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Opened 5 months ago
Closed 5 months ago
#18043 closed defect (can't reproduce)
Crash in drawing after 'view matrix'
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Graphics | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Linux-6.8.0-59-generic-x86_64-with-glibc2.35
ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Aborted
Thread 0x000073683ae3ab80 (most recent call first):
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/graphics/opengl.py", line 703 in shader
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/graphics/drawing.py", line 818 in _draw_geometry
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/graphics/drawing.py", line 787 in draw_self
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/graphics/drawing.py", line 780 in draw
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/graphics/drawing.py", line 1567 in _draw_multiple
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/graphics/drawing.py", line 1554 in draw_opaque
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/graphics/drawing.py", line 1579 in draw_depth
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/graphics/opengl.py", line 1723 in use_multishadow_map
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/graphics/view.py", line 632 in _compute_shadowmaps
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/graphics/view.py", line 227 in _draw_scene
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/graphics/view.py", line 188 in draw
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/core/updateloop.py", line 84 in draw_new_frame
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/core/updateloop.py", line 150 in _redraw_timer_callback
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/ui/gui.py", line 330 in event_loop
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1037 in init
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1200 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.pdb_lib._load_libs, chimerax.surface._surface, chimerax.map._map, charset_normalizer.md, requests.packages.charset_normalizer.md, requests.packages.chardet.md, PIL._imaging, kiwisolver._cext, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, psutil._psutil_linux, psutil._psutil_posix, PIL._imagingmath, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif (total: 53)
===== Log before crash start =====
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.9.dev202408090049 (2024-08-09)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /home/ananya/Downloads/cryosparc_P16_J1366_007_volume_map_half_A.mrc
> /home/ananya/Downloads/cryosparc_P16_J1365_007_volume_map_half_A.mrc
> /home/ananya/Downloads/cryosparc_P16_J1364_005_volume_map_half_A.mrc
Opened cryosparc_P16_J1366_007_volume_map_half_A.mrc as #1.1, grid size
320,320,320, pixel 1.07, shown at level 0.232, step 2, values float32
Opened cryosparc_P16_J1365_007_volume_map_half_A.mrc as #1.2, grid size
320,320,320, pixel 1.07, shown at level 0.257, step 2, values float32
Opened cryosparc_P16_J1364_005_volume_map_half_A.mrc as #1.3, grid size
320,320,320, pixel 1.07, shown at level 0.265, step 2, values float32
> set bgColor white
> volume all step 1 level 0.75
> surface dust #1.1 size 10.7
> surface dust #1.2 size 10.7
> surface dust #1.3 size 10.7
> volume all step 1 level 0.5
> tile
3 models tiled
> lighting full
> volume all step 1 level 0.67
> lighting soft
> lighting simple
> lighting soft
> lighting full
> hide #!1.2 models
> hide #!1.3 models
> open /home/ananya/Downloads/cryosparc_P16_J1094_010_volume_map_half_A.mrc
Opened cryosparc_P16_J1094_010_volume_map_half_A.mrc as #2, grid size
320,320,320, pixel 1.07, shown at level 0.242, step 2, values float32
> volume #2 step 1
> select add #2
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #2,-0.89036,0.3921,0.23136,212.21,0.42376,0.89951,0.10636,-71.307,-0.16641,0.19274,-0.96704,316.84
> view matrix models
> #2,-0.19027,0.97302,0.13051,13.677,0.98142,0.18517,0.050269,-34.968,0.024745,0.13765,-0.99017,297.94
> view matrix models
> #2,0.15663,0.92026,0.3586,-72.72,0.97765,-0.19601,0.075977,25.723,0.14021,0.33869,-0.93039,234.97
> view matrix models
> #2,0.56444,0.70377,0.43141,-116.32,0.78377,-0.62092,-0.01253,144.25,0.25906,0.3452,-0.90207,209.36
> view matrix models
> #2,0.52412,0.8418,0.12912,-83.441,0.85163,-0.51901,-0.073219,125.64,0.0053812,0.14834,-0.98892,299.17
> tile
2 models tiled
> volume all step 1 level 0.6
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.56145,0.79412,0.23271,-34.324,0.79294,-0.59672,0.12319,-72.617,0.23669,0.11536,-0.96471,208.19
> view matrix models
> #2,0.86664,0.42263,0.26517,-26.96,0.43721,-0.89935,0.0045101,59.378,0.24039,0.11203,-0.96419,208.05
> view matrix models
> #2,-0.024813,0.92203,0.38633,16.069,0.93214,-0.1183,0.34222,-215.55,0.36123,0.3686,-0.85653,125.3
> hide #!2 models
> select add #1.1
4 models selected
> view matrix models
> #1.1,-0.18299,-0.45397,-0.87202,428.43,0.98098,-0.025825,-0.19241,31.559,0.064827,-0.89064,0.45006,226.02,#2,-0.8537,-0.51096,-0.10059,574.73,-0.52025,0.82826,0.20815,218.88,-0.023036,0.23003,-0.97291,301.5
> hide #!1.1 models
> show #!1.1 models
> select subtract #1.1
2 models selected
> show #!2 models
> ui mousemode right "rotate selected models"
> view matrix models
> #2,-0.82118,-0.53249,-0.20522,590.67,-0.54923,0.63983,0.53756,200.57,-0.15493,0.55415,-0.81787,241.52
> view matrix models
> #2,-0.79348,-0.43971,-0.42076,606.45,-0.43589,-0.071867,0.89712,243.55,-0.42472,0.89526,-0.13464,112.48
> view matrix models
> #2,-0.87195,-0.48637,-0.056101,566.03,-0.48847,0.87199,0.032176,235.74,0.033269,0.05546,-0.99791,326.39
> view matrix models
> #2,-0.80628,-0.52454,-0.27344,598.33,-0.54038,0.4651,0.70119,201.57,-0.24062,0.71312,-0.65846,201.53
> view matrix models
> #2,0.5731,0.68034,0.45683,35.443,0.7148,-0.68764,0.12733,286.72,0.40076,0.25357,-0.88039,210.65
> vop flip #2
Opened cryosparc_P16_J1094_010_volume_map_half_A.mrc z flip as #3, grid size
320,320,320, pixel 1.07, shown at step 1, values float32
> select subtract #2
Nothing selected
> select add #3
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.92548,0.32412,0.19603,82.673,-0.25733,0.91775,-0.30252,247.02,-0.27796,0.22954,0.93276,16.341
> view matrix models
> #3,0.91915,0.37646,0.11591,88.51,-0.3791,0.92536,0.00077239,213.9,-0.10697,-0.044653,0.99326,24.515
> view matrix models
> #3,0.92568,0.33825,0.16944,84.784,-0.30128,0.92999,-0.21057,236.45,-0.22881,0.14387,0.96278,17.696
> view matrix models
> #3,-0.93349,-0.33547,-0.12673,564.18,0.35767,-0.89655,-0.26129,449.67,-0.025969,-0.28924,0.9569,59.376
> view matrix models
> #3,-0.19061,0.90388,-0.38298,269.79,-0.97486,-0.22014,-0.034365,517.6,-0.11537,0.3668,0.92312,-32.975
> ui mousemode right "translate selected models"
> view matrix models
> #3,-0.19061,0.90388,-0.38298,290.58,-0.97486,-0.22014,-0.034365,402.22,-0.11537,0.3668,0.92312,-6.8414
> fitmap #3 inMap #1.1
Fit map cryosparc_P16_J1094_010_volume_map_half_A.mrc z flip in map
cryosparc_P16_J1366_007_volume_map_half_A.mrc using 45052 points
correlation = 0.105, correlation about mean = -0.02164, overlap = 45.07
steps = 76, shift = 3.96, angle = 2.15 degrees
Position of cryosparc_P16_J1094_010_volume_map_half_A.mrc z flip (#3) relative
to cryosparc_P16_J1366_007_volume_map_half_A.mrc (#1.1) coordinates:
Matrix rotation and translation
-0.92533952 -0.35761502 0.12592968 369.12438788
0.19001212 -0.72484419 -0.66219056 268.71214028
0.32808868 -0.58882292 0.73867816 -53.39075828
Axis 0.12470233 -0.34360784 0.93079696
Axis point 169.09239282 155.29313493 -0.00000000
Rotation angle (degrees) 162.89216025
Shift along axis -95.99688334
> select subtract #3
Nothing selected
> hide #!1.1 models
> show #!1.1 models
> select add #1.1
2 models selected
> view matrix models
> #1.1,-0.18299,-0.45397,-0.87202,376.76,0.98098,-0.025825,-0.19241,116.22,0.064827,-0.89064,0.45006,132.46
> select subtract #1.1
Nothing selected
> select add #3
2 models selected
> view matrix models
> #3,0.84375,-0.53525,-0.039941,336.28,0.5043,0.81604,-0.28241,-102.52,0.18375,0.21814,0.95846,-72.641
> fitmap #3 inMap #1.1
Fit map cryosparc_P16_J1094_010_volume_map_half_A.mrc z flip in map
cryosparc_P16_J1366_007_volume_map_half_A.mrc using 45052 points
correlation = 0.07359, correlation about mean = 0.01623, overlap = 44.58
steps = 92, shift = 2.57, angle = 5.55 degrees
Position of cryosparc_P16_J1094_010_volume_map_half_A.mrc z flip (#3) relative
to cryosparc_P16_J1366_007_volume_map_half_A.mrc (#1.1) coordinates:
Matrix rotation and translation
0.42670199 0.88866543 -0.16792648 -237.70821837
-0.49975902 0.07693687 -0.86274090 192.65730813
-0.75376818 0.45205599 0.47694768 -16.38909883
Axis 0.65742936 0.29293462 -0.69424487
Axis point 29.28158822 220.93532670 0.00000000
Rotation angle (degrees) 90.55616349
Shift along axis -88.46231832
> close #1
> surface dust #3 size 10.7
