mask.mrc as #7, grid size 600,600,600, pixel 0.765,
shown at level 5e-05, step 4, values float32
> hide #!7 models
> show #!7 models
> hide #!7 models
> hide #!5 models
> hide #!4 models
> hide #!2 models
> hide #!1 models
> hide #!3 models
> show #!7 models
> show #!1 models
> open /Users/toni/Downloads/cryosparc_P89_P89_J1334_onlye3bp.mrc
Opened cryosparc_P89_P89_J1334_onlye3bp.mrc as #8, grid size 600,600,600,
pixel 0.765, shown at level 2.66e-05, step 4, values float32
> hide #!7 models
> hide #!8 models
> show #!8 models
> open /Users/toni/Library/CloudStorage/OneDrive-
> Personal/Desktop/cryoem/PDH/E3BP/biological_assembly_e3BP_A.pdb
Summary of feedback from opening /Users/toni/Library/CloudStorage/OneDrive-
Personal/Desktop/cryoem/PDH/E3BP/biological_assembly_e3BP_A.pdb
---
warnings | Ignored bad PDB record found on line 995
Duplicate atom serial number found: 1
Duplicate atom serial number found: 2
Duplicate atom serial number found: 3
Duplicate atom serial number found: 4
Duplicate atom serial number found: 5
987 messages similar to the above omitted
Ignored bad PDB record found on line 1989
Duplicate atom serial number found: 1
Duplicate atom serial number found: 2
Duplicate atom serial number found: 3
Duplicate atom serial number found: 4
Duplicate atom serial number found: 5
987 messages similar to the above omitted
Ignored bad PDB record found on line 2983
Duplicate atom serial number found: 1
Duplicate atom serial number found: 2
Duplicate atom serial number found: 3
Duplicate atom serial number found: 4
Duplicate atom serial number found: 5
987 messages similar to the above omitted
Ignored bad PDB record found on line 3977
Duplicate atom serial number found: 1
Duplicate atom serial number found: 2
Duplicate atom serial number found: 3
Duplicate atom serial number found: 4
Duplicate atom serial number found: 5
987 messages similar to the above omitted
Ignored bad PDB record found on line 4971
Duplicate atom serial number found: 1
Duplicate atom serial number found: 2
Duplicate atom serial number found: 3
Duplicate atom serial number found: 4
Duplicate atom serial number found: 5
987 messages similar to the above omitted
Ignored bad PDB record found on line 5965
Duplicate atom serial number found: 1
Duplicate atom serial number found: 2
Duplicate atom serial number found: 3
Duplicate atom serial number found: 4
Duplicate atom serial number found: 5
987 messages similar to the above omitted
Ignored bad PDB record found on line 6959
Duplicate atom serial number found: 1
Duplicate atom serial number found: 2
Duplicate atom serial number found: 3
Duplicate atom serial number found: 4
Duplicate atom serial number found: 5
987 messages similar to the above omitted
Ignored bad PDB record found on line 7953
Duplicate atom serial number found: 1
Duplicate atom serial number found: 2
Duplicate atom serial number found: 3
Duplicate atom serial number found: 4
Duplicate atom serial number found: 5
987 messages similar to the above omitted
Ignored bad PDB record found on line 8947
Duplicate atom serial number found: 1
Duplicate atom serial number found: 2
Duplicate atom serial number found: 3
Duplicate atom serial number found: 4
Duplicate atom serial number found: 5
987 messages similar to the above omitted
Ignored bad PDB record found on line 9941
Duplicate atom serial number found: 1
Duplicate atom serial number found: 2
Duplicate atom serial number found: 3
Duplicate atom serial number found: 4
Duplicate atom serial number found: 5
987 messages similar to the above omitted
Ignored bad PDB record found on line 10935
Duplicate atom serial number found: 1
Duplicate atom serial number found: 2
Duplicate atom serial number found: 3
Duplicate atom serial number found: 4
Duplicate atom serial number found: 5
987 messages similar to the above omitted
Ignored bad PDB record found on line 11929
Ignored bad PDB record found on line 11930
Chain information for biological_assembly_e3BP_A.pdb #9
---
Chain | Description
A B C D E F G H I J K L | No description available
> close #9
> open /Users/toni/Library/CloudStorage/OneDrive-
> Personal/Desktop/cryoem/PDH/Paper/Data/Cryo_EM/SPA/E3BP_core/E3BP_3_1_monomer_real_space_refined_037.cif
Summary of feedback from opening /Users/toni/Library/CloudStorage/OneDrive-
Personal/Desktop/cryoem/PDH/Paper/Data/Cryo_EM/SPA/E3BP_core/E3BP_3_1_monomer_real_space_refined_037.cif
---
warnings | Skipping chem_comp category: Missing column 'type' on line 252
Missing entity information. Treating each chain as a separate entity.
Bad residue range for struct_conf "1" on line 130
Bad residue range for struct_conf "2" on line 131
Bad residue range for struct_conf "3" on line 132
Bad residue range for struct_conf "4" on line 133
Bad residue range for struct_conf "5" on line 134
2 messages similar to the above omitted
Invalid sheet range for struct_sheet_range "A 1" on line 232
Invalid sheet range for struct_sheet_range "A 2" on line 234
Missing or incomplete sequence information. Inferred polymer connectivity.
