The following bug report has been submitted:
Platform: macOS-12.2.1-arm64-arm-64bit
ChimeraX Version: 1.7.1 (2024-01-23 01:58:08 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault
Thread 0x0000000104b28580 (most recent call first):
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/chem_group/support.py", line 40 in call_c_plus_plus
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/chem_group/chem_group.py", line 233 in find_group
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/chem_group/chem_group.py", line 239 in select
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/chem_group/chem_group.py", line 246 in
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/toolshed/info.py", line 357 in selector_cb
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/atomspec.py", line 941 in find_matches
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/atomspec.py", line 1004 in find_matches
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/atomspec.py", line 1001 in evaluate
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/atomspec.py", line 1091 in evaluate
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 1309 in parse
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 2499 in _parse_arg
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 2640 in _process_positional_arguments
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 2864 in run
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/run.py", line 49 in run
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 1648 in select_by_mode
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 1846 in
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 275 in event_loop
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 918 in init
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1069 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtWebChannel, PyQt6.QtNetwork, PyQt6.QtWebEngineCore, PyQt6.QtPrintSupport, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.surface._surface, openmm._openmm, openmm.app.internal.compiled, lxml._elementpath, lxml.etree, chimerax.pdb_lib._load_libs, chimerax.core._mac_util, chimerax.graphics._graphics, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, PIL._imagingmath, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.chem_group._chem_group (total: 58)
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{
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"procLaunch" : "2024-07-20 15:55:18.3545 -0400",
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"version" : 2,
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"incident" : "B8696695-4D5A-47B2-A79F-1DDE8DDEE8F8",
"bug_type" : "309",
"pid" : 47758,
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"translated" : false,
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"procName" : "ChimeraX",
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"wakeTime" : 1698,
"sleepWakeUUID" : "34FAFA9F-3617-41B5-99AC-1305674EDE4F",
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"path" : "\/Applications\/ChimeraX-1.7.1.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/QtWidgets.abi3.so",
"name" : "QtWidgets.abi3.so"
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"path" : "\/Applications\/ChimeraX-1.7.1.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/Qt6\/plugins\/platforms\/libqcocoa.dylib",
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"path" : "\/Applications\/ChimeraX-1.7.1.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/Qt6\/lib\/QtWebEngineCore.framework\/Versions\/A\/QtWebEngineCore",
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"path" : "\/Applications\/ChimeraX-1.7.1.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/numpy\/.dylibs\/libopenblas64_.0.dylib",
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"name" : "libsystem_c.dylib"
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"uuid" : "49cf1536-27e5-3a34-9724-d75552cbab56",
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===== Log before crash start =====
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> /Users/lingxiaobin/Desktop/ROOL:GOLLD/map/cryosparc_P104_J132_8mers_6dot8_map_emready_zflip.mrc
Opened cryosparc_P104_J132_8mers_6dot8_map_emready_zflip.mrc as #1, grid size
512,512,512, pixel 1.07, shown at level 1.97, step 2, values float32
> open
> /Users/lingxiaobin/Desktop/ROOL:GOLLD/map/cryosparc_P104_J81_mono_3dot25_map_emready.mrc
Opened cryosparc_P104_J81_mono_3dot25_map_emready.mrc as #2, grid size
384,384,384, pixel 1.07, shown at level 0.00179, step 2, values float32
> open /Users/lingxiaobin/Desktop/ROOL:GOLLD/map/R-combine-new-3-coot-0.pdb
Summary of feedback from opening
/Users/lingxiaobin/Desktop/ROOL:GOLLD/map/R-combine-new-3-coot-0.pdb
---
warning | PDB SEQRES record for chain M is incomplete. Ignoring input sequence
records as basis for sequence.
Chain information for R-combine-new-3-coot-0.pdb #3
---
Chain | Description
A C D | No description available
B | No description available
G | No description available
H | No description available
M | No description available
> volume #1 step 1
> volume #2 step 1
> volume #2 level 1.338
> volume #2 level 3.081
> select /H:571@P
1 atom, 1 residue, 1 model selected
> select up
23 atoms, 25 bonds, 1 residue, 1 model selected
> select up
6069 atoms, 6801 bonds, 283 residues, 1 model selected
> select up
10332 atoms, 11566 bonds, 482 residues, 1 model selected
> style sel stick
Changed 10332 atom styles
> cartoon sel
> open /Users/lingxiaobin/Desktop/ROOL:GOLLD/fold_r_e_m/fold_r_e_m_model_0.cif
Chain information for fold_r_e_m_model_0.cif #4
---
Chain | Description
B | .