> open /home/ananya/Downloads/cryosparc_P16_J1366_007_volume_map_half_A.mrc
Opened cryosparc_P16_J1366_007_volume_map_half_A.mrc as #1, grid size
320,320,320, pixel 1.07, shown at level 0.232, step 2, values float32
> volume all step 1 level 0.6
> surface dust #3 size 10.7
> select subtract #3
Nothing selected
> select add #1
2 models selected
> view matrix models #1,1,0,0,9.3175,0,1,0,-58.847,0,0,1,19.853
> view matrix models #1,1,0,0,209.99,0,1,0,-108,0,0,1,-17.734
> fitmap #1 inMap #3
Fit map cryosparc_P16_J1366_007_volume_map_half_A.mrc in map
cryosparc_P16_J1094_010_volume_map_half_A.mrc z flip using 44404 points
correlation = 0.9902, correlation about mean = 0.8413, overlap = 3.01e+04
steps = 236, shift = 12.7, angle = 33.6 degrees
Position of cryosparc_P16_J1366_007_volume_map_half_A.mrc (#1) relative to
cryosparc_P16_J1094_010_volume_map_half_A.mrc z flip (#3) coordinates:
Matrix rotation and translation
-0.99996913 -0.00772375 0.00137051 343.41423384
0.00770440 -0.99987770 -0.01360158 343.26663728
0.00147540 -0.01359060 0.99990639 0.82471797
Axis 0.00071154 -0.00679818 0.99997664
Axis point 171.04480292 172.29844556 0.00000000
Rotation angle (degrees) 179.55800119
Shift along axis -1.26453661
> surface dust #1 size 10.7
> tile
2 models tiled
> lighting soft
> select subtract #1
Nothing selected
> close #1
> close
> open /home/ananya/Downloads/cryosparc_P16_J1383_007_volume_map_half_A.mrc
Opened cryosparc_P16_J1383_007_volume_map_half_A.mrc as #1, grid size
320,320,320, pixel 1.07, shown at level 0.247, step 2, values float32
> volume #1 step 1
> open /home/ananya/Downloads/cryosparc_P16_J1379_010_volume_map_half_A.mrc
Opened cryosparc_P16_J1379_010_volume_map_half_A.mrc as #2, grid size
320,320,320, pixel 1.07, shown at level 0.246, step 2, values float32
> surface dust #1 size 10.7
> surface dust #2 size 10.7
> volume all step 1 level 0.6
> volume all step 1 level 0.5
> tile
2 models tiled
> lighting soft
> color #2 #cdab8fff models
> close #2
> close
> open /home/ananya/Downloads/cryosparc_P16_J1383_007_volume_map_sharp.mrc
> /home/ananya/Downloads/cryosparc_P16_J1379_010_volume_map_sharp.mrc
Opened cryosparc_P16_J1383_007_volume_map_sharp.mrc as #1.1, grid size
320,320,320, pixel 1.07, shown at level 0.242, step 2, values float32
Opened cryosparc_P16_J1379_010_volume_map_sharp.mrc as #1.2, grid size
320,320,320, pixel 1.07, shown at level 0.245, step 2, values float32
> surface dust #1.1 size 10.7
> surface dust #1.2 size 10.7
> tile
2 models tiled
> lighting soft
> lighting full
> lighting simple
> lighting soft
> volume all step 1 level 0.5
> color #1.2 #cdab8fff models
> volume all step 1 level 0.65
> close #1.2
> close #1.1
> open /home/ananya/Downloads/cryosparc_P16_J1291_007_volume_map_half_B.mrc
Opened cryosparc_P16_J1291_007_volume_map_half_B.mrc as #2, grid size
320,320,320, pixel 1.07, shown at level 0.28, step 2, values float32
> volume all step 1 level 0.65
> surface dust #2 size 10.7
> open /home/ananya/Desktop/Latest_models/WT-
> ATPgs_forJ890_real_space_refined_000.pdb
Chain information for WT-ATPgs_forJ890_real_space_refined_000.pdb #3
---
Chain | Description
A | No description available
B C | No description available
D E | No description available
> hide atoms
> show cartoons
> hide #!3 models
> show #!3 models
> hide #!2 models
> show #!2 models
> hide #!3 models
> volume #2 level 0.2358
> volume #2 level 0.4291
> volume #2 level 0.269
> volume #2 level 0.1585
> volume #2 level 0.2634
> volume #2 level 0.1916
> close #2
> close #3
> close
> open /home/ananya/Desktop/BceABS/nanodisc/EQ_ATPgS/56/run_it025_class003.mrc
> /home/ananya/Desktop/BceABS/nanodisc/EQ_ATPgS/56/run_it025_class002.mrc
> /home/ananya/Desktop/BceABS/nanodisc/EQ_ATPgS/56/run_it025_class001.mrc
Opened run_it025_class003.mrc as #1.1, grid size 320,320,320, pixel 1.07,
shown at level 9.31e-07, step 2, values float32
Opened run_it025_class002.mrc as #1.2, grid size 320,320,320, pixel 1.07,
shown at level 8.71e-07, step 2, values float32
Opened run_it025_class001.mrc as #1.3, grid size 320,320,320, pixel 1.07,
shown at level 1.44e-06, step 2, values float32
> volume all step 1 level 0.65
> volume all step 1 level 0.001
> lighting soft
> tile
3 models tiled
> close
> open /home/ananya/Downloads/cryosparc_P16_J1396_002_volume_map_half_A.mrc
Opened cryosparc_P16_J1396_002_volume_map_half_A.mrc as #1, grid size
320,320,320, pixel 1.07, shown at level 0.119, step 2, values float32
> volume #1 step 1
> volume #1 level 0.09765
> close #1
> open /home/ananya/Downloads/cryosparc_P16_J1395_005_volume_map_sharp.mrc
> /home/ananya/Downloads/cryosparc_P16_J1395_005_volume_map_half_A.mrc
Opened cryosparc_P16_J1395_005_volume_map_sharp.mrc as #1.1, grid size
320,320,320, pixel 1.07, shown at level 0.26, step 2, values float32
Opened cryosparc_P16_J1395_005_volume_map_half_A.mrc as #1.2, grid size
320,320,320, pixel 1.07, shown at level 0.274, step 2, values float32
> hide #!1.1 models
> volume all step 1 level 0.35
> lighting soft
> surface dust #1.2 size 10.7
> volume all step 1 level 0.5
> show #!1.1 models
> hide #!1.2 models
> volume all step 1 level 0.7
> open /home/ananya/Downloads/cryosparc_P16_J1291_007_volume_map_sharp.mrc
Opened cryosparc_P16_J1291_007_volume_map_sharp.mrc as #2, grid size
320,320,320, pixel 1.07, shown at level 0.267, step 2, values float32
> surface dust #1.1 size 10.7
> surface dust #2 size 10.7
> volume all step 1 level 0.7
> tile
2 models tiled
> lighting soft
> hide #!2 models
> hide #!1.1 models
> show #!1.2 models
> open
> /home/ananya/Downloads/cryosparc_P16_J1291_007_volume_map_half1_unfil.mrc
Opened cryosparc_P16_J1291_007_volume_map_half1_unfil.mrc as #3, grid size
320,320,320, pixel 1.07, shown at level 0.28, step 2, values float32
> volume all step 1 level 0.7
> surface dust #1.2 size 10.7
> surface dust #3 size 10.7
> select add #3
2 models selected
> ui mousemode right "translate selected models"
> view matrix models #3,1,0,0,115.75,0,1,0,-6.4305,0,0,1,-5.7633
> select subtract #3
Nothing selected
> select add #3
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.12369,-0.95058,0.28478,378.94,0.98258,0.15745,0.098775,-47.481,-0.13873,0.2676,0.95349,-19.755
> view matrix models
> #3,0.62202,-0.7185,0.31121,250.45,0.78163,0.5933,-0.1925,-39.039,-0.046327,0.36298,0.93064,-47.869
> view matrix models
> #3,0.96311,-0.21669,0.15956,132.42,0.26709,0.84205,-0.46863,51.976,-0.032811,0.49396,0.86887,-62.159
> view matrix models
> #3,0.99583,0.09041,0.012368,99.125,-0.069356,0.83797,-0.54129,121.93,-0.059303,0.53818,0.84074,-60.498
> view matrix models
> #3,0.98715,-0.12727,0.096641,123.56,0.14034,0.97968,-0.14332,-3.2927,-0.076435,0.15504,0.98495,-16.5
> view matrix models
> #3,0.95792,-0.27153,0.093057,153.54,0.25631,0.95512,0.14852,-66.946,-0.12921,-0.11842,0.98452,38.828
> view matrix models
> #3,0.88951,-0.45606,0.027792,207.16,0.40441,0.81415,0.41667,-112.47,-0.21265,-0.35939,0.90863,106.31
> view matrix models
> #3,0.87623,-0.48186,-0.0056001,219.28,0.48162,0.87528,0.043956,-74.592,-0.016279,-0.041213,0.99902,4.1442
> view matrix models
> #3,0.96479,-0.26205,0.022499,162.38,0.2624,0.96485,-0.01443,-42.797,-0.017926,0.019826,0.99964,-6.0059
> view matrix models
> #3,0.98996,-0.13874,0.026955,136.49,0.14048,0.98684,-0.0801,-14.939,-0.015487,0.083082,0.99642,-16.594
> view matrix models
> #3,0.94958,-0.31352,0.0024744,176.98,0.2947,0.89519,0.33435,-93.945,-0.10704,-0.31676,0.94245,75.541
> view matrix models
> #3,0.87195,-0.48577,-0.061117,229.81,0.47544,0.86991,-0.1312,-43.787,0.1169,0.085346,0.98947,-38.38
> view matrix models
> #3,0.9717,-0.23244,-0.042105,166.83,0.23204,0.9726,-0.014141,-38.986,0.044238,0.0039704,0.99901,-13.807
> view matrix models
> #3,0.96743,-0.25205,-0.023219,167.77,0.24269,0.89757,0.36806,-91.042,-0.071931,-0.36171,0.92951,79.296
> view matrix models
> #3,0.9749,-0.212,-0.067982,167.09,0.16537,0.89399,-0.41645,51.919,0.14906,0.39476,0.90661,-82.565
> view matrix models
> #3,0.95302,-0.30142,-0.03002,179.69,0.29665,0.94877,-0.10882,-30.365,0.061284,0.094805,0.99361,-31.189
> view matrix models
> #3,0.79102,0.59282,0.15116,26.143,-0.61177,0.76819,0.18873,105.91,-0.0042328,-0.24177,0.97033,40.751
> view matrix models
> #3,0.98017,-0.18294,-0.076203,162.63,0.18826,0.97963,0.069824,-46.546,0.061877,-0.082785,0.99464,-1.4127
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.98017,-0.18294,-0.076203,40.813,0.18826,0.97963,0.069824,-39.249,0.061877,-0.082785,0.99464,-0.013202
> fitmap #3 inMap #1.2
Fit map cryosparc_P16_J1291_007_volume_map_half1_unfil.mrc in map
cryosparc_P16_J1395_005_volume_map_half_A.mrc using 50269 points
correlation = 0.9374, correlation about mean = 0.2834, overlap = 3.224e+04
steps = 108, shift = 5.3, angle = 8.34 degrees
Position of cryosparc_P16_J1291_007_volume_map_half1_unfil.mrc (#3) relative
to cryosparc_P16_J1395_005_volume_map_half_A.mrc (#1.2) coordinates:
Matrix rotation and translation
-0.66901197 -0.59608032 0.44397219 319.98566276