Chain information for E3BP_3_1_monomer_real_space_refined_037.cif #9
---
Chain | Description
A | No description available
Computing secondary structure
> hide #!8 models
> select add #9
992 atoms, 1008 bonds, 46 pseudobonds, 126 residues, 3 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #9,0.94097,-0.013942,0.33821,-54.481,-0.15444,-0.90677,0.39231,356.81,0.30121,-0.42139,-0.8554,409.48
> view matrix models
> #9,0.70952,-0.2054,0.67409,-28.306,-0.61737,-0.6424,0.45408,402.61,0.33976,-0.73833,-0.5826,408.66
> ui mousemode right "translate selected models"
> view matrix models
> #9,0.70952,-0.2054,0.67409,-13.745,-0.61737,-0.6424,0.45408,411.2,0.33976,-0.73833,-0.5826,418.32
> view matrix models
> #9,0.70952,-0.2054,0.67409,-14.2,-0.61737,-0.6424,0.45408,411.21,0.33976,-0.73833,-0.5826,418.55
> view matrix models
> #9,0.70952,-0.2054,0.67409,-15.874,-0.61737,-0.6424,0.45408,408.77,0.33976,-0.73833,-0.5826,417.86
> ui mousemode right "rotate selected models"
> view matrix models
> #9,0.74292,-0.010994,0.66929,-64.126,-0.58096,-0.50725,0.63654,332.38,0.3325,-0.86173,-0.38323,403.21
> view matrix models
> #9,0.49608,0.16787,0.8519,-79.581,-0.53488,-0.71378,0.45212,403.8,0.68397,-0.67995,-0.2643,252.45
> ui mousemode right "translate selected models"
> view matrix models
> #9,0.49608,0.16787,0.8519,-69.079,-0.53488,-0.71378,0.45212,397.54,0.68397,-0.67995,-0.2643,266.48
> ui tool show "Fit in Map"
> fitmap #9 inMap #1
Fit molecule E3BP_3_1_monomer_real_space_refined_037.cif (#9) to map
J1473_class_00_01013_volume.mrc (#1) using 992 atoms
average map value = 0.1065, steps = 176
shifted from previous position = 8.91
rotated from previous position = 29 degrees
atoms outside contour = 651, contour level = 0.1237
Position of E3BP_3_1_monomer_real_space_refined_037.cif (#9) relative to
J1473_class_00_01013_volume.mrc (#1) coordinates:
Matrix rotation and translation
0.74405201 -0.02881021 0.66750025 -52.18022232
-0.61404554 -0.42323302 0.66619958 305.46963556
0.26331479 -0.90556269 -0.33259816 427.31867377
Axis -0.91106276 0.23428372 -0.33922822
Axis point 0.00000000 277.60361246 125.44013394
Rotation angle (degrees) 120.39042292
Shift along axis -25.85253200
> show #!8 models
> select add #7
992 atoms, 1008 bonds, 46 pseudobonds, 126 residues, 5 models selected
> select subtract #7
992 atoms, 1008 bonds, 46 pseudobonds, 126 residues, 3 models selected
> select add #8
992 atoms, 1008 bonds, 46 pseudobonds, 126 residues, 5 models selected
> select subtract #8
992 atoms, 1008 bonds, 46 pseudobonds, 126 residues, 3 models selected
> select add #8
992 atoms, 1008 bonds, 46 pseudobonds, 126 residues, 5 models selected
> view matrix models
> #8,1,0,0,-4.5027,0,1,0,-13.415,0,0,1,-27.193,#9,0.74405,-0.02881,0.6675,-56.683,-0.61405,-0.42323,0.6662,292.05,0.26331,-0.90556,-0.3326,400.13
> view matrix models
> #8,1,0,0,-7.8697,0,1,0,-27.038,0,0,1,-42.023,#9,0.74405,-0.02881,0.6675,-60.05,-0.61405,-0.42323,0.6662,278.43,0.26331,-0.90556,-0.3326,385.3
> ui mousemode right "rotate selected models"
> view matrix models
> #8,0.95568,0.17905,0.2337,-99.181,0.08132,0.60237,-0.79407,250.24,-0.28295,0.77788,0.56111,-45.869,#9,0.66267,-0.31494,0.67948,5.5094,-0.51846,0.46179,0.71968,90.678,-0.54044,-0.82919,0.14273,446.29
> view matrix models
> #8,0.94584,0.28524,0.15499,-103.5,0.098914,0.2015,-0.97448,389.63,-0.3092,0.93703,0.16238,19.932,#9,0.56941,-0.28833,0.76983,0.50744,-0.30673,0.79432,0.52438,29.607,-0.76268,-0.53472,0.36386,391.69
> view matrix models
> #8,0.93527,0.34869,0.060769,-92.39,0.1451,-0.22113,-0.96439,477.59,-0.32283,0.91078,-0.25741,134.97,#9,0.49778,-0.22955,0.83638,-8.7109,-0.010189,0.96272,0.27029,-9.6359,-0.86724,-0.14307,0.47688,320.03
> view matrix models
> #8,0.94798,0.20983,-0.23937,13.637,0.10109,-0.91151,-0.39865,523.95,-0.30184,0.35372,-0.88531,425.64,#9,0.51348,0.10065,0.85218,-74.021,0.52996,0.74388,-0.40718,69.887,-0.6749,0.6607,0.32862,171.13
> view matrix models
> #8,0.98133,-0.06555,-0.18081,56.652,-0.10149,-0.97506,-0.19735,544.88,-0.16337,0.21202,-0.96351,441.38,#9,0.7228,0.16321,0.67151,-91.843,0.47125,0.59432,-0.6517,167.99,-0.50545,0.78749,0.35266,102.95
> fitmap #8 inMap #1
Fit map cryosparc_P89_P89_J1334_onlye3bp.mrc in map
J1473_class_00_01013_volume.mrc using 7049 points
correlation = 0.781, correlation about mean = 0.6826, overlap = 56.66
steps = 104, shift = 19.6, angle = 32.8 degrees
Position of cryosparc_P89_P89_J1334_onlye3bp.mrc (#8) relative to
J1473_class_00_01013_volume.mrc (#1) coordinates:
Matrix rotation and translation
0.90747772 0.34103784 -0.24531077 -0.21948162
0.12755608 -0.78004945 -0.61257841 519.38463105
-0.40026695 0.52461038 -0.75137895 373.00034346
Axis 0.97413472 0.13273802 -0.18287201
