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Opened 8 months ago
Closed 8 months ago
#16835 closed defect (duplicate)
Crash in python_instances_of_class
| Reported by: | Owned by: | pett | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Core | 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-14.1-arm64-arm-64bit
ChimeraX Version: 1.8.dev202403220040 (2024-03-22 00:40:30 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Bus error
Current thread 0x00000001dd3b5ec0 (most recent call first):
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molobject.py", line 44 in python_instances_of_class
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/structure.py", line 176 in _copy_custom_attrs
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/structure.py", line 162 in copy
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/cmd.py", line 65 in combine_cmd
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 2904 in run
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/cmd_line/tool.py", line 319 in execute
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/cmd_line/tool.py", line 146 in keyPressEvent
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 280 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 918 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 1069 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, chimerax.surface._surface, chimerax.pdb_lib._load_libs, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, 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, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, PIL._imagingmath (total: 53)
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===== Log before crash start =====
UCSF ChimeraX version: 1.8.dev202403220040 (2024-03-22)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/Users/melvinshen/Desktop/Sinica /Protein Purification/New Phage
> Proteins/Structure/CryoEM/cryosparc/Corndog
> /cryosparc_P2_J308_008_volume_map_sharp.mrc"
Opened cryosparc_P2_J308_008_volume_map_sharp.mrc as #1, grid size
640,640,640, pixel 1.06, shown at level 0.234, step 4, values float32
> open "/Users/melvinshen/Desktop/Sinica /Protein Purification/New Phage
> Proteins/Structure/CryoEM/cryosparc/Corndog /Capsid/Corndog-Head-
> Cap-C5-2_96A/cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc"
Opened cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc as #2, grid size
512,512,512, pixel 1.06, shown at level 0.327, step 2, values float32
> open "/Users/melvinshen/Desktop/Sinica /Protein Purification/New Phage
> Proteins/Structure/CryoEM/cryosparc/Corndog /Capsid/Fitting/6mer_Fit/6mer-
> coot-3.pdb"
Chain information for 6mer-coot-3.pdb #3
---
Chain | Description
A B D | No description available
C E F | No description available
> close #2
> select add #3
12123 atoms, 12345 bonds, 1683 residues, 1 model selected
Already setting window visible!
> hide sel atoms
> show sel cartoons
> set bgColor white
> volume #1 level 0.3
> surface dust #1 size 10.6
> volume #1 step 1
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.98044,0.14401,0.13418,-40.776,-0.18643,0.46068,0.86777,0.077441,0.06315,-0.87581,0.47851,215.17
> view matrix models
> #3,0.98044,0.14401,0.13418,-0.75543,-0.18643,0.46068,0.86777,-4.8346,0.06315,-0.87581,0.47851,250.78
> view matrix models
> #3,0.98044,0.14401,0.13418,37.644,-0.18643,0.46068,0.86777,14.187,0.06315,-0.87581,0.47851,295.33
> view matrix models
> #3,0.91718,-0.16951,-0.36062,186.13,0.38972,0.5702,0.72318,-129.49,0.083039,-0.80383,0.58904,260.35
> view matrix models
> #3,0.91718,-0.16951,-0.36062,222.14,0.38972,0.5702,0.72318,-110.01,0.083039,-0.80383,0.58904,287.95
> view matrix models
> #3,0.91718,-0.16951,-0.36062,236.11,0.38972,0.5702,0.72318,-150.02,0.083039,-0.80383,0.58904,288.45
> view matrix models
> #3,0.91718,-0.16951,-0.36062,276.1,0.38972,0.5702,0.72318,-128.26,0.083039,-0.80383,0.58904,291.1
> view matrix models
> #3,0.91718,-0.16951,-0.36062,273.52,0.38972,0.5702,0.72318,-129.7,0.083039,-0.80383,0.58904,290.3
> transparency 50
> ui tool show "Fit in Map"
> fitmap #3 inMap #1
Fit molecule 6mer-coot-3.pdb (#3) to map
cryosparc_P2_J308_008_volume_map_sharp.mrc (#1) using 12123 atoms
average map value = 0.2418, steps = 160
shifted from previous position = 8.63
rotated from previous position = 15.1 degrees
atoms outside contour = 7506, contour level = 0.3
Position of 6mer-coot-3.pdb (#3) relative to
cryosparc_P2_J308_008_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.84261453 -0.38271410 -0.37885441 326.54028885
0.52383844 0.41937070 0.74143206 -134.59076251
-0.12487607 -0.82319994 0.55384820 350.91497833
Axis -0.85684513 -0.13908709 0.49645867
Axis point 0.00000000 260.77193047 402.03773569
Rotation angle (degrees) 65.92596685
Shift along axis -86.85983363
> fitmap #3 inMap #1
Fit molecule 6mer-coot-3.pdb (#3) to map
cryosparc_P2_J308_008_volume_map_sharp.mrc (#1) using 12123 atoms
average map value = 0.2418, steps = 48
shifted from previous position = 0.00947
rotated from previous position = 0.0042 degrees
atoms outside contour = 7507, contour level = 0.3
Position of 6mer-coot-3.pdb (#3) relative to
cryosparc_P2_J308_008_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.84258481 -0.38271910 -0.37891545 326.55056252
0.52388806 0.41932416 0.74142333 -134.59738496
-0.12486847 -0.82322131 0.55381814 350.91702061
Axis -0.85682976 -0.13912106 0.49647567
Axis point 0.00000000 260.74387185 402.04814614
Rotation angle (degrees) 65.92930256
Shift along axis -86.85114701
> view #3 clip false
> view matrix models
> #3,0.84258,-0.38272,-0.37892,326.28,0.52389,0.41932,0.74142,-134.77,-0.12487,-0.82322,0.55382,350.71
> fitmap #3 inMap #1
Fit molecule 6mer-coot-3.pdb (#3) to map
cryosparc_P2_J308_008_volume_map_sharp.mrc (#1) using 12123 atoms
average map value = 0.2418, steps = 60
shifted from previous position = 0.391
rotated from previous position = 0.0107 degrees
atoms outside contour = 7497, contour level = 0.3
Position of 6mer-coot-3.pdb (#3) relative to
cryosparc_P2_J308_008_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.84267695 -0.38258336 -0.37884764 326.49847832
0.52376413 0.41943036 0.74145081 -134.58628787
-0.12476654 -0.82323031 0.55382774 350.90205268
Axis -0.85689333 -0.13914682 0.49635872
Axis point 0.00000000 260.75614250 401.99781091
Rotation angle (degrees) 65.92277808
Shift along axis -86.87382093
> fitmap #3 inMap #1
Fit molecule 6mer-coot-3.pdb (#3) to map
cryosparc_P2_J308_008_volume_map_sharp.mrc (#1) using 12123 atoms
average map value = 0.2417, steps = 48
shifted from previous position = 0.023
rotated from previous position = 0.0149 degrees
atoms outside contour = 7496, contour level = 0.3
Position of 6mer-coot-3.pdb (#3) relative to
cryosparc_P2_J308_008_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.84260202 -0.38252716 -0.37907098 326.52334004
0.52392869 0.41943907 0.74132961 -134.62203718
-0.12458153 -0.82325199 0.55383716 350.85585367
Axis -0.85682692 -0.13936851 0.49641116
Axis point 0.00000000 260.65617536 402.05062130
Rotation angle (degrees) 65.92456077
Shift along axis -86.84315209
> split #3
Split 6mer-coot-3.pdb (#3) into 6 models
Chain information for 6mer-coot-3.pdb A #3.1
---
Chain | Description
A | No description available
Chain information for 6mer-coot-3.pdb B #3.2
---
Chain | Description
B | No description available
Chain information for 6mer-coot-3.pdb C #3.3
---
Chain | Description
C | No description available
Chain information for 6mer-coot-3.pdb D #3.4
---
Chain | Description
D | No description available
Chain information for 6mer-coot-3.pdb E #3.5
---
Chain | Description
E | No description available
Chain information for 6mer-coot-3.pdb F #3.6
---
Chain | Description
F | No description available
> select add #3.1
2018 atoms, 2055 bonds, 280 residues, 1 model selected
> fitmap #3.1 inMap #1
Fit molecule 6mer-coot-3.pdb A (#3.1) to map
cryosparc_P2_J308_008_volume_map_sharp.mrc (#1) using 2018 atoms
average map value = 0.3083, steps = 52
shifted from previous position = 0.425
rotated from previous position = 4.11 degrees
atoms outside contour = 973, contour level = 0.3
Position of 6mer-coot-3.pdb A (#3.1) relative to
cryosparc_P2_J308_008_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.81113638 -0.42452191 -0.40229209 345.75117612
0.57215767 0.43342210 0.69626208 -143.40161342
-0.12121622 -0.79493801 0.59445790 338.84802790
Axis -0.82137016 -0.15481982 0.54898258
Axis point 0.00000000 257.86610663 432.64316077
Rotation angle (degrees) 65.19645863
Shift along axis -75.76662249
> fitmap #3.1 inMap #1
Fit molecule 6mer-coot-3.pdb A (#3.1) to map
cryosparc_P2_J308_008_volume_map_sharp.mrc (#1) using 2018 atoms
average map value = 0.3083, steps = 44
shifted from previous position = 0.0167
rotated from previous position = 0.0119 degrees
atoms outside contour = 972, contour level = 0.3
Position of 6mer-coot-3.pdb A (#3.1) relative to
cryosparc_P2_J308_008_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.81103019 -0.42466568 -0.40235445 345.80302081
0.57230308 0.43341938 0.69614426 -143.43314756
-0.12124036 -0.79486269 0.59455368 338.81977160
Axis -0.82126104 -0.15484036 0.54914003
Axis point 0.00000000 257.84515231 432.73879275
Rotation angle (degrees) 65.19687316
Shift along axis -75.72580953
> fitmap #3.2 inMap #1
Fit molecule 6mer-coot-3.pdb B (#3.2) to map
cryosparc_P2_J308_008_volume_map_sharp.mrc (#1) using 2018 atoms
average map value = 0.3114, steps = 68
shifted from previous position = 0.38
rotated from previous position = 2.94 degrees
atoms outside contour = 914, contour level = 0.3
Position of 6mer-coot-3.pdb B (#3.2) relative to
cryosparc_P2_J308_008_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.84327236 -0.36715860 -0.39253826 325.26546576
0.52097740 0.37873188 0.76494752 -129.31220126
-0.13219031 -0.84956266 0.51065546 363.76358055
Axis -0.86756374 -0.13989905 0.47724356
Axis point 0.00000000 253.51382307 391.49389778
Rotation angle (degrees) 68.51055306
Shift along axis -90.49404375
> fitmap #3.2 inMap #1
Fit molecule 6mer-coot-3.pdb B (#3.2) to map
cryosparc_P2_J308_008_volume_map_sharp.mrc (#1) using 2018 atoms
average map value = 0.3114, steps = 44
shifted from previous position = 0.00262
rotated from previous position = 0.00778 degrees
atoms outside contour = 916, contour level = 0.3
Position of 6mer-coot-3.pdb B (#3.2) relative to
cryosparc_P2_J308_008_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.84320663 -0.36727192 -0.39257345 325.30954766
0.52106413 0.37868703 0.76491065 -129.32048220
-0.13226773 -0.84953368 0.51068364 363.77072406
Axis -0.86751323 -0.13987392 0.47734274
Axis point 0.00000000 253.52032150 391.53791700
Rotation angle (degrees) 68.51309011
Shift along axis -90.47845810
> fitmap #3.3 inMap #1
Fit molecule 6mer-coot-3.pdb C (#3.3) to map
cryosparc_P2_J308_008_volume_map_sharp.mrc (#1) using 2023 atoms
average map value = 0.32, steps = 60
shifted from previous position = 0.0558
rotated from previous position = 3.24 degrees
atoms outside contour = 892, contour level = 0.3
Position of 6mer-coot-3.pdb C (#3.3) relative to
cryosparc_P2_J308_008_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.83827903 -0.36205316 -0.40768344 327.94736774
0.53161836 0.37663160 0.75863730 -131.22439850
-0.12112056 -0.85268174 0.50819648 361.76852579
Axis -0.86411579 -0.15367751 0.47925684
Axis point 0.00000000 247.29971971 394.37731680
Rotation angle (degrees) 68.80436414
Shift along axis -89.83821786
> fitmap #3.3 inMap #1
Fit molecule 6mer-coot-3.pdb C (#3.3) to map
cryosparc_P2_J308_008_volume_map_sharp.mrc (#1) using 2023 atoms
average map value = 0.3201, steps = 28
shifted from previous position = 0.0256
rotated from previous position = 0.00174 degrees
atoms outside contour = 893, contour level = 0.3
Position of 6mer-coot-3.pdb C (#3.3) relative to
cryosparc_P2_J308_008_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.83828156 -0.36204891 -0.40768199 327.92570599
0.53161860 0.37665863 0.75862371 -131.24302901
-0.12110195 -0.85267160 0.50821792 361.76318141
Axis -0.86411224 -0.15368835 0.47925978
Axis point 0.00000000 247.28812275 394.38728970
Rotation angle (degrees) 68.80279706
Shift along axis -89.81554786
> fitmap #3.4 inMap #1
Fit molecule 6mer-coot-3.pdb D (#3.4) to map
cryosparc_P2_J308_008_volume_map_sharp.mrc (#1) using 2018 atoms
average map value = 0.2975, steps = 108
shifted from previous position = 3.68
rotated from previous position = 13 degrees
atoms outside contour = 1012, contour level = 0.3
Position of 6mer-coot-3.pdb D (#3.4) relative to
cryosparc_P2_J308_008_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.87145457 -0.40923463 -0.27035894 306.54020735
0.48007336 0.59876156 0.64110387 -137.16721670
-0.10048136 -0.68848502 0.71825614 296.75252507
Axis -0.82655997 -0.10560708 0.55285238
Axis point 0.00000000 317.25586261 424.83724294
Rotation angle (degrees) 53.54180329
Shift along axis -74.82769555
> fitmap #3.4 inMap #1
Fit molecule 6mer-coot-3.pdb D (#3.4) to map
cryosparc_P2_J308_008_volume_map_sharp.mrc (#1) using 2018 atoms
average map value = 0.2975, steps = 44
shifted from previous position = 0.0197
rotated from previous position = 0.00651 degrees
atoms outside contour = 1018, contour level = 0.3
Position of 6mer-coot-3.pdb D (#3.4) relative to
cryosparc_P2_J308_008_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.87144771 -0.40919029 -0.27044812 306.53337560
0.48010838 0.59878512 0.64105564 -137.17786947
-0.10037343 -0.68849088 0.71826561 296.73249539
Axis -0.82654357 -0.10573090 0.55285324
Axis point 0.00000000 317.20802439 424.85571367
Rotation angle (degrees) 53.54087077
Shift along axis -74.80973057
> fitmap #3.5 inMap #1
Fit molecule 6mer-coot-3.pdb E (#3.5) to map
cryosparc_P2_J308_008_volume_map_sharp.mrc (#1) using 2023 atoms
average map value = 0.3137, steps = 92
shifted from previous position = 5.25
rotated from previous position = 12.9 degrees
atoms outside contour = 938, contour level = 0.3
Position of 6mer-coot-3.pdb E (#3.5) relative to
cryosparc_P2_J308_008_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.80068386 -0.48670659 -0.34931655 348.87001390