> hide #!3 models
> hide #!1 models
> ui tool show "Show Sequence Viewer"
> sequence chain #3/A #3/C #3/D #4/B
Alignment identifier is 1
> select #4/B:302
20 atoms, 21 bonds, 1 residue, 1 model selected
> select add #4/B:435
43 atoms, 46 bonds, 2 residues, 1 model selected
> select #4/B:302
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #4/B:302-434
2838 atoms, 3180 bonds, 133 residues, 1 model selected
> select ~sel & ##selected
9508 atoms, 10652 bonds, 445 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #4/B:302
20 atoms, 21 bonds, 1 residue, 1 model selected
> select add #4/B:332
42 atoms, 45 bonds, 2 residues, 1 model selected
> select #4/B:302
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #4/B:302-332
665 atoms, 745 bonds, 31 residues, 1 model selected
> save /Users/lingxiaobin/Desktop/ROOL:GOLLD/map/R-302-332.pdb models #4
> selectedOnly true relModel #4
> open /Users/lingxiaobin/Desktop/ROOL:GOLLD/map/R-302-332.pdb
Chain information for R-302-332.pdb #5
---
Chain | Description
B | No description available
> delete atoms sel
> delete bonds sel
> select #4/B:347
22 atoms, 24 bonds, 1 residue, 1 model selected
> select add #4/B:415
42 atoms, 45 bonds, 2 residues, 1 model selected
> select add #4/B:359
64 atoms, 69 bonds, 3 residues, 1 model selected
> select add #4/B:434
84 atoms, 90 bonds, 4 residues, 1 model selected
> select #4/B:347
22 atoms, 24 bonds, 1 residue, 1 model selected
> select #4/B:347-359
278 atoms, 311 bonds, 13 residues, 1 model selected
> select add #4/B:415
298 atoms, 332 bonds, 14 residues, 1 model selected
> select add #4/B:416
321 atoms, 357 bonds, 15 residues, 1 model selected
> select add #4/B:417
343 atoms, 381 bonds, 16 residues, 1 model selected
> select add #4/B:418
365 atoms, 405 bonds, 17 residues, 1 model selected
> select add #4/B:419
385 atoms, 426 bonds, 18 residues, 1 model selected
> select add #4/B:420
408 atoms, 451 bonds, 19 residues, 1 model selected
> select add #4/B:421
428 atoms, 472 bonds, 20 residues, 1 model selected
> select add #4/B:422
448 atoms, 493 bonds, 21 residues, 1 model selected
> select add #4/B:423
468 atoms, 514 bonds, 22 residues, 1 model selected
> select add #4/B:424
490 atoms, 538 bonds, 23 residues, 1 model selected
> select add #4/B:425
513 atoms, 563 bonds, 24 residues, 1 model selected
> select add #4/B:426
536 atoms, 588 bonds, 25 residues, 1 model selected
> select add #4/B:427
556 atoms, 609 bonds, 26 residues, 1 model selected
> select add #5/B:312
578 atoms, 633 bonds, 27 residues, 2 models selected
> select subtract #5/B:312
556 atoms, 609 bonds, 26 residues, 1 model selected
> select add #4/B:428
579 atoms, 634 bonds, 27 residues, 1 model selected
> select add #4/B:429
601 atoms, 658 bonds, 28 residues, 1 model selected
> select add #4/B:430
623 atoms, 682 bonds, 29 residues, 1 model selected
> select add #4/B:431
643 atoms, 703 bonds, 30 residues, 1 model selected
> select add #4/B:432
666 atoms, 728 bonds, 31 residues, 1 model selected
> select add #4/B:433
686 atoms, 749 bonds, 32 residues, 1 model selected
> select add #4/B:434
706 atoms, 770 bonds, 33 residues, 1 model selected
> save /Users/lingxiaobin/Desktop/ROOL:GOLLD/map/R_mid_2.pdb models #4
> selectedOnly true relModel #4
> open /Users/lingxiaobin/Desktop/ROOL:GOLLD/map/R_mid_2.pdb
Chain information for R_mid_2.pdb #6
---
Chain | Description
B | No description available
> delete atoms sel
> delete bonds sel
> select clear
> select #4/B:334
22 atoms, 24 bonds, 1 residue, 1 model selected
> select add #4/B:333
42 atoms, 45 bonds, 2 residues, 1 model selected
> select add #4/B:335
64 atoms, 69 bonds, 3 residues, 1 model selected
> select add #4/B:336
87 atoms, 94 bonds, 4 residues, 1 model selected
> select add #4/B:338
110 atoms, 119 bonds, 5 residues, 1 model selected
> select add #4/B:337
132 atoms, 143 bonds, 6 residues, 1 model selected
> select add #4/B:339
154 atoms, 167 bonds, 7 residues, 1 model selected
> select add #4/B:340
174 atoms, 188 bonds, 8 residues, 1 model selected
> select add #4/B:341
194 atoms, 209 bonds, 9 residues, 1 model selected
> select add #4/B:342
214 atoms, 230 bonds, 10 residues, 1 model selected
> select add #4/B:343
234 atoms, 251 bonds, 11 residues, 1 model selected
> select add #4/B:344
257 atoms, 276 bonds, 12 residues, 1 model selected
> select add #4/B:345
280 atoms, 301 bonds, 13 residues, 1 model selected
> select add #4/B:346
300 atoms, 322 bonds, 14 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> show #!1 models
> select clear
> select #4/B:386
23 atoms, 25 bonds, 1 residue, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models #4,1,0,0,202.24,0,1,0,247.47,0,0,1,303.1
> view matrix models #4,1,0,0,380.86,0,1,0,234.98,0,0,1,233.37
> view matrix models #4,1,0,0,371.91,0,1,0,289.72,0,0,1,302.59
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.5986,-0.22508,-0.76877,369.76,-0.58142,0.53809,-0.61026,305.21,0.55102,0.81228,0.19124,236.56
> view matrix models
> #4,0.27007,-0.67944,-0.68222,396.77,-0.89153,0.091148,-0.44371,333.71,0.36365,0.72805,-0.58112,222.87
> view matrix models
> #4,0.60941,-0.49088,-0.62262,381.45,-0.71962,-0.012803,-0.69425,323.85,0.33282,0.87113,-0.36105,225.93
> view matrix models