0.60658454 -0.78307183 -0.13730905 196.94636320
0.42950932 0.17744526 0.88545752 -87.22821084
Axis 0.25316961 0.01163307 0.96735196
Axis point 135.92071944 156.69941992 0.00000000
Rotation angle (degrees) 141.56493155
Shift along axis -1.07864372
> select subtract #3
Nothing selected
> select add #3
2 models selected
> tile
2 models tiled
> lighting soft
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.91117,-0.31966,0.25998,155.42,0.34003,0.93971,-0.036274,-58.697,-0.23272,0.12145,0.96493,-0.20949
> select subtract #3
Nothing selected
> close
> open
> /home/ananya/Downloads/cryosparc_P29_J339_class_02_00042_volume_sharp.mrc
> /home/ananya/Downloads/cryosparc_P29_J339_class_00_00042_volume_sharp.mrc
> /home/ananya/Downloads/cryosparc_P29_J339_class_01_00042_volume_sharp.mrc
Opened cryosparc_P29_J339_class_02_00042_volume_sharp.mrc as #1.1, grid size
128,128,128, pixel 2.14, shown at level 0.389, step 1, values float32
Opened cryosparc_P29_J339_class_00_00042_volume_sharp.mrc as #1.2, grid size
128,128,128, pixel 2.14, shown at level 0.219, step 1, values float32
Opened cryosparc_P29_J339_class_01_00042_volume_sharp.mrc as #1.3, grid size
128,128,128, pixel 2.14, shown at level 0.397, step 1, values float32
> volume #1.2 level 0.2374
> hide #!1.2 models
> volume #1.2 level 0.2631
> hide #!1.2 models
> volume #1.1 level 0.2764
> select add #1.1
2 models selected
> ui mousemode right "translate selected models"
> view matrix models #1.1,1,0,0,-127.93,0,1,0,-9.5029,0,0,1,-1.7428
> volume #1.3 level 0.3191
> volume #1.1 level 0.319
> volume #1.1 level 0.402
> volume #1.3 level 0.3289
> close
> open
> /home/ananya/Downloads/cryosparc_P29_J208_007_volume_map_sym_sharp(1).mrc
> /home/ananya/Downloads/cryosparc_P29_J340_006_volume_map_sym_sharp.mrc
Opened cryosparc_P29_J208_007_volume_map_sym_sharp(1).mrc as #1.1, grid size
256,256,256, pixel 1.07, shown at level 0.212, step 1, values float32
Opened cryosparc_P29_J340_006_volume_map_sym_sharp.mrc as #1.2, grid size
256,256,256, pixel 1.07, shown at level 0.221, step 1, values float32
> tile
2 models tiled
> lighting soft
> volume all step 1 level 0.7
> select add #1.2
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #1.2,-0.30713,0.95165,0.0064041,-31.95,-0.94653,-0.30477,-0.10583,155.37,-0.098762,-0.038565,0.99436,19.959
> view matrix models
> #1.2,-0.8796,-0.46988,-0.074265,239.26,0.42751,-0.84925,0.30984,-9.6488,-0.20866,0.24078,0.94788,4.1963
> view matrix models
> #1.2,-0.16323,-0.91712,0.36367,144.28,0.9855,-0.13427,0.10373,-147.54,-0.046299,0.37533,0.92573,-31.509
> view matrix models
> #1.2,-0.0016618,-0.9995,0.031596,179.38,0.96079,0.0071646,0.27717,-186.5,-0.27726,0.030818,0.9603,38.846
> view matrix models
> #1.2,-0.25063,-0.96556,-0.069774,221.29,0.92627,-0.26014,0.27266,-146.5,-0.28142,0.0037091,0.95958,43.026
> view matrix models
> #1.2,-0.62351,-0.72659,-0.28862,268.68,0.70028,-0.68318,0.20707,-52.842,-0.34763,-0.073001,0.93479,65.063
> view matrix models
> #1.2,-0.75631,-0.65409,0.012759,235.31,0.65421,-0.75614,0.016129,-11.197,-0.00090247,0.020546,0.99979,-1.2605
> view matrix models
> #1.2,-0.68167,-0.71877,0.13671,217.07,0.71987,-0.69228,-0.050328,-19.003,0.13082,0.064105,0.98933,-22.695
> view matrix models
> #1.2,-0.701,-0.70991,0.068042,227.82,0.7109,-0.70318,-0.012612,-21.57,0.0568,0.03953,0.9976,-10.965
> view matrix models
> #1.2,-0.90359,-0.4284,-0.0013013,227,0.42832,-0.90348,0.016226,37.482,-0.008127,0.014105,0.99987,0.51154
> view matrix models
> #1.2,-0.9019,-0.33498,0.2727,177.11,0.31174,-0.94179,-0.12587,77.124,0.29899,-0.028514,0.95383,-27.688
> view matrix models
> #1.2,-0.92403,-0.3805,0.037219,218.14,0.38063,-0.92472,-0.0036141,49.188,0.035792,0.010827,0.9993,-4.7117
> view matrix models
> #1.2,0.077409,-0.99699,-0.0053489,173.79,0.99003,0.076233,0.11846,-177.62,-0.1177,-0.014466,0.99294,19.479
> view matrix models
> #1.2,-0.10687,-0.99427,0.0020356,196.47,0.99006,-0.10623,0.092136,-150.21,-0.091391,0.011862,0.99574,12.229
> view matrix models
> #1.2,-0.31861,-0.94321,-0.094001,230.56,0.93851,-0.32781,0.10832,-116.78,-0.13298,-0.053709,0.98966,27.043
> view matrix models
> #1.2,-0.43352,-0.89007,-0.14083,245.02,0.88775,-0.44868,0.1029,-93.649,-0.15478,-0.080416,0.98467,34.053
> ui mousemode right "rotate selected models"
> view matrix models
> #1.2,0.97633,0.20979,0.052544,-108.86,-0.213,0.97486,0.065456,-130.72,-0.037491,-0.075099,0.99647,16.447
> vop flip #1.2
Opened cryosparc_P29_J340_006_volume_map_sym_sharp.mrc z flip as #2, grid size
256,256,256, pixel 1.07, shown at step 1, values float32
> select subtract #1.2
Nothing selected
> select add #2
2 models selected
> view matrix models
> #2,0.54526,0.83177,0.1042,-140.83,-0.82978,0.5532,-0.073779,23.698,-0.11901,-0.046238,0.99182,23.947
> open
> /home/ananya/Downloads/refined_expanded_all_real_space_refined_001(1).pdb
Chain information for refined_expanded_all_real_space_refined_001(1).pdb #3
---
Chain | Description
A B C D | No description available
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.12829,0.99053,0.048999,-99.645,-0.98884,0.13153,-0.069919,98.947,-0.075702,-0.039482,0.99635,16.8
> view matrix models
> #2,-0.42741,0.90051,-0.080002,2.1366,-0.90405,-0.42528,0.04282,145.21,0.0045361,0.090627,0.99587,-10.58
> view matrix models
> #2,-0.67235,0.73972,-0.027631,47.941,-0.73984,-0.67029,0.057831,153.72,0.024258,0.059325,0.99794,-9.3496
> view matrix models
> #2,-0.87377,0.48309,0.056072,96.314,-0.48181,-0.87556,0.035357,149.91,0.066176,0.0038784,0.9978,-7.5618
> view matrix models
> #2,-0.94914,0.2891,0.12471,122.12,-0.29214,-0.95635,-0.0064178,141.4,0.11741,-0.042525,0.99217,-7.4236
> view matrix models
> #2,-0.94541,-0.31107,0.097171,203.7,0.3088,-0.95037,-0.037921,66.523,0.10414,-0.0058438,0.99454,-10.803
> view matrix models
> #2,-0.99453,0.049813,0.09177,163.75,-0.051715,-0.99849,-0.018468,117.18,0.090712,-0.023113,0.99561,-6.9416
> view matrix models
> #2,-0.95515,0.29042,0.057813,131.84,-0.29065,-0.95682,0.0044897,139.78,0.05662,-0.012515,0.99832,-4.2465
> view matrix models
> #2,-0.88816,0.45942,-0.010264,110.31,-0.45949,-0.88752,0.034444,148.68,0.0067146,0.035308,0.99935,-4.119
> view matrix models
> #2,-0.83053,0.55673,-0.016064,90.879,-0.55696,-0.83009,0.027309,154.88,0.0018691,0.031628,0.9995,-3.0263
> view matrix models
> #2,-0.66926,0.73529,-0.10701,58.917,-0.74184,-0.66936,0.040258,156.25,-0.042026,0.10633,0.99344,-6.2251
> view matrix models
> #2,-0.58594,0.79602,-0.15176,46.215,-0.80841,-0.58715,0.041527,154.03,-0.056052,0.14702,0.98754,-8.9034
> view matrix models
> #2,-0.41826,0.88611,-0.1997,19.109,-0.90572,-0.4235,0.017824,148.6,-0.068777,0.18833,0.9797,-11.566
> view matrix models
> #2,-0.31183,0.92484,-0.21779,2.6358,-0.94735,-0.32019,-0.0032349,143.41,-0.072725,0.20531,0.97599,-12.764
> view matrix models
> #2,-0.46231,0.88646,0.021236,-5.2541,-0.88208,-0.45731,-0.11313,167.74,-0.090574,-0.071032,0.99335,23.264
> view matrix models
> #2,-0.24323,0.96887,-0.046053,-35.427,-0.9656,-0.24637,-0.083152,147.03,-0.09191,0.024244,0.99547,10.717
> view matrix models
> #2,-0.085361,0.99356,-0.074549,-55.362,-0.99265,-0.091247,-0.079482,129.82,-0.085773,0.067217,0.99404,4.5027
> view matrix models
> #2,0.023364,0.9921,-0.12329,-62.72,-0.99757,0.01503,-0.068093,115.04,-0.065702,0.12458,0.99003,-5.0552
> view matrix models
> #2,-0.096548,0.99525,0.012379,-65.953,-0.9862,-0.093976,-0.13627,137.06,-0.13446,-0.025365,0.99059,23.405
> view matrix models
> #2,-0.082068,0.98578,0.14662,-84.872,-0.98866,-0.099091,0.11284,104.15,0.12577,-0.1357,0.98274,4.9302
> view matrix models
> #2,-0.094865,0.99531,-0.018923,-61.921,-0.9764,-0.096734,-0.19308,143.87,-0.194,0.00016008,0.981,29.145
> view matrix models
> #2,0.075611,0.99674,-0.02832,-83.063,-0.98047,0.069146,-0.18411,121.53,-0.18155,0.041688,0.9825,21.898
> view matrix models
> #2,0.089427,0.98576,0.14237,-106.66,-0.98877,0.07068,0.13169,79.445,0.11975,-0.15255,0.98101,8.1483
> view matrix models
> #2,0.074261,0.997,0.021903,-89.756,-0.99279,0.075985,-0.0927,109.81,-0.094086,-0.014861,0.99545,16.106
> select subtract #2
Nothing selected
> select add #3
8996 atoms, 9076 bonds, 1212 residues, 1 model selected
> ui mousemode right "rotate selected models"
> view matrix models
> #3,-0.048264,0.99119,0.12333,-8.42,-0.98805,-0.029287,-0.1513,291.35,-0.14635,-0.12916,0.98076,39.604
> ui mousemode right "translate selected models"
> view matrix models
> #3,-0.048264,0.99119,0.12333,-64.763,-0.98805,-0.029287,-0.1513,187.91,-0.14635,-0.12916,0.98076,32.989
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.12644,0.98984,0.065098,-80.134,-0.9858,0.1327,-0.10291,159.32,-0.1105,-0.051161,0.99256,16.117
> view matrix models
> #3,0.28183,0.95792,0.054362,-95.306,-0.95423,0.28575,-0.088287,132.6,-0.10011,-0.026991,0.99461,11.204
> view matrix models
> #3,0.46954,0.88217,0.036087,-107.93,-0.87924,0.47092,-0.071889,95.488,-0.080413,0.0020258,0.99676,4.3778
> view matrix models