0.59041904 0.54224599 0.59780820 -148.06513787
-0.10154169 -0.68489852 0.72152845 295.62794952
Axis -0.75756332 -0.14633520 0.63614765
Axis point 0.00000000 286.86912161 480.69734991
Rotation angle (degrees) 57.84380674
Shift along axis -54.56095820
> fitmap #3.5 inMap #1
Fit molecule 6mer-coot-3.pdb E (#3.5) to map
cryosparc_P2_J308_008_volume_map_sharp.mrc (#1) using 2023 atoms
average map value = 0.3137, steps = 40
shifted from previous position = 0.00419
rotated from previous position = 0.00215 degrees
atoms outside contour = 941, contour level = 0.3
Position of 6mer-coot-3.pdb E (#3.5) relative to
cryosparc_P2_J308_008_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.80068337 -0.48672354 -0.34929405 348.86893093
0.59041335 0.54223101 0.59782741 -148.06503062
-0.10157861 -0.68489833 0.72152343 295.63443711
Axis -0.75756879 -0.14629900 0.63614946
Axis point 0.00000000 286.87860657 480.69331663
Rotation angle (degrees) 57.84449998
Shift along axis -54.56275842
> fitmap #3.6 inMap #1
Fit molecule 6mer-coot-3.pdb F (#3.6) to map
cryosparc_P2_J308_008_volume_map_sharp.mrc (#1) using 2023 atoms
average map value = 0.3192, steps = 56
shifted from previous position = 0.834
rotated from previous position = 2.54 degrees
atoms outside contour = 889, contour level = 0.3
Position of 6mer-coot-3.pdb F (#3.6) relative to
cryosparc_P2_J308_008_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.86387856 -0.36530066 -0.34679860 313.77340577
0.48614709 0.42450685 0.76384222 -129.86234096
-0.13181369 -0.82846204 0.54431222 354.93245578
Axis -0.87565749 -0.11822687 0.46823752
Axis point 0.00000000 268.42033124 386.67223614
Rotation angle (degrees) 65.39571338
Shift along axis -93.21212060
> fitmap #3.6 inMap #1
Fit molecule 6mer-coot-3.pdb F (#3.6) to map
cryosparc_P2_J308_008_volume_map_sharp.mrc (#1) using 2023 atoms
average map value = 0.3192, steps = 36
shifted from previous position = 0.00841
rotated from previous position = 0.00928 degrees
atoms outside contour = 890, contour level = 0.3
Position of 6mer-coot-3.pdb F (#3.6) relative to
cryosparc_P2_J308_008_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.86386964 -0.36531412 -0.34680664 313.77239743
0.48618229 0.42463426 0.76374899 -129.88196216
-0.13174231 -0.82839081 0.54443790 354.88069670
Axis -0.87562090 -0.11827781 0.46829308
Axis point 0.00000000 268.41932750 386.70320902
Rotation angle (degrees) 65.38801969
Shift along axis -93.19533942
> fitmap #3.1 inMap #1
Fit molecule 6mer-coot-3.pdb A (#3.1) to map
cryosparc_P2_J308_008_volume_map_sharp.mrc (#1) using 2018 atoms
average map value = 0.3083, steps = 44
shifted from previous position = 0.0203
rotated from previous position = 0.00597 degrees
atoms outside contour = 975, contour level = 0.3
Position of 6mer-coot-3.pdb A (#3.1) relative to
cryosparc_P2_J308_008_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.81107383 -0.42463999 -0.40229358 345.79089250
0.57223120 0.43339883 0.69621614 -143.41048885
-0.12128765 -0.79488763 0.59451070 338.85437617
Axis -0.82131021 -0.15478000 0.54908351
Axis point 0.00000000 257.88521684 432.69952591
Rotation angle (degrees) 65.19750091
Shift along axis -75.74516419
> fitmap #3.1 inMap #1
Fit molecule 6mer-coot-3.pdb A (#3.1) to map
cryosparc_P2_J308_008_volume_map_sharp.mrc (#1) using 2018 atoms
average map value = 0.3084, steps = 44
shifted from previous position = 0.0224
rotated from previous position = 0.0185 degrees
atoms outside contour = 971, contour level = 0.3
Position of 6mer-coot-3.pdb A (#3.1) relative to
cryosparc_P2_J308_008_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.81097283 -0.42464827 -0.40248841 345.83716030
0.57241961 0.43350288 0.69599644 -143.45699969
-0.12107380 -0.79482646 0.59463605 338.75052380
Axis -0.82118235 -0.15501016 0.54920980
Axis point 0.00000000 257.78206275 432.79829872
Rotation angle (degrees) 65.19344835
Shift along axis -75.71297157
> fitmap #3.2 inMap #1
Fit molecule 6mer-coot-3.pdb B (#3.2) to map
cryosparc_P2_J308_008_volume_map_sharp.mrc (#1) using 2018 atoms
average map value = 0.3114, steps = 44
shifted from previous position = 0.0141
rotated from previous position = 0.00403 degrees
atoms outside contour = 915, contour level = 0.3
Position of 6mer-coot-3.pdb B (#3.2) relative to
cryosparc_P2_J308_008_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.84323588 -0.36727306 -0.39250955 325.29006333
0.52101071 0.37871225 0.76493456 -129.31645904
-0.13229168 -0.84952194 0.51069696 363.78609314
Axis -0.86753221 -0.13982871 0.47732149
Axis point 0.00000000 253.54869452 391.52904261
Rotation angle (degrees) 68.51100298
Shift along axis -90.47453316
> fitmap #3.2 inMap #1
Fit molecule 6mer-coot-3.pdb B (#3.2) to map
cryosparc_P2_J308_008_volume_map_sharp.mrc (#1) using 2018 atoms
average map value = 0.3114, steps = 40
shifted from previous position = 0.00855
rotated from previous position = 0.00212 degrees
atoms outside contour = 917, contour level = 0.3
Position of 6mer-coot-3.pdb B (#3.2) relative to
cryosparc_P2_J308_008_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.84323802 -0.36728481 -0.39249398 325.29192841
0.52099933 0.37868879 0.76495392 -129.31029399
-0.13232289 -0.84952732 0.51067992 363.78905421
Axis -0.86753846 -0.13980245 0.47731781
Axis point 0.00000000 253.55201477 391.51987176
Rotation angle (degrees) 68.51218431
Shift along axis -90.48236841
> select subtract #3.1
Nothing selected
> select add #3.2
2018 atoms, 2055 bonds, 280 residues, 1 model selected
> save /Users/melvinshen/Desktop/Monomer_1.pdb models #3.2 selectedOnly true
> relModel #1
> open /Users/melvinshen/Desktop/Monomer_1-coot-0.pdb
Chain information for Monomer_1-coot-0.pdb #2
---
Chain | Description
B | No description available
> fitmap #2 inMap #1
Fit molecule Monomer_1-coot-0.pdb (#2) to map
cryosparc_P2_J308_008_volume_map_sharp.mrc (#1) using 2018 atoms
average map value = 0.3304, steps = 44
shifted from previous position = 0.0432
rotated from previous position = 0.0534 degrees
atoms outside contour = 846, contour level = 0.3
Position of Monomer_1-coot-0.pdb (#2) relative to
cryosparc_P2_J308_008_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.99999970 -0.00067167 -0.00039272 0.19527230
0.00067187 0.99999964 0.00051266 -0.41334400
0.00039237 -0.00051293 0.99999979 -0.10284596
Axis -0.55030293 -0.42125800 0.72090803
Axis point 620.05038296 284.32040989 0.00000000
Rotation angle (degrees) 0.05339064
Shift along axis -0.00747693
> fitmap #2 inMap #1
Fit molecule Monomer_1-coot-0.pdb (#2) to map
cryosparc_P2_J308_008_volume_map_sharp.mrc (#1) using 2018 atoms
average map value = 0.3304, steps = 28
shifted from previous position = 0.0153
rotated from previous position = 0.00451 degrees
atoms outside contour = 846, contour level = 0.3
Position of Monomer_1-coot-0.pdb (#2) relative to
cryosparc_P2_J308_008_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.99999965 -0.00070234 -0.00046478 0.20372449
0.00070258 0.99999963 0.00050449 -0.42991758
0.00046442 -0.00050482 0.99999976 -0.13699510
Axis -0.51399676 -0.47320181 0.71546305
Axis point 611.59361626 290.27509930 0.00000000
Rotation angle (degrees) 0.05625433
Shift along axis 0.00070912
> hide #3.1 models
> show #3.1 models
> hide #3.1 models
> hide #3.2 models
> show #3.2 models
> select subtract #3.2
Nothing selected
> hide #3.3 models
> show #3.3 models
> show #3.1 models
> hide #3.1 models
> select add #3.2
2018 atoms, 2055 bonds, 280 residues, 1 model selected
> hide #2 models
> show #2 models
> color #2 #0433ffff
> hide #3.2 models
> show #3.2 models
> select subtract #3.2
Nothing selected
> volume #1 level 0.2
> fitmap #2 inMap #1
Fit molecule Monomer_1-coot-0.pdb (#2) to map
cryosparc_P2_J308_008_volume_map_sharp.mrc (#1) using 2018 atoms
average map value = 0.3304, steps = 40
shifted from previous position = 0.0145
rotated from previous position = 0.00266 degrees
atoms outside contour = 375, contour level = 0.2
Position of Monomer_1-coot-0.pdb (#2) relative to
cryosparc_P2_J308_008_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.99999968 -0.00067369 -0.00042835 0.20336635
0.00067390 0.99999965 0.00050482 -0.41262612
0.00042801 -0.00050511 0.99999978 -0.12000025
Axis -0.53456306 -0.45327516 0.71329094
Axis point 617.33957691 295.80605248 0.00000000
Rotation angle (degrees) 0.05412338
Shift along axis -0.00727406
> volume #1 level 0.25
> fitmap #2 inMap #1
Fit molecule Monomer_1-coot-0.pdb (#2) to map
cryosparc_P2_J308_008_volume_map_sharp.mrc (#1) using 2018 atoms
average map value = 0.3304, steps = 44
shifted from previous position = 0.0213
rotated from previous position = 0.000621 degrees
atoms outside contour = 593, contour level = 0.25
Position of Monomer_1-coot-0.pdb (#2) relative to
cryosparc_P2_J308_008_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.99999969 -0.00067009 -0.00041891 0.19866907
0.00067030 0.99999965 0.00050093 -0.40870470
0.00041857 -0.00050121 0.99999979 -0.09570865
Axis -0.53548906 -0.44750612 0.71623302
Axis point 604.57960233 302.56480824 0.00000000
Rotation angle (degrees) 0.05361259
Shift along axis 0.00796304
> open /Users/melvinshen/Desktop/Monomer_1-coot-1.pdb
Chain information for Monomer_1-coot-1.pdb #4
---
Chain | Description
B | No description available
> fitmap #4 inMap #1
Fit molecule Monomer_1-coot-1.pdb (#4) to map
cryosparc_P2_J308_008_volume_map_sharp.mrc (#1) using 2018 atoms
average map value = 0.3302, steps = 44
shifted from previous position = 0.0418
rotated from previous position = 0.0741 degrees
atoms outside contour = 588, contour level = 0.25
Position of Monomer_1-coot-1.pdb (#4) relative to
cryosparc_P2_J308_008_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.99999948 -0.00067213 -0.00076724 0.27928394
0.00067274 0.99999946 0.00079624 -0.47979169
0.00076670 -0.00079676 0.99999939 -0.20119429
Axis -0.61546272 -0.59264380 0.51959500
Axis point 0.00000000 -258.13726465 596.50186744
Rotation angle (degrees) 0.07414917
Shift along axis 0.00791717
> fitmap #4 inMap #1
Fit molecule Monomer_1-coot-1.pdb (#4) to map
cryosparc_P2_J308_008_volume_map_sharp.mrc (#1) using 2018 atoms
average map value = 0.3302, steps = 44
shifted from previous position = 0.0191
rotated from previous position = 0.00585 degrees
atoms outside contour = 594, contour level = 0.25
Position of Monomer_1-coot-1.pdb (#4) relative to
cryosparc_P2_J308_008_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.99999955 -0.00066883 -0.00067023 0.25311332
0.00066938 0.99999943 0.00082766 -0.48492058
0.00066968 -0.00082811 0.99999943 -0.13718431
Axis -0.65822753 -0.53266119 0.53198550
Axis point 0.00000000 -178.07392935 573.72975621
Rotation angle (degrees) 0.07206354
Shift along axis 0.01871215
> fitmap #4 inMap #1
Fit molecule Monomer_1-coot-1.pdb (#4) to map
cryosparc_P2_J308_008_volume_map_sharp.mrc (#1) using 2018 atoms
average map value = 0.3302, steps = 40
shifted from previous position = 0.00273
rotated from previous position = 0.000327 degrees
atoms outside contour = 592, contour level = 0.25
Position of Monomer_1-coot-1.pdb (#4) relative to
cryosparc_P2_J308_008_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.99999956 -0.00066926 -0.00066472 0.25214897
0.00066981 0.99999943 0.00082912 -0.48560003
0.00066417 -0.00082957 0.99999944 -0.13739029
Axis -0.66029600 -0.52900959 0.53306477
Axis point 0.00000000 -177.03231568 574.61240387
Rotation angle (degrees) 0.07196460
Shift along axis 0.01715619
> fitmap #4 inMap #1
Fit molecule Monomer_1-coot-1.pdb (#4) to map
cryosparc_P2_J308_008_volume_map_sharp.mrc (#1) using 2018 atoms
average map value = 0.3302, steps = 40
shifted from previous position = 0.00271
rotated from previous position = 0.0108 degrees
atoms outside contour = 593, contour level = 0.25
Position of Monomer_1-coot-1.pdb (#4) relative to
cryosparc_P2_J308_008_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.99999965 -0.00067478 -0.00048610 0.21268872
0.00067521 0.99999938 0.00088775 -0.50086022
0.00048550 -0.00088808 0.99999949 -0.05139089
Axis -0.72985871 -0.39932490 0.55483862
Axis point 0.00000000 -68.34720922 556.82978514
Rotation angle (degrees) 0.06970343
Shift along axis 0.01625960
> rename #4 4
> hide #2 models
> hide #!3 models
> combine #4
> rename #5 5
> rename #6 6
> rename #7 7
> rename #8 8
> rename #9 9
> select add #5
2018 atoms, 2055 bonds, 280 residues, 1 model selected
> view orient
> turn x 90
> turn z 72 models #5
> turn x 90
> zoom 1.3
> turn y 20
> undo
> turn y 180
> zoom 0.5
> turn y 35
> move x -50
> move y -30
> zoom 1.3
> turn y 30 models #5
> color #4 #0096ffff
> color #5 #fffb00ff
> color #5 #4f8f00ff
> turn y 30 models #5
> turn y 60 models #5
> undo
> turn y 60 models #5
> undo
> select ~sel & ##selected
Nothing selected
> select ~sel & ##selected
Nothing selected
> select ~sel & ##selected
Nothing selected
> select add #5
2018 atoms, 2055 bonds, 280 residues, 1 model selected
> turn xy 30 model #5
Expected an axis vector or a keyword
> turn x 30 models #5
> turn z 30 models #5
> view sel
> turn z 30 models #5
> view orient
> undo
> view orient
> turn x 90
> turn y 180
> turn y 50
> view matrix models
> #5,0.32858,-0.18814,-0.92555,522.57,-0.44161,0.83564,-0.32664,285.03,0.83487,0.51606,0.19149,-242.34
> view matrix models
> #5,0.32858,-0.18814,-0.92555,557.46,-0.44161,0.83564,-0.32664,300.9,0.83487,0.51606,0.19149,-236.24
> view matrix models
> #5,-0.018711,-0.35307,-0.93541,730.28,-0.6029,0.75033,-0.27115,368.68,0.7976,0.55888,-0.2269,-130.98
> view matrix models
> #5,-0.018711,-0.35307,-0.93541,730.59,-0.6029,0.75033,-0.27115,368.79,0.7976,0.55888,-0.2269,-130.75
> view matrix models
> #5,-0.018711,-0.35307,-0.93541,738.57,-0.6029,0.75033,-0.27115,372.23,0.7976,0.55888,-0.2269,-128.07
> view matrix models
> #5,0.42075,-0.14842,-0.89495,514.07,-0.39478,0.85826,-0.32794,281.7,0.81677,0.49129,0.30252,-247.5
> view matrix models
> #5,0.42075,-0.14842,-0.89495,509.56,-0.39478,0.85826,-0.32794,279.37,0.81677,0.49129,0.30252,-246.36
> view matrix models
> #5,0.35924,0.012142,-0.93317,514.93,-0.44692,0.88004,-0.1606,257.62,0.81927,0.47475,0.32157,-248.87