> #4,0.70711,-0.41414,-0.57313,377.3,-0.64711,-0.052288,-0.7606,320.71,0.28503,0.90871,-0.30497,228
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.70711,-0.41414,-0.57313,320.01,-0.64711,-0.052288,-0.7606,380.09,0.28503,0.90871,-0.30497,228.62
> view matrix models
> #4,0.70711,-0.41414,-0.57313,301.15,-0.64711,-0.052288,-0.7606,369.94,0.28503,0.90871,-0.30497,246.56
> view matrix models
> #4,0.70711,-0.41414,-0.57313,298.08,-0.64711,-0.052288,-0.7606,369.76,0.28503,0.90871,-0.30497,247.08
> view matrix models
> #4,0.70711,-0.41414,-0.57313,304.51,-0.64711,-0.052288,-0.7606,355.26,0.28503,0.90871,-0.30497,230.18
> view matrix models
> #4,0.70711,-0.41414,-0.57313,302.4,-0.64711,-0.052288,-0.7606,360.41,0.28503,0.90871,-0.30497,224.64
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.55953,0.36013,-0.74648,279.17,-0.82809,0.28044,-0.48541,364.32,0.034533,0.88975,0.45514,255.33
> view matrix models
> #4,0.6018,0.24071,-0.7615,280.89,-0.79658,0.24945,-0.55067,362.29,0.057401,0.93799,0.34187,249.82
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.6018,0.24071,-0.7615,267.35,-0.79658,0.24945,-0.55067,366.25,0.057401,0.93799,0.34187,243.02
> view matrix models
> #4,0.6018,0.24071,-0.7615,270.72,-0.79658,0.24945,-0.55067,367.48,0.057401,0.93799,0.34187,238.94
> view matrix models
> #4,0.6018,0.24071,-0.7615,269.91,-0.79658,0.24945,-0.55067,367.93,0.057401,0.93799,0.34187,239.14
> view matrix models
> #4,0.6018,0.24071,-0.7615,271.05,-0.79658,0.24945,-0.55067,365.4,0.057401,0.93799,0.34187,236.83
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.75714,-0.040537,-0.65199,277.47,-0.65252,-0.094004,-0.75191,365.08,-0.030809,0.99475,-0.097626,225.43
> select clear
> select #5/B:327
23 atoms, 25 bonds, 1 residue, 1 model selected
> select clear
> select #5/B:327
23 atoms, 25 bonds, 1 residue, 1 model selected
> view matrix models
> #5,0.9987,0.049293,-0.013173,0.67923,-0.048341,0.99672,0.064832,1.735,0.016326,-0.064111,0.99781,-1.4315
> ui mousemode right "translate selected models"
> view matrix models
> #5,0.9987,0.049293,-0.013173,319.93,-0.048341,0.99672,0.064832,299.71,0.016326,-0.064111,0.99781,321.77
> view matrix models
> #5,0.9987,0.049293,-0.013173,337.71,-0.048341,0.99672,0.064832,327.36,0.016326,-0.064111,0.99781,320.01
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.45204,0.8773,0.16126,362.65,-0.82211,0.33961,0.45695,331.9,0.34612,-0.33913,0.87475,308.79
> view matrix models
> #5,-0.70409,0.65439,0.27574,374.3,-0.59737,-0.75577,0.26825,305.78,0.38393,0.024159,0.92304,315.87
> view matrix models
> #5,-0.37792,0.86497,0.33014,375.33,-0.62722,-0.50149,0.59591,316.95,0.68101,0.018138,0.73205,308.67
> view matrix models
> #5,-0.36978,0.92352,0.1019,371.99,-0.7612,-0.364,0.53673,319.91,0.53277,0.12091,0.83758,314.28
> view matrix models
> #5,0.10594,0.97404,0.20008,369.19,-0.81646,-0.029642,0.57664,327.53,0.5676,-0.22445,0.79212,306.66
> ui mousemode right "translate selected models"
> view matrix models
> #5,0.10594,0.97404,0.20008,337.22,-0.81646,-0.029642,0.57664,372.12,0.5676,-0.22445,0.79212,261.67
> view matrix models
> #5,0.10594,0.97404,0.20008,339.3,-0.81646,-0.029642,0.57664,374.29,0.5676,-0.22445,0.79212,259.44
> view matrix models
> #5,0.10594,0.97404,0.20008,337.69,-0.81646,-0.029642,0.57664,376.46,0.5676,-0.22445,0.79212,261.89
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.26353,0.94313,-0.20262,327.67,-0.93115,0.30358,0.20199,376.8,0.25202,0.13543,0.9582,275.28
> view matrix models
> #5,0.17522,0.95091,-0.25509,327.86,-0.95854,0.2239,0.17624,375.19,0.2247,0.21363,0.95072,276.88
> ui mousemode right "translate selected models"
> view matrix models
> #5,0.17522,0.95091,-0.25509,330.49,-0.95854,0.2239,0.17624,370.78,0.2247,0.21363,0.95072,269.81
> select clear
> view matrix models #6,1,0,0,48.665,0,1,0,35.738,0,0,1,302.88
> view matrix models #6,1,0,0,375.25,0,1,0,377.51,0,0,1,281.3
> ui mousemode right "rotate selected models"
> view matrix models
> #6,0.51238,-0.47431,-0.71589,359.01,-0.22208,0.73209,-0.64399,365.1,0.82955,0.48895,0.26977,278.08
> view matrix models
> #6,0.082215,-0.54055,-0.83729,355.83,-0.54218,0.68067,-0.49268,366.02,0.83623,0.49447,-0.23712,271.24
> view matrix models
> #6,-0.28364,-0.27109,-0.91982,356.88,-0.58675,0.80775,-0.057125,373.5,0.75847,0.5235,-0.38817,269.24
> ui mousemode right "translate selected models"
> view matrix models
> #6,-0.28364,-0.27109,-0.91982,333.8,-0.58675,0.80775,-0.057125,406.36,0.75847,0.5235,-0.38817,254.52
> view matrix models
> #6,-0.28364,-0.27109,-0.91982,295.6,-0.58675,0.80775,-0.057125,386.9,0.75847,0.5235,-0.38817,266.43
> view matrix models
> #6,-0.28364,-0.27109,-0.91982,296.07,-0.58675,0.80775,-0.057125,384.8,0.75847,0.5235,-0.38817,259.92
> ui mousemode right "rotate selected models"
> view matrix models
> #6,0.46385,-0.59112,-0.65987,297.62,-0.10549,0.70269,-0.70363,375.61,0.87961,0.39599,0.26358,267.97
> view matrix models
> #6,0.79063,-0.43192,-0.43399,303.13,0.14255,0.81917,-0.55556,379.43,0.59547,0.37737,0.70923,273.19
> view matrix models
> #6,0.62799,-0.40628,-0.66375,299.92,-0.043556,0.83322,-0.55122,379.24,0.777,0.37508,0.50556,270.76
> ui mousemode right "translate selected models"
> view matrix models