> #3,0.58211,0.81288,0.019231,-111.51,-0.81075,0.58206,-0.062333,70.095,-0.061863,0.020693,0.99787,-0.76794
> view matrix models
> #3,0.60259,0.79756,0.028086,-113.42,-0.79494,0.60297,-0.067086,65.818,-0.07044,0.018099,0.99735,0.80425
> view matrix models
> #3,0.80627,0.59138,-0.014186,-107.46,-0.5913,0.80498,-0.048749,8.8814,-0.01741,0.047693,0.99871,-10.477
> view matrix models
> #3,0.85482,0.51856,-0.019298,-103.56,-0.51883,0.85339,-0.050399,-7.1219,-0.0096659,0.053094,0.99854,-12.219
> view matrix models
> #3,0.93183,0.36104,-0.036617,-90.474,-0.36255,0.93058,-0.050749,-38.433,0.015753,0.060565,0.99804,-16.57
> view matrix models
> #3,0.94673,0.32011,-0.035206,-87.195,-0.32165,0.94529,-0.054479,-45.395,0.015841,0.062901,0.99789,-16.875
> view matrix models
> #3,0.98741,0.14946,-0.051744,-67.577,-0.15238,0.98662,-0.057944,-73.229,0.042391,0.0651,0.99698,-20.617
> view matrix models
> #3,0.99588,0.080871,-0.041082,-60.995,-0.083566,0.99413,-0.068777,-82.012,0.035278,0.071927,0.99679,-20.547
> view matrix models
> #3,0.99858,-0.040878,-0.03428,-45.997,0.038068,0.99615,-0.078969,-97.258,0.037376,0.077552,0.99629,-21.513
> view matrix models
> #3,0.99722,-0.066942,-0.032715,-42.541,0.064107,0.99464,-0.081142,-100.26,0.037972,0.078819,0.99617,-21.746
> view matrix models
> #3,0.99028,-0.13617,-0.02827,-32.952,0.13328,0.98728,-0.086726,-107.82,0.03972,0.082116,0.99583,-22.377
> view matrix models
> #3,0.96168,-0.27295,-0.02594,-11.119,0.26955,0.9585,-0.092835,-121.47,0.050203,0.082286,0.99534,-23.744
> view matrix models
> #3,0.91725,-0.39707,-0.031592,12.239,0.39272,0.91475,-0.09482,-131.92,0.066549,0.074566,0.99499,-24.863
> view matrix models
> #3,0.90178,-0.4299,-0.044368,20.459,0.425,0.90075,-0.089651,-135.1,0.078505,0.061989,0.99498,-24.788
> view matrix models
> #3,0.80177,-0.59523,-0.053539,57.292,0.58913,0.80224,-0.096648,-143.05,0.10048,0.045948,0.99388,-25.447
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.90118,-0.43344,-0.001078,15.098,0.43019,0.89473,-0.12001,-130.84,0.052983,0.10769,0.99277,-27.166
> view matrix models
> #3,0.84566,-0.5337,-0.0050021,36.522,0.52952,0.84013,-0.11745,-137.25,0.066886,0.096674,0.99307,-27.603
> view matrix models
> #3,0.61534,-0.7837,-0.084646,111.85,0.77849,0.62106,-0.090754,-145.09,0.12369,-0.010051,0.99227,-20.858
> view matrix models
> #3,0.61518,-0.78337,-0.088801,112.39,0.77723,0.62149,-0.098315,-143.95,0.13221,-0.0085371,0.99119,-22.058
> view matrix models
> #3,0.49038,-0.85894,-0.14749,147.32,0.85887,0.50501,-0.085444,-141.11,0.14788,-0.084775,0.98537,-13.17
> view matrix models
> #3,0.2389,-0.95975,-0.14764,194.67,0.95751,0.25813,-0.12859,-115.45,0.16153,-0.11064,0.98065,-10.901
> view matrix models
> #3,0.71743,-0.68826,-0.10767,88.485,0.68298,0.72537,-0.085909,-146.86,0.13723,-0.011902,0.99047,-22.185
> view matrix models
> #3,0.93628,-0.33451,-0.10715,11.632,0.3336,0.94233,-0.0269,-136.94,0.10997,-0.010558,0.99388,-19.163
> view matrix models
> #3,0.93739,0.34823,-0.0060767,-93.681,-0.34816,0.93738,0.009873,-49.563,0.0091342,-0.0071392,0.99993,-6.8793
> view matrix models
> #3,0.79719,0.59895,0.075832,-119.56,-0.59892,0.8004,-0.025701,7.3705,-0.07609,-0.024929,0.99679,7.3986
> view matrix models
> #3,0.52383,0.84311,0.12151,-121.68,-0.84277,0.5337,-0.069946,81.915,-0.12382,-0.065768,0.99012,20.197
> view matrix models
> #3,0.16641,0.97913,0.11669,-91.129,-0.97755,0.17933,-0.11063,153.03,-0.12925,-0.095659,0.98699,25.356
> view matrix models
> #3,-0.35406,0.9332,0.061452,-7.3989,-0.9296,-0.34398,-0.13235,219.56,-0.10237,-0.10399,0.9893,22.537
> view matrix models
> #3,-0.30575,0.94914,0.075196,-17.91,-0.94618,-0.2941,-0.13505,215.49,-0.10607,-0.11244,0.98798,24.346
> view matrix models
> #3,-0.22964,0.97027,0.076477,-31.154,-0.96725,-0.21878,-0.12869,207.38,-0.10813,-0.10353,0.98873,23.328
> view matrix models
> #3,-0.052839,0.99748,0.04745,-54.62,-0.99369,-0.047811,-0.10149,184.34,-0.098965,-0.052513,0.9937,14.589
> view matrix models
> #3,0.15033,0.98835,0.023699,-77.493,-0.98487,0.15181,-0.083576,154,-0.0862,-0.010777,0.99622,6.9434
> view matrix models
> #3,0.46754,0.88372,-0.020832,-100.09,-0.88247,0.46525,-0.069212,96.316,-0.051472,0.050743,0.99738,-6.1206
> view matrix models
> #3,0.32109,0.947,0.0096303,-93.015,-0.94376,0.3208,-0.080019,125.37,-0.078868,0.016604,0.99675,2.2209
> view matrix models
> #3,0.25068,0.96712,0.043003,-90.792,-0.96217,0.2538,-0.099066,139.41,-0.10672,-0.016543,0.99415,10.759
> view matrix models
> #3,0.22538,0.97341,0.040943,-87.949,-0.96853,0.22841,-0.098869,143.64,-0.10559,-0.017371,0.99426,10.703
> view matrix models
> #3,0.10555,0.99392,0.031429,-73.268,-0.98937,0.10814,-0.097242,162.31,-0.10005,-0.020831,0.99476,10.351
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.10555,0.99392,0.031429,-78.323,-0.98937,0.10814,-0.097242,152.86,-0.10005,-0.020831,0.99476,11.277
> view matrix models
> #3,0.10555,0.99392,0.031429,-82.483,-0.98937,0.10814,-0.097242,145.08,-0.10005,-0.020831,0.99476,12.019
> view matrix models
> #3,0.10555,0.99392,0.031429,-86.099,-0.98937,0.10814,-0.097242,137.83,-0.10005,-0.020831,0.99476,17.076
> view matrix models
> #3,0.10555,0.99392,0.031429,-93.323,-0.98937,0.10814,-0.097242,124.25,-0.10005,-0.020831,0.99476,19.066
> view matrix models
> #3,0.10555,0.99392,0.031429,-97.435,-0.98937,0.10814,-0.097242,116.64,-0.10005,-0.020831,0.99476,19.116
> view matrix models
> #3,0.10555,0.99392,0.031429,-100.13,-0.98937,0.10814,-0.097242,111.61,-0.10005,-0.020831,0.99476,19.495
Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps,
got 1 atomic models, 2 maps.
> hide #!1.1 models
> fitmap #3 inMap #2
Fit molecule refined_expanded_all_real_space_refined_001(1).pdb (#3) to map
cryosparc_P29_J340_006_volume_map_sym_sharp.mrc z flip (#2) using 8996 atoms
average map value = 0.3356, steps = 212
shifted from previous position = 1.66
rotated from previous position = 16.4 degrees
atoms outside contour = 7485, contour level = 0.7
Position of refined_expanded_all_real_space_refined_001(1).pdb (#3) relative
to cryosparc_P29_J340_006_volume_map_sym_sharp.mrc z flip (#2) coordinates:
Matrix rotation and translation
0.94972435 -0.31308336 -0.00156290 42.01845049
0.31308664 0.94972055 0.00275999 -40.05601763
0.00062021 -0.00311055 0.99999498 2.49013700
Axis -0.00937484 -0.00348627 0.99994998
Axis point 145.71997187 110.87541049 0.00000000
Rotation angle (degrees) 18.24619064
Shift along axis 2.23574260
> select subtract #3
Nothing selected
> hide #3 models
> hide #!2 models
> show #3 models
> hide #3 models
> show #!2 models
> show #3 models
> fitmap #3 inMap #2
Fit molecule refined_expanded_all_real_space_refined_001(1).pdb (#3) to map
cryosparc_P29_J340_006_volume_map_sym_sharp.mrc z flip (#2) using 8996 atoms
average map value = 0.3421, steps = 160
shifted from previous position = 4.38
rotated from previous position = 12.8 degrees
atoms outside contour = 7387, contour level = 0.7
Position of refined_expanded_all_real_space_refined_001(1).pdb (#3) relative
to cryosparc_P29_J340_006_volume_map_sym_sharp.mrc z flip (#2) coordinates:
Matrix rotation and translation
0.99883673 0.04802442 -0.00433436 -13.01264799
-0.04794875 0.99871939 0.01613877 0.60258839
0.00510385 -0.01591217 0.99986036 -0.66803575
Axis -0.31539124 -0.09287488 -0.94440596
Axis point 15.20460684 240.59874875 0.00000000
Rotation angle (degrees) 2.91253294
Shift along axis 4.67900681
> transparency #2-3#!1 20
> hide #3 models
> show #3 models
> hide #!2 models
> show #!1.2 models
> select add #1.2
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #1.2,0.8678,0.4943,0.05091,-131.6,-0.4969,0.86392,0.082074,-81.488,-0.003413,-0.096521,0.99533,14.954
> view matrix models
> #1.2,0.48884,0.86894,0.077302,-134.67,-0.8709,0.48094,0.10112,14.667,0.050685,-0.11675,0.99187,11.011
> view matrix models
> #1.2,0.1458,0.96352,0.22443,-122.4,-0.98902,0.14748,0.0093448,86.142,-0.024095,-0.22333,0.97445,37.056
> view matrix models
> #1.2,-0.40791,0.88794,0.21256,-38.689,-0.91301,-0.39797,-0.089624,160.95,0.005011,-0.23063,0.97303,34.406
> view matrix models
> #1.2,-0.79391,0.59471,0.12662,61.68,-0.6077,-0.78303,-0.13258,177.25,0.020299,-0.1822,0.98305,24.721
> view matrix models
> #1.2,-0.99434,0.075217,-0.075088,183.2,-0.073205,-0.99689,-0.029202,121.3,-0.077051,-0.02354,0.99675,14.841
> view matrix models
> #1.2,-0.85448,0.49716,-0.15066,120.24,-0.49418,-0.86733,-0.059328,163.42,-0.16017,0.02376,0.9868,20.87
> view matrix models
> #1.2,-0.477,0.85094,-0.21994,34.309,-0.85168,-0.50932,-0.12342,172.1,-0.21704,0.12845,0.96767,17.242
> view matrix models
> #1.2,0.33008,0.93528,-0.12768,-94.587,-0.91371,0.28261,-0.29201,99.904,-0.23702,0.21305,0.94785,11.519
> volume #1.2 level 0.9295
> ui mousemode right "rotate selected models"
> view matrix models
> #1.2,0.54172,0.82439,-0.16407,-102.74,-0.82625,0.48639,-0.28413,60.804,-0.15443,0.28949,0.94464,-8.7981
> view matrix models
> #1.2,0.72148,0.67555,-0.15201,-108.35,-0.68465,0.66313,-0.30252,21.746,-0.10356,0.32233,0.94094,-19.218