Axis point 0.00000000 198.01914799 272.34413332
Rotation angle (degrees) 144.28937859
Shift along axis 0.51696245
> hide #!8 models
> select subtract #8
992 atoms, 1008 bonds, 46 pseudobonds, 126 residues, 3 models selected
> select add #8
992 atoms, 1008 bonds, 46 pseudobonds, 126 residues, 5 models selected
> select subtract #8
992 atoms, 1008 bonds, 46 pseudobonds, 126 residues, 3 models selected
> show #!8 models
> hide #!8 models
> hide #!9 models
> select subtract #9
Nothing selected
> show #!9 models
> select add #9
992 atoms, 1008 bonds, 46 pseudobonds, 126 residues, 3 models selected
> view matrix models
> #9,0.30418,-0.42358,-0.85326,460.45,0.91757,-0.11044,0.38193,-14.169,-0.25601,-0.8991,0.35508,396.3
> view matrix models
> #9,-0.49038,0.72261,-0.4872,337.64,0.50482,0.69121,0.51709,-109.75,0.71041,0.0076224,-0.70375,191.18
> ui mousemode right "translate selected models"
> view matrix models
> #9,-0.49038,0.72261,-0.4872,322.7,0.50482,0.69121,0.51709,-104.36,0.71041,0.0076224,-0.70375,202.61
> open /Users/toni/Downloads/cryosparc_P89_J1338_011_volume_map_sharp.mrc
Opened cryosparc_P89_J1338_011_volume_map_sharp.mrc as #10, grid size
600,600,600, pixel 0.765, shown at level 0.0448, step 4, values float32
> volume #10 step 1
> volume #10 level 0.05954
> surface dust #1 size 19.1
> surface dust #10 size 7.65
> hide #!1 models
> ui mousemode right "translate selected models"
> view matrix models
> #9,-0.49038,0.72261,-0.4872,326.28,0.50482,0.69121,0.51709,-171.8,0.71041,0.0076224,-0.70375,202.25
> view matrix models
> #9,-0.49038,0.72261,-0.4872,329.38,0.50482,0.69121,0.51709,-171.89,0.71041,0.0076224,-0.70375,200.5
> ui mousemode right "rotate selected models"
> view matrix models
> #9,0.39533,0.71488,-0.57677,130.62,-0.75289,0.6119,0.24237,215,0.52619,0.33843,0.78012,-139.73
> view matrix models
> #9,0.87114,0.43749,-0.22296,-4.1559,-0.48145,0.67172,-0.56303,306.7,-0.096551,0.59782,0.79579,-43.457
> view matrix models
> #9,0.96863,0.23495,0.080963,-50.345,-0.15614,0.82884,-0.53726,187.47,-0.19334,0.50776,0.83952,-9.7976
> view matrix models
> #9,0.83774,0.49998,-0.21959,-9.7757,0.38021,-0.82268,-0.42266,378.44,-0.39197,0.27059,-0.87928,455.6
> view matrix models
> #9,0.97204,0.1072,-0.20894,37.512,0.23475,-0.46779,0.85209,68.082,-0.0063987,-0.87731,-0.47988,517.05
> view matrix models
> #9,0.56856,0.079117,0.81883,-75.534,-0.73864,-0.38909,0.55047,356.93,0.36215,-0.91779,-0.16278,366.71
> volume #10 level 0.07539
> fitmap #9 inMap #10
Fit molecule E3BP_3_1_monomer_real_space_refined_037.cif (#9) to map
cryosparc_P89_J1338_011_volume_map_sharp.mrc (#10) using 992 atoms
average map value = 0.02353, steps = 140
shifted from previous position = 4.21
rotated from previous position = 7.39 degrees
atoms outside contour = 926, contour level = 0.075394
Position of E3BP_3_1_monomer_real_space_refined_037.cif (#9) relative to
cryosparc_P89_J1338_011_volume_map_sharp.mrc (#10) coordinates:
Matrix rotation and translation
0.46052523 0.10935370 0.88088494 -65.13837139
-0.79689697 -0.38618778 0.46455809 387.89791415
0.39098814 -0.91591526 -0.09070559 346.99675159
Axis -0.80143732 0.28441083 -0.52612613
Axis point 0.00000000 302.25831154 54.65413271
Rotation angle (degrees) 120.54294694
Shift along axis -20.03736834
> show #!8 models
> hide #!8 models
> show #!7 models
> hide #!7 models
> show #!1 models
> hide #!9 models
> show #!9 models
> select subtract #9
Nothing selected
> hide #!10 models
> fitmap #9 inMap #1
Fit molecule E3BP_3_1_monomer_real_space_refined_037.cif (#9) to map
J1473_class_00_01013_volume.mrc (#1) using 992 atoms
average map value = 0.1065, steps = 80
shifted from previous position = 10.4
rotated from previous position = 22.1 degrees
atoms outside contour = 649, contour level = 0.1237
Position of E3BP_3_1_monomer_real_space_refined_037.cif (#9) relative to
J1473_class_00_01013_volume.mrc (#1) coordinates:
Matrix rotation and translation
0.74407238 -0.02758108 0.66752945 -52.43283439
-0.61374840 -0.42295679 0.66664867 305.24018121
0.26394922 -0.90573000 -0.33163831 426.96504474
Axis -0.91103126 0.23383312 -0.33962350
Axis point 0.00000000 277.46906048 125.31099316
Rotation angle (degrees) 120.34870348
Shift along axis -25.86414757
> close #10
> open /Users/toni/Library/CloudStorage/OneDrive-
> Personal/Desktop/cryoem/PDH/Paper/Data/Cryo_EM/SPA/E3BP_core/E3BP_3_1_monomer_real_space_refined_037.cif
Summary of feedback from opening /Users/toni/Library/CloudStorage/OneDrive-
Personal/Desktop/cryoem/PDH/Paper/Data/Cryo_EM/SPA/E3BP_core/E3BP_3_1_monomer_real_space_refined_037.cif
---
warnings | Skipping chem_comp category: Missing column 'type' on line 252
Missing entity information. Treating each chain as a separate entity.