> #6,0.62799,-0.40628,-0.66375,302.85,-0.043556,0.83322,-0.55122,378.46,0.777,0.37508,0.50556,282.04
> ui mousemode right "rotate selected models"
> view matrix models
> #6,0.2357,-0.92023,-0.31245,301.3,-0.65864,0.085149,-0.74763,366.4,0.7146,0.382,-0.58603,266.94
> view matrix models
> #6,0.98235,-0.17802,-0.057376,314.63,-0.065308,-0.039015,-0.9971,362.88,0.17527,0.98325,-0.049953,279.92
> view matrix models
> #6,0.78369,-0.35154,-0.51211,305.93,-0.51675,0.088516,-0.85155,365.45,0.34469,0.93198,-0.11229,278.81
> view matrix models
> #6,0.7776,-0.1999,-0.59613,306.36,-0.55532,0.22631,-0.80025,367.56,0.29488,0.95332,0.064977,281.39
> view matrix models
> #6,0.86303,-0.11037,-0.49295,308.89,-0.45721,0.24426,-0.85516,367.17,0.21479,0.96341,0.16034,282.66
> view matrix models
> #6,0.82245,-0.4005,-0.40395,306.82,-0.38298,0.13521,-0.91381,365.35,0.4206,0.90626,-0.042185,279.6
> ui mousemode right "translate selected models"
> view matrix models
> #6,0.82245,-0.4005,-0.40395,306.5,-0.38298,0.13521,-0.91381,363.57,0.4206,0.90626,-0.042185,273.09
> view matrix models
> #6,0.82245,-0.4005,-0.40395,300.74,-0.38298,0.13521,-0.91381,358.01,0.4206,0.90626,-0.042185,280.09
> view matrix models
> #6,0.82245,-0.4005,-0.40395,300.27,-0.38298,0.13521,-0.91381,358.18,0.4206,0.90626,-0.042185,277.31
> view matrix models
> #6,0.82245,-0.4005,-0.40395,296.16,-0.38298,0.13521,-0.91381,356.91,0.4206,0.90626,-0.042185,275.04
> view matrix models
> #6,0.82245,-0.4005,-0.40395,295.87,-0.38298,0.13521,-0.91381,356.86,0.4206,0.90626,-0.042185,275.71
> view matrix models
> #6,0.82245,-0.4005,-0.40395,297.16,-0.38298,0.13521,-0.91381,356.06,0.4206,0.90626,-0.042185,275.92
> select #4/B:378
20 atoms, 21 bonds, 1 residue, 1 model selected
> view matrix models
> #4,0.75714,-0.040537,-0.65199,298.26,-0.65252,-0.094004,-0.75191,362.3,-0.030809,0.99475,-0.097626,271.58
> volume #1 color #b2b2b280
> volume #2 color #ffffb280
> ui tool show "Side View"
> view matrix models
> #4,0.75714,-0.040537,-0.65199,308.35,-0.65252,-0.094004,-0.75191,351.25,-0.030809,0.99475,-0.097626,223.87
> view matrix models
> #4,0.75714,-0.040537,-0.65199,293.89,-0.65252,-0.094004,-0.75191,347.11,-0.030809,0.99475,-0.097626,239.74
> view matrix models
> #4,0.75714,-0.040537,-0.65199,292.98,-0.65252,-0.094004,-0.75191,355.72,-0.030809,0.99475,-0.097626,255.91
> select #5/B:325
23 atoms, 25 bonds, 1 residue, 1 model selected
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.041482,0.94471,-0.32527,330.66,-0.91308,-0.096336,-0.39625,353.6,-0.40567,0.31343,0.8586,277.44
> ui mousemode right "translate selected models"
> view matrix models
> #5,0.041482,0.94471,-0.32527,330.3,-0.91308,-0.096336,-0.39625,353.05,-0.40567,0.31343,0.8586,276.08
> view matrix models
> #5,0.041482,0.94471,-0.32527,329.77,-0.91308,-0.096336,-0.39625,352.68,-0.40567,0.31343,0.8586,276.65
> view matrix models
> #5,0.041482,0.94471,-0.32527,330.37,-0.91308,-0.096336,-0.39625,350.89,-0.40567,0.31343,0.8586,275.4
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.16479,0.87409,-0.45697,325.15,-0.9061,-0.048875,-0.42023,351.22,-0.38965,0.48331,0.78395,276.89
> ui mousemode right "translate selected models"
> view matrix models
> #5,0.16479,0.87409,-0.45697,325.42,-0.9061,-0.048875,-0.42023,352.29,-0.38965,0.48331,0.78395,280.6
> view matrix models
> #5,0.16479,0.87409,-0.45697,325.52,-0.9061,-0.048875,-0.42023,352.25,-0.38965,0.48331,0.78395,280.63
> view matrix models
> #5,0.16479,0.87409,-0.45697,325.41,-0.9061,-0.048875,-0.42023,352.56,-0.38965,0.48331,0.78395,279.53
> view matrix models
> #5,0.16479,0.87409,-0.45697,325.61,-0.9061,-0.048875,-0.42023,352.54,-0.38965,0.48331,0.78395,280.01
> select #4/B:411
22 atoms, 24 bonds, 1 residue, 1 model selected
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.95574,0.21715,-0.19853,291.75,-0.29061,0.80216,-0.52162,323.87,0.045981,0.55623,0.82976,293.51
> view matrix models
> #4,0.27268,0.48417,-0.8314,287.74,-0.9621,0.13363,-0.23773,374.58,-0.004004,0.86471,0.50226,276.25
> view matrix models
> #4,0.33995,0.45217,-0.82461,286.64,-0.86675,-0.1896,-0.46129,374.49,-0.36492,0.87155,0.32746,282.96
> view matrix models
> #4,0.43759,0.50616,-0.74318,284.13,-0.70162,-0.3247,-0.63427,367.96,-0.56235,0.79898,0.21305,288.4
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.43759,0.50616,-0.74318,289.99,-0.70162,-0.3247,-0.63427,362.87,-0.56235,0.79898,0.21305,279.18
> view matrix models
> #4,0.43759,0.50616,-0.74318,289.08,-0.70162,-0.3247,-0.63427,364.35,-0.56235,0.79898,0.21305,279.9
> view matrix models
> #4,0.43759,0.50616,-0.74318,292.91,-0.70162,-0.3247,-0.63427,365.33,-0.56235,0.79898,0.21305,277.3
> view matrix models
> #4,0.43759,0.50616,-0.74318,293.37,-0.70162,-0.3247,-0.63427,365.43,-0.56235,0.79898,0.21305,279.47
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.62991,0.71731,-0.2978,293.48,-0.18139,-0.23695,-0.95444,336.13,-0.75519,0.65523,-0.019144,283.54
> view matrix models
> #4,0.54759,0.76624,-0.33619,293.65,-0.50754,-0.015276,-0.86149,343,-0.66524,0.64237,0.38053,292.41
> view matrix models
> #4,0.51446,0.80082,-0.30663,294.56,-0.66072,0.14225,-0.73703,346.95,-0.54661,0.58177,0.6023,296.65
> view matrix models
> #4,0.48944,0.74646,-0.45083,292.89,-0.22561,-0.391,-0.89231,344.04,-0.84235,0.53845,-0.022963,289.78