> view matrix models
> #5,0.35924,0.012142,-0.93317,512.03,-0.44692,0.88004,-0.1606,256.41,0.81927,0.47475,0.32157,-250.09
> fitmap #5 inMap #1
Fit molecule 5 (#5) to map cryosparc_P2_J308_008_volume_map_sharp.mrc (#1)
using 2018 atoms
average map value = 0.295, steps = 224
shifted from previous position = 7.53
rotated from previous position = 31.6 degrees
atoms outside contour = 788, contour level = 0.25
Position of 5 (#5) relative to cryosparc_P2_J308_008_volume_map_sharp.mrc (#1)
coordinates:
Matrix rotation and translation
0.58768361 -0.38040448 -0.71408711 434.59309548
-0.03277056 0.87066419 -0.49078505 168.08628437
0.80842691 0.31182737 0.49920900 -263.15322081
Axis 0.45710201 -0.86709874 0.19798368
Axis point 517.34982628 0.00000000 309.36406521
Rotation angle (degrees) 61.39435218
Shift along axis 0.80592775
> fitmap #5 inMap #1
Fit molecule 5 (#5) to map cryosparc_P2_J308_008_volume_map_sharp.mrc (#1)
using 2018 atoms
average map value = 0.2949, steps = 40
shifted from previous position = 0.022
rotated from previous position = 0.0135 degrees
atoms outside contour = 788, contour level = 0.25
Position of 5 (#5) relative to cryosparc_P2_J308_008_volume_map_sharp.mrc (#1)
coordinates:
Matrix rotation and translation
0.58783928 -0.38045042 -0.71393449 434.48556800
-0.03263644 0.87064307 -0.49083145 168.03349740
0.80831915 0.31183028 0.49938165 -263.14326171
Axis 0.45717372 -0.86703319 0.19810514
Axis point 517.35487367 0.00000000 309.38375655
Rotation angle (degrees) 61.38432773
Shift along axis 0.81473198
> select add #6
4036 atoms, 4110 bonds, 560 residues, 2 models selected
> select subtract #5
2018 atoms, 2055 bonds, 280 residues, 1 model selected
> select add #7
4036 atoms, 4110 bonds, 560 residues, 2 models selected
> select add #8
6054 atoms, 6165 bonds, 840 residues, 3 models selected
> select add #9
8072 atoms, 8220 bonds, 1120 residues, 4 models selected
> color #6 #9437ffff
> color #7 #ff8ad8ff
> color #8 #00fa92ff
> color #8 #4f8f00ff
> color #8 silver
> color #8 #919191ff
> color #8 black
> color #9 #ff7e79ff
> select subtract #7
6054 atoms, 6165 bonds, 840 residues, 3 models selected
> select subtract #8
4036 atoms, 4110 bonds, 560 residues, 2 models selected
> select subtract #9
2018 atoms, 2055 bonds, 280 residues, 1 model selected
> view matrix models
> #6,-0.47282,-0.73608,-0.48439,842.87,-0.88088,0.40871,0.23876,407.61,0.022228,0.53958,-0.84164,324.86
> view matrix models
> #6,-0.47282,-0.73608,-0.48439,887.28,-0.88088,0.40871,0.23876,418.58,0.022228,0.53958,-0.84164,378.94
> view matrix models
> #6,-0.37158,-0.6157,-0.69487,873.83,-0.88988,0.44956,0.077518,452.61,0.26465,0.64715,-0.71495,231.66
> view matrix models
> #6,-0.37158,-0.6157,-0.69487,872.25,-0.88988,0.44956,0.077518,452.06,0.26465,0.64715,-0.71495,230.3
> view matrix models
> #6,-0.36772,-0.61186,-0.7003,871.26,-0.88948,0.45111,0.072912,452.69,0.2713,0.64971,-0.71012,226.02
> view matrix models
> #6,-0.36772,-0.61186,-0.7003,870.97,-0.88948,0.45111,0.072912,452.66,0.2713,0.64971,-0.71012,225.53
> fitmap #6 inMap #1
Fit molecule 6 (#6) to map cryosparc_P2_J308_008_volume_map_sharp.mrc (#1)
using 2018 atoms
average map value = 0.1666, steps = 168
shifted from previous position = 16.3
rotated from previous position = 25.8 degrees
atoms outside contour = 1460, contour level = 0.25
Position of 6 (#6) relative to cryosparc_P2_J308_008_volume_map_sharp.mrc (#1)
coordinates:
Matrix rotation and translation
-0.45139064 -0.79065144 -0.41366264 868.92414722
-0.81194600 0.55621363 -0.17711603 472.73483723
0.37012184 0.25592321 -0.89303591 288.14383201
Axis 0.48345975 -0.87504369 -0.02377397
Axis point 526.12612832 0.00000000 255.07414850
Rotation angle (degrees) 153.39388682
Shift along axis -0.42410567
> view matrix models
> #6,-0.45139,-0.79065,-0.41366,866.7,-0.81195,0.55621,-0.17712,467.47,0.37012,0.25592,-0.89304,301.98
> view matrix models
> #6,-0.52975,-0.65707,-0.53631,903.28,-0.78871,0.61419,0.026574,400.05,0.31194,0.43707,-0.8436,281.64
> view matrix models
> #6,-0.66978,-0.5405,-0.50916,932.94,-0.6335,0.77365,0.012067,311.89,0.38739,0.33064,-0.86058,274.01
> view matrix models
> #6,-0.77586,-0.50269,-0.38124,939.34,-0.4498,0.86446,-0.22447,276.35,0.44241,-0.002676,-0.89681,319.78
> view matrix models
> #6,-0.69064,-0.47234,-0.54764,938.2,-0.59858,0.79831,0.066326,280.62,0.40586,0.37361,-0.83408,252.63
> view matrix models
> #6,-0.4472,-0.42655,-0.78617,886.92,-0.54126,0.82881,-0.1418,300.54,0.71207,0.36212,-0.60152,76.006
> view matrix models
> #6,-0.26802,-0.37048,-0.88933,828.25,-0.8007,0.59901,-0.0082283,415.77,0.53576,0.70988,-0.45719,51.635
> view matrix models
> #6,-0.26802,-0.37048,-0.88933,829.19,-0.8007,0.59901,-0.0082283,418.92,0.53576,0.70988,-0.45719,42.546
> view matrix models
> #6,-0.24249,-0.42087,-0.87411,824.28,-0.80072,0.59554,-0.064615,432.73,0.54776,0.68425,-0.48141,47.92
> view matrix models
> #6,-0.24249,-0.42087,-0.87411,824.73,-0.80072,0.59554,-0.064615,433.59,0.54776,0.68425,-0.48141,45.84
> fitmap #6 inMap #1
Fit molecule 6 (#6) to map cryosparc_P2_J308_008_volume_map_sharp.mrc (#1)
using 2018 atoms
average map value = 0.1191, steps = 152
shifted from previous position = 6.33
rotated from previous position = 7.06 degrees
atoms outside contour = 1637, contour level = 0.25
Position of 6 (#6) relative to cryosparc_P2_J308_008_volume_map_sharp.mrc (#1)
coordinates:
Matrix rotation and translation
-0.19379636 -0.51938212 -0.83227711 809.19534378
-0.80255598 0.57184699 -0.16998506 467.94949956
0.56422236 0.63500648 -0.52765509 57.48681359
Axis 0.49187282 -0.85330105 -0.17302731
Axis point 522.55721465 0.00000000 229.35977669
Rotation angle (degrees) 125.08578372
Shift along axis -11.22739411
> fitmap #6 inMap #1
Fit molecule 6 (#6) to map cryosparc_P2_J308_008_volume_map_sharp.mrc (#1)
using 2018 atoms
average map value = 0.1191, steps = 44
shifted from previous position = 0.0571
rotated from previous position = 0.256 degrees
atoms outside contour = 1641, contour level = 0.25
Position of 6 (#6) relative to cryosparc_P2_J308_008_volume_map_sharp.mrc (#1)
coordinates:
Matrix rotation and translation
-0.19181215 -0.52290048 -0.83053187 808.58881574
-0.80289942 0.57027312 -0.17361191 469.15953054
0.56441175 0.63353268 -0.52922181 58.05265006
Axis 0.49343348 -0.85277396 -0.17117237
Axis point 522.93136340 0.00000000 229.73229886
Rotation angle (degrees) 125.12627771
Shift along axis -11.03924324
> view matrix models
> #6,-0.19181,-0.5229,-0.83053,814.19,-0.8029,0.57027,-0.17361,468.24,0.56441,0.63353,-0.52922,62.361
> view matrix models
> #6,-0.19181,-0.5229,-0.83053,809.98,-0.8029,0.57027,-0.17361,463.17,0.56441,0.63353,-0.52922,65.234
> fitmap #6 inMap #1
Fit molecule 6 (#6) to map cryosparc_P2_J308_008_volume_map_sharp.mrc (#1)
using 2018 atoms
average map value = 0.1715, steps = 172
shifted from previous position = 6.85
rotated from previous position = 20.4 degrees
atoms outside contour = 1416, contour level = 0.25
Position of 6 (#6) relative to cryosparc_P2_J308_008_volume_map_sharp.mrc (#1)
coordinates:
Matrix rotation and translation
-0.32145393 -0.69499796 -0.64315255 853.41017757
-0.68877255 0.63770452 -0.34485551 450.18596101
0.64981516 0.33213066 -0.68368814 119.70839774
Axis 0.46385081 -0.88590306 0.00426547
Axis point 515.27652227 0.00000000 269.97479941
Rotation angle (degrees) 133.13492938
Shift along axis -2.45550642
> fitmap #6 inMap #1
Fit molecule 6 (#6) to map cryosparc_P2_J308_008_volume_map_sharp.mrc (#1)
using 2018 atoms
average map value = 0.1715, steps = 56
shifted from previous position = 0.0166
rotated from previous position = 0.00503 degrees
atoms outside contour = 1413, contour level = 0.25
Position of 6 (#6) relative to cryosparc_P2_J308_008_volume_map_sharp.mrc (#1)
coordinates:
Matrix rotation and translation
-0.32139238 -0.69498905 -0.64319294 853.39399346
-0.68874930 0.63770431 -0.34490232 450.20381553
0.64987025 0.33214971 -0.68362653 119.66896390
Axis 0.46385933 -0.88589856 0.00427495
Axis point 515.28196603 0.00000000 269.98026347
Rotation angle (degrees) 133.13010278
Shift along axis -2.46856820
> view matrix models
> #6,-0.32139,-0.69499,-0.64319,847.93,-0.68875,0.6377,-0.3449,447.12,0.64987,0.33215,-0.68363,118.49
> view matrix models
> #6,-0.19383,-0.6358,-0.74712,809.84,-0.61936,0.66991,-0.4094,428.26,0.7608,0.38338,-0.52364,26.894
> view matrix models
> #6,-0.19383,-0.6358,-0.74712,814.01,-0.61936,0.66991,-0.4094,430.87,0.7608,0.38338,-0.52364,19.801
> fitmap #6 inMap #1
Fit molecule 6 (#6) to map cryosparc_P2_J308_008_volume_map_sharp.mrc (#1)
using 2018 atoms
average map value = 0.1802, steps = 76
shifted from previous position = 1.11
rotated from previous position = 4.73 degrees
atoms outside contour = 1391, contour level = 0.25
Position of 6 (#6) relative to cryosparc_P2_J308_008_volume_map_sharp.mrc (#1)
coordinates:
Matrix rotation and translation
-0.17915494 -0.64171140 -0.74572782 809.60373313
-0.55822527 0.69046438 -0.46004728 413.51809902
0.81011608 0.33386437 -0.48191962 -0.49553363
Axis 0.45400371 -0.88971980 0.04774211
Axis point 510.46428678 0.00000000 278.73153635
Rotation angle (degrees) 119.03246316
Shift along axis -0.37579489
> fitmap #6 inMap #1
Fit molecule 6 (#6) to map cryosparc_P2_J308_008_volume_map_sharp.mrc (#1)
using 2018 atoms
average map value = 0.1802, steps = 48
shifted from previous position = 0.0265
rotated from previous position = 0.0251 degrees
atoms outside contour = 1393, contour level = 0.25
Position of 6 (#6) relative to cryosparc_P2_J308_008_volume_map_sharp.mrc (#1)
coordinates:
Matrix rotation and translation
-0.17936249 -0.64183756 -0.74556935 809.67304879
-0.55849898 0.69032651 -0.45992195 413.61849295
0.80988146 0.33390697 -0.48228430 -0.34862644
Axis 0.45405880 -0.88969563 0.04766847
Axis point 510.49165194 0.00000000 278.69608637
Rotation angle (degrees) 119.05573218
Shift along axis -0.37201187
> view matrix models
> #6,-0.11854,-0.61876,-0.77659,788.1,-0.52478,0.70299,-0.48002,402.36,0.84294,0.35064,-0.40804,-34.119
> view matrix models
> #6,-0.14021,-0.54318,-0.82783,795.35,-0.51026,0.75615,-0.40973,370.52,0.84852,0.36496,-0.38318,-44.754
> view matrix models
> #6,-0.12732,-0.60022,-0.78964,791.4,-0.48723,0.73129,-0.47731,381.42,0.86394,0.32396,-0.38555,-43.129
> fitmap #6 inMap #1
Fit molecule 6 (#6) to map cryosparc_P2_J308_008_volume_map_sharp.mrc (#1)
using 2018 atoms
average map value = 0.2977, steps = 76
shifted from previous position = 4.72
rotated from previous position = 11.1 degrees
atoms outside contour = 799, contour level = 0.25
Position of 6 (#6) relative to cryosparc_P2_J308_008_volume_map_sharp.mrc (#1)
coordinates:
Matrix rotation and translation
-0.11013919 -0.71624917 -0.68909831 783.72801189
-0.59937029 0.60092971 -0.52880879 464.41322957
0.79285851 0.35478248 -0.49548439 1.82615479
Axis 0.51094360 -0.85695318 0.06758613
Axis point 529.75861245 0.00000000 281.96559681
Rotation angle (degrees) 120.15539378
Shift along axis 2.58383934
> fitmap #6 inMap #1
Fit molecule 6 (#6) to map cryosparc_P2_J308_008_volume_map_sharp.mrc (#1)
using 2018 atoms
average map value = 0.2976, steps = 28
shifted from previous position = 0.0196
rotated from previous position = 0.0127 degrees
atoms outside contour = 797, contour level = 0.25
Position of 6 (#6) relative to cryosparc_P2_J308_008_volume_map_sharp.mrc (#1)
coordinates:
Matrix rotation and translation
-0.11030453 -0.71625562 -0.68906517 783.80447789
-0.59947545 0.60093448 -0.52868416 464.43651117
0.79275601 0.35476139 -0.49566345 1.92002238
Axis 0.51091764 -0.85697255 0.06753676
Axis point 529.76211601 0.00000000 281.96041639
Rotation angle (degrees) 120.16664706
Shift along axis 2.57986910
> select subtract #6
Nothing selected
> select add #7
2018 atoms, 2055 bonds, 280 residues, 1 model selected
> view matrix models
> #7,0.13206,-0.69451,0.70726,311.33,-0.74387,0.40215,0.53379,284.2,-0.65515,-0.5966,-0.46352,714.79
> view matrix models
> #7,0.13206,-0.69451,0.70726,312.3,-0.74387,0.40215,0.53379,287.42,-0.65515,-0.5966,-0.46352,779.52
> view matrix models
> #7,0.13206,-0.69451,0.70726,306.07,-0.74387,0.40215,0.53379,284.24,-0.65515,-0.5966,-0.46352,777.05
> view matrix models
> #7,-0.044241,-0.86207,0.50486,454.93,-0.8447,0.30211,0.44183,364.57,-0.53341,-0.40691,-0.74155,758.66
> view matrix models
> #7,0.13049,-0.69609,0.70599,307.28,-0.74474,0.40123,0.53326,284.88,-0.65447,-0.59537,-0.46605,777.14
> view matrix models
> #7,-0.075796,-0.69222,0.7177,387.61,-0.53995,0.6336,0.55408,155.29,-0.83828,-0.34552,-0.42179,796.72
> view matrix models
> #7,-0.075796,-0.69222,0.7177,392.35,-0.53995,0.6336,0.55408,157.79,-0.83828,-0.34552,-0.42179,797.19
> view matrix models
> #7,-0.39534,-0.82346,0.40696,618.19,-0.72581,0.55159,0.41103,281.36,-0.56294,-0.13289,-0.81574,739.44
> view matrix models
> #7,-0.39534,-0.82346,0.40696,628.49,-0.72581,0.55159,0.41103,286.51,-0.56294,-0.13289,-0.81574,745.34
> view matrix models
> #7,-0.090126,-0.95632,0.27808,558.47,-0.83596,0.22441,0.50081,368.79,-0.54133,-0.18733,-0.81967,747.23
> view matrix models
> #7,-0.090126,-0.95632,0.27808,559.56,-0.83596,0.22441,0.50081,369.35,-0.54133,-0.18733,-0.81967,747.42
> view matrix models
> #7,-0.015633,-0.96158,0.27408,531.19,-0.86784,0.14919,0.47392,402.04,-0.4966,-0.23045,-0.83683,740.98
> view matrix models
> #7,-0.091993,-0.99076,0.099688,608.17,-0.91433,0.1237,0.38562,446.11,-0.39438,-0.055673,-0.91726,687.01
> view matrix models
> #7,-0.091993,-0.99076,0.099688,611.15,-0.91433,0.1237,0.38562,447.65,-0.39438,-0.055673,-0.91726,687.93
> fitmap #7 inMap #1
Fit molecule 7 (#7) to map cryosparc_P2_J308_008_volume_map_sharp.mrc (#1)
using 2018 atoms
average map value = 0.124, steps = 88
shifted from previous position = 3
rotated from previous position = 6.87 degrees
atoms outside contour = 1628, contour level = 0.25
Position of 7 (#7) relative to cryosparc_P2_J308_008_volume_map_sharp.mrc (#1)
coordinates:
Matrix rotation and translation
-0.11010973 -0.97526813 0.19164532 597.08619228
-0.87697306 0.18607399 0.44305159 406.35961160