> ui mousemode right "rotate selected models"
> view matrix models
> #1.2,0.93843,-0.34357,0.036035,-28.931,0.33429,0.87683,-0.34557,-133.13,0.087132,0.33634,0.9377,-45.46
> view matrix models
> #1.2,0.89659,-0.42349,-0.12955,9.4292,0.38259,0.88802,-0.25504,-153.17,0.22305,0.1791,0.95821,-45.403
> view matrix models
> #1.2,0.83139,-0.40146,-0.3842,49.593,0.39,0.91407,-0.1112,-177.05,0.39583,-0.057389,0.91653,-31.356
> view matrix models
> #1.2,0.95252,-0.25607,-0.16474,-14.965,0.22229,0.95456,-0.1985,-148.64,0.20809,0.15245,0.96616,-41.049
> view matrix models
> #1.2,0.73867,-0.66341,-0.11938,59.987,0.62129,0.73877,-0.26116,-163.94,0.26145,0.11874,0.95788,-42.475
> view matrix models
> #1.2,0.15047,-0.98538,0.079925,151.68,0.94287,0.11873,-0.3113,-118,0.29726,0.1222,0.94695,-46.109
> view matrix models
> #1.2,-0.031676,-0.99341,0.11013,172.37,0.95503,-0.062582,-0.28983,-98.803,0.29481,0.095995,0.95072,-42.877
> view matrix models
> #1.2,-0.47952,-0.86106,0.16923,205.42,0.83292,-0.5073,-0.22109,-34.091,0.27622,0.034933,0.96046,-33.795
> view matrix models
> #1.2,-0.55002,-0.83508,0.010772,232.71,0.82727,-0.54656,-0.12998,-40.583,0.11443,-0.062582,0.99146,-4.1715
> view matrix models
> #1.2,-0.57703,-0.81534,-0.047537,241.55,0.81499,-0.57104,-0.098468,-40.058,0.053139,-0.095562,0.994,7.7809
> view matrix models
> #1.2,-0.65381,-0.75332,-0.070997,246.64,0.75628,-0.64764,-0.092741,-23.173,0.023883,-0.11433,0.99316,14.161
> volume #1.2 level 0.8443
> volume #1.2 level 0.8246
> volume #1.2 level 0.7393
> volume #1.2 level 0.6016
> ui mousemode right "rotate selected models"
> view matrix models
> #1.2,-0.78596,-0.60828,-0.11076,250.41,0.61749,-0.78129,-0.091079,12.102,-0.031134,-0.13998,0.98966,25.153
> view matrix models
> #1.2,-0.95604,-0.24983,-0.15356,231.73,0.26938,-0.95512,-0.12323,84.535,-0.11589,-0.15918,0.98042,39.968
> view matrix models
> #1.2,-0.94687,0.29557,-0.12678,155.77,-0.26748,-0.94261,-0.19984,163.38,-0.17857,-0.15531,0.97159,48.844
> view matrix models
> #1.2,-0.56372,0.82134,-0.087245,31.889,-0.78544,-0.56575,-0.25103,188.78,-0.25554,-0.072988,0.96404,49.182
> view matrix models
> #1.2,-0.36809,0.92372,-0.10608,-4.3576,-0.89054,-0.38305,-0.24539,177.89,-0.26731,0.0041456,0.9636,40.721
> ui mousemode right "translate selected models"
> view matrix models
> #1.2,-0.36809,0.92372,-0.10608,-10.201,-0.89054,-0.38305,-0.24539,166.49,-0.26731,0.0041456,0.9636,45.992
> ui mousemode right "rotate selected models"
> view matrix models
> #1.2,-0.23146,0.96732,-0.10356,-34.035,-0.93517,-0.25057,-0.25035,155.72,-0.26812,0.038899,0.9626,41.705
> view matrix models
> #1.2,-0.041637,0.99594,-0.079774,-65.766,-0.96232,-0.061447,-0.26487,136.6,-0.2687,0.06574,0.96098,38.505
> view matrix models
> #1.2,0.11205,0.99258,-0.047239,-89.822,-0.95595,0.094692,-0.27784,117.2,-0.2713,0.07629,0.95947,37.677
> view matrix models
> #1.2,0.2035,0.97883,-0.022073,-103.4,-0.93951,0.18888,-0.28574,103.87,-0.27552,0.078885,0.95805,38.083
> ui mousemode right "rotate selected models"
> view matrix models
> #1.2,0.042293,0.99521,-0.088185,-75.451,-0.96654,0.018402,-0.25587,125.51,-0.25302,0.096056,0.96268,32.277
> view matrix models
> #1.2,0.31894,0.94272,-0.097744,-103.35,-0.92423,0.28651,-0.25241,84.575,-0.20995,0.17084,0.96267,16.919
> view matrix models
> #1.2,0.17007,0.9695,-0.1765,-76.62,-0.97096,0.13428,-0.198,103.03,-0.16827,0.20505,0.96418,6.8218
> view matrix models
> #1.2,-0.14698,0.9833,-0.10729,-46.614,-0.96248,-0.16719,-0.21374,143.38,-0.22811,0.071848,0.97098,31.047
> view matrix models
> #1.2,0.06953,0.99058,-0.118,-74.302,-0.97485,0.042363,-0.2188,118.38,-0.21174,0.13024,0.96861,21.628
> view matrix models
> #1.2,0.25979,0.96044,-0.10034,-97.591,-0.94373,0.2305,-0.23716,92.322,-0.20465,0.1563,0.96628,17.628
> view matrix models
> #1.2,0.31005,0.92479,0.22052,-143.56,-0.90611,0.21723,0.363,6.7202,0.2878,-0.31237,0.90532,22.921
> view matrix models
> #1.2,0.60944,0.79245,-0.024461,-131.68,-0.70968,0.55902,0.42879,-72.46,0.35347,-0.24396,0.90307,5.7558
> view matrix models
> #1.2,0.69933,0.7009,-0.14028,-115.55,-0.59455,0.67932,0.43015,-103.33,0.39678,-0.21741,0.89179,-1.799
> view matrix models
> #1.2,0.78238,0.62232,-0.024454,-132.04,-0.57764,0.73978,0.34505,-101.72,0.23282,-0.25583,0.93827,18.19
> view matrix models
> #1.2,0.80212,0.59704,-0.012077,-133.01,-0.56007,0.75917,0.33164,-104.7,0.20717,-0.25925,0.94333,21.282
> view matrix models
> #1.2,0.84357,0.53457,0.051289,-138.98,-0.52515,0.80118,0.28694,-108.59,0.1123,-0.26899,0.95657,33.095
> view matrix models
> #1.2,0.85328,0.49875,0.1522,-149.43,-0.52137,0.82132,0.23155,-104.1,-0.0095146,-0.27693,0.96084,49.416
> view matrix models
> #1.2,0.87084,0.40987,0.27138,-156.5,-0.46263,0.86998,0.17061,-109.72,-0.16616,-0.27412,0.94723,71.33
> view matrix models
> #1.2,0.69771,0.6458,0.31007,-170.01,-0.69966,0.70726,0.10131,-48.11,-0.15387,-0.28763,0.9453,71.755
> view matrix models
> #1.2,0.54131,0.76819,0.34185,-169.95,-0.82447,0.56472,0.036521,-4.3686,-0.16499,-0.30161,0.93905,75.886
> view matrix models
> #1.2,0.44663,0.83069,0.33237,-164.46,-0.88264,0.4699,0.01165,18.985,-0.1465,-0.29857,0.94308,72.526
> view matrix models
> #1.2,0.45911,0.87066,0.17658,-149.89,-0.88837,0.44912,0.095323,10.949,0.0036895,-0.20063,0.97966,35.166
> view matrix models
> #1.2,0.45533,0.88617,0.085885,-138.97,-0.88576,0.44112,0.14437,4.9131,0.090053,-0.14181,0.98579,15.404
> view matrix models
> #1.2,0.45128,0.89236,-0.0065499,-126.55,-0.87497,0.44391,0.19332,-3.5784,0.17542,-0.081511,0.98111,-2.9364
> view matrix models
> #1.2,0.60172,0.79412,-0.08546,-122.51,-0.77139,0.60555,0.19564,-38.461,0.20711,-0.051797,0.97695,-10.366
> view matrix models
> #1.2,0.68204,0.73131,0.0036488,-137.03,-0.72557,0.67605,0.12844,-44.391,0.09146,-0.090247,0.99171,7.6867
> view matrix models
> #1.2,0.77392,0.62606,0.095415,-147.89,-0.63264,0.77113,0.071605,-61.088,-0.028749,-0.11578,0.99286,26.52
> select subtract #1.2
Nothing selected
> select add #3
8996 atoms, 9076 bonds, 1212 residues, 1 model selected
> ui mousemode right "rotate selected models"
> view matrix models
> #3,-0.66317,0.74673,-0.05093,49.396,-0.74845,-0.66204,0.03896,164.9,-0.0046254,0.063956,0.99794,-8.3689
> ui mousemode right "rotate selected models"
> view matrix models
> #3,-0.94525,-0.32062,0.060833,214.9,0.32542,-0.94003,0.10219,48.953,0.024419,0.1164,0.9929,-18.605
> ui mousemode right "translate selected models"
> view matrix models
> #3,-0.94525,-0.32062,0.060833,181.64,0.32542,-0.94003,0.10219,-13.094,0.024419,0.1164,0.9929,-13.692
> ui mousemode right "rotate selected models"
> view matrix models
> #3,-0.22515,-0.96882,0.1034,165.66,0.96997,-0.21286,0.11771,-199.24,-0.092029,0.12679,0.98765,1.3046
> view matrix models
> #3,-0.18455,-0.97394,0.13181,157,0.97979,-0.17179,0.10242,-203.97,-0.077107,0.14805,0.98597,-3.3182
> view matrix models
> #3,0.079752,-0.97006,0.22939,107.58,0.99587,0.087559,0.024042,-230.13,-0.043407,0.22652,0.97304,-16.585
> view matrix models
> #3,0.29413,-0.93306,0.20711,76.826,0.95347,0.30146,0.004032,-250.31,-0.066197,0.19629,0.97831,-10.194
> view matrix models
> #3,0.64064,-0.70529,0.30356,-13.456,0.76188,0.63306,-0.13702,-249.62,-0.095528,0.31906,0.94291,-17.837
> open /home/ananya/Downloads/cryosparc_P29_J350_007_volume_map_sym_sharp.mrc
Opened cryosparc_P29_J350_007_volume_map_sym_sharp.mrc as #4, grid size
256,256,256, pixel 1.07, shown at level 0.196, step 1, values float32
> volume #4 level 0.9713
> select subtract #3
Nothing selected
> select add #4
2 models selected
> view matrix models
> #4,-0.91245,0.3519,0.20878,169.21,-0.32735,-0.93394,0.14352,306.33,0.2455,0.062606,0.96737,-36.712
> view matrix models
> #4,-0.82196,0.55092,0.14444,137.12,-0.52456,-0.83108,0.18478,311.3,0.22184,0.076111,0.97211,-36.257
> view matrix models
> #4,-0.75738,0.64589,0.095916,121.47,-0.6197,-0.75728,0.20615,309.95,0.20578,0.096692,0.97381,-37.413
> view matrix models
> #4,-0.61805,0.78596,-0.016716,98.3,-0.76609,-0.59737,0.23718,301.34,0.17643,0.1594,0.97132,-42.427
> view matrix models
> #4,-0.2744,0.91615,-0.2922,72.39,-0.94881,-0.20852,0.23724,268.19,0.15642,0.34234,0.92646,-60.435
> view matrix models
> #4,-0.41613,0.90279,0.10866,37.527,-0.90338,-0.42408,0.063773,317.79,0.10365,-0.071619,0.99203,-1.9327
> view matrix models
> #4,-0.24372,0.96964,0.019852,17.483,-0.96405,-0.24445,0.10422,293.8,0.10591,0.0062632,0.99436,-13.962
> view matrix models
> #4,-0.33071,0.92644,0.17984,13.089,-0.94076,-0.33874,0.015012,316.89,0.074826,-0.16422,0.98358,16.566
> view matrix models
> #4,-0.52465,0.8278,0.19872,50.251,-0.84694,-0.53118,-0.023327,338.14,0.086245,-0.18054,0.97978,17.992
> view matrix models
> #4,-0.68794,0.69716,0.20176,90.288,-0.71906,-0.69242,-0.059217,350.03,0.09842,-0.18582,0.97764,17.471
> view matrix models
> #4,-0.69908,0.7138,0.042011,111.35,-0.71337,-0.70026,0.02725,338.51,0.04887,-0.010919,0.99875,-4.6048
> volume #4 level 0.5837