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.48944,0.74646,-0.45083,287.66,-0.22561,-0.391,-0.89231,347.5,-0.84235,0.53845,-0.022963,290.79
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.75434,0.34472,-0.55869,287.76,-0.45063,-0.34697,-0.82252,355.64,-0.47739,0.87223,-0.10639,266.45
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.75434,0.34472,-0.55869,291.43,-0.45063,-0.34697,-0.82252,355.71,-0.47739,0.87223,-0.10639,269.48
> view matrix models
> #4,0.75434,0.34472,-0.55869,292.4,-0.45063,-0.34697,-0.82252,355.39,-0.47739,0.87223,-0.10639,269.33
> view matrix models
> #4,0.75434,0.34472,-0.55869,281.65,-0.45063,-0.34697,-0.82252,365.43,-0.47739,0.87223,-0.10639,258.18
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.27787,0.55499,-0.78407,284.63,-0.82576,0.55505,0.10024,377.97,0.49083,0.6196,0.61252,254.45
> view matrix models
> #4,0.98965,-0.12372,-0.072712,301.83,0.076691,0.88423,-0.46071,321.91,0.12129,0.45037,0.88457,279.78
> view matrix models
> #4,0.55475,-0.26646,-0.7882,299.48,-0.54851,0.59519,-0.58727,347.43,0.62561,0.75812,0.18402,233.52
> view matrix models
> #4,0.60398,-0.33691,-0.72229,301.91,-0.66786,0.28061,-0.68936,357.82,0.43493,0.89875,-0.055525,228.5
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.60398,-0.33691,-0.72229,299.82,-0.66786,0.28061,-0.68936,353.48,0.43493,0.89875,-0.055525,211.93
> view matrix models
> #4,0.60398,-0.33691,-0.72229,301.62,-0.66786,0.28061,-0.68936,353.28,0.43493,0.89875,-0.055525,213.72
> view matrix models
> #4,0.60398,-0.33691,-0.72229,300.07,-0.66786,0.28061,-0.68936,353.78,0.43493,0.89875,-0.055525,215.2
> view matrix models
> #4,0.60398,-0.33691,-0.72229,301.44,-0.66786,0.28061,-0.68936,352.45,0.43493,0.89875,-0.055525,214.54
> hide #5 models
> hide #!6 models
> fitmap #4 inMap #1
Fit molecule fold_r_e_m_model_0.cif (#4) to map
cryosparc_P104_J132_8mers_6dot8_map_emready_zflip.mrc (#1) using 1167 atoms
average map value = 3.606, steps = 140
shifted from previous position = 14.2
rotated from previous position = 23.6 degrees
atoms outside contour = 314, contour level = 1.9745
Position of fold_r_e_m_model_0.cif (#4) relative to
cryosparc_P104_J132_8mers_6dot8_map_emready_zflip.mrc (#1) coordinates:
Matrix rotation and translation
0.77847777 -0.14057086 -0.61172885 278.88091620
-0.62227612 -0.04532615 -0.78148446 359.81500925
0.08212663 0.98903254 -0.12275929 215.61005543
Axis 0.90254934 -0.35370392 -0.24555696
Axis point 0.00000000 128.51448011 320.87931660
Rotation angle (degrees) 101.23326445
Shift along axis 71.49125948
> view matrix models
> #4,0.77848,-0.14057,-0.61173,282.11,-0.62228,-0.045326,-0.78148,360.01,0.082127,0.98903,-0.12276,221.02
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.88554,-0.19395,-0.42214,285.61,-0.45482,-0.17681,-0.87285,355.8,0.094655,0.96495,-0.24479,217.82
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.88554,-0.19395,-0.42214,287.68,-0.45482,-0.17681,-0.87285,355.33,0.094655,0.96495,-0.24479,216.1
> view matrix models
> #4,0.88554,-0.19395,-0.42214,286.81,-0.45482,-0.17681,-0.87285,356.72,0.094655,0.96495,-0.24479,215.57
> view matrix models
> #4,0.88554,-0.19395,-0.42214,288.56,-0.45482,-0.17681,-0.87285,355.88,0.094655,0.96495,-0.24479,217.72
> view matrix models
> #4,0.88554,-0.19395,-0.42214,287.98,-0.45482,-0.17681,-0.87285,355.99,0.094655,0.96495,-0.24479,217.47
> fitmap #4 inMap #1
Fit molecule fold_r_e_m_model_0.cif (#4) to map
cryosparc_P104_J132_8mers_6dot8_map_emready_zflip.mrc (#1) using 1167 atoms
average map value = 3.606, steps = 132
shifted from previous position = 7.38
rotated from previous position = 13.7 degrees
atoms outside contour = 314, contour level = 1.9745
Position of fold_r_e_m_model_0.cif (#4) relative to
cryosparc_P104_J132_8mers_6dot8_map_emready_zflip.mrc (#1) coordinates:
Matrix rotation and translation
0.78190674 -0.14055302 -0.60734397 278.91732459
-0.61828693 -0.05037854 -0.78433620 359.77982024
0.07964372 0.98879060 -0.12629341 215.63023855
Axis 0.90435521 -0.35038717 -0.24366060
Axis point 0.00000000 128.19411064 319.92545337
Rotation angle (degrees) 101.38394223
Shift along axis 73.63750578
> view matrix models
> #4,0.78191,-0.14055,-0.60734,282.29,-0.61829,-0.050379,-0.78434,359.46,0.079644,0.98879,-0.12629,219.46
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.9807,-0.065199,-0.18433,285.54,-0.19479,-0.2444,-0.94991,346.6,0.016883,0.96748,-0.25238,218.53
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.9807,-0.065199,-0.18433,285.97,-0.19479,-0.2444,-0.94991,344.44,0.016883,0.96748,-0.25238,217.9
> view matrix models
> #4,0.9807,-0.065199,-0.18433,286.06,-0.19479,-0.2444,-0.94991,344.41,0.016883,0.96748,-0.25238,217.92
> view matrix models
> #4,0.9807,-0.065199,-0.18433,285.22,-0.19479,-0.2444,-0.94991,343.87,0.016883,0.96748,-0.25238,217.85
> volume #1 level 1.618
> show #5 models
> show #!3 models
> show #!6 models
> hide #!1 models
> select #3/M:329
20 atoms, 21 bonds, 1 residue, 1 model selected
> select add #3/M:328
40 atoms, 42 bonds, 2 residues, 1 model selected
> select add #3/M:330
60 atoms, 63 bonds, 3 residues, 1 model selected
> select add #3/M:305
83 atoms, 88 bonds, 4 residues, 1 model selected