Bad residue range for struct_conf "1" on line 130
Bad residue range for struct_conf "2" on line 131
Bad residue range for struct_conf "3" on line 132
Bad residue range for struct_conf "4" on line 133
Bad residue range for struct_conf "5" on line 134
2 messages similar to the above omitted
Invalid sheet range for struct_sheet_range "A 1" on line 232
Invalid sheet range for struct_sheet_range "A 2" on line 234
Missing or incomplete sequence information. Inferred polymer connectivity.
Chain information for E3BP_3_1_monomer_real_space_refined_037.cif #10
---
Chain | Description
A | No description available
Computing secondary structure
> select add #10
992 atoms, 1008 bonds, 46 pseudobonds, 126 residues, 3 models selected
> view matrix models
> #10,-0.25543,-0.83776,-0.48261,590.57,0.39744,0.36406,-0.84232,215.07,0.88136,-0.40696,0.23997,29.339
> view matrix models
> #10,-0.80113,-0.58323,0.1343,540.69,-0.39439,0.34567,-0.85145,417.1,0.45017,-0.73509,-0.50695,364.5
> view matrix models
> #10,-0.66796,-0.4155,0.61741,369.4,-0.71705,0.58137,-0.38451,347.87,-0.19918,-0.69955,-0.68626,556.1
> view matrix models
> #10,0.14765,0.040409,0.98821,-7.8353,0.76662,0.62662,-0.14016,-81.36,-0.62489,0.77828,0.06154,190.63
> ui mousemode right "translate selected models"
> view matrix models
> #10,0.14765,0.040409,0.98821,8.1246,0.76662,0.62662,-0.14016,-66.481,-0.62489,0.77828,0.06154,195.81
> view matrix models
> #10,0.14765,0.040409,0.98821,13.773,0.76662,0.62662,-0.14016,-72.51,-0.62489,0.77828,0.06154,199.05
> fitmap #10 inMap #1
Fit molecule E3BP_3_1_monomer_real_space_refined_037.cif (#10) to map
J1473_class_00_01013_volume.mrc (#1) using 992 atoms
average map value = 0.08083, steps = 140
shifted from previous position = 12.3
rotated from previous position = 43.5 degrees
atoms outside contour = 799, contour level = 0.1237
Position of E3BP_3_1_monomer_real_space_refined_037.cif (#10) relative to
J1473_class_00_01013_volume.mrc (#1) coordinates:
Matrix rotation and translation
-0.28329892 0.56251511 0.77673578 53.73033503
0.87996380 0.47449881 -0.02268461 -104.25674533
-0.38132064 0.67707284 -0.62941793 309.82382815
Axis 0.50349706 0.83325729 0.22841412
Axis point 132.90618760 0.00000000 157.50603715
Rotation angle (degrees) 135.98096887
Shift along axis 10.94850925
> view matrix models
> #10,-0.2833,0.56252,0.77674,67.315,0.87996,0.4745,-0.022685,-106.96,-0.38132,0.67707,-0.62942,305.2
> ui mousemode right "rotate selected models"
> view matrix models
> #10,-0.25354,0.39472,0.88313,72.662,0.90842,0.41089,0.07715,-121.87,-0.33241,0.82181,-0.46274,227.05
> view matrix models
> #10,0.75531,0.42376,0.49992,-101.81,0.37749,0.34225,-0.86045,223.9,-0.53572,0.83862,0.098534,154.31
> ui mousemode right "translate selected models"
> view matrix models
> #10,0.75531,0.42376,0.49992,-109.38,0.37749,0.34225,-0.86045,238.05,-0.53572,0.83862,0.098534,151.52
> fitmap #10 inMap #1
Fit molecule E3BP_3_1_monomer_real_space_refined_037.cif (#10) to map
J1473_class_00_01013_volume.mrc (#1) using 992 atoms
average map value = 0.07891, steps = 104
shifted from previous position = 6.53
rotated from previous position = 44.4 degrees
atoms outside contour = 764, contour level = 0.1237
Position of E3BP_3_1_monomer_real_space_refined_037.cif (#10) relative to
J1473_class_00_01013_volume.mrc (#1) coordinates:
Matrix rotation and translation
0.89241176 0.41876133 -0.16804818 -2.65854356
-0.05553114 -0.26767125 -0.96190872 492.34295104
-0.44779184 0.86775057 -0.21561868 184.57739511
Axis 0.95757425 0.14640722 -0.24822668
Axis point 0.00000000 173.03079056 280.19711101
Rotation angle (degrees) 107.18386873
Shift along axis 23.71977587
> view matrix models
> #10,0.89241,0.41876,-0.16805,-1.8841,-0.055531,-0.26767,-0.96191,495.03,-0.44779,0.86775,-0.21562,186.32
> fitmap #10 inMap #1
Fit molecule E3BP_3_1_monomer_real_space_refined_037.cif (#10) to map
J1473_class_00_01013_volume.mrc (#1) using 992 atoms
average map value = 0.07893, steps = 56
shifted from previous position = 3.3
rotated from previous position = 0.0554 degrees
atoms outside contour = 764, contour level = 0.1237
Position of E3BP_3_1_monomer_real_space_refined_037.cif (#10) relative to
J1473_class_00_01013_volume.mrc (#1) coordinates:
Matrix rotation and translation
0.89249000 0.41850331 -0.16827532 -2.57263341
-0.05618702 -0.26700805 -0.96205494 492.38609970
-0.44755405 0.86807930 -0.21478757 184.28094744
Axis 0.95757946 0.14612675 -0.24837178
Axis point 0.00000000 173.09580830 280.24034989
Rotation angle (degrees) 107.13671967
Shift along axis 23.71709286
> ui mousemode right "rotate selected models"
> view matrix models
> #10,0.6602,0.71576,-0.22765,4.9474,-0.124,-0.19507,-0.97292,496.33,-0.74078,0.67055,-0.040033,261.37
> view matrix models
> #10,0.71814,-0.59604,-0.35917,295.25,-0.62259,-0.78088,0.051034,525.29,-0.31089,0.18697,-0.93188,446.82
> view matrix models
> #10,0.87295,0.44502,-0.19978,3.3888,-0.12,-0.20106,-0.9722,496.45,-0.47282,0.87266,-0.12211,169.83
> view matrix models
> #10,0.75808,0.65214,-0.0054976,-53.214,0.46129,-0.54215,-0.70234,366.86,-0.461,0.52989,-0.71182,364.82
> fitmap #10 inMap #1
Fit molecule E3BP_3_1_monomer_real_space_refined_037.cif (#10) to map