> ui mousemode right "rotate selected models"
> view matrix models
> #4,-0.77344,0.6291,0.077596,128.69,-0.63034,-0.77625,0.01038,341.36,0.066764,-0.040884,0.99693,-2.2205
> view matrix models
> #4,-0.81378,0.57212,0.10214,139.01,-0.57553,-0.81776,-0.0048437,342.52,0.080759,-0.062729,0.99476,-0.48859
> view matrix models
> #4,-0.94407,0.29588,0.14556,190.98,-0.30602,-0.95057,-0.0526,333.9,0.1228,-0.094203,0.98795,-0.3231
> view matrix models
> #4,-0.97979,0.040294,0.19592,226.69,-0.065066,-0.99043,-0.1217,318.09,0.18914,-0.13198,0.97304,-1.2553
> view matrix models
> #4,-0.90228,-0.40779,0.14001,290.91,0.38104,-0.90614,-0.18361,256.27,0.20174,-0.11232,0.97298,-5.8018
> view matrix models
> #4,-0.75321,-0.6577,-0.009879,329.3,0.65305,-0.74592,-0.13091,190,0.078731,-0.10505,0.99135,6.5323
> view matrix models
> #4,-0.7756,-0.55653,0.29787,274.95,0.62784,-0.63131,0.45527,95.827,-0.06532,0.54012,0.83905,-49.799
> view matrix models
> #4,-0.4459,-0.76849,0.45891,241.65,0.89035,-0.32815,0.31559,35.933,-0.091936,0.54931,0.83054,-46.551
> view matrix models
> #4,-0.29279,-0.81385,0.50192,222.66,0.9504,-0.19008,0.2462,17.154,-0.10497,0.54911,0.82913,-44.64
> view matrix models
> #4,0.12949,-0.85965,0.49421,175.83,0.97227,0.20796,0.10698,-25.734,-0.19474,0.46665,0.86274,-25.367
> view matrix models
> #4,0.60089,-0.62762,0.49499,80.182,0.76778,0.62546,-0.139,-27.551,-0.22235,0.46357,0.85771,-20.642
> view matrix models
> #4,0.64024,-0.71593,0.27845,117.91,0.74856,0.66285,-0.016871,-47.372,-0.17249,0.21924,0.9603,-4.8635
> view matrix models
> #4,0.67872,-0.72665,0.10637,138.13,0.72333,0.6865,0.074312,-60.125,-0.12702,0.026505,0.99155,13.604
> view matrix models
> #4,0.70081,-0.71142,-0.052377,154.78,0.70901,0.68659,0.1609,-70.164,-0.078509,-0.1499,0.98558,34.354
> view matrix models
> #4,0.79799,-0.60201,0.028288,114.87,0.59288,0.79258,0.14254,-68.353,-0.10823,-0.096974,0.98938,29.817
> view matrix models
> #4,0.90737,-0.41109,0.087657,64.183,0.39876,0.90782,0.12982,-58.591,-0.13295,-0.082842,0.98766,31.155
> view matrix models
> #4,0.9159,-0.3977,-0.054474,80.584,0.38806,0.91195,-0.13321,-21.739,0.10266,0.10087,0.98959,-26.929
> view matrix models
> #4,0.82476,-0.56093,-0.071667,119.01,0.54942,0.82486,-0.13322,-29.694,0.13384,0.070501,0.98849,-26.304
> view matrix models
> #4,0.4337,-0.89833,0.07004,200.36,0.88931,0.41424,-0.19374,-4.394,0.14503,0.14631,0.97855,-37.656
> view matrix models
> #4,0.017222,-0.9898,0.14145,258.1,0.98568,-0.0069232,-0.16846,42.245,0.16772,0.14232,0.97551,-39.585
> view matrix models
> #4,-0.2762,-0.94821,0.15688,287.81,0.94664,-0.2966,-0.12607,84.537,0.16608,0.11369,0.97954,-35.669
> view matrix models
> #4,-0.35478,-0.92527,0.1342,297.69,0.92382,-0.36901,-0.10195,94.946,0.14385,0.087808,0.9857,-29.789
> view matrix models
> #4,-0.5591,-0.82161,0.11118,311.91,0.82112,-0.56728,-0.062909,132.36,0.11475,0.056116,0.99181,-22.149
> view matrix models
> #4,-0.78777,-0.61597,-0.0014213,326.41,0.61597,-0.78777,0.00093887,182.94,-0.0016979,-0.00013584,1,0.17062
> view matrix models
> #4,-0.95582,-0.29305,-0.022884,303.13,0.29345,-0.95584,-0.016234,252.05,-0.017116,-0.022232,0.99961,5.5052
> view matrix models
> #4,-0.9897,-0.13983,-0.030669,285.82,0.1406,-0.98977,-0.024274,277.99,-0.026961,-0.028336,0.99923,7.7384
> view matrix models
> #4,-0.90191,0.42995,-0.04116,191.21,-0.42689,-0.90185,-0.066575,344.23,-0.065745,-0.042474,0.99693,15.179
> view matrix models
> #4,-0.77601,0.62916,-0.04438,145.74,-0.6249,-0.77648,-0.081117,353.24,-0.085495,-0.035215,0.99572,16.825
> view matrix models
> #4,-0.51553,0.85668,-0.017917,74.56,-0.85065,-0.5142,-0.10952,347.4,-0.10304,-0.041223,0.99382,20.25
> show #!1.1 models
> vop flip #1.1
Opened cryosparc_P29_J208_007_volume_map_sym_sharp(1).mrc z flip as #5, grid
size 256,256,256, pixel 1.07, shown at step 1, values float32
> hide #!1.2 models
> hide #3 models
> fitmap #4 inMap #5
Fit map cryosparc_P29_J350_007_volume_map_sym_sharp.mrc in map
cryosparc_P29_J208_007_volume_map_sym_sharp(1).mrc z flip using 67343 points
correlation = 0.6446, correlation about mean = 0.04937, overlap = 2.246e+04
steps = 472, shift = 9.88, angle = 10.8 degrees
Position of cryosparc_P29_J350_007_volume_map_sym_sharp.mrc (#4) relative to
cryosparc_P29_J208_007_volume_map_sym_sharp(1).mrc z flip (#5) coordinates:
Matrix rotation and translation
0.53978957 0.84179881 0.00138520 -59.62245911
-0.84179916 0.53978608 0.00225508 168.07040787
0.00115061 -0.00238333 0.99999644 -2.71877604
Axis -0.00275505 0.00013934 -0.99999620
Axis point 123.90607507 138.55723387 0.00000000
Rotation angle (degrees) 57.33092291
Shift along axis 2.90644712
> tile
2 models tiled
> lighting soft
> close #1.1
> select add #5
4 models selected
> select subtract #4
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #5,-0.040435,0.99916,-0.0072103,-79.97,-0.9941,-0.039502,0.10098,104.46,0.10061,0.011251,0.99486,-15.038
> view matrix models
> #5,-0.72149,0.68604,0.09378,42.906,-0.67793,-0.72745,0.10598,154.74,0.14093,0.012888,0.98994,-20.136
> view matrix models
> #5,-0.98703,0.11013,0.11682,155.32,-0.097859,-0.98954,0.10602,110.97,0.12727,0.09321,0.98748,-28.949
> view matrix models
> #5,-0.91168,-0.30118,0.27951,179.32,0.30479,-0.9519,-0.031569,69.149,0.27557,0.05641,0.95962,-40.499
> view matrix models
> #5,-0.64287,-0.73747,0.20699,212.1,0.73377,-0.67047,-0.10982,-17.816,0.21977,0.081286,0.97216,-37.946
> view matrix models
> #5,-0.32045,-0.94021,0.11537,208.06,0.93437,-0.33376,-0.12468,-89.587,0.15573,0.067841,0.98547,-29.107
> view matrix models
> #5,-0.14652,-0.98917,0.0090489,205.31,0.98624,-0.14678,-0.076124,-128.98,0.076627,-0.002229,0.99706,-10.189
> view matrix models
> #5,0.025428,-0.99943,-0.022124,187.32,0.99817,0.026599,-0.054352,-157.38,0.05491,-0.020701,0.99828,-4.8344
> view matrix models
> #5,0.45784,-0.88108,0.11861,92.512,0.88533,0.43969,-0.15125,-185.4,0.081108,0.17426,0.98135,-32.896
> view matrix models
> #5,0.28249,-0.95665,0.070913,133.47,0.9559,0.27454,-0.10429,-178.81,0.080305,0.097248,0.99202,-23.664
> view matrix models
> #5,0.098333,-0.99491,0.021856,170.7,0.9927,0.096526,-0.072298,-163.78,0.06982,0.028805,0.99714,-13.525
> view matrix models
> #5,-0.059354,-0.99813,0.014852,193.77,0.99586,-0.060232,-0.068057,-143.28,0.068824,0.010752,0.99757,-10.968
> view matrix models
> #5,-0.15566,-0.9878,0.004186,207.04,0.98581,-0.15561,-0.063014,-129.49,0.062896,-0.0056818,0.998,-7.9567
> view matrix models
> #5,0.1365,-0.98787,-0.074033,177.52,0.99063,0.1364,0.0063791,-179.66,0.0037967,-0.07421,0.99724,9.6778
> view matrix models
> #5,0.16448,-0.98632,0.010864,161.93,0.98579,0.16399,-0.036336,-176.98,0.034057,0.016686,0.99928,-7.2359
> select subtract #5
Nothing selected
> show #3 models
> select add #3
8996 atoms, 9076 bonds, 1212 residues, 1 model selected
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.82424,-0.4993,0.26706,-60.738,0.55531,0.80499,-0.20887,-235.01,-0.11069,0.32046,0.94077,-15.692
> view matrix models
> #3,0.7757,-0.47673,0.41353,-77.241,0.49684,0.86536,0.065649,-272.73,-0.38915,0.15453,0.90812,48.442
> view matrix models
> #3,0.9553,-0.059244,0.28965,-140.34,0.058107,0.99823,0.012534,-224.22,-0.28988,0.0048568,0.95705,48.424
> view matrix models
> #3,0.92186,0.26009,0.28729,-178.25,-0.2519,0.96551,-0.065806,-167.42,-0.2945,-0.011704,0.95558,51.463
> view matrix models
> #3,0.73221,0.65761,0.17724,-190.88,-0.6511,0.75222,-0.10116,-80.334,-0.19984,-0.041331,0.97896,39.496
> view matrix models
> #3,0.41738,0.9085,0.020392,-160.65,-0.90758,0.41788,-0.040939,-9.3131,-0.045714,-0.0014201,0.99895,10.683
> view matrix models
> #3,0.42218,0.89833,-0.12153,-140.54,-0.87892,0.3728,-0.29753,27.923,-0.22198,0.23243,0.94694,10.218
> view matrix models
> #3,0.41615,0.90909,-0.019401,-155.13,-0.90426,0.41151,-0.11389,1.0604,-0.095549,0.064938,0.9933,9.2822
> view matrix models
> #3,0.41868,0.90727,0.039471,-163.27,-0.90787,0.41921,-0.0056877,-14.268,-0.021707,-0.033453,0.9992,11.705
> view matrix models
> #3,0.42039,0.90112,-0.10609,-142.79,-0.88434,0.38077,-0.27009,23.838,-0.20299,0.20736,0.95697,9.6477
> view matrix models
> #3,0.42173,0.90402,0.069969,-167.41,-0.90656,0.41897,0.05104,-22.164,0.016826,-0.084957,0.99624,13.816
> view matrix models
> #3,0.086441,0.99397,0.067449,-133.99,-0.99461,0.08221,0.063181,33.085,0.057255,-0.072547,0.99572,6.7863
> view matrix models
> #3,0.080344,0.99657,0.019599,-126.98,-0.9964,0.080836,-0.025723,45.657,-0.027219,-0.017461,0.99948,10.269
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.080344,0.99657,0.019599,-100.01,-0.9964,0.080836,-0.025723,96.224,-0.027219,-0.017461,0.99948,4.0674
> view matrix models
> #3,0.080344,0.99657,0.019599,-98.948,-0.9964,0.080836,-0.025723,98.185,-0.027219,-0.017461,0.99948,4.0544
> view matrix models
> #3,0.080344,0.99657,0.019599,-95.53,-0.9964,0.080836,-0.025723,104.62,-0.027219,-0.017461,0.99948,3.0002
Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps,
got 1 atomic models, 2 maps.