> select add #3/M:306
105 atoms, 112 bonds, 5 residues, 1 model selected
> select add #3/M:307
125 atoms, 133 bonds, 6 residues, 1 model selected
> select add #3/M:308
148 atoms, 158 bonds, 7 residues, 1 model selected
> select add #3/M:309
170 atoms, 182 bonds, 8 residues, 1 model selected
> select add #3/M:310
193 atoms, 207 bonds, 9 residues, 1 model selected
> select add #3/M:327
216 atoms, 232 bonds, 10 residues, 1 model selected
> select add #3/M:326
239 atoms, 257 bonds, 11 residues, 1 model selected
> select add #3/M:325
262 atoms, 282 bonds, 12 residues, 1 model selected
> select add #3/M:324
282 atoms, 303 bonds, 13 residues, 1 model selected
> select add #3/M:317
304 atoms, 327 bonds, 14 residues, 1 model selected
> select add #3/M:315
326 atoms, 351 bonds, 15 residues, 1 model selected
> select add #3/M:314
346 atoms, 372 bonds, 16 residues, 1 model selected
> select add #3/M:316
366 atoms, 393 bonds, 17 residues, 1 model selected
> select add #3/M:318
389 atoms, 418 bonds, 18 residues, 1 model selected
> select add #3/M:319
411 atoms, 442 bonds, 19 residues, 1 model selected
> select add #3/M:320
433 atoms, 466 bonds, 20 residues, 1 model selected
> delete atoms sel
> delete bonds sel
Drag select of 92 atoms, 6 residues, 1 pseudobonds, 102 bonds
> delete atoms (#!3 & sel)
> delete bonds (#!3 & sel)
Drag select of 92 atoms, 11 pseudobonds
> delete atoms (#!3 & sel)
> delete bonds (#!3 & sel)
> show #!1 models
> select clear
> select #3/M:295
22 atoms, 24 bonds, 1 residue, 1 model selected
> view matrix models #3,1,0,0,133.62,0,1,0,-39.474,0,0,1,91.588
> ui mousemode right "rotate selected models"
> view matrix models
> #3,-0.63941,0.61147,0.46611,194.58,-0.60418,-0.024668,-0.79647,636.24,-0.47552,-0.79088,0.38521,614.74
> view matrix models
> #3,-0.41915,0.74798,-0.51463,324.09,0.022139,-0.55824,-0.82939,681.82,-0.90765,-0.35903,0.21742,605.36
> view matrix models
> #3,-0.70882,0.66532,0.23436,245.11,0.28421,0.57345,-0.76836,219.27,-0.6456,-0.47802,-0.59556,774.23
> view matrix models
> #3,-0.81102,0.52266,-0.26281,432.82,0.44966,0.26957,-0.85155,304.39,-0.37423,-0.8088,-0.45365,791.75
> ui mousemode right "translate selected models"
> view matrix models
> #3,-0.81102,0.52266,-0.26281,379.55,0.44966,0.26957,-0.85155,302.8,-0.37423,-0.8088,-0.45365,699.67
> ui mousemode right "rotate selected models"
> view matrix models
> #3,-0.97997,0.19907,0.005374,467.07,0.042708,0.23644,-0.97071,435.74,-0.19451,-0.95103,-0.24021,657.35
> view matrix models
> #3,-0.98691,0.03425,-0.15758,563.03,0.15832,0.02,-0.98719,486.99,-0.03066,-0.99921,-0.025161,586.01
> view matrix models
> #3,-0.95216,-0.020931,-0.30489,608.16,0.30533,-0.10793,-0.94611,487.36,-0.013102,-0.99394,0.10915,548.93
> ui mousemode right "translate selected models"
> view matrix models
> #3,-0.95216,-0.020931,-0.30489,610.61,0.30533,-0.10793,-0.94611,503.77,-0.013102,-0.99394,0.10915,561.58
> hide #!4 models
> hide #5 models
> hide #!6 models
> fitmap #3 inMap #1
Fit molecule R-combine-new-3-coot-0.pdb (#3) to map
cryosparc_P104_J132_8mers_6dot8_map_emready_zflip.mrc (#1) using 9771 atoms
average map value = 3.93, steps = 184
shifted from previous position = 23.4
rotated from previous position = 16.6 degrees
atoms outside contour = 1748, contour level = 1.6178
Position of R-combine-new-3-coot-0.pdb (#3) relative to
cryosparc_P104_J132_8mers_6dot8_map_emready_zflip.mrc (#1) coordinates:
Matrix rotation and translation
-0.99816076 0.04052911 -0.04508306 548.23447691
0.04492687 -0.00475678 -0.99897895 554.51550216
-0.04070218 -0.99916703 0.00292719 576.50119861
Axis -0.03028550 -0.70542216 0.70814007
Axis point 285.83679744 565.00302863 0.00000000
Rotation angle (degrees) 179.82208787
Shift along axis 0.47252070
> show #!4 models
> show #5 models
> show #!6 models
> select clear
> hide #!4 models
> show #!4 models
> hide #!4 models
> hide #5 models
> hide #!6 models
> show #!4 models
> show #5 models
> hide #!4 models
> show #!4 models
> hide #5 models
> hide #!3 models
> show #5 models
> hide #5 models
> show #!6 models
> hide #!4 models
> show #!4 models
> hide #!1 models
> show #!1 models
> hide #!6 models
> select #4/B:399
20 atoms, 21 bonds, 1 residue, 1 model selected
> view matrix models
> #4,0.9807,-0.065199,-0.18433,286.41,-0.19479,-0.2444,-0.94991,344.25,0.016883,0.96748,-0.25238,218.87
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.97889,-0.19216,-0.069607,293.59,-0.11505,-0.2366,-0.96477,340.93,0.16892,0.95242,-0.25371,214.2
> view matrix models
> #4,0.80338,-0.58513,-0.1105,310.1,-0.58681,-0.74643,-0.31384,390.96,0.10116,0.31698,-0.94302,215.58
> view matrix models
> #4,0.61034,-0.78369,0.11536,329.01,-0.27179,-0.070388,0.95978,397.11,-0.74405,-0.61715,-0.25596,291.41
> view matrix models
> #4,0.60121,-0.79829,0.035718,327.45,-0.20182,-0.10844,0.9734,396.33,-0.77319,-0.59243,-0.22631,292.48
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.60121,-0.79829,0.035718,314.78,-0.20182,-0.10844,0.9734,394.15,-0.77319,-0.59243,-0.22631,307.79
> view matrix models
> #4,0.60121,-0.79829,0.035718,297.57,-0.20182,-0.10844,0.9734,386.05,-0.77319,-0.59243,-0.22631,293.68
> show #!6 models
> view matrix models