-0.46775430 -0.11928349 -0.87577244 719.46720529
Axis -0.64474974 0.75603986 0.11270098
Axis point 580.97153691 0.00000000 238.48261828
Rotation angle (degrees) 154.14546304
Shift along axis 3.33755674
> fitmap #7 inMap #1
Fit molecule 7 (#7) to map cryosparc_P2_J308_008_volume_map_sharp.mrc (#1)
using 2018 atoms
average map value = 0.1241, steps = 48
shifted from previous position = 0.0191
rotated from previous position = 0.0239 degrees
atoms outside contour = 1630, contour level = 0.25
Position of 7 (#7) relative to cryosparc_P2_J308_008_volume_map_sharp.mrc (#1)
coordinates:
Matrix rotation and translation
-0.11045179 -0.97527437 0.19141657 597.28783862
-0.87698239 0.18625867 0.44295553 406.35789183
-0.46765617 -0.11894373 -0.87587105 719.40553071
Axis -0.64464064 0.75612322 0.11276578
Axis point 580.92817845 0.00000000 238.47784706
Rotation angle (degrees) 154.16228534
Shift along axis 3.34494507
> view #7 clip false
> view matrix models
> #7,-0.21345,-0.96971,-0.11878,710.61,-0.94221,0.17219,0.28739,471.72,-0.25823,0.17326,-0.95042,599.52
> view matrix models
> #7,-0.21345,-0.96971,-0.11878,712.14,-0.94221,0.17219,0.28739,472.6,-0.25823,0.17326,-0.95042,597.8
> view matrix models
> #7,-0.083339,-0.9863,-0.14236,667.79,-0.96448,0.043895,0.2605,510.88,-0.25068,0.15901,-0.95492,598.34
> view matrix models
> #7,-0.083339,-0.9863,-0.14236,673.15,-0.96448,0.043895,0.2605,513.49,-0.25068,0.15901,-0.95492,600.91
> view matrix models
> #7,-0.083339,-0.9863,-0.14236,673.19,-0.96448,0.043895,0.2605,513.51,-0.25068,0.15901,-0.95492,600.96
> fitmap #7 inMap #1
Fit molecule 7 (#7) to map cryosparc_P2_J308_008_volume_map_sharp.mrc (#1)
using 2018 atoms
average map value = 0.1143, steps = 180
shifted from previous position = 3.75
rotated from previous position = 9.06 degrees
atoms outside contour = 1669, contour level = 0.25
Position of 7 (#7) relative to cryosparc_P2_J308_008_volume_map_sharp.mrc (#1)
coordinates:
Matrix rotation and translation
-0.11464869 -0.99339550 0.00458951 651.85755539
-0.94379671 0.11036385 0.31155672 479.03761415
-0.31000556 0.03138800 -0.95021647 644.45043318
Axis -0.66050234 0.74166303 0.11692995
Axis point 585.83834876 0.00000000 237.32091598
Rotation angle (degrees) 167.75528057
Shift along axis 0.08660921
> fitmap #7 inMap #1
Fit molecule 7 (#7) to map cryosparc_P2_J308_008_volume_map_sharp.mrc (#1)
using 2018 atoms
average map value = 0.1143, steps = 44
shifted from previous position = 0.0164
rotated from previous position = 0.0277 degrees
atoms outside contour = 1665, contour level = 0.25
Position of 7 (#7) relative to cryosparc_P2_J308_008_volume_map_sharp.mrc (#1)
coordinates:
Matrix rotation and translation
-0.11434958 -0.99343113 0.00433257 651.81182564
-0.94375262 0.10999123 0.31182194 479.02980256
-0.31025016 0.03156783 -0.95013068 644.50974527
Axis -0.66061552 0.74153503 0.11710227
Axis point 585.90401585 0.00000000 237.27739601
Rotation angle (degrees) 167.75362184
Shift along axis 0.09392637
> view matrix models
> #7,-0.69673,-0.71194,0.087832,818.38,-0.66114,0.68482,0.30647,262.69,-0.27834,0.15546,-0.94782,608.85
> fitmap #7 inMap #1
Fit molecule 7 (#7) to map cryosparc_P2_J308_008_volume_map_sharp.mrc (#1)
using 2018 atoms
average map value = 0.3528, steps = 148
shifted from previous position = 6.08
rotated from previous position = 21 degrees
atoms outside contour = 551, contour level = 0.25
Position of 7 (#7) relative to cryosparc_P2_J308_008_volume_map_sharp.mrc (#1)
coordinates:
Matrix rotation and translation
-0.57787824 -0.81612275 -0.00062028 812.94588043
-0.81612280 0.57787742 0.00112361 420.12946410
-0.00055856 0.00115554 -0.99999918 534.98132712
Axis 0.45941307 -0.88822250 -0.00064094
Axis point 515.11895728 0.00000000 267.34703122
Rotation angle (degrees) 179.99800942
Shift along axis -0.03337000
> select subtract #7
Nothing selected
> select add #8
2018 atoms, 2055 bonds, 280 residues, 1 model selected
> view matrix models
> #8,0.035896,-0.50728,0.86103,280.93,-0.32333,0.80935,0.49031,50.768,-0.9456,-0.296,-0.13497,702.14
> view matrix models
> #8,0.035896,-0.50728,0.86103,277.77,-0.32333,0.80935,0.49031,43.424,-0.9456,-0.296,-0.13497,761.28
> view matrix models
> #8,-0.27266,-0.62783,0.72903,455.47,-0.4682,0.74855,0.46953,117.98,-0.8405,-0.21331,-0.49805,788.67
> view matrix models
> #8,-0.29529,-0.61887,0.72788,463.32,-0.43089,0.76624,0.47667,97.994,-0.85272,-0.17287,-0.49293,785.2
> view matrix models
> #8,-0.29529,-0.61887,0.72788,462.97,-0.43089,0.76624,0.47667,96.185,-0.85272,-0.17287,-0.49293,782.93
> fitmap #8 inMap #1
Fit molecule 8 (#8) to map cryosparc_P2_J308_008_volume_map_sharp.mrc (#1)
using 2018 atoms
average map value = 0.1578, steps = 140
shifted from previous position = 6.34
rotated from previous position = 9.91 degrees
atoms outside contour = 1490, contour level = 0.25
Position of 8 (#8) relative to cryosparc_P2_J308_008_volume_map_sharp.mrc (#1)
coordinates:
Matrix rotation and translation
-0.42330964 -0.54994909 0.71997566 504.77685513
-0.46760367 0.81328216 0.34629315 137.86762952
-0.77598696 -0.19007403 -0.60142839 775.84459139
Axis -0.33705301 0.94006257 0.05174584
Axis point 481.58904218 0.00000000 251.12439206
Rotation angle (degrees) 127.28124186
Shift along axis -0.38562850
> fitmap #8 inMap #1
Fit molecule 8 (#8) to map cryosparc_P2_J308_008_volume_map_sharp.mrc (#1)
using 2018 atoms
average map value = 0.1578, steps = 80
shifted from previous position = 0.0105
rotated from previous position = 0.0083 degrees
atoms outside contour = 1490, contour level = 0.25
Position of 8 (#8) relative to cryosparc_P2_J308_008_volume_map_sharp.mrc (#1)
coordinates:
Matrix rotation and translation
-0.42340267 -0.54993175 0.71993420 504.81422430
-0.46750647 0.81332525 0.34632317 137.80585172
-0.77599477 -0.18993974 -0.60146073 775.82895935
Axis -0.33700076 0.94007843 0.05179807
Axis point 481.57158727 0.00000000 251.11575758
Rotation angle (degrees) 127.28420413
Shift along axis -0.38802517
> view matrix models
> #8,-0.4234,-0.54993,0.71993,503.29,-0.46751,0.81333,0.34632,135.56,-0.77599,-0.18994,-0.60146,785.11
> fitmap #8 inMap #1
Fit molecule 8 (#8) to map cryosparc_P2_J308_008_volume_map_sharp.mrc (#1)
using 2018 atoms
average map value = 0.3041, steps = 88
shifted from previous position = 4.28
rotated from previous position = 9.46 degrees
atoms outside contour = 774, contour level = 0.25
Position of 8 (#8) relative to cryosparc_P2_J308_008_volume_map_sharp.mrc (#1)
coordinates:
Matrix rotation and translation
-0.31311916 -0.48935964 0.81393091 424.18937092
-0.49776107 0.81444596 0.29818066 162.55258223
-0.80882032 -0.31177705 -0.49860281 798.05931598
Axis -0.35184035 0.93604748 -0.00484617
Axis point 489.21009992 0.00000000 268.49783205
Rotation angle (degrees) 119.90993228
Shift along axis -0.95753789
> fitmap #8 inMap #1
Fit molecule 8 (#8) to map cryosparc_P2_J308_008_volume_map_sharp.mrc (#1)
using 2018 atoms
average map value = 0.3041, steps = 28
shifted from previous position = 0.0206
rotated from previous position = 0.0161 degrees
atoms outside contour = 771, contour level = 0.25
Position of 8 (#8) relative to cryosparc_P2_J308_008_volume_map_sharp.mrc (#1)
coordinates:
Matrix rotation and translation
-0.31334545 -0.48942252 0.81380601 424.30387344
-0.49782776 0.81442917 0.29811516 162.59123126
-0.80869163 -0.31172219 -0.49884579 798.06035378
Axis -0.35182770 0.93605222 -0.00484916
Axis point 489.19268029 0.00000000 268.50639732
Rotation angle (degrees) 119.92599751
Shift along axis -0.95789185
> select subtract #8
Nothing selected
> select add #9
2018 atoms, 2055 bonds, 280 residues, 1 model selected
> view matrix models
> #9,0.57473,-0.37524,0.72724,69.802,-0.0029252,0.88773,0.46036,-86.343,-0.81834,-0.26671,0.50911,494.69
> view matrix models
> #9,0.57473,-0.37524,0.72724,53.034,-0.0029252,0.88773,0.46036,-101.23,-0.81834,-0.26671,0.50911,523.95
> view matrix models
> #9,0.49732,-0.41931,0.75951,84.807,-0.027602,0.86736,0.49692,-96.112,-0.86713,-0.26809,0.41978,564.89
> view matrix models
> #9,0.49732,-0.41931,0.75951,83.899,-0.027602,0.86736,0.49692,-97.304,-0.86713,-0.26809,0.41978,568.09
> fitmap #9 inMap #1
Fit molecule 9 (#9) to map cryosparc_P2_J308_008_volume_map_sharp.mrc (#1)
using 2018 atoms
average map value = 0.2928, steps = 112
shifted from previous position = 9.88
rotated from previous position = 20.7 degrees
atoms outside contour = 825, contour level = 0.25
Position of 9 (#9) relative to cryosparc_P2_J308_008_volume_map_sharp.mrc (#1)
coordinates:
Matrix rotation and translation
0.55187908 -0.07696878 0.83036455 -18.82012199
-0.25822652 0.93101846 0.25792186 49.72802120
-0.79293666 -0.35676382 0.49393423 533.84134245
Axis -0.35221060 0.93014026 -0.10385942
Axis point 489.24383334 0.00000000 287.78059185
Rotation angle (degrees) 60.76348452
Shift along axis -2.56176988
> select subtract #9
Nothing selected
> select add #4
2018 atoms, 2055 bonds, 280 residues, 1 model selected
> select add #5
4036 atoms, 4110 bonds, 560 residues, 2 models selected
> select subtract #4
2018 atoms, 2055 bonds, 280 residues, 1 model selected
> save /Users/melvinshen/Desktop/Monomer_2.pdb models #5 selectedOnly true
> relModel #1
> select subtract #5
Nothing selected
> select add #6
2018 atoms, 2055 bonds, 280 residues, 1 model selected
> save /Users/melvinshen/Desktop/Monomer_3.pdb models #6 selectedOnly true
> relModel #1
> select subtract #6
Nothing selected
> select add #7
2018 atoms, 2055 bonds, 280 residues, 1 model selected
> save /Users/melvinshen/Desktop/Monomer_4.pdb models #7 selectedOnly true
> relModel #1
> select subtract #7
Nothing selected
> select add #8
2018 atoms, 2055 bonds, 280 residues, 1 model selected
> save /Users/melvinshen/Desktop/Monomer_5.pdb models #8 selectedOnly true
> relModel #1
> select subtract #8
Nothing selected
> select add #9
2018 atoms, 2055 bonds, 280 residues, 1 model selected
> save /Users/melvinshen/Desktop/Monomer_6.pdb selectedOnly true relModel #1
> select subtract #9
Nothing selected
> hide #6 models
> show #6 models
> select add #7
2018 atoms, 2055 bonds, 280 residues, 1 model selected
> fitmap #7 inMap #1
Fit molecule 7 (#7) to map cryosparc_P2_J308_008_volume_map_sharp.mrc (#1)
using 2018 atoms
average map value = 0.3528, steps = 44
shifted from previous position = 0.00109
rotated from previous position = 0.015 degrees
atoms outside contour = 551, contour level = 0.25
Position of 7 (#7) relative to cryosparc_P2_J308_008_volume_map_sharp.mrc (#1)
coordinates:
Matrix rotation and translation
-0.57786112 -0.81613501 -0.00041010 812.89240334
-0.81613472 0.57786027 0.00127960 420.10137058
-0.00080734 0.00107412 -0.99999910 535.09858916
Axis -0.45942302 0.88821734 0.00066257
Axis point 515.12684730 0.00000000 267.34144093
Rotation angle (degrees) 179.98718748
Shift along axis 0.03438358
> ui tool show "Show Sequence Viewer"
> sequence chain #6/B
Alignment identifier is 6/B
> select #6/B:192
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #6/B:192
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #6/B:189
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #6/B:189-190
13 atoms, 12 bonds, 2 residues, 1 model selected
> select #6/B:189
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #6/B:189-190
13 atoms, 12 bonds, 2 residues, 1 model selected
> select #6/B:188-189
17 atoms, 16 bonds, 2 residues, 1 model selected
> select #6/B:188-189
17 atoms, 16 bonds, 2 residues, 1 model selected
> select #6/B:193-194
8 atoms, 7 bonds, 2 residues, 1 model selected
> select #6/B:193-194
8 atoms, 7 bonds, 2 residues, 1 model selected
> select clear
> open /Users/melvinshen/Desktop/Monomer_3-coot-0.pdb
Chain information for Monomer_3-coot-0.pdb #10
---
Chain | Description
B | No description available
> fitmap #10 inMap #1
Fit molecule Monomer_3-coot-0.pdb (#10) to map
cryosparc_P2_J308_008_volume_map_sharp.mrc (#1) using 2010 atoms
average map value = 0.3542, steps = 48
shifted from previous position = 0.0157
rotated from previous position = 0.0424 degrees
atoms outside contour = 513, contour level = 0.25
Position of Monomer_3-coot-0.pdb (#10) relative to
cryosparc_P2_J308_008_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.99999981 0.00043141 -0.00044524 0.03356244
-0.00043123 0.99999983 0.00040467 0.08743172
0.00044541 -0.00040447 0.99999982 -0.13371860
Axis -0.54650257 -0.60155590 -0.58263663
Axis point 291.12647813 0.00000000 83.81331488
Rotation angle (degrees) 0.04241546
Shift along axis 0.00697233
> fitmap #10 inMap #1
Fit molecule Monomer_3-coot-0.pdb (#10) to map
cryosparc_P2_J308_008_volume_map_sharp.mrc (#1) using 2010 atoms
average map value = 0.3542, steps = 40
shifted from previous position = 0.00803
rotated from previous position = 0.00927 degrees
atoms outside contour = 519, contour level = 0.25
Position of Monomer_3-coot-0.pdb (#10) relative to
cryosparc_P2_J308_008_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.99999971 0.00048998 -0.00059042 0.06710372
-0.00048976 0.99999981 0.00036406 0.12967821
0.00059059 -0.00036377 0.99999976 -0.20410936
Axis -0.42854888 -0.69538534 -0.57687528
Axis point 346.80667622 0.00000000 112.62002593
Rotation angle (degrees) 0.04865418
Shift along axis -0.00118791
> hide #10 models
> show #10 models
> hide #10 models
> show #10 models
> hide #10 models
> hide #6 models
> close #6
> rename #10 y
> rename #10 t
> rename #10 6
> rename #10 id #6
> show #6 models
> ui tool show "Show Sequence Viewer"
> sequence chain #8/B
Alignment identifier is 8/B
> select #8/B:187
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #8/B:187
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #8/B:189
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #8/B:189
9 atoms, 8 bonds, 1 residue, 1 model selected
> open /Users/melvinshen/Desktop/Monomer_1-coot-1.pdb
Chain information for Monomer_1-coot-1.pdb #10
---
Chain | Description
B | No description available
> select add #8
2018 atoms, 2055 bonds, 280 residues, 1 model selected
> select subtract #8
Nothing selected
> fitmap #10 inMap #1
Fit molecule Monomer_1-coot-1.pdb (#10) to map
