id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 18043 Crash in drawing after 'view matrix' kananya@… Tom Goddard "{{{ 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 }}} " defect closed normal Graphics can't reproduce all ChimeraX