> #4,0.60121,-0.79829,0.035718,294.08,-0.20182,-0.10844,0.9734,383.52,-0.77319,-0.59243,-0.22631,290.43
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.50516,-0.83164,0.23065,303.88,-0.076998,0.22276,0.97183,369.38,-0.85959,-0.50868,0.048497,298.72
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.50516,-0.83164,0.23065,305.04,-0.076998,0.22276,0.97183,367.25,-0.85959,-0.50868,0.048497,301.05
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.61339,-0.72554,0.312,300.7,-0.5604,-0.12146,0.81927,389.12,-0.55652,-0.67737,-0.4811,280.89
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.61339,-0.72554,0.312,298.04,-0.5604,-0.12146,0.81927,383.54,-0.55652,-0.67737,-0.4811,290.01
> view matrix models
> #4,0.61339,-0.72554,0.312,302.7,-0.5604,-0.12146,0.81927,381.01,-0.55652,-0.67737,-0.4811,288.26
> ui mousemode right "rotate selected models"
> view matrix models
> #4,-0.17824,-0.79705,-0.57702,305.08,0.57657,-0.55979,0.59515,349.87,-0.79737,-0.22661,0.55933,313.36
> view matrix models
> #4,-0.82447,-0.31227,-0.47195,314.71,0.30996,-0.94694,0.085079,355.54,-0.47348,-0.076141,0.87751,307.37
> view matrix models
> #4,-0.95495,-0.064127,-0.28974,316.82,0.087716,-0.99374,-0.069163,359.9,-0.28349,-0.091462,0.9546,303.74
> ui mousemode right "translate selected models"
> view matrix models
> #4,-0.95495,-0.064127,-0.28974,322.89,0.087716,-0.99374,-0.069163,365.48,-0.28349,-0.091462,0.9546,308.63
> ui mousemode right "rotate selected models"
> view matrix models
> #4,-0.66713,0.36634,0.64864,327.91,-0.61304,-0.76468,-0.19864,377.92,0.42323,-0.53016,0.73472,292.08
> view matrix models
> #4,-0.37161,0.24255,0.89615,329.18,-0.81207,-0.55274,-0.18714,378.39,0.44994,-0.79728,0.40237,289.62
> view matrix models
> #4,-0.35844,0.23802,0.9027,329.08,-0.81769,-0.54662,-0.18056,378.58,0.45045,-0.80284,0.39055,289.43
> view matrix models
> #4,0.57688,-0.34699,0.73946,310.89,-0.81225,-0.14801,0.56421,387.88,-0.086329,-0.92611,-0.36723,289.14
> view matrix models
> #4,0.59632,-0.56868,0.56657,311.83,-0.71579,-0.057203,0.69597,385.87,-0.36337,-0.82057,-0.44117,292.87
> view matrix models
> #4,0.618,-0.33205,0.71261,308.31,-0.78444,-0.20026,0.58698,389.2,-0.052198,-0.92176,-0.38424,287.4
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.618,-0.33205,0.71261,308.73,-0.78444,-0.20026,0.58698,387.44,-0.052198,-0.92176,-0.38424,282.93
> view matrix models
> #4,0.618,-0.33205,0.71261,303.15,-0.78444,-0.20026,0.58698,393.35,-0.052198,-0.92176,-0.38424,286.22
> view matrix models
> #4,0.618,-0.33205,0.71261,305.07,-0.78444,-0.20026,0.58698,395.11,-0.052198,-0.92176,-0.38424,282.5
> view matrix models
> #4,0.618,-0.33205,0.71261,303.62,-0.78444,-0.20026,0.58698,394.7,-0.052198,-0.92176,-0.38424,282.63
> view matrix models
> #4,0.618,-0.33205,0.71261,302.69,-0.78444,-0.20026,0.58698,394.1,-0.052198,-0.92176,-0.38424,282.23
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.78587,-0.47337,0.39791,292.15,-0.49338,-0.092027,0.86493,389.43,-0.37281,-0.87604,-0.30587,293.7
> view matrix models
> #4,0.77081,-0.63522,-0.048413,284.55,-0.031079,-0.1134,0.99306,378.59,-0.63631,-0.76396,-0.10715,304.79
> view matrix models
> #4,-0.10147,-0.84291,-0.5284,305.73,0.89161,-0.31266,0.32754,334.5,-0.4413,-0.43789,0.78327,314.58
> view matrix models
> #4,-0.95365,-0.21272,-0.21283,324.16,0.25932,-0.93977,-0.22269,358.25,-0.15264,-0.26756,0.95137,304.77
> view matrix models
> #4,-0.99635,-0.016626,0.083708,328.42,-0.022773,-0.89348,-0.44852,359.63,0.082249,-0.44879,0.88984,300.56
> ui mousemode right "translate selected models"
> view matrix models
> #4,-0.99635,-0.016626,0.083708,323.7,-0.022773,-0.89348,-0.44852,360.64,0.082249,-0.44879,0.88984,301.99
> ui mousemode right "rotate selected models"
> view matrix models
> #4,-0.31554,-0.20512,0.92648,331.49,-0.91394,0.32831,-0.23858,359.05,-0.25524,-0.92203,-0.29106,293.41
> view matrix models
> #4,0.27098,-0.89763,0.34762,316.17,-0.56717,0.1429,0.81111,383.99,-0.77775,-0.41695,-0.47039,290.04
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.27098,-0.89763,0.34762,309.19,-0.56717,0.1429,0.81111,382.41,-0.77775,-0.41695,-0.47039,289.35
> view matrix models
> #4,0.27098,-0.89763,0.34762,306.94,-0.56717,0.1429,0.81111,380.46,-0.77775,-0.41695,-0.47039,288.82
> view matrix models
> #4,0.27098,-0.89763,0.34762,311.81,-0.56717,0.1429,0.81111,378.53,-0.77775,-0.41695,-0.47039,288.03
> view matrix models
> #4,0.27098,-0.89763,0.34762,313.19,-0.56717,0.1429,0.81111,378.47,-0.77775,-0.41695,-0.47039,289.41
> view matrix models
> #4,0.27098,-0.89763,0.34762,311.09,-0.56717,0.1429,0.81111,377.82,-0.77775,-0.41695,-0.47039,289.68
> view matrix models
> #4,0.27098,-0.89763,0.34762,310.37,-0.56717,0.1429,0.81111,377.4,-0.77775,-0.41695,-0.47039,289.83
> view matrix models
> #4,0.27098,-0.89763,0.34762,310.96,-0.56717,0.1429,0.81111,375.72,-0.77775,-0.41695,-0.47039,292.77
> view matrix models
> #4,0.27098,-0.89763,0.34762,310.99,-0.56717,0.1429,0.81111,374.71,-0.77775,-0.41695,-0.47039,290.06
> view matrix models
> #4,0.27098,-0.89763,0.34762,310.84,-0.56717,0.1429,0.81111,375.1,-0.77775,-0.41695,-0.47039,290.4
> open /Users/lingxiaobin/Desktop/ROOL:GOLLD/fold_r_e/fold_r_e_model_0.cif
Chain information for fold_r_e_model_0.cif #7
---
Chain | Description
A | .