cryosparc_P2_J308_008_volume_map_sharp.mrc (#1) using 2018 atoms
average map value = 0.3302, steps = 44
shifted from previous position = 0.0418
rotated from previous position = 0.0741 degrees
atoms outside contour = 588, contour level = 0.25
Position of Monomer_1-coot-1.pdb (#10) relative to
cryosparc_P2_J308_008_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.99999948 -0.00067213 -0.00076724 0.27928394
0.00067274 0.99999946 0.00079624 -0.47979169
0.00076670 -0.00079676 0.99999939 -0.20119429
Axis -0.61546272 -0.59264380 0.51959500
Axis point 0.00000000 -258.13726465 596.50186744
Rotation angle (degrees) 0.07414917
Shift along axis 0.00791717
> fitmap #10 inMap #1
Fit molecule Monomer_1-coot-1.pdb (#10) to map
cryosparc_P2_J308_008_volume_map_sharp.mrc (#1) using 2018 atoms
average map value = 0.3302, steps = 44
shifted from previous position = 0.0191
rotated from previous position = 0.00585 degrees
atoms outside contour = 594, contour level = 0.25
Position of Monomer_1-coot-1.pdb (#10) relative to
cryosparc_P2_J308_008_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.99999955 -0.00066883 -0.00067023 0.25311332
0.00066938 0.99999943 0.00082766 -0.48492058
0.00066968 -0.00082811 0.99999943 -0.13718431
Axis -0.65822753 -0.53266119 0.53198550
Axis point 0.00000000 -178.07392935 573.72975621
Rotation angle (degrees) 0.07206354
Shift along axis 0.01871215
> fitmap #2 inMap #1
Fit molecule Monomer_1-coot-0.pdb (#2) to map
cryosparc_P2_J308_008_volume_map_sharp.mrc (#1) using 2018 atoms
average map value = 0.3304, steps = 40
shifted from previous position = 0.0027
rotated from previous position = 0.00398 degrees
atoms outside contour = 592, contour level = 0.25
Position of Monomer_1-coot-0.pdb (#2) relative to
cryosparc_P2_J308_008_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.99999971 -0.00067190 -0.00035354 0.18389380
0.00067209 0.99999964 0.00052438 -0.41513175
0.00035318 -0.00052462 0.99999980 -0.06749700
Axis -0.56838691 -0.38292497 0.72822029
Axis point 614.81081774 277.90102129 0.00000000
Rotation angle (degrees) 0.05287212
Shift along axis 0.00528880
> fitmap #2 inMap #1
Fit molecule Monomer_1-coot-0.pdb (#2) to map
cryosparc_P2_J308_008_volume_map_sharp.mrc (#1) using 2018 atoms
average map value = 0.3304, steps = 40
shifted from previous position = 0.00146
rotated from previous position = 0.000606 degrees
atoms outside contour = 593, contour level = 0.25
Position of Monomer_1-coot-0.pdb (#2) relative to
cryosparc_P2_J308_008_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.99999971 -0.00067262 -0.00036375 0.18563565
0.00067281 0.99999964 0.00052175 -0.41499894
0.00036340 -0.00052199 0.99999980 -0.07089943
Axis -0.56370224 -0.39272415 0.72664126
Axis point 612.98589834 281.43655463 0.00000000
Rotation angle (degrees) 0.05304372
Shift along axis 0.00681842
> fitmap #10 inMap #1
Fit molecule Monomer_1-coot-1.pdb (#10) to map
cryosparc_P2_J308_008_volume_map_sharp.mrc (#1) using 2018 atoms
average map value = 0.3302, steps = 40
shifted from previous position = 0.00273
rotated from previous position = 0.000327 degrees
atoms outside contour = 592, contour level = 0.25
Position of Monomer_1-coot-1.pdb (#10) relative to
cryosparc_P2_J308_008_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.99999956 -0.00066926 -0.00066472 0.25214897
0.00066981 0.99999943 0.00082912 -0.48560003
0.00066417 -0.00082957 0.99999944 -0.13739029
Axis -0.66029600 -0.52900959 0.53306477
Axis point 0.00000000 -177.03231568 574.61240387
Rotation angle (degrees) 0.07196460
Shift along axis 0.01715619
> fitmap #10 inMap #1
Fit molecule Monomer_1-coot-1.pdb (#10) to map
cryosparc_P2_J308_008_volume_map_sharp.mrc (#1) using 2018 atoms
average map value = 0.3302, steps = 40
shifted from previous position = 0.00271
rotated from previous position = 0.0108 degrees
atoms outside contour = 593, contour level = 0.25
Position of Monomer_1-coot-1.pdb (#10) relative to
cryosparc_P2_J308_008_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.99999965 -0.00067478 -0.00048610 0.21268872
0.00067521 0.99999938 0.00088775 -0.50086022
0.00048550 -0.00088808 0.99999949 -0.05139089
Axis -0.72985871 -0.39932490 0.55483862
Axis point 0.00000000 -68.34720922 556.82978514
Rotation angle (degrees) 0.06970343
Shift along axis 0.01625960
> close #10
> fitmap #4 inMap #1
Fit molecule 4 (#4) to map cryosparc_P2_J308_008_volume_map_sharp.mrc (#1)
using 2018 atoms
average map value = 0.3302, steps = 40
shifted from previous position = 0.00368
rotated from previous position = 0.000787 degrees
atoms outside contour = 592, contour level = 0.25
Position of 4 (#4) relative to cryosparc_P2_J308_008_volume_map_sharp.mrc (#1)
coordinates:
Matrix rotation and translation
0.99999966 -0.00067379 -0.00047334 0.21053407
0.00067421 0.99999937 0.00089273 -0.50152381
0.00047273 -0.00089305 0.99999949 -0.04882964
Axis -0.73512238 -0.38945164 0.55490766
Axis point 0.00000000 -63.35546031 555.87061017
Rotation angle (degrees) 0.06959247
Shift along axis 0.01345502
> fitmap #4 inMap #1
Fit molecule 4 (#4) to map cryosparc_P2_J308_008_volume_map_sharp.mrc (#1)
using 2018 atoms
average map value = 0.3302, steps = 40
shifted from previous position = 0.000754
rotated from previous position = 0.0128 degrees
atoms outside contour = 592, contour level = 0.25
Position of 4 (#4) relative to cryosparc_P2_J308_008_volume_map_sharp.mrc (#1)
coordinates:
Matrix rotation and translation
0.99999954 -0.00066665 -0.00068603 0.25773778
0.00066721 0.99999944 0.00082245 -0.48270990
0.00068548 -0.00082290 0.99999943 -0.14861708
Axis -0.65204345 -0.54352372 0.52860317
Axis point 0.00000000 -191.11865738 576.38108900
Rotation angle (degrees) 0.07228946
Shift along axis 0.01574860
> fitmap #5 inMap #1
Fit molecule 5 (#5) to map cryosparc_P2_J308_008_volume_map_sharp.mrc (#1)
using 2018 atoms
average map value = 0.2949, steps = 40
shifted from previous position = 0.00164
rotated from previous position = 0.00117 degrees
atoms outside contour = 788, contour level = 0.25
Position of 5 (#5) relative to cryosparc_P2_J308_008_volume_map_sharp.mrc (#1)
coordinates:
Matrix rotation and translation
0.58785378 -0.38043687 -0.71392977 434.47502021
-0.03264048 0.87064698 -0.49082425 168.03169694
0.80830844 0.31183590 0.49939548 -263.14256141
Axis 0.45717740 -0.86703308 0.19809710
Axis point 517.35430091 0.00000000 309.38147916
Rotation angle (degrees) 61.38327549
Shift along axis 0.81534079
> fitmap #5 inMap #1
Fit molecule 5 (#5) to map cryosparc_P2_J308_008_volume_map_sharp.mrc (#1)
using 2018 atoms
average map value = 0.2949, steps = 40
shifted from previous position = 0.000585
rotated from previous position = 0.000369 degrees
atoms outside contour = 788, contour level = 0.25
Position of 5 (#5) relative to cryosparc_P2_J308_008_volume_map_sharp.mrc (#1)
coordinates:
Matrix rotation and translation
0.58785725 -0.38043950 -0.71392552 434.47273325
-0.03263958 0.87064460 -0.49082852 168.03234483
0.80830595 0.31183933 0.49939735 -263.14236032
Axis 0.45718221 -0.86703005 0.19809929
Axis point 517.35522982 0.00000000 309.38179212
Rotation angle (degrees) 61.38317882
Shift along axis 0.81579526
> open /Users/melvinshen/Desktop/Monomer_2.pdb
Chain information for Monomer_2.pdb #10
---
Chain | Description
B | No description available
> fitmap #10 inMap #1
Fit molecule Monomer_2.pdb (#10) to map
cryosparc_P2_J308_008_volume_map_sharp.mrc (#1) using 2018 atoms
average map value = 0.3395, steps = 40
shifted from previous position = 0.0318
rotated from previous position = 0.0817 degrees
atoms outside contour = 560, contour level = 0.25
Position of Monomer_2.pdb (#10) relative to
cryosparc_P2_J308_008_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.99999952 0.00024640 -0.00094383 0.18306828
-0.00024542 0.99999943 0.00104007 -0.13211989
0.00094408 -0.00103984 0.99999901 -0.24216933
Axis -0.72936294 -0.66203156 -0.17246425
Axis point 0.00000000 -233.72525266 129.63189334
Rotation angle (degrees) 0.08169481
Shift along axis -0.00429013
> fitmap #10 inMap #1
Fit molecule Monomer_2.pdb (#10) to map
cryosparc_P2_J308_008_volume_map_sharp.mrc (#1) using 2018 atoms
average map value = 0.3395, steps = 28
shifted from previous position = 0.0119
rotated from previous position = 0.0122 degrees
atoms outside contour = 563, contour level = 0.25
Position of Monomer_2.pdb (#10) relative to
cryosparc_P2_J308_008_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.99999967 0.00022374 -0.00078264 0.14001856
-0.00022282 0.99999928 0.00117745 -0.18160527
0.00078290 -0.00117728 0.99999900 -0.14026947
Axis -0.82255408 -0.54687315 -0.15599535
Axis point 0.00000000 -118.47788441 151.36610662
Rotation angle (degrees) 0.08201035
Shift along axis 0.00602359
> fitmap #5 inMap #1
Fit molecule 5 (#5) to map cryosparc_P2_J308_008_volume_map_sharp.mrc (#1)
using 2018 atoms
average map value = 0.2949, steps = 40
shifted from previous position = 0.000583
rotated from previous position = 0.000844 degrees
atoms outside contour = 788, contour level = 0.25
Position of 5 (#5) relative to cryosparc_P2_J308_008_volume_map_sharp.mrc (#1)
coordinates:
Matrix rotation and translation
0.58786623 -0.38044492 -0.71391524 434.46723286
-0.03263453 0.87064044 -0.49083624 168.03247318
0.80829963 0.31184434 0.49940447 -263.14211019
Axis 0.45719115 -0.86702380 0.19810599
Axis point 517.35739981 0.00000000 309.38340705
Rotation angle (degrees) 61.38278937
Shift along axis 0.81639132
> fitmap #5 inMap #1
Fit molecule 5 (#5) to map cryosparc_P2_J308_008_volume_map_sharp.mrc (#1)
using 2018 atoms
average map value = 0.2949, steps = 40
shifted from previous position = 0.000858
rotated from previous position = 0.00135 degrees
atoms outside contour = 788, contour level = 0.25
Position of 5 (#5) relative to cryosparc_P2_J308_008_volume_map_sharp.mrc (#1)
coordinates:
Matrix rotation and translation
0.58785199 -0.38043585 -0.71393179 434.47587379
-0.03264385 0.87064686 -0.49082423 168.03278129
0.80830960 0.31183748 0.49939260 -263.14261717
Axis 0.45717761 -0.86703361 0.19809431
Axis point 517.35414384 0.00000000 309.38047659
Rotation angle (degrees) 61.38343161
Shift along axis 0.81551934
> close #5
> rename #10 id #5
> open /Users/melvinshen/Desktop/Monomer_3-coot-0.pdb
Chain information for Monomer_3-coot-0.pdb #10
---
Chain | Description
B | No description available
> fitmap #10 inMap #1
Fit molecule Monomer_3-coot-0.pdb (#10) to map
cryosparc_P2_J308_008_volume_map_sharp.mrc (#1) using 2010 atoms
average map value = 0.3542, steps = 48
shifted from previous position = 0.0157
rotated from previous position = 0.0424 degrees
atoms outside contour = 513, contour level = 0.25
Position of Monomer_3-coot-0.pdb (#10) relative to
cryosparc_P2_J308_008_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.99999981 0.00043141 -0.00044524 0.03356244
-0.00043123 0.99999983 0.00040467 0.08743172
0.00044541 -0.00040447 0.99999982 -0.13371860
Axis -0.54650257 -0.60155590 -0.58263663
Axis point 291.12647813 0.00000000 83.81331488
Rotation angle (degrees) 0.04241546
Shift along axis 0.00697233
> fitmap #6 inMap #1
Fit molecule 6 (#6) to map cryosparc_P2_J308_008_volume_map_sharp.mrc (#1)
using 2010 atoms
average map value = 0.3542, steps = 40
shifted from previous position = 0.00118
rotated from previous position = 0.00115 degrees
atoms outside contour = 519, contour level = 0.25
Position of 6 (#6) relative to cryosparc_P2_J308_008_volume_map_sharp.mrc (#1)
coordinates:
Matrix rotation and translation
0.99999969 0.00049742 -0.00060751 0.07097949
-0.00049720 0.99999981 0.00035659 0.13585694
0.00060768 -0.00035629 0.99999975 -0.21278336
Axis -0.41336471 -0.70463382 -0.57673287
Axis point 352.43212551 0.00000000 115.05896612
Rotation angle (degrees) 0.04940537
Shift along axis -0.00235065
> fitmap #6 inMap #1
Fit molecule 6 (#6) to map cryosparc_P2_J308_008_volume_map_sharp.mrc (#1)
using 2010 atoms
average map value = 0.3542, steps = 40
shifted from previous position = 0.0167
rotated from previous position = 0.0124 degrees
atoms outside contour = 520, contour level = 0.25
Position of 6 (#6) relative to cryosparc_P2_J308_008_volume_map_sharp.mrc (#1)
coordinates:
Matrix rotation and translation
0.99999959 0.00050103 -0.00075119 0.12079661
-0.00050089 0.99999986 0.00019426 0.19210232
0.00075129 -0.00019388 0.99999970 -0.30323027
Axis -0.21013111 -0.81340651 -0.54241567
Axis point 416.06732275 0.00000000 155.77959498
Rotation angle (degrees) 0.05291687
Shift along axis -0.01716355
> close #10
> open /Users/melvinshen/Desktop/Monomer_4.pdb
Chain information for Monomer_4.pdb #10
---
Chain | Description
B | No description available
> fitmap #10 inMap #1
Fit molecule Monomer_4.pdb (#10) to map
cryosparc_P2_J308_008_volume_map_sharp.mrc (#1) using 2018 atoms
average map value = 0.3528, steps = 44
shifted from previous position = 0.00086
rotated from previous position = 0.0151 degrees
atoms outside contour = 550, contour level = 0.25
Position of Monomer_4.pdb (#10) relative to
cryosparc_P2_J308_008_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.99999998 -0.00002077 -0.00021104 0.06797814
0.00002074 0.99999999 -0.00015686 0.03877896
0.00021104 0.00015685 0.99999997 -0.11989977
Axis 0.59468052 -0.80010108 0.07869785
Axis point 568.17947689 0.00000000 322.16253420
Rotation angle (degrees) 0.01511252
Shift along axis -0.00003767
> fitmap #10 inMap #1
Fit molecule Monomer_4.pdb (#10) to map
cryosparc_P2_J308_008_volume_map_sharp.mrc (#1) using 2018 atoms
average map value = 0.3528, steps = 40
shifted from previous position = 0.012
rotated from previous position = 0.00207 degrees
atoms outside contour = 551, contour level = 0.25
Position of Monomer_4.pdb (#10) relative to
cryosparc_P2_J308_008_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.99999998 -0.00003230 -0.00018104 0.06310910
0.00003227 0.99999999 -0.00014048 0.03078261
0.00018105 0.00014048 0.99999997 -0.11555893
Axis 0.60704093 -0.78232715 0.13951894
Axis point 636.87498542 0.00000000 354.88283751
Rotation angle (degrees) 0.01325924
Shift along axis -0.00189493
> fitmap #7 inMap #1
Fit molecule 7 (#7) to map cryosparc_P2_J308_008_volume_map_sharp.mrc (#1)