J1473_class_00_01013_volume.mrc (#1) using 992 atoms
average map value = 0.1089, steps = 92
shifted from previous position = 5.23
rotated from previous position = 23.6 degrees
atoms outside contour = 623, contour level = 0.1237
Position of E3BP_3_1_monomer_real_space_refined_037.cif (#10) relative to
J1473_class_00_01013_volume.mrc (#1) coordinates:
Matrix rotation and translation
0.90148490 0.35685504 -0.24490703 22.91886922
0.13736913 -0.77250423 -0.61997333 484.42737943
-0.41043232 0.52525393 -0.74542177 358.25267936
Axis 0.97237761 0.14054249 -0.18635880
Axis point 0.00000000 179.82785253 261.88910419
Rotation angle (degrees) 143.92243695
Shift along axis 23.60488578
> open /Users/toni/Library/CloudStorage/OneDrive-
> Personal/Desktop/cryoem/PDH/Paper/Data/Cryo_EM/SPA/E3BP_core/E3BP_3_1_monomer_real_space_refined_037.cif
Summary of feedback from opening /Users/toni/Library/CloudStorage/OneDrive-
Personal/Desktop/cryoem/PDH/Paper/Data/Cryo_EM/SPA/E3BP_core/E3BP_3_1_monomer_real_space_refined_037.cif
---
warnings | Skipping chem_comp category: Missing column 'type' on line 252
Missing entity information. Treating each chain as a separate entity.
Bad residue range for struct_conf "1" on line 130
Bad residue range for struct_conf "2" on line 131
Bad residue range for struct_conf "3" on line 132
Bad residue range for struct_conf "4" on line 133
Bad residue range for struct_conf "5" on line 134
2 messages similar to the above omitted
Invalid sheet range for struct_sheet_range "A 1" on line 232
Invalid sheet range for struct_sheet_range "A 2" on line 234
Missing or incomplete sequence information. Inferred polymer connectivity.
Chain information for E3BP_3_1_monomer_real_space_refined_037.cif #11
---
Chain | Description
A | No description available
Computing secondary structure
> select add #11
1984 atoms, 2016 bonds, 92 pseudobonds, 252 residues, 6 models selected
> select subtract #10
992 atoms, 1008 bonds, 46 pseudobonds, 126 residues, 3 models selected
> view matrix models
> #11,0.01914,-0.89621,0.44322,337.63,0.85245,-0.21702,-0.47564,146.75,0.52246,0.38692,0.75982,-159.89
> view matrix models
> #11,-0.51092,-0.61235,0.60331,375.01,0.52025,-0.77897,-0.35006,320.82,0.68432,0.13502,0.71657,-137.66
> view matrix models
> #11,-0.87184,-0.20112,0.4466,411.1,-0.17044,-0.73025,-0.66158,548.06,0.45918,-0.65291,0.60238,108.61
> view matrix models
> #11,-0.78005,0.37807,0.49858,255.14,-0.572,-0.10786,-0.81313,548.59,-0.25364,-0.91947,0.30039,405.79
> view matrix models
> #11,-0.58137,0.53872,0.60975,148.35,-0.57258,0.26154,-0.77701,463.14,-0.57806,-0.80086,0.15641,491.84
> view matrix models
> #11,-0.17579,0.71849,0.67296,-3.5315,-0.14711,0.65675,-0.73962,266.4,-0.97337,-0.22901,-0.009751,504.6
> view matrix models
> #11,-0.12104,0.47493,0.87166,-8.0612,-0.076511,0.87104,-0.48521,149.52,-0.98969,-0.12542,-0.069097,499.44
> view matrix models
> #11,0.08568,0.2685,0.95946,-34.456,0.29656,0.91248,-0.28183,5.0106,-0.95116,0.30868,-0.0014431,383.93
> view matrix models
> #11,0.12213,0.88893,0.44145,-63.981,-0.095124,0.45322,-0.88631,327.69,-0.98794,0.066255,0.13991,414.05
> view matrix models
> #11,0.52491,0.78051,0.33953,-119.21,-0.35544,0.56346,-0.74577,339.01,-0.77339,0.27078,0.57319,225.46
> view matrix models
> #11,0.25048,0.86657,0.43164,-88.977,-0.18284,0.48017,-0.85791,337.69,-0.9507,0.13597,0.27872,360.55
> ui mousemode right "translate selected models"
> view matrix models
> #11,0.25048,0.86657,0.43164,-80.114,-0.18284,0.48017,-0.85791,329.76,-0.9507,0.13597,0.27872,350.89
> fitmap #11 inMap #1
Fit molecule E3BP_3_1_monomer_real_space_refined_037.cif (#11) to map
J1473_class_00_01013_volume.mrc (#1) using 992 atoms
average map value = 0.1047, steps = 104
shifted from previous position = 7.21
rotated from previous position = 34.3 degrees
atoms outside contour = 671, contour level = 0.1237
Position of E3BP_3_1_monomer_real_space_refined_037.cif (#11) relative to
J1473_class_00_01013_volume.mrc (#1) coordinates:
Matrix rotation and translation
0.33325705 0.84798050 0.41215144 -94.43626399
-0.66702743 0.52099541 -0.53257694 368.09366017
-0.66634387 -0.09743130 0.73925164 235.07951891
Axis 0.22783578 0.56468410 -0.79323561
Axis point 301.67135835 348.52601768 0.00000000
Rotation angle (degrees) 72.73737232
Shift along axis -0.13276833
> select subtract #11
Nothing selected
> combine #9-11
Remapping chain ID 'A' in E3BP_3_1_monomer_real_space_refined_037.cif #10 to
'B'
Remapping chain ID 'A' in E3BP_3_1_monomer_real_space_refined_037.cif #11 to
'C'
> hide #!11 models
> hide #!10 models
> hide #!9 models
> save /Users/toni/Desktop/testtrimer_e3bp_B.pdb models #12 relModel #1
> close #11
> close #2-10,12
> open /Users/toni/Desktop/test_combination.pdb
Chain information for test_combination.pdb #2
---
Chain | Description
A | No description available
> close #2
> open /Users/toni/Desktop/testtrimer_e3bp_B.pdb
Chain information for testtrimer_e3bp_B.pdb #2
---
Chain | Description
A B C | No description available
> molmap #2 20
Opened testtrimer_e3bp_B.pdb map 20 as #3, grid size 28,29,28, pixel 6.67,
shown at level 0.0197, step 1, values float32