> hide #3 models
> show #3 models
> hide #!4 models
> fitmap #3 inMap #5
Fit molecule refined_expanded_all_real_space_refined_001(1).pdb (#3) to map
cryosparc_P29_J208_007_volume_map_sym_sharp(1).mrc z flip (#5) using 8996
atoms
average map value = 0.3371, steps = 152
shifted from previous position = 6.92
rotated from previous position = 7.34 degrees
atoms outside contour = 7381, contour level = 0.7
Position of refined_expanded_all_real_space_refined_001(1).pdb (#3) relative
to cryosparc_P29_J208_007_volume_map_sym_sharp(1).mrc z flip (#5) coordinates:
Matrix rotation and translation
-0.93127518 0.36431568 -0.00075147 213.67352377
-0.36430085 -0.93125240 -0.00733430 310.94176619
-0.00337181 -0.00655649 0.99997279 -7.80507318
Axis 0.00106751 0.00359630 -0.99999296
Axis point 136.15729617 135.30423615 0.00000000
Rotation angle (degrees) 158.63482335
Shift along axis 9.15135741
> ui mousemode right "translate selected models"
> view matrix models
> #3,-0.94432,0.31621,0.090944,110.51,-0.31827,-0.94796,-0.0087088,121.81,0.083458,-0.037169,0.99582,-11.609
> view matrix models
> #3,-0.94432,0.31621,0.090944,104.43,-0.31827,-0.94796,-0.0087088,110.58,0.083458,-0.037169,0.99582,-11.737
> view matrix models
> #3,-0.94432,0.31621,0.090944,102.38,-0.31827,-0.94796,-0.0087088,106.85,0.083458,-0.037169,0.99582,-12.319
> ui mousemode right "rotate selected models"
> view matrix models
> #3,-0.92887,0.34066,-0.14545,129.33,-0.24957,-0.86573,-0.43384,144.7,-0.27371,-0.36668,0.88917,94.406
> view matrix models
> #3,-0.81297,-0.43494,-0.38717,250.54,0.52306,-0.83766,-0.15729,-0.81746,-0.2559,-0.33039,0.90849,84.513
> view matrix models
> #3,-0.34566,-0.864,-0.36608,242.19,0.90461,-0.41052,0.11474,-146.48,-0.24942,-0.2915,0.92348,76.389
> view matrix models
> #3,0.35292,-0.91729,-0.18444,130.49,0.88804,0.26632,0.37477,-270.35,-0.29466,-0.29605,0.90859,85.121
> view matrix models
> #3,0.73683,-0.67459,0.044885,15.026,0.59451,0.67811,0.4321,-293.79,-0.32193,-0.2917,0.90071,89.285
> view matrix models
> #3,0.93003,0.018433,0.36703,-147.72,-0.13651,0.9446,0.29848,-212.82,-0.3412,-0.3277,0.88102,99.384
> view matrix models
> #3,0.43153,0.79605,0.42437,-192.52,-0.87514,0.48356,-0.017178,-8.602,-0.21888,-0.36397,0.90532,84.458
> view matrix models
> #3,-0.081778,0.94389,0.31998,-128.97,-0.98605,-0.029931,-0.16372,95.054,-0.14496,-0.32891,0.93317,66.013
> view matrix models
> #3,-0.050609,0.86475,0.49964,-147.12,-0.97096,-0.15972,0.17809,63.684,0.23381,-0.47612,0.84773,46.418
> view matrix models
> #3,-0.38285,0.74732,0.54308,-92.639,-0.88677,-0.46209,0.010734,115.68,0.25897,-0.47747,0.83961,44.322
> view matrix models
> #3,-0.58804,0.58149,0.56221,-45.453,-0.76108,-0.63309,-0.14126,142.42,0.27379,-0.51095,0.81484,50.193
> view matrix models
> #3,-0.76571,0.38397,0.516,11.198,-0.5743,-0.76937,-0.27972,154.44,0.28959,-0.51053,0.80963,48.722
> ui mousemode right "translate selected models"
> view matrix models
> #3,-0.76571,0.38397,0.516,30.957,-0.5743,-0.76937,-0.27972,194.46,0.28959,-0.51053,0.80963,17.706
> fitmap #3 inMap #5
Fit molecule refined_expanded_all_real_space_refined_001(1).pdb (#3) to map
cryosparc_P29_J208_007_volume_map_sym_sharp(1).mrc z flip (#5) using 8996
atoms
average map value = 0.3295, steps = 628
shifted from previous position = 3.1
rotated from previous position = 36.5 degrees
atoms outside contour = 7475, contour level = 0.7
Position of refined_expanded_all_real_space_refined_001(1).pdb (#3) relative
to cryosparc_P29_J208_007_volume_map_sym_sharp(1).mrc z flip (#5) coordinates:
Matrix rotation and translation
-0.58819390 0.80865946 -0.00988536 110.62346990
-0.80857199 -0.58827615 -0.01193364 327.03492239
-0.01546558 0.00097374 0.99987988 -35.05243795
Axis 0.00798086 0.00345034 -0.99996220
Axis point 138.39384885 135.37044219 0.00000000
Rotation angle (degrees) 126.03611708
Shift along axis 37.06236561
> view matrix models
> #3,-0.77539,-0.60713,0.17371,209.46,0.60304,-0.79352,-0.081605,10.975,0.18738,0.041476,0.98141,-57.428
> view matrix models
> #3,-0.77539,-0.60713,0.17371,211.32,0.60304,-0.79352,-0.081605,13.696,0.18738,0.041476,0.98141,-50.972
> view matrix models
> #3,-0.77539,-0.60713,0.17371,212.03,0.60304,-0.79352,-0.081605,14.278,0.18738,0.041476,0.98141,-44.502
> fitmap #3 inMap #5
Fit molecule refined_expanded_all_real_space_refined_001(1).pdb (#3) to map
cryosparc_P29_J208_007_volume_map_sym_sharp(1).mrc z flip (#5) using 8996
atoms
average map value = 0.5642, steps = 240
shifted from previous position = 5.09
rotated from previous position = 22.2 degrees
atoms outside contour = 5821, contour level = 0.7
Position of refined_expanded_all_real_space_refined_001(1).pdb (#3) relative
to cryosparc_P29_J208_007_volume_map_sym_sharp(1).mrc z flip (#5) coordinates:
Matrix rotation and translation
-0.23894753 0.97102412 -0.00401965 42.26245227
-0.97102003 -0.23896334 -0.00406496 299.84008649
-0.00490772 0.00293185 0.99998361 -16.06914950
Axis 0.00360278 0.00045728 -0.99999341
Axis point 138.59883910 133.37791434 0.00000000
Rotation angle (degrees) 103.82538147
Shift along axis 16.35841833
> save /home/ananya/Desktop/odin/208RH.mrc models #5
> save /home/ananya/Desktop/odin/FtsZ1modelwrt208.pdb relModel #5
> show #!4 models
> select add #4
8996 atoms, 9076 bonds, 1212 residues, 3 models selected
> select subtract #3
2 models selected
> view matrix models
> #4,-0.32998,0.94202,-0.060984,33.681,-0.94389,-0.32832,0.035711,274.93,0.013617,0.069346,0.9975,-10.422
> ui mousemode right "rotate selected models"
> view matrix models
> #4,-0.15101,0.95373,0.25997,-35.268,-0.69085,-0.28993,0.66232,150.5,0.70705,-0.079585,0.70267,-37.663
> view matrix models
> #4,0.65867,0.66473,-0.35256,-13.168,-0.47142,0.72976,0.4952,-6.5372,0.58645,-0.15997,0.79403,-22.629
> view matrix models
> #4,0.85615,-0.40379,-0.32243,115.91,0.37816,0.91485,-0.14156,-56.739,0.35214,-0.00073188,0.93595,-35.411
> view matrix models
> #4,0.27855,-0.96035,-0.012079,230.87,0.88122,0.26056,-0.39442,10.024,0.38192,0.099219,0.91885,-51.778
> view matrix models
> #4,-0.57808,-0.74766,0.32684,263.72,0.69906,-0.66039,-0.27423,153.99,0.42087,0.069955,0.90442,-50.494
> view matrix models
> #4,-0.67886,-0.72567,0.11207,302.97,0.49954,-0.56829,-0.65384,218.22,0.53816,-0.38788,0.74829,23.772
> view matrix models
> #4,-0.40329,-0.8846,-0.23418,338.39,0.79221,-0.20943,-0.57319,115.92,0.45799,-0.41668,0.78525,33.364
> view matrix models
> #4,-0.57515,-0.69408,-0.43296,359.61,0.44907,0.1745,-0.87629,144.89,0.68377,-0.69842,0.21133,124.72
> view matrix models
> #4,-0.86966,-0.15752,-0.46784,322.8,0.48879,-0.14213,-0.86075,184.67,0.069088,-0.97723,0.2006,247.24
> view matrix models
> #4,-0.88332,0.26931,-0.38368,249.59,0.2936,-0.3202,-0.90071,241.89,-0.36543,-0.90826,0.20377,292.84
> view matrix models
> #4,-0.69092,0.71162,-0.12736,123.78,-0.12217,-0.28857,-0.94963,297.76,-0.71253,-0.64056,0.28632,286.69
> ui mousemode right "rotate selected models"
> view matrix models
> #4,-0.61469,0.44331,0.65241,46.812,-0.14827,-0.87731,0.45644,195.75,0.77471,0.18384,0.605,-72.177
> view matrix models
> #4,-0.47003,0.79532,0.38281,12.746,-0.43028,-0.58514,0.68737,157.18,0.77067,0.15837,0.61724,-69.548
> view matrix models
> #4,-0.35405,0.9276,0.11915,14.232,-0.55249,-0.31025,0.77363,120.33,0.75459,0.20808,0.62233,-75.551
> view matrix models
> #4,0.16331,0.93243,-0.32234,7.0635,-0.68997,0.34148,0.63823,59.854,0.70517,0.11817,0.69912,-66.322
> view matrix models
> #4,0.22751,0.87012,-0.43719,23.763,-0.65335,0.4693,0.59405,42.175,0.72206,0.15049,0.67526,-70.04
> view matrix models
> #4,0.45585,0.82759,-0.32757,-14.528,-0.69583,0.56085,0.44862,54.021,0.55499,0.023432,0.83152,-50.953
> view matrix models
> #4,0.5882,0.79933,-0.12282,-55.56,-0.73905,0.59296,0.3197,72.532,0.32837,-0.09728,0.93953,-18.476
> view matrix models
> #4,0.65398,0.75594,0.02925,-78.492,-0.74056,0.63181,0.22889,79.41,0.15455,-0.17135,0.97301,10.453
> view matrix models
> #4,0.6167,0.74254,-0.26137,-31.806,-0.78289,0.54385,-0.30217,170.81,-0.08223,0.39098,0.91672,-34.725
> view matrix models
> #4,0.90132,0.38948,-0.18957,-26.049,-0.43314,0.81472,-0.38552,96.691,0.0042986,0.42959,0.90302,-49.791
> vop flip #4
Opened cryosparc_P29_J350_007_volume_map_sym_sharp.mrc z flip as #6, grid size
256,256,256, pixel 1.07, shown at step 1, values float32
> select add #6
4 models selected
> select subtract #4
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #6,0.75447,-0.65628,0.0090722,121.43,0.60435,0.68925,-0.39962,-17.131,0.25601,0.30698,0.91664,-66.021
> view matrix models
> #6,0.3555,-0.92506,0.13373,196.14,0.8888,0.2903,-0.35463,-0.79056,0.28923,0.24493,0.92539,-62.291
> view matrix models
> #6,-0.012346,-0.96674,0.25545,233.47,0.95105,-0.090247,-0.29558,39.69,0.3088,0.23929,0.92053,-63.328
> view matrix models
> #6,-0.13935,-0.94905,0.28266,243.59,0.94053,-0.21615,-0.26208,55.218,0.30982,0.22933,0.92272,-62.276
> view matrix models