using 2018 atoms
average map value = 0.3528, steps = 40
shifted from previous position = 0.0118
rotated from previous position = 0.00199 degrees
atoms outside contour = 551, contour level = 0.25
Position of 7 (#7) relative to cryosparc_P2_J308_008_volume_map_sharp.mrc (#1)
coordinates:
Matrix rotation and translation
-0.57785202 -0.81614144 -0.00043894 812.89845819
-0.81614119 0.57785116 0.00126392 420.11117456
-0.00077790 0.00108859 -0.99999910 535.07244635
Axis -0.45942799 0.88821478 0.00066225
Axis point 515.12895661 0.00000000 267.33594896
Rotation angle (degrees) 179.98906741
Shift along axis 0.03500043
> fitmap #7 inMap #1
Fit molecule 7 (#7) to map cryosparc_P2_J308_008_volume_map_sharp.mrc (#1)
using 2018 atoms
average map value = 0.3528, steps = 40
shifted from previous position = 0.00699
rotated from previous position = 0.0137 degrees
atoms outside contour = 550, contour level = 0.25
Position of 7 (#7) relative to cryosparc_P2_J308_008_volume_map_sharp.mrc (#1)
coordinates:
Matrix rotation and translation
-0.57787627 -0.81612415 -0.00062805 812.94774144
-0.81612420 0.57787544 0.00111974 420.13194913
-0.00055091 0.00115963 -0.99999918 534.97380890
Axis 0.45941426 -0.88822189 -0.00064111
Axis point 515.11957945 0.00000000 267.34521705
Rotation angle (degrees) 179.99751212
Shift along axis -0.03358521
> close #10
> open /Users/melvinshen/Desktop/Monomer_5-coot-0.pdb
Chain information for Monomer_5-coot-0.pdb #10
---
Chain | Description
B | No description available
> fitmap #10 inMap #1
Fit molecule Monomer_5-coot-0.pdb (#10) to map
cryosparc_P2_J308_008_volume_map_sharp.mrc (#1) using 2018 atoms
average map value = 0.3468, steps = 44
shifted from previous position = 0.0289
rotated from previous position = 0.0833 degrees
atoms outside contour = 583, contour level = 0.25
Position of Monomer_5-coot-0.pdb (#10) relative to
cryosparc_P2_J308_008_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.99999992 -0.00020368 -0.00035653 0.15904324
0.00020319 0.99999901 -0.00139480 0.33745620
0.00035682 0.00139473 0.99999896 -0.36079829
Axis 0.95929324 -0.24531481 0.13991831
Axis point 0.00000000 260.80615322 245.14828411
Rotation angle (degrees) 0.08330514
Shift along axis 0.01930381
> fitmap #10 inMap #1
Fit molecule Monomer_5-coot-0.pdb (#10) to map
cryosparc_P2_J308_008_volume_map_sharp.mrc (#1) using 2018 atoms
average map value = 0.3468, steps = 40
shifted from previous position = 0.0146
rotated from previous position = 0.013 degrees
atoms outside contour = 583, contour level = 0.25
Position of Monomer_5-coot-0.pdb (#10) relative to
cryosparc_P2_J308_008_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.99999997 -0.00018788 -0.00014392 0.08038281
0.00018769 0.99999911 -0.00131815 0.31651918
0.00014417 0.00131812 0.99999912 -0.25773290
Axis 0.98426038 -0.10755825 0.14022382
Axis point 0.00000000 196.64109783 240.72047873
Rotation angle (degrees) 0.07673140
Shift along axis 0.00893308
> select add #10
2018 atoms, 2055 bonds, 280 residues, 1 model selected
> select subtract #10
Nothing selected
> select add #8
2018 atoms, 2055 bonds, 280 residues, 1 model selected
> select subtract #8
Nothing selected
> fitmap #8 inMap #1
Fit molecule 8 (#8) to map cryosparc_P2_J308_008_volume_map_sharp.mrc (#1)
using 2018 atoms
average map value = 0.3041, steps = 28
shifted from previous position = 0.0216
rotated from previous position = 0.0213 degrees
atoms outside contour = 775, contour level = 0.25
Position of 8 (#8) relative to cryosparc_P2_J308_008_volume_map_sharp.mrc (#1)
coordinates:
Matrix rotation and translation
-0.31307947 -0.48927614 0.81399638 424.14402186
-0.49773400 0.81448138 0.29812910 162.54732201
-0.80885234 -0.31181557 -0.49852676 798.06151588
Axis -0.35181519 0.93605677 -0.00487848
Axis point 489.20697110 0.00000000 268.50413122
Rotation angle (degrees) 119.90493644
Shift along axis -0.96011801
> fitmap #8 inMap #1
Fit molecule 8 (#8) to map cryosparc_P2_J308_008_volume_map_sharp.mrc (#1)
using 2018 atoms
average map value = 0.3041, steps = 28
shifted from previous position = 0.0201
rotated from previous position = 0.0206 degrees
atoms outside contour = 772, contour level = 0.25
Position of 8 (#8) relative to cryosparc_P2_J308_008_volume_map_sharp.mrc (#1)
coordinates:
Matrix rotation and translation
-0.31335873 -0.48938340 0.81382443 424.29924788
-0.49781412 0.81445063 0.29807930 162.59065471
-0.80869488 -0.31172754 -0.49883718 798.06010628
Axis -0.35180813 0.93605950 -0.00486383
Axis point 489.18907923 0.00000000 268.50864302
Rotation angle (degrees) 119.92544224
Shift along axis -0.95902563
> close #8
> select add #10
2018 atoms, 2055 bonds, 280 residues, 1 model selected
> color #10 black
> rename #10 id #8
> fitmap #8 inMap #1
Fit molecule Monomer_5-coot-0.pdb (#8) to map
cryosparc_P2_J308_008_volume_map_sharp.mrc (#1) using 2018 atoms
average map value = 0.3468, steps = 60
shifted from previous position = 0.00415
rotated from previous position = 0.0118 degrees
atoms outside contour = 584, contour level = 0.25
Position of Monomer_5-coot-0.pdb (#8) relative to
cryosparc_P2_J308_008_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.99999991 -0.00026095 -0.00033270 0.14587639
0.00026050 0.99999904 -0.00135802 0.29797590
0.00033305 0.00135793 0.99999902 -0.33740366
Axis 0.95478785 -0.23404207 0.18331524
Axis point 0.00000000 249.66588593 220.56937481
Rotation angle (degrees) 0.08149061
Shift along axis 0.00769088
> fitmap #8 inMap #1
Fit molecule Monomer_5-coot-0.pdb (#8) to map
cryosparc_P2_J308_008_volume_map_sharp.mrc (#1) using 2018 atoms
average map value = 0.3468, steps = 40
shifted from previous position = 0.0129
rotated from previous position = 0.0151 degrees
atoms outside contour = 583, contour level = 0.25
Position of Monomer_5-coot-0.pdb (#8) relative to
cryosparc_P2_J308_008_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.99999998 -0.00018602 -0.00008417 0.06989912
0.00018590 0.99999912 -0.00131333 0.31850322
0.00008441 0.00131331 0.99999913 -0.23670376
Axis 0.98813044 -0.06342070 0.13991447
Axis point 0.00000000 182.07229469 243.15441223
Rotation angle (degrees) 0.07615174
Shift along axis 0.01575147
> select subtract #8
Nothing selected
> select add #9
2018 atoms, 2055 bonds, 280 residues, 1 model selected
> fitmap #9 inMap #1
Fit molecule 9 (#9) to map cryosparc_P2_J308_008_volume_map_sharp.mrc (#1)
using 2018 atoms
average map value = 0.2928, steps = 28
shifted from previous position = 0.0213
rotated from previous position = 0.0109 degrees
atoms outside contour = 825, contour level = 0.25
Position of 9 (#9) relative to cryosparc_P2_J308_008_volume_map_sharp.mrc (#1)
coordinates:
Matrix rotation and translation
0.55172136 -0.07698359 0.83046798 -18.76327659
-0.25826594 0.93101816 0.25788346 49.76219535
-0.79303357 -0.35676141 0.49378037 533.92960957
Axis -0.35215200 0.93016204 -0.10386314
Axis point 489.24628022 0.00000000 287.77010155
Rotation angle (degrees) 60.77372291
Shift along axis -2.56117277
> fitmap #9 inMap #1
Fit molecule 9 (#9) to map cryosparc_P2_J308_008_volume_map_sharp.mrc (#1)
using 2018 atoms
average map value = 0.2928, steps = 28
shifted from previous position = 0.0189
rotated from previous position = 0.00383 degrees
atoms outside contour = 823, contour level = 0.25
Position of 9 (#9) relative to cryosparc_P2_J308_008_volume_map_sharp.mrc (#1)
coordinates:
Matrix rotation and translation
0.55177692 -0.07697883 0.83043151 -18.79105754
-0.25825109 0.93101856 0.25789690 49.74472104
-0.79299975 -0.35676140 0.49383469 533.89185489
Axis -0.35217215 0.93015465 -0.10386103
Axis point 489.23426209 0.00000000 287.77763533
Rotation angle (degrees) 60.77010265
Shift along axis -2.56258649
> select subtract #9
Nothing selected
> fitmap #4 inMap #1
Fit molecule 4 (#4) to map cryosparc_P2_J308_008_volume_map_sharp.mrc (#1)
using 2018 atoms
average map value = 0.3302, steps = 40
shifted from previous position = 0.00501
rotated from previous position = 0.0013 degrees
atoms outside contour = 595, contour level = 0.25
Position of 4 (#4) relative to cryosparc_P2_J308_008_volume_map_sharp.mrc (#1)
coordinates:
Matrix rotation and translation
0.99999956 -0.00066961 -0.00066451 0.25137061
0.00067016 0.99999943 0.00082910 -0.48573032
0.00066395 -0.00082954 0.99999944 -0.13401763
Axis -0.66024801 -0.52881372 0.53331850
Axis point 0.00000000 -174.43131418 573.34819158
Rotation angle (degrees) 0.07196775
Shift along axis 0.01941983
> fitmap #5 inMap #1
Fit molecule Monomer_2.pdb (#5) to map
cryosparc_P2_J308_008_volume_map_sharp.mrc (#1) using 2018 atoms
average map value = 0.3395, steps = 36
shifted from previous position = 0.00546
rotated from previous position = 0.00704 degrees
atoms outside contour = 563, contour level = 0.25
Position of Monomer_2.pdb (#5) relative to
cryosparc_P2_J308_008_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.99999973 0.00011660 -0.00073201 0.14475078
-0.00011576 0.99999934 0.00114489 -0.22409126
0.00073214 -0.00114480 0.99999908 -0.12263526
Axis -0.83941908 -0.53676719 -0.08518565
Axis point 0.00000000 -106.59144562 191.34552366
Rotation angle (degrees) 0.07814306
Shift along axis 0.00922503
> fitmap #6 inMap #1
Fit molecule 6 (#6) to map cryosparc_P2_J308_008_volume_map_sharp.mrc (#1)
using 2010 atoms
average map value = 0.3542, steps = 36
shifted from previous position = 0.0211
rotated from previous position = 0.00422 degrees
atoms outside contour = 519, contour level = 0.25
Position of 6 (#6) relative to cryosparc_P2_J308_008_volume_map_sharp.mrc (#1)
coordinates:
Matrix rotation and translation
0.99999965 0.00045322 -0.00071013 0.10517912
-0.00045311 0.99999989 0.00015599 0.16906445
0.00071020 -0.00015567 0.99999974 -0.30269008
Axis -0.18189041 -0.82892985 -0.52895291
Axis point 425.63515461 0.00000000 148.11316530
Rotation angle (degrees) 0.04908694
Shift along axis 0.00083515
> fitmap #6 inMap #1
Fit molecule 6 (#6) to map cryosparc_P2_J308_008_volume_map_sharp.mrc (#1)
using 2010 atoms
average map value = 0.3542, steps = 44
shifted from previous position = 0.0275
rotated from previous position = 0.0106 degrees
atoms outside contour = 521, contour level = 0.25
Position of 6 (#6) relative to cryosparc_P2_J308_008_volume_map_sharp.mrc (#1)
coordinates:
Matrix rotation and translation
0.99999948 0.00055069 -0.00086259 0.14526945
-0.00055052 0.99999983 0.00019067 0.21984470
0.00086269 -0.00019019 0.99999961 -0.35149690
Axis -0.18294058 -0.82870390 -0.52894479
Axis point 421.51880070 0.00000000 163.31135023
Rotation angle (degrees) 0.05964215
Shift along axis -0.02283938
> fitmap #7 inMap #1
Fit molecule 7 (#7) to map cryosparc_P2_J308_008_volume_map_sharp.mrc (#1)
using 2018 atoms
average map value = 0.3528, steps = 40
shifted from previous position = 0.0102
rotated from previous position = 0.0134 degrees
atoms outside contour = 552, contour level = 0.25
Position of 7 (#7) relative to cryosparc_P2_J308_008_volume_map_sharp.mrc (#1)
coordinates:
Matrix rotation and translation
-0.57785071 -0.81614236 -0.00044169 812.89927208
-0.81614212 0.57784986 0.00125822 420.11369591
-0.00077165 0.00108754 -0.99999911 535.06699398
Axis -0.45942870 0.88821441 0.00066035
Axis point 515.12946686 0.00000000 267.33482871
Rotation angle (degrees) 179.98935762
Shift along axis 0.03511207
> fitmap #8 inMap #1
Fit molecule Monomer_5-coot-0.pdb (#8) to map
cryosparc_P2_J308_008_volume_map_sharp.mrc (#1) using 2018 atoms
average map value = 0.3468, steps = 36
shifted from previous position = 0.00939
rotated from previous position = 0.0161 degrees
atoms outside contour = 581, contour level = 0.25
Position of Monomer_5-coot-0.pdb (#8) relative to
cryosparc_P2_J308_008_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.99999990 -0.00031606 -0.00032654 0.15657051
0.00031561 0.99999901 -0.00137153 0.28107335
0.00032697 0.00137143 0.99999901 -0.33899233
Axis 0.94924546 -0.22615968 0.21859746
Axis point 0.00000000 249.07766927 206.56035026
Rotation angle (degrees) 0.08278155
Shift along axis 0.01095352
> fitmap #8 inMap #1
Fit molecule Monomer_5-coot-0.pdb (#8) to map
cryosparc_P2_J308_008_volume_map_sharp.mrc (#1) using 2018 atoms
average map value = 0.3468, steps = 40
shifted from previous position = 0.00612
rotated from previous position = 0.00383 degrees
atoms outside contour = 585, contour level = 0.25
Position of Monomer_5-coot-0.pdb (#8) relative to
cryosparc_P2_J308_008_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.99999991 -0.00025339 -0.00034919 0.14715659
0.00025291 0.99999902 -0.00137780 0.30579105
0.00034953 0.00137771 0.99999899 -0.34660923
Axis 0.95430472 -0.24198513 0.17534450
Axis point 0.00000000 252.46729884 222.75605451
Rotation angle (degrees) 0.08271938
Shift along axis 0.00565932
> fitmap #9 inMap #1
Fit molecule 9 (#9) to map cryosparc_P2_J308_008_volume_map_sharp.mrc (#1)
using 2018 atoms
average map value = 0.2928, steps = 28
shifted from previous position = 0.0166
rotated from previous position = 0.000754 degrees
atoms outside contour = 825, contour level = 0.25
Position of 9 (#9) relative to cryosparc_P2_J308_008_volume_map_sharp.mrc (#1)
coordinates:
Matrix rotation and translation
0.55177399 -0.07696728 0.83043452 -18.78153609
-0.25826159 0.93101783 0.25788901 49.75834624
-0.79299837 -0.35676579 0.49383374 533.90222411
Axis -0.35216962 0.93015421 -0.10387351
Axis point 489.24990826 0.00000000 287.77464702
Rotation angle (degrees) 60.77025415
Shift along axis -2.56107600
> fitmap #9 inMap #1
Fit molecule 9 (#9) to map cryosparc_P2_J308_008_volume_map_sharp.mrc (#1)
using 2018 atoms
average map value = 0.2928, steps = 28
shifted from previous position = 0.0158
rotated from previous position = 0.00455 degrees
atoms outside contour = 823, contour level = 0.25
Position of 9 (#9) relative to cryosparc_P2_J308_008_volume_map_sharp.mrc (#1)
coordinates:
Matrix rotation and translation
0.55177140 -0.07704455 0.83042908 -18.77596359
-0.25820804 0.93101829 0.25794099 49.71710173
-0.79301761 -0.35674792 0.49381574 533.90187449
Axis -0.35218689 0.93015611 -0.10379788
Axis point 489.23776481 0.00000000 287.76463499