> open /Users/toni/Downloads/cryosparc_P89_P89_J1334_onlye3bp.mrc
Opened cryosparc_P89_P89_J1334_onlye3bp.mrc as #4, grid size 600,600,600,
pixel 0.765, shown at level 2.66e-05, step 4, values float32
> fitmap #4 inMap #3
Fit map cryosparc_P89_P89_J1334_onlye3bp.mrc in map testtrimer_e3bp_B.pdb map
20 using 7049 points
correlation = 0.6488, correlation about mean = 0.4047, overlap = 81.14
steps = 108, shift = 59.1, angle = 65.2 degrees
Position of cryosparc_P89_P89_J1334_onlye3bp.mrc (#4) relative to
testtrimer_e3bp_B.pdb map 20 (#3) coordinates:
Matrix rotation and translation
0.88600142 -0.28343672 0.36696744 13.81257916
0.45991734 0.43653956 -0.77324592 162.61267531
0.05897049 0.85387167 0.51713214 -149.85647360
Axis 0.89638502 0.16967664 0.40951646
Axis point 0.00000000 203.11936015 66.98167563
Rotation angle (degrees) 65.17573068
Shift along axis -21.39573114
> select add #4
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.65944,0.68458,-0.31063,-3.4316,0.18073,-0.54546,-0.81842,500.68,-0.72971,0.48355,-0.48342,408.03
> view matrix models
> #4,0.098254,0.94795,0.30288,-71.887,-0.53984,0.30645,-0.784,469.3,-0.83601,-0.086478,0.54186,326.88
> fitmap #4 inMap #3
Fit map cryosparc_P89_P89_J1334_onlye3bp.mrc in map testtrimer_e3bp_B.pdb map
20 using 7049 points
correlation = 0.8988, correlation about mean = 0.8699, overlap = 120.1
steps = 56, shift = 2.88, angle = 21.6 degrees
Position of cryosparc_P89_P89_J1334_onlye3bp.mrc (#4) relative to
testtrimer_e3bp_B.pdb map 20 (#3) coordinates:
Matrix rotation and translation
0.34389382 0.84487784 0.40977859 -136.76376659
-0.66369315 0.52740963 -0.53042482 382.13340810
-0.66426534 -0.08955742 0.74211254 232.14552109
Axis 0.23159577 0.56421506 -0.79248013
Axis point 296.55843400 392.16144316 0.00000000
Rotation angle (degrees) 72.13904959
Shift along axis -0.03919735
> select subtract #4
Nothing selected
> hide #!2 models
> show #!2 models
> hide #!2 models
> hide #!1 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> hide #!3 models
> show #!3 models
> show #!4 models
> hide #!4 models
> show #!4 models
> vop resample #4 onGrid #1
Opened cryosparc_P89_P89_J1334_onlye3bp.mrc resampled as #5, grid size
240,240,240, pixel 1.91, shown at step 1, values float32
> save /Users/toni/Desktop/fixed_maskE3BP_config_B.mrc models #5
> close #2-5
> open /Users/toni/Desktop/fixed_maskE3BP_config_B.mrc
Opened fixed_maskE3BP_config_B.mrc as #2, grid size 240,240,240, pixel 1.91,
shown at level 2.62e-05, step 1, values float32
> show #!1 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> select add #2
2 models selected
> select subtract #2
Nothing selected
> select add #2
2 models selected
> transparency sel 50
> open /Users/toni/Downloads/cryosparc_P89_P89_J1334_onlye3bp.mrc
Opened cryosparc_P89_P89_J1334_onlye3bp.mrc as #3, grid size 600,600,600,
pixel 0.765, shown at level 2.66e-05, step 4, values float32
> hide #!3 models
> volume #2 level 0.04
> open /Users/toni/Downloads/cryosparc_P89_J2846_mask.mrc
Opened cryosparc_P89_J2846_mask.mrc as #4, grid size 240,240,240, pixel 1.91,
shown at level 5e-05, step 1, values float32
> volume #4 level 0.9029
> open /Users/toni/Downloads/cryosparc_P89_J1470_mask(1).mrc
Opened cryosparc_P89_J1470_mask(1).mrc as #5, grid size 600,600,600, pixel
0.765, shown at level 5e-05, step 4, values float32
> volume #5 level 0.8133
> open /Users/toni/Documents/Phenix/ApplyNCS_55/Kastritis_Lab_apply_ncs_55.pdb
Summary of feedback from opening
/Users/toni/Documents/Phenix/ApplyNCS_55/Kastritis_Lab_apply_ncs_55.pdb
---
warnings | Ignored bad PDB record found on line 995
Duplicate atom serial number found: 1
Duplicate atom serial number found: 2
Duplicate atom serial number found: 3
Duplicate atom serial number found: 4
Duplicate atom serial number found: 5
987 messages similar to the above omitted
Ignored bad PDB record found on line 1989
Duplicate atom serial number found: 1
Duplicate atom serial number found: 2
Duplicate atom serial number found: 3
Duplicate atom serial number found: 4
Duplicate atom serial number found: 5
987 messages similar to the above omitted
Ignored bad PDB record found on line 2983
Duplicate atom serial number found: 1
Duplicate atom serial number found: 2
Duplicate atom serial number found: 3
Duplicate atom serial number found: 4
Duplicate atom serial number found: 5
987 messages similar to the above omitted
Ignored bad PDB record found on line 3977
Duplicate atom serial number found: 1
Duplicate atom serial number found: 2
Duplicate atom serial number found: 3
Duplicate atom serial number found: 4
Duplicate atom serial number found: 5
987 messages similar to the above omitted
Ignored bad PDB record found on line 4971
Duplicate atom serial number found: 1
Duplicate atom serial number found: 2
Duplicate atom serial number found: 3
Duplicate atom serial number found: 4
Duplicate atom serial number found: 5
987 messages similar to the above omitted
Ignored bad PDB record found on line 5965
Duplicate atom serial number found: 1
Duplicate atom serial number found: 2
Duplicate atom serial number found: 3
Duplicate atom serial number found: 4
Duplicate atom serial number found: 5
987 messages similar to the above omitted