> #6,-0.2204,-0.9754,-0.0048027,297.01,0.97011,-0.21868,-0.10522,30.481,0.10158,-0.027849,0.99444,-6.814
> view matrix models
> #6,-0.23675,-0.96238,0.13334,278.45,0.96445,-0.21622,0.15192,-4.0401,-0.11737,0.16457,0.97936,-5.0037
> view matrix models
> #6,-0.803,-0.59532,0.028062,311.53,0.59128,-0.78988,0.16274,128.08,-0.074715,0.14727,0.98627,-8.8961
> view matrix models
> #6,-0.94435,-0.32881,-0.0091362,295.28,0.32416,-0.935,0.14386,186.81,-0.055845,0.13289,0.98956,-9.6495
> view matrix models
> #6,-0.99876,0.029799,-0.0398,253.19,-0.033758,-0.99413,0.10282,247.52,-0.036502,0.10403,0.9939,-8.4561
> view matrix models
> #6,-0.91256,0.39777,-0.094882,194.81,-0.40464,-0.91187,0.068972,287.93,-0.059085,0.10133,0.9931,-5.0202
> view matrix models
> #6,-0.57681,0.79879,-0.17095,102.05,-0.80989,-0.58653,-0.0079795,302.51,-0.10664,0.13385,0.98525,-2.6273
> view matrix models
> #6,-0.56567,0.82224,-0.062738,82.44,-0.81522,-0.54612,0.19279,269.96,0.12426,0.1602,0.97923,-35.635
> view matrix models
> #6,-0.5724,0.81391,-0.09957,89.547,-0.81875,-0.56066,0.12378,281.94,0.04492,0.15237,0.9873,-25.29
> select subtract #6
Nothing selected
> select add #5
2 models selected
> select subtract #5
Nothing selected
> select add #3
8996 atoms, 9076 bonds, 1212 residues, 1 model selected
> select subtract #3
Nothing selected
> open /home/ananya/Downloads/refined_expanded_all_real_space_refined_001.pdb
Chain information for refined_expanded_all_real_space_refined_001.pdb #7
---
Chain | Description
A B C D | No description available
> select add #7
8996 atoms, 9076 bonds, 1212 residues, 1 model selected
> view matrix models
> #7,0.62684,-0.72271,0.29112,107.14,-0.64011,-0.26466,0.72126,156.8,-0.44421,-0.63847,-0.62852,367.73
> view matrix models
> #7,0.54805,-0.83642,0.0063382,171.87,-0.81417,-0.5317,0.23328,282.63,-0.19175,-0.13301,-0.97239,313.11
> ui mousemode right "rotate selected models"
> view matrix models
> #7,0.69102,-0.51429,-0.50794,179.8,-0.61417,-0.047174,-0.78777,330.4,0.38118,0.85632,-0.34846,18.386
> view matrix models
> #7,0.61579,-0.66256,-0.42641,198.62,-0.74065,-0.30214,-0.60012,355.9,0.26878,0.68537,-0.67678,101.25
> view matrix models
> #7,0.84975,-0.51162,-0.12718,106.05,-0.43625,-0.54695,-0.71452,363.33,0.296,0.66264,-0.68796,102.15
> select subtract #7
Nothing selected
> select add #7
8996 atoms, 9076 bonds, 1212 residues, 1 model selected
> view matrix models
> #7,0.93642,-0.31741,0.14954,30.592,-0.12081,-0.69182,-0.71189,339.9,0.32942,0.64857,-0.68618,99.298
> view matrix models
> #7,0.99702,0.07005,0.032464,-13.407,0.076523,-0.84073,-0.53602,309.24,-0.010255,0.53691,-0.84358,181.45
===== Log before crash end =====
Log:
Startup Messages
---
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle
You can double click a model's Name or ID in the model panel to edit those
fields
UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 3.3 (Core Profile) Mesa 23.2.1-1ubuntu3.1~22.04.2
OpenGL renderer: Mesa Intel(R) HD Graphics 2000 (SNB GT1)
OpenGL vendor: Intel
Python: 3.9.11
Locale: en_IN.ISO8859-1
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: xcb
XDG_SESSION_TYPE=wayland
DESKTOP_SESSION=ubuntu
XDG_SESSION_DESKTOP=ubuntu
XDG_CURRENT_DESKTOP=ubuntu:GNOME
WAYLAND_DISPLAY=wayland-0
GNOME_SETUP_DISPLAY=:1
DISPLAY=:0
Manufacturer: LENOVO
Model: 5030AR8
OS: Ubuntu 22.04 Jammy Jellyfish
Architecture: 64bit ELF
Virtual Machine: none
CPU: 4 Intel(R) Core(TM) i5-2400 CPU @ 3.10GHz
Cache Size: 6144 KB
Memory:
total used free shared buff/cache available
Mem: 15Gi 3.7Gi 2.5Gi 686Mi 9.3Gi 10Gi
Swap: 2.0Gi 75Mi 1.9Gi
Graphics:
00:02.0 VGA compatible controller [0300]: Intel Corporation 2nd Generation Core Processor Family Integrated Graphics Controller [8086:0102] (rev 09)
DeviceName: Onboard IGD
Subsystem: Lenovo 2nd Generation Core Processor Family Integrated Graphics Controller [17aa:3077]
Installed Packages:
alabaster: 0.7.13
appdirs: 1.4.4
asttokens: 2.2.1
Babel: 2.12.1
backcall: 0.2.0
beautifulsoup4: 4.11.2
blockdiag: 3.0.0
build: 0.10.0
certifi: 2023.5.7
cftime: 1.6.2
charset-normalizer: 3.1.0
ChimeraX-AddCharge: 1.5.9.1
ChimeraX-AddH: 2.2.5
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.3.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.9.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.3
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.43.10
ChimeraX-AtomicLibrary: 10.0.6
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3.2
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.1
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.8
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: 1.3.2
ChimeraX-ChangeChains: 1.0.2
ChimeraX-CheckWaters: 1.3.1
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.3
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.6.1
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.4.2
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
ChimeraX-DockPrep: 1.1.1
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: 1.2.1
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-Label: 1.1.7
ChimeraX-LinuxSupport: 1.0.1
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.5
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.2
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: 2.0.12
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.12
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.9
ChimeraX-ModelPanel: 1.3.7
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.0
ChimeraX-NRRD: 1.0
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.10.1
ChimeraX-PDB: 2.7.2
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 3.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.1
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.8.3
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.1
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.10.3
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1.2
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.2.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Topography: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.28.4
ChimeraX-uniprot: 2.2.2
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.1
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.1.3
contourpy: 1.0.7
cxservices: 1.2.2
cycler: 0.11.0
Cython: 0.29.33
debugpy: 1.6.7
decorator: 5.1.1
distro: 1.7.0
docutils: 0.19
executing: 1.2.0
filelock: 3.9.0
fonttools: 4.39.3
funcparserlib: 1.0.1
grako: 3.16.5
h5py: 3.8.0
html2text: 2020.1.16
idna: 3.4
ihm: 0.35
imagecodecs: 2022.9.26
imagesize: 1.4.1
importlib-metadata: 6.6.0
ipykernel: 6.21.1
ipython: 8.10.0
ipython-genutils: 0.2.0
ipywidgets: 8.0.6
jedi: 0.18.2
Jinja2: 3.1.2
jupyter-client: 8.0.2
jupyter-core: 5.3.0
jupyterlab-widgets: 3.0.7
kiwisolver: 1.4.4
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.2
matplotlib: 3.6.3
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.5.6
netCDF4: 1.6.2
networkx: 2.8.8
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.8.4
numpy: 1.23.5
openvr: 1.23.701
packaging: 23.1
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 9.3.0
pip: 23.0
pkginfo: 1.9.6
platformdirs: 3.5.0
prompt-toolkit: 3.0.38
psutil: 5.9.4
ptyprocess: 0.7.0
pure-eval: 0.2.2
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.14.0
pynrrd: 1.0.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.9
pyproject-hooks: 1.0.0
PyQt6-commercial: 6.4.2
PyQt6-Qt6: 6.4.3
PyQt6-sip: 13.4.1
PyQt6-WebEngine-commercial: 6.4.0
PyQt6-WebEngine-Qt6: 6.4.3
python-dateutil: 2.8.2
pytz: 2023.3
pyzmq: 25.0.2
qtconsole: 5.4.0
QtPy: 2.3.1
RandomWords: 0.4.0
requests: 2.28.2
scipy: 1.9.3
setuptools: 67.4.0
sfftk-rw: 0.7.3
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.4.1
sphinx: 6.1.3
sphinx-autodoc-typehints: 1.22
sphinxcontrib-applehelp: 1.0.4
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.1
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
stack-data: 0.6.2
tables: 3.7.0
tcia-utils: 1.2.0
tifffile: 2022.10.10
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.3.1
traitlets: 5.9.0
typing-extensions: 4.5.0
tzdata: 2023.3
urllib3: 1.26.15
wcwidth: 0.2.6
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.7
zipp: 3.15.0
Change History (2)
comment:1 by , 5 months ago
| Component: | Unassigned → Graphics |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash in drawing after 'view matrix' |
comment:2 by , 5 months ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | assigned → closed |
There is no indication in this Linux ChimeraX crash report of what caused the crash. While it appears to be in graphics rendering the actual line of code from the Python traceback where it crashed
if self.SHADER_STEREO_360 & c:
was not doing any graphics. So I suspect it crashed in Python garbage collection. That is generally caused by previous memory overwriting errors.
My only suggestion is to use a more current version of ChimeraX, either 1.9 or the 1.10 release candidate instead of the older version 1.6.
Note:
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Reported by Ananya Kundu