Rotation angle (degrees) 60.77091523
Shift along axis -2.56056866
> fitmap #9 inMap #1
Fit molecule 9 (#9) to map cryosparc_P2_J308_008_volume_map_sharp.mrc (#1)
using 2018 atoms
average map value = 0.2928, steps = 28
shifted from previous position = 0.0231
rotated from previous position = 0.0135 degrees
atoms outside contour = 825, contour level = 0.25
Position of 9 (#9) relative to cryosparc_P2_J308_008_volume_map_sharp.mrc (#1)
coordinates:
Matrix rotation and translation
0.55159175 -0.07697890 0.83055451 -18.72778371
-0.25832930 0.93100922 0.25785228 49.79898498
-0.79310309 -0.35678575 0.49365111 533.99531237
Axis -0.35211786 0.93017160 -0.10389321
Axis point 489.23897245 0.00000000 287.77024596
Rotation angle (degrees) 60.78251400
Shift along axis -2.56249690
> fitmap #9 inMap #1
Fit molecule 9 (#9) to map cryosparc_P2_J308_008_volume_map_sharp.mrc (#1)
using 2018 atoms
average map value = 0.2928, steps = 28
shifted from previous position = 0.0228
rotated from previous position = 0.0158 degrees
atoms outside contour = 824, contour level = 0.25
Position of 9 (#9) relative to cryosparc_P2_J308_008_volume_map_sharp.mrc (#1)
coordinates:
Matrix rotation and translation
0.55182090 -0.07697129 0.83040298 -18.80308203
-0.25827334 0.93100475 0.25792449 49.75065872
-0.79296190 -0.35679907 0.49386825 533.87599083
Axis -0.35221674 0.93013562 -0.10388022
Axis point 489.24674436 0.00000000 287.78251862
Rotation angle (degrees) 60.76801087
Shift along axis -2.56153360
> fitmap #9 inMap #1
Fit molecule 9 (#9) to map cryosparc_P2_J308_008_volume_map_sharp.mrc (#1)
using 2018 atoms
average map value = 0.2928, steps = 36
shifted from previous position = 0.0184
rotated from previous position = 0.0229 degrees
atoms outside contour = 824, contour level = 0.25
Position of 9 (#9) relative to cryosparc_P2_J308_008_volume_map_sharp.mrc (#1)
coordinates:
Matrix rotation and translation
0.55156487 -0.07673259 0.83059515 -18.77317950
-0.25846228 0.93102959 0.25764541 49.89533304
-0.79307846 -0.35678567 0.49369073 533.97349035
Axis -0.35200304 0.93019064 -0.10411160
Axis point 489.21039083 0.00000000 287.81508500
Rotation angle (degrees) 60.78142741
Shift along axis -2.57244566
> open /Users/melvinshen/Desktop/Monomer_6.pdb
Summary of feedback from opening /Users/melvinshen/Desktop/Monomer_6.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 PRO A 160 LEU A 165 1 6
Start residue of secondary structure not found: HELIX 2 2 ARG A 227 ASP A 231
1 5
Start residue of secondary structure not found: HELIX 3 3 ALA A 237 SER A 263
1 27
Start residue of secondary structure not found: HELIX 4 4 ALA A 276 VAL A 294
1 19
Start residue of secondary structure not found: HELIX 5 5 PRO A 306 PHE A 312
1 7
13 messages similar to the above omitted
Chain information for Monomer_6.pdb #10
---
Chain | Description
B | No description available
> hide #9 models
> hide #8 models
> hide #7 models
> hide #6 models
> hide #5 models
> hide #4 models
> view #10 clip false
> fitmap #10 inMap #1
Fit molecule Monomer_6.pdb (#10) to map
cryosparc_P2_J308_008_volume_map_sharp.mrc (#1) using 2018 atoms
average map value = 0.2928, steps = 28
shifted from previous position = 0.0213
rotated from previous position = 0.0107 degrees
atoms outside contour = 825, contour level = 0.25
Position of Monomer_6.pdb (#10) relative to
cryosparc_P2_J308_008_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.99999998 0.00005425 0.00017813 -0.04193406
-0.00005426 1.00000000 0.00001465 0.02618912
-0.00017813 -0.00001466 0.99999998 0.08453083
Axis -0.07845017 0.95366219 -0.29047202
Axis point 480.57881436 0.00000000 233.82472249
Rotation angle (degrees) 0.01070199
Shift along axis 0.00371147
> fitmap #10 inMap #1
Fit molecule Monomer_6.pdb (#10) to map
cryosparc_P2_J308_008_volume_map_sharp.mrc (#1) using 2018 atoms
average map value = 0.2928, steps = 28
shifted from previous position = 0.0191
rotated from previous position = 0.00381 degrees
atoms outside contour = 823, contour level = 0.25
Position of Monomer_6.pdb (#10) relative to
cryosparc_P2_J308_008_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.99999999 0.00003605 0.00011445 -0.03510179
-0.00003605 1.00000000 0.00000807 0.01257727
-0.00011445 -0.00000808 0.99999999 0.04744399
Axis -0.06714713 0.95165778 -0.29973110
Axis point 414.81267171 0.00000000 306.67357133
Rotation angle (degrees) 0.00689038
Shift along axis 0.00010580
> close #10
> show #9 models
> select add #9
2018 atoms, 2055 bonds, 280 residues, 1 model selected
> save /Users/melvinshen/Desktop/Monomer_6.pdb models #9 selectedOnly true
> relModel #1
> fitmap #9 inMap #1
Fit molecule 9 (#9) to map cryosparc_P2_J308_008_volume_map_sharp.mrc (#1)
using 2018 atoms
average map value = 0.2928, steps = 28
shifted from previous position = 0.0191
rotated from previous position = 0.0242 degrees
atoms outside contour = 825, contour level = 0.25
Position of 9 (#9) relative to cryosparc_P2_J308_008_volume_map_sharp.mrc (#1)
coordinates:
Matrix rotation and translation
0.55180702 -0.07702069 0.83040762 -18.79007966
-0.25822086 0.93101495 0.25794019 49.72314459
-0.79298865 -0.35676178 0.49385224 533.88382078
Axis -0.35220214 0.93014774 -0.10382119
Axis point 489.24222923 0.00000000 287.77058206
Rotation angle (degrees) 60.76865681
Shift along axis -2.56067429
> fitmap #9 inMap #1
Fit molecule 9 (#9) to map cryosparc_P2_J308_008_volume_map_sharp.mrc (#1)
using 2018 atoms
average map value = 0.2928, steps = 28
shifted from previous position = 0.0219
rotated from previous position = 0.012 degrees
atoms outside contour = 824, contour level = 0.25
Position of 9 (#9) relative to cryosparc_P2_J308_008_volume_map_sharp.mrc (#1)
coordinates:
Matrix rotation and translation
0.55163923 -0.07698188 0.83052269 -18.74032757
-0.25830519 0.93101251 0.25786457 49.78503676
-0.79307792 -0.35677654 0.49369821 533.97164846
Axis -0.35213067 0.93016813 -0.10388094
Axis point 489.24208057 0.00000000 287.76990080
Rotation angle (degrees) 60.77930162
Shift along axis -2.56197919
> open /Users/melvinshen/Desktop/Monomer_6-coot-0.pdb
Chain information for Monomer_6-coot-0.pdb #10
---
Chain | Description
B | No description available
> fitmap #10 inMap #1
Fit molecule Monomer_6-coot-0.pdb (#10) to map
cryosparc_P2_J308_008_volume_map_sharp.mrc (#1) using 2018 atoms
average map value = 0.3445, steps = 44
shifted from previous position = 0.0283
rotated from previous position = 0.0566 degrees
atoms outside contour = 559, contour level = 0.25
Position of Monomer_6-coot-0.pdb (#10) relative to
cryosparc_P2_J308_008_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.99999951 -0.00074100 0.00064987 -0.04587201
0.00074105 0.99999972 -0.00007830 -0.27538472
-0.00064981 0.00007879 0.99999979 0.26260488
Axis 0.07944102 0.65724869 0.74947534
Axis point 382.39002980 -63.46173978 0.00000000
Rotation angle (degrees) 0.05664960
Shift along axis 0.01217551
> close #9
> show #!3 models
> show #3.1 models
> fitmap #3.1 inMap #1
Fit molecule 6mer-coot-3.pdb A (#3.1) to map
cryosparc_P2_J308_008_volume_map_sharp.mrc (#1) using 2018 atoms
average map value = 0.3083, steps = 40
shifted from previous position = 0.0234
rotated from previous position = 0.0249 degrees
atoms outside contour = 762, contour level = 0.25
Position of 6mer-coot-3.pdb A (#3.1) relative to
cryosparc_P2_J308_008_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.81120018 -0.42438808 -0.40230466 345.71672161
0.57209618 0.43351147 0.69625697 -143.39382693
-0.12107947 -0.79496073 0.59445538 338.81355868
Axis -0.82141137 -0.15490801 0.54889604
Axis point 0.00000000 257.84409306 432.59879862
Rotation angle (degrees) 65.19170432
Shift along axis -75.78937221
> fitmap #3.1 inMap #1
Fit molecule 6mer-coot-3.pdb A (#3.1) to map
cryosparc_P2_J308_008_volume_map_sharp.mrc (#1) using 2018 atoms
average map value = 0.3083, steps = 40
shifted from previous position = 0.0239
rotated from previous position = 0.0189 degrees
atoms outside contour = 764, contour level = 0.25
Position of 6mer-coot-3.pdb A (#3.1) relative to
cryosparc_P2_J308_008_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.81103731 -0.42455699 -0.40245477 345.79797781
0.57233735 0.43353711 0.69604277 -143.44585556
-0.12103074 -0.79485655 0.59460459 338.74750972
Axis -0.82123850 -0.15501801 0.54912361
Axis point 0.00000000 257.78261960 432.74627522
Rotation angle (degrees) 65.19132585
Shift along axis -75.73166912
> fitmap #3.2 inMap #1
Fit molecule 6mer-coot-3.pdb B (#3.2) to map
cryosparc_P2_J308_008_volume_map_sharp.mrc (#1) using 2018 atoms
average map value = 0.3114, steps = 44
shifted from previous position = 0.00701
rotated from previous position = 0.00436 degrees
atoms outside contour = 697, contour level = 0.25
Position of 6mer-coot-3.pdb B (#3.2) relative to
cryosparc_P2_J308_008_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.84319990 -0.36731082 -0.39255151 325.31575901
0.52106396 0.37867756 0.76491545 -129.31958877
-0.13231127 -0.84952108 0.51069331 363.77627503
Axis -0.86750784 -0.13983854 0.47736289
Axis point 0.00000000 253.53315725 391.54336852
Rotation angle (degrees) 68.51329077
Shift along axis -90.47681615
> fitmap #3.2 inMap #1
Fit molecule 6mer-coot-3.pdb B (#3.2) to map
cryosparc_P2_J308_008_volume_map_sharp.mrc (#1) using 2018 atoms
average map value = 0.3114, steps = 44
shifted from previous position = 0.000756
rotated from previous position = 0.00211 degrees
atoms outside contour = 697, contour level = 0.25
Position of 6mer-coot-3.pdb B (#3.2) relative to
cryosparc_P2_J308_008_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.84320510 -0.36732998 -0.39252241 325.31503334
0.52104764 0.37867515 0.76492777 -129.31664558
-0.13234242 -0.84951387 0.51069723 363.78236404
Axis -0.86751181 -0.13980637 0.47736509
Axis point 0.00000000 253.54653312 391.54135781
Rotation angle (degrees) 68.51308454
Shift along axis -90.47834223
> fitmap #3.3 inMap #1
Fit molecule 6mer-coot-3.pdb C (#3.3) to map
cryosparc_P2_J308_008_volume_map_sharp.mrc (#1) using 2023 atoms
average map value = 0.32, steps = 28
shifted from previous position = 0.0194
rotated from previous position = 0.0023 degrees
atoms outside contour = 673, contour level = 0.25
Position of 6mer-coot-3.pdb C (#3.3) relative to
cryosparc_P2_J308_008_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.83828842 -0.36201347 -0.40769935 327.93447915
0.53161534 0.37665959 0.75862553 -131.23090905
-0.12106879 -0.85268623 0.50820129 361.75475092
Axis -0.86411947 -0.15371516 0.47923814
Axis point 0.00000000 247.28336203 394.37340625
Rotation angle (degrees) 68.80306780
Shift along axis -89.83571238
> fitmap #3.3 inMap #1
Fit molecule 6mer-coot-3.pdb C (#3.3) to map
cryosparc_P2_J308_008_volume_map_sharp.mrc (#1) using 2023 atoms
average map value = 0.32, steps = 28
shifted from previous position = 0.0136
rotated from previous position = 0.0218 degrees
atoms outside contour = 673, contour level = 0.25
Position of 6mer-coot-3.pdb C (#3.3) relative to
cryosparc_P2_J308_008_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.83822790 -0.36229329 -0.40757523 327.97627526
0.53162533 0.37645846 0.75871835 -131.21706696
-0.12144343 -0.85265620 0.50816227 361.86343682
Axis -0.86409913 -0.15343809 0.47936359
Axis point 0.00000000 247.37674093 394.41042334
Rotation angle (degrees) 68.81230633
Shift along axis -89.80615914
> fitmap #3.4 inMap #1
Fit molecule 6mer-coot-3.pdb D (#3.4) to map
cryosparc_P2_J308_008_volume_map_sharp.mrc (#1) using 2018 atoms
average map value = 0.2975, steps = 28
shifted from previous position = 0.0147
rotated from previous position = 0.02 degrees
atoms outside contour = 810, contour level = 0.25
Position of 6mer-coot-3.pdb D (#3.4) relative to
cryosparc_P2_J308_008_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.87145720 -0.40935450 -0.27016890 306.52000497
0.48002110 0.59873102 0.64117152 -137.16436570
-0.10070794 -0.68844031 0.71826725 296.79774654
Axis -0.82656786 -0.10534727 0.55289015
Axis point 0.00000000 317.34576929 424.82663750
Rotation angle (degrees) 53.54240127
Shift along axis -74.81314284
> fitmap #3.4 inMap #1
Fit molecule 6mer-coot-3.pdb D (#3.4) to map
cryosparc_P2_J308_008_volume_map_sharp.mrc (#1) using 2018 atoms
average map value = 0.2975, steps = 40
shifted from previous position = 0.0154
rotated from previous position = 0.0107 degrees
atoms outside contour = 808, contour level = 0.25
Position of 6mer-coot-3.pdb D (#3.4) relative to
cryosparc_P2_J308_008_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.87145801 -0.40925661 -0.27031456 306.51682558
0.48005739 0.59876023 0.64111706 -137.17340867
-0.10052778 -0.68847310 0.71826106 296.76556209
Axis -0.82656344 -0.10555098 0.55285791
Axis point 0.00000000 317.26807423 424.83660485
Rotation angle (degrees) 53.54155243
Shift along axis -74.80762559
> fitmap #3.5 inMap #1
Fit molecule 6mer-coot-3.pdb E (#3.5) to map
cryosparc_P2_J308_008_volume_map_sharp.mrc (#1) using 2023 atoms
average map value = 0.3137, steps = 40
shifted from previous position = 0.0165
rotated from previous position = 0.0113 degrees
atoms outside contour = 728, contour level = 0.25
Position of 6mer-coot-3.pdb E (#3.5) relative to
cryosparc_P2_J308_008_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.80068596 -0.48681577 -0.34915957 348.86368425
0.59037648 0.54217032 0.59791886 -148.05885268
-0.10177237 -0.68488083 0.72151274 295.67089415
Axis -0.75759311 -0.14610141 0.63616590
Axis point 0.00000000 286.94681698 480.67439339
Rotation angle (degrees) 57.84682767
Shift along axis -54.56937634
> fitmap #3.5 inMap #1
Fit molecule 6mer-coot-3.pdb E (#3.5) to map
cryosparc_P2_J308_008_volume_map_sharp.mrc (#1) using 2023 atoms
average map value = 0.3136, steps = 28
shifted from previous position = 0.0182
rotated from previous position = 0.00542 degrees
atoms outside contour = 723, contour level = 0.25
Position of 6mer-coot-3.pdb E (#3.5) relative to
cryosparc_P2_J308_008_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.80069050 -0.48684998 -0.34910145 348.84825961
0.59035462 0.54213426 0.59797313 -148.06364579
-0.10186335 -0.68488506 0.72149589 295.71362716