Ignored bad PDB record found on line 6959
Duplicate atom serial number found: 1
Duplicate atom serial number found: 2
Duplicate atom serial number found: 3
Duplicate atom serial number found: 4
Duplicate atom serial number found: 5
987 messages similar to the above omitted
Ignored bad PDB record found on line 7953
Duplicate atom serial number found: 1
Duplicate atom serial number found: 2
Duplicate atom serial number found: 3
Duplicate atom serial number found: 4
Duplicate atom serial number found: 5
987 messages similar to the above omitted
Ignored bad PDB record found on line 8947
Duplicate atom serial number found: 1
Duplicate atom serial number found: 2
Duplicate atom serial number found: 3
Duplicate atom serial number found: 4
Duplicate atom serial number found: 5
987 messages similar to the above omitted
Ignored bad PDB record found on line 9941
Duplicate atom serial number found: 1
Duplicate atom serial number found: 2
Duplicate atom serial number found: 3
Duplicate atom serial number found: 4
Duplicate atom serial number found: 5
987 messages similar to the above omitted
Ignored bad PDB record found on line 10935
Duplicate atom serial number found: 1
Duplicate atom serial number found: 2
Duplicate atom serial number found: 3
Duplicate atom serial number found: 4
Duplicate atom serial number found: 5
987 messages similar to the above omitted
Ignored bad PDB record found on line 11929
Ignored bad PDB record found on line 11930
Chain information for Kastritis_Lab_apply_ncs_55.pdb #6
---
Chain | Description
A B C D E F G H I J K L | No description available
> close
> open /Users/toni/Downloads/cryosparc_P89_J1792_map_locres.mrc
Opened cryosparc_P89_J1792_map_locres.mrc as #1, grid size 600,600,600, pixel
0.68, shown at level 3.64, step 4, values float32
> open /Users/toni/Library/CloudStorage/OneDrive-
> Personal/Desktop/cryoem/PDH/Paper/Data/Cryo_EM/SPA/E2_core/cryosparc_P89_J1787_015_volume_map_sharp.mrc
Opened cryosparc_P89_J1787_015_volume_map_sharp.mrc as #2, grid size
600,600,600, pixel 0.68, shown at level 0.0518, step 4, values float32
> hide #!1 models
> volume #2 step 1
> volume #2 level 0.05473
> surface dust #2 size 6.8
> ui tool show "Surface Color"
> color sample #2.1 map #1 palette #ff0000:#ffffff:#0000ff outsideColor
> #808080
Map values for surface "surface": minimum 0, mean 2.454, maximum 3.801
> color sample #2.1 map #1 palette 4,#ff0000:3.5,#fffb00:3,#0000ff:2.5,#00fa92
> outsideColor #808080
Map values for surface "surface": minimum 0, mean 2.454, maximum 3.801
> color single #2.1
> color sample #2.1 map #1 palette 4,#ff0000:3.5,#fffb00:3,#0000ff:2.5,#00fa92
> outsideColor #808080
Map values for surface "surface": minimum 0, mean 2.454, maximum 3.801
> volume #2 level 0.0727
> color sample #2.1 map #1 palette 4,#00fa92:3.5,#0000ff:3,#fffb00:2.5,#ff0000
> outsideColor #808080
Map values for surface "surface": minimum 0, mean 2.438, maximum 3.572
> volume #2 level 0.07569
> surface dust #2 size 6.8
> volume #2 level 0.08318
> volume #2 level 0.197
> color sample #2.1 map #1 palette 4,#00fa92:3.5,#0000ff:3,#fffb00
> outsideColor #808080
Map values for surface "surface": minimum 1.777, mean 2.411, maximum 2.661
> color sample #2.1 map #1 palette 4,#00fa92:3.5,#0000ff:3,#fffb00
> outsideColor #808080
Map values for surface "surface": minimum 1.777, mean 2.411, maximum 2.661
> color sample #2.1 map #1 palette 4,#00fa92:3.5,#0000ff:3,#fffb00
> outsideColor #808080
Map values for surface "surface": minimum 1.777, mean 2.411, maximum 2.661
> color sample #2.1 map #1 palette 4,#00fa92:3.5,#0000ff:3,#fffb00
> outsideColor #808080
Map values for surface "surface": minimum 1.777, mean 2.411, maximum 2.661
> color sample #2.1 map #1 palette 4,#00fa92:3.5,#0000ff:3,#fffb00
> outsideColor #808080
Map values for surface "surface": minimum 1.777, mean 2.411, maximum 2.661
> color sample #2.1 map #1 palette 4,#00fa92:3.5,#0000ff:3,#fffb00
> outsideColor #808080
Map values for surface "surface": minimum 1.777, mean 2.411, maximum 2.661
> color sample #2.1 map #1 palette 10,#00fa92:5,#0000ff:3,#fffb00 outsideColor
> #808080
Map values for surface "surface": minimum 1.777, mean 2.411, maximum 2.661
===== Log before crash end =====
Log:
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.10.dev202502120650 (2025-02-12)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 Metal - 89.4
OpenGL renderer: Apple M3 Max
OpenGL vendor: Apple
Python: 3.11.4
Locale: en_US.UTF-8
Qt version: PyQt6 6.8.1, Qt 6.8.2
Qt runtime version: 6.8.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: Mac15,9
Model Number: MUW63D/A
Chip: Apple M3 Max
Total Number of Cores: 16 (12 performance and 4 efficiency)
Memory: 48 GB
System Firmware Version: 11881.101.1
OS Loader Version: 11881.101.1
Software:
System Software Overview:
System Version: macOS 15.4.1 (24E263)
Kernel Version: Darwin 24.4.0
Time since boot: 7 days, 7 hours, 16 minutes
Graphics/Displays:
Apple M3 Max:
Chipset Model: Apple M3 Max
Type: GPU
Bus: Built-In
Total Number of Cores: 40
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3456 x 2234 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
VA24DQLB:
Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