> hide #!6 models
> hide #!4 models
> hide #!1 models
> close #3
> open /Users/lingxiaobin/Desktop/ROOL:GOLLD/map/R-combine-new-3-coot-0.pdb
Summary of feedback from opening
/Users/lingxiaobin/Desktop/ROOL:GOLLD/map/R-combine-new-3-coot-0.pdb
---
warning | PDB SEQRES record for chain M is incomplete. Ignoring input sequence
records as basis for sequence.
Chain information for R-combine-new-3-coot-0.pdb #3
---
Chain | Description
A C D | No description available
B | No description available
G | No description available
H | No description available
M | No description available
> select #7/A:293
22 atoms, 24 bonds, 1 residue, 1 model selected
> select add #7/A:237
44 atoms, 48 bonds, 2 residues, 1 model selected
> select add #7/A:236
66 atoms, 72 bonds, 3 residues, 1 model selected
> select add #7/A:238
88 atoms, 96 bonds, 4 residues, 1 model selected
> select add #7/A:239
110 atoms, 120 bonds, 5 residues, 1 model selected
> select add #7/A:292
132 atoms, 144 bonds, 6 residues, 1 model selected
> select add #7/A:291
154 atoms, 168 bonds, 7 residues, 1 model selected
> select add #7/A:290
174 atoms, 189 bonds, 8 residues, 1 model selected
> select add #7/A:240
197 atoms, 214 bonds, 9 residues, 1 model selected
> select add #7/A:289
217 atoms, 235 bonds, 10 residues, 1 model selected
> select add #7/A:288
237 atoms, 256 bonds, 11 residues, 1 model selected
> select add #7/A:287
257 atoms, 277 bonds, 12 residues, 1 model selected
> select add #7/A:286
279 atoms, 301 bonds, 13 residues, 1 model selected
> select add #7/A:285
301 atoms, 325 bonds, 14 residues, 1 model selected
> select add #7/A:284
323 atoms, 349 bonds, 15 residues, 1 model selected
> select add #7/A:283
346 atoms, 374 bonds, 16 residues, 1 model selected
> select add #7/A:241
368 atoms, 398 bonds, 17 residues, 1 model selected
> select add #7/A:242
390 atoms, 422 bonds, 18 residues, 1 model selected
> select add #7/A:243
410 atoms, 443 bonds, 19 residues, 1 model selected
> select add #7/A:244
430 atoms, 464 bonds, 20 residues, 1 model selected
> select add #7/A:245
450 atoms, 485 bonds, 21 residues, 1 model selected
> select add #7/A:246
472 atoms, 509 bonds, 22 residues, 1 model selected
> select add #7/A:247
494 atoms, 533 bonds, 23 residues, 1 model selected
> select add #7/A:248
517 atoms, 558 bonds, 24 residues, 1 model selected
> select add #7/A:249
537 atoms, 579 bonds, 25 residues, 1 model selected
> select add #7/A:250
557 atoms, 600 bonds, 26 residues, 1 model selected
> select add #7/A:251
579 atoms, 624 bonds, 27 residues, 1 model selected
> select add #7/A:252
602 atoms, 649 bonds, 28 residues, 1 model selected
> select add #7/A:253
625 atoms, 674 bonds, 29 residues, 1 model selected
> select add #7/A:254
645 atoms, 695 bonds, 30 residues, 1 model selected
> select add #7/A:255
668 atoms, 720 bonds, 31 residues, 1 model selected
> select add #7/A:256
691 atoms, 745 bonds, 32 residues, 1 model selected
> select add #7/A:257
713 atoms, 769 bonds, 33 residues, 1 model selected
> select add #7/A:258
735 atoms, 793 bonds, 34 residues, 1 model selected
> select add #7/A:259
758 atoms, 818 bonds, 35 residues, 1 model selected
> select add #7/A:260
778 atoms, 839 bonds, 36 residues, 1 model selected
> select add #7/A:261
801 atoms, 864 bonds, 37 residues, 1 model selected
> select add #7/A:262
821 atoms, 885 bonds, 38 residues, 1 model selected
> select add #7/A:263
844 atoms, 910 bonds, 39 residues, 1 model selected
> select add #7/A:264
866 atoms, 934 bonds, 40 residues, 1 model selected
> select add #7/A:265
889 atoms, 959 bonds, 41 residues, 1 model selected
> select add #7/A:266
911 atoms, 983 bonds, 42 residues, 1 model selected
> select add #7/A:267
933 atoms, 1007 bonds, 43 residues, 1 model selected
> select add #7/A:268
955 atoms, 1031 bonds, 44 residues, 1 model selected
> select add #7/A:269
975 atoms, 1052 bonds, 45 residues, 1 model selected
> select add #7/A:270
995 atoms, 1073 bonds, 46 residues, 1 model selected
> select add #7/A:271
1015 atoms, 1094 bonds, 47 residues, 1 model selected
> select add #7/A:272
1038 atoms, 1119 bonds, 48 residues, 1 model selected
> select add #7/A:273
1060 atoms, 1143 bonds, 49 residues, 1 model selected
> select add #7/A:274
1080 atoms, 1164 bonds, 50 residues, 1 model selected
> select add #7/A:275
1102 atoms, 1188 bonds, 51 residues, 1 model selected
> select add #7/A:276
1125 atoms, 1213 bonds, 52 residues, 1 model selected
> select add #7/A:277
1147 atoms, 1237 bonds, 53 residues, 1 model selected
> select add #7/A:278
1167 atoms, 1258 bonds, 54 residues, 1 model selected
> select add #7/A:279
1187 atoms, 1279 bonds, 55 residues, 1 model selected
> select add #7/A:280
1207 atoms, 1300 bonds, 56 residues, 1 model selected
> select add #7/A:281
1227 atoms, 1321 bonds, 57 residues, 1 model selected
> select add #7/A:282
1249 atoms, 1345 bonds, 58 residues, 1 model selected
> show #!4 models
> hide #!