Axis -0.75761406 -0.14601072 0.63616178
Axis point 0.00000000 286.98087495 480.66958623
Rotation angle (degrees) 57.84846434
Shift along axis -54.55175930
> fitmap #3.6 inMap #1
Fit molecule 6mer-coot-3.pdb F (#3.6) to map
cryosparc_P2_J308_008_volume_map_sharp.mrc (#1) using 2023 atoms
average map value = 0.3192, steps = 28
shifted from previous position = 0.0223
rotated from previous position = 0.0145 degrees
atoms outside contour = 678, contour level = 0.25
Position of 6mer-coot-3.pdb F (#3.6) relative to
cryosparc_P2_J308_008_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.86388858 -0.36541692 -0.34665112 313.78008327
0.48608707 0.42452469 0.76387051 -129.85184134
-0.13196925 -0.82840163 0.54436647 354.95515203
Axis -0.87565793 -0.11806266 0.46827813
Axis point 0.00000000 268.49700847 386.67617549
Rotation angle (degrees) 65.39312643
Shift along axis -93.21563072
> fitmap #3.6 inMap #1
Fit molecule 6mer-coot-3.pdb F (#3.6) to map
cryosparc_P2_J308_008_volume_map_sharp.mrc (#1) using 2023 atoms
average map value = 0.3192, steps = 40
shifted from previous position = 0.0026
rotated from previous position = 0.00432 degrees
atoms outside contour = 677, contour level = 0.25
Position of 6mer-coot-3.pdb F (#3.6) relative to
cryosparc_P2_J308_008_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.86387779 -0.36543453 -0.34665945 313.78484897
0.48609406 0.42445811 0.76390306 -129.84705197
-0.13201414 -0.82842798 0.54431549 354.97608190
Axis -0.87566201 -0.11803874 0.46827652
Axis point 0.00000000 268.49272724 386.67067014
Rotation angle (degrees) 65.39717049
Shift along axis -93.21552643
> fitmap #4 inMap #1
Fit molecule 4 (#4) to map cryosparc_P2_J308_008_volume_map_sharp.mrc (#1)
using 2018 atoms
average map value = 0.3302, steps = 44
shifted from previous position = 0.0049
rotated from previous position = 0.0108 degrees
atoms outside contour = 592, contour level = 0.25
Position of 4 (#4) relative to cryosparc_P2_J308_008_volume_map_sharp.mrc (#1)
coordinates:
Matrix rotation and translation
0.99999965 -0.00067406 -0.00048695 0.21429469
0.00067449 0.99999938 0.00089059 -0.50087941
0.00048634 -0.00089092 0.99999948 -0.05416876
Axis -0.73098167 -0.39935761 0.55333470
Axis point 0.00000000 -69.45228699 556.35183812
Rotation angle (degrees) 0.06981891
Shift along axis 0.01341106
> fitmap #4 inMap #1
Fit molecule 4 (#4) to map cryosparc_P2_J308_008_volume_map_sharp.mrc (#1)
using 2018 atoms
average map value = 0.3302, steps = 40
shifted from previous position = 0.00606
rotated from previous position = 0.00364 degrees
atoms outside contour = 595, contour level = 0.25
Position of 4 (#4) relative to cryosparc_P2_J308_008_volume_map_sharp.mrc (#1)
coordinates:
Matrix rotation and translation
0.99999968 -0.00067558 -0.00042593 0.19778982
0.00067596 0.99999936 0.00090796 -0.50603248
0.00042532 -0.00090824 0.99999950 -0.02073985
Axis -0.75091479 -0.35195210 0.55879933
Axis point 0.00000000 -34.20608190 550.33542506
Rotation angle (degrees) 0.06928920
Shift along axis 0.01798648
> fitmap #5 inMap #1
Fit molecule Monomer_2.pdb (#5) to map
cryosparc_P2_J308_008_volume_map_sharp.mrc (#1) using 2018 atoms
average map value = 0.3395, steps = 24
shifted from previous position = 0.00722
rotated from previous position = 0.00661 degrees
atoms outside contour = 563, contour level = 0.25
Position of Monomer_2.pdb (#5) relative to
cryosparc_P2_J308_008_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.99999969 0.00021612 -0.00075633 0.12531910
-0.00021521 0.99999926 0.00119808 -0.19706788
0.00075659 -0.00119792 0.99999900 -0.12141507
Axis -0.83591347 -0.52782905 -0.15048309
Axis point 0.00000000 -99.28391455 156.70051660
Rotation angle (degrees) 0.08211412
Shift along axis 0.01753314
> fitmap #5 inMap #1
Fit molecule Monomer_2.pdb (#5) to map
cryosparc_P2_J308_008_volume_map_sharp.mrc (#1) using 2018 atoms
average map value = 0.3394, steps = 28
shifted from previous position = 0.0288
rotated from previous position = 0.00146 degrees
atoms outside contour = 560, contour level = 0.25
Position of Monomer_2.pdb (#5) relative to
cryosparc_P2_J308_008_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.99999968 0.00023635 -0.00076124 0.14443077
-0.00023542 0.99999924 0.00121288 -0.17503803
0.00076153 -0.00121270 0.99999897 -0.12910493
Axis -0.83566897 -0.52463230 -0.16253713
Axis point -0.00000000 -107.64219855 147.65784259
Rotation angle (degrees) 0.08315203
Shift along axis -0.00788137
> fitmap #6 inMap #1
Fit molecule 6 (#6) to map cryosparc_P2_J308_008_volume_map_sharp.mrc (#1)
using 2010 atoms
average map value = 0.3542, steps = 36
shifted from previous position = 0.026
rotated from previous position = 0.00989 degrees
atoms outside contour = 520, contour level = 0.25
Position of 6 (#6) relative to cryosparc_P2_J308_008_volume_map_sharp.mrc (#1)
coordinates:
Matrix rotation and translation
0.99999964 0.00046118 -0.00071754 0.10659712
-0.00046106 0.99999988 0.00016279 0.17153405
0.00071762 -0.00016246 0.99999973 -0.30362312
Axis -0.18728842 -0.82638700 -0.53104385
Axis point 423.51120500 0.00000000 148.21868973
Rotation angle (degrees) 0.04975180
Shift along axis -0.00048073
> fitmap #6 inMap #1
Fit molecule 6 (#6) to map cryosparc_P2_J308_008_volume_map_sharp.mrc (#1)
using 2010 atoms
average map value = 0.3542, steps = 44
shifted from previous position = 0.024
rotated from previous position = 0.00827 degrees
atoms outside contour = 520, contour level = 0.25
Position of 6 (#6) relative to cryosparc_P2_J308_008_volume_map_sharp.mrc (#1)
coordinates:
Matrix rotation and translation
0.99999951 0.00053587 -0.00083585 0.13987579
-0.00053570 0.99999984 0.00019860 0.20962494
0.00083596 -0.00019816 0.99999963 -0.33883456
Axis -0.19593037 -0.82558335 -0.52917239
Axis point 418.79663260 0.00000000 162.13706319
Rotation angle (degrees) 0.05801193
Shift along axis -0.02116688
> fitmap #7 inMap #1
Fit molecule 7 (#7) to map cryosparc_P2_J308_008_volume_map_sharp.mrc (#1)
using 2018 atoms
average map value = 0.3528, steps = 40
shifted from previous position = 0.0114
rotated from previous position = 0.00223 degrees
atoms outside contour = 551, contour level = 0.25
Position of 7 (#7) relative to cryosparc_P2_J308_008_volume_map_sharp.mrc (#1)
coordinates:
Matrix rotation and translation
-0.57786084 -0.81613521 -0.00041290 812.89349450
-0.81613491 0.57785999 0.00128116 420.10168784
-0.00080700 0.00107731 -0.99999909 535.09436590
Axis -0.45942317 0.88821727 0.00066391
Axis point 515.12725366 0.00000000 267.33941751
Rotation angle (degrees) 179.98728884
Shift along axis 0.03472091
> fitmap #7 inMap #1
Fit molecule 7 (#7) to map cryosparc_P2_J308_008_volume_map_sharp.mrc (#1)
using 2018 atoms
average map value = 0.3528, steps = 44
shifted from previous position = 0.00399
rotated from previous position = 0.00321 degrees
atoms outside contour = 552, contour level = 0.25
Position of 7 (#7) relative to cryosparc_P2_J308_008_volume_map_sharp.mrc (#1)
coordinates:
Matrix rotation and translation
-0.57786439 -0.81613272 -0.00036484 812.88274489
-0.81613235 0.57786354 0.00130949 420.09280288
-0.00085789 0.00105446 -0.99999908 535.12312310
Axis -0.45942121 0.88821828 0.00066543
Axis point 515.12738625 0.00000000 267.34069650
Rotation angle (degrees) 179.98409756
Shift along axis 0.03461427
> fitmap #8 inMap #1
Fit molecule Monomer_5-coot-0.pdb (#8) to map
cryosparc_P2_J308_008_volume_map_sharp.mrc (#1) using 2018 atoms
average map value = 0.3468, steps = 44
shifted from previous position = 0.00491
rotated from previous position = 0.00155 degrees
atoms outside contour = 586, contour level = 0.25
Position of Monomer_5-coot-0.pdb (#8) relative to
cryosparc_P2_J308_008_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.99999992 -0.00025385 -0.00032262 0.13545767
0.00025340 0.99999903 -0.00137273 0.30246356
0.00032297 0.00137265 0.99999901 -0.33269181
Axis 0.95807402 -0.22529695 0.17701823
Axis point 0.00000000 242.88591895 220.61512370
Rotation angle (degrees) 0.08209097
Shift along axis 0.00274185
> fitmap #8 inMap #1
Fit molecule Monomer_5-coot-0.pdb (#8) to map
cryosparc_P2_J308_008_volume_map_sharp.mrc (#1) using 2018 atoms
average map value = 0.3468, steps = 40
shifted from previous position = 0.0184
rotated from previous position = 0.016 degrees
atoms outside contour = 583, contour level = 0.25
Position of Monomer_5-coot-0.pdb (#8) relative to
cryosparc_P2_J308_008_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.99999998 -0.00017431 -0.00006275 0.05985753
0.00017423 0.99999913 -0.00130609 0.32028018
0.00006298 0.00130607 0.99999915 -0.22617609
Axis 0.99008935 -0.04765423 0.13210661
Axis point 0.00000000 174.76157452 245.62048522
Rotation angle (degrees) 0.07558199
Shift along axis 0.01412224
> fitmap #10 inMap #1
Fit molecule Monomer_6-coot-0.pdb (#10) to map
cryosparc_P2_J308_008_volume_map_sharp.mrc (#1) using 2018 atoms
average map value = 0.3445, steps = 40
shifted from previous position = 0.02
rotated from previous position = 0.016 degrees
atoms outside contour = 563, contour level = 0.25
Position of Monomer_6-coot-0.pdb (#10) relative to
cryosparc_P2_J308_008_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.99999928 -0.00076362 0.00092706 -0.12983676
0.00076368 0.99999971 -0.00006029 -0.29568181
-0.00092702 0.00006100 0.99999957 0.36218799
Axis 0.05042724 0.77086326 0.63500152
Axis point 393.71129683 0.00000000 140.11384110
Rotation angle (degrees) 0.06890394
Shift along axis -0.00448763
> combine #4-10
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.8.dev202403220040 (2024-03-22)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 Metal - 88
OpenGL renderer: Apple M2
OpenGL vendor: Apple
Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: Mac14,7
Model Number: Z16U0000PTA/A
Chip: Apple M2
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 16 GB
System Firmware Version: 10151.41.12
OS Loader Version: 10151.41.12
Software:
System Software Overview:
System Version: macOS 14.1 (23B74)
Kernel Version: Darwin 23.1.0
Time since boot: 46 days, 21 hours, 24 minutes
Graphics/Displays:
Apple M2:
Chipset Model: Apple M2
Type: GPU
Bus: Built-In
Total Number of Cores: 10
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2560 x 1600 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
alabaster: 0.7.16
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 2.4.1
Babel: 2.14.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 2.0.0
build: 1.1.1
certifi: 2023.11.17
cftime: 1.6.3
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.16
ChimeraX-AddH: 2.2.5
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.4.3
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.5
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.56
ChimeraX-AtomicLibrary: 14.0.2
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.12.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.5
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.8.dev202403220040
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
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: 1.1.9
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.1.4
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
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.15
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: 1.1
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.1
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.3
ChimeraX-PDB: 2.7.5
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.3
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: 1.0
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.11.2
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.16.3
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2
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: 1.37.1
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.3.2
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: 1.1.3
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.2.0
cxservices: 1.2.2
cycler: 0.12.1
Cython: 3.0.9
debugpy: 1.8.1
decorator: 5.1.1
docutils: 0.20.1
executing: 2.0.1
filelock: 3.13.1
fonttools: 4.50.0
funcparserlib: 2.0.0a0
glfw: 2.7.0
grako: 3.16.5
h5py: 3.10.0
html2text: 2024.2.26
idna: 3.6
ihm: 0.43
imagecodecs: 2024.1.1
imagesize: 1.4.1
ipykernel: 6.29.2
ipython: 8.21.0
ipywidgets: 8.1.2
jedi: 0.19.1
Jinja2: 3.1.3
jupyter-client: 8.6.0
jupyter-core: 5.7.2
jupyterlab-widgets: 3.0.10
kiwisolver: 1.4.5
line-profiler: 4.1.2
lxml: 5.1.0
lz4: 4.3.3
MarkupSafe: 2.1.5
matplotlib: 3.8.3
matplotlib-inline: 0.1.6
MolecularDynamicsViewer: 1.6
msgpack: 1.0.8
ndindex: 1.8
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.2.1
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.9.0
numpy: 1.26.4
openvr: 1.26.701
packaging: 23.2
ParmEd: 4.2.2
parso: 0.8.3
pep517: 0.13.1
pexpect: 4.9.0
pillow: 10.2.0
pip: 24.0
pkginfo: 1.10.0
platformdirs: 4.2.0
prompt-toolkit: 3.0.43
psutil: 5.9.8
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.3.0
pygments: 2.17.2
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3302
pyparsing: 3.1.2
pyproject-hooks: 1.0.0
PyQt6-commercial: 6.6.1
PyQt6-Qt6: 6.6.2
PyQt6-sip: 13.6.0
PyQt6-WebEngine-commercial: 6.6.0
PyQt6-WebEngine-Qt6: 6.6.2
python-dateutil: 2.9.0.post0
pytz: 2024.1
pyzmq: 25.1.2
qtconsole: 5.5.1
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.12.0
setuptools: 69.2.0
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: 2.0.0
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: 0.6.1
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2024.1.30
tinyarray: 1.2.4
tornado: 6.4
traitlets: 5.14.1
typing-extensions: 4.10.0
tzdata: 2024.1
urllib3: 2.2.1
wcwidth: 0.2.13
webcolors: 1.13
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.10
Change History (2)
comment:1 by , 8 months ago
| Component: | Unassigned → Core |
|---|---|
| Description: | modified (diff) |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Crash in python_instances_of_class |
comment:2 by , 8 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | accepted → closed |
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