UI Looks like: 1920 x 1080 @ 60.00Hz
Mirror: Off
Online: Yes
Rotation: 180
BenQ BL2381T:
Resolution: 1200 x 1920
UI Looks like: 1200 x 1920 @ 60.00Hz
Mirror: Off
Online: Yes
Rotation: 90
Installed Packages:
alabaster: 1.0.0
anyio: 4.8.0
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.0
auditwheel: 6.2.0
babel: 2.17.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 3.0.0
build: 1.2.1
certifi: 2023.11.17
cftime: 1.6.4.post1
charset-normalizer: 3.4.1
ChimeraX-AddCharge: 1.5.18
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.6
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.19.1
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Aniso: 1.0.1
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.60.5
ChimeraX-AtomicLibrary: 14.1.13
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.3
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.2
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.4.0
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: 2.3
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.8
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.10.dev202502120650
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.4
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.7
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: 1.4.1
ChimeraX-Hbonds: 2.5
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.3
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.5.1
ChimeraX-Label: 1.1.14
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.3
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.1.7
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.2
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.2
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.18
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-MutationScores: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.14.1
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.7
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.2
ChimeraX-ProfileGrids: 1.0.1
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.3
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.3
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.7
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.17
ChimeraX-Shape: 1.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.0
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-SimilarStructures: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.19.1
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.2.3
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.43
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.4
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.4
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.3.1
coverage: 7.6.12
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.12
decorator: 5.1.1
docutils: 0.21.2
executing: 2.2.0
filelock: 3.15.4
fonttools: 4.56.0
funcparserlib: 2.0.0a0
glfw: 2.8.0
grako: 3.16.5
h11: 0.14.0
h5py: 3.12.1
html2text: 2024.2.26
httpcore: 1.0.7
httpx: 0.28.1
idna: 3.10
ihm: 1.3
imagecodecs: 2024.6.1
imagesize: 1.4.1
iniconfig: 2.0.0
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.5
jedi: 0.19.1
Jinja2: 3.1.5
jupyter_client: 8.6.2
jupyter_core: 5.7.2
jupyterlab_widgets: 3.0.13
kiwisolver: 1.4.8
line_profiler: 4.1.3
lxml: 5.2.2
lz4: 4.3.3
MarkupSafe: 3.0.2
matplotlib: 3.9.2
matplotlib-inline: 0.1.7
msgpack: 1.0.8
ndindex: 1.9.2
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.2
numpy: 1.26.4
OpenMM: 8.2.0
openvr: 1.26.701
packaging: 23.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pickleshare: 0.7.5
pillow: 10.4.0
pip: 25.0.1
pkginfo: 1.11.1
platformdirs: 4.3.6
pluggy: 1.5.0
prompt_toolkit: 3.0.50
psutil: 6.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pyelftools: 0.31
Pygments: 2.18.0
pynmrstar: 3.3.5
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.2.1
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.8.1
PyQt6-Qt6: 6.8.2
PyQt6-WebEngine-commercial: 6.8.0
PyQt6-WebEngine-Qt6: 6.8.2
PyQt6_sip: 13.10.0
pytest: 8.3.4
pytest-cov: 6.0.0
python-dateutil: 2.9.0.post0
pytz: 2025.1
pyzmq: 26.2.1
qtconsole: 5.5.2
QtPy: 2.4.3
qtshim: 1.1
RandomWords: 0.4.0
requests: 2.32.3
scipy: 1.14.0
setuptools: 72.1.0
sfftk-rw: 0.8.1
six: 1.16.0
sniffio: 1.3.1
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.6
Sphinx: 8.1.3
sphinx-autodoc-typehints: 3.0.1
sphinxcontrib-applehelp: 2.0.0
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 2.0.0
sphinxcontrib-htmlhelp: 2.1.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 2.0.0
sphinxcontrib-serializinghtml: 2.0.0
stack-data: 0.6.3
superqt: 0.7.1
tables: 3.10.2
tcia_utils: 1.5.1
tifffile: 2024.7.24
tinyarray: 1.2.4
tornado: 6.4.2
traitlets: 5.14.3
typing_extensions: 4.12.2
tzdata: 2025.1
urllib3: 2.3.0
wcwidth: 0.2.13
webcolors: 24.6.0
wheel: 0.45.1
wheel-filename: 1.4.2
widgetsnbextension: 4.0.13
Change History (2)
comment:1 by , 5 months ago
| Component: | Unassigned → Window Toolkit |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash destroying OpenGL context on exit |
comment:2 by , 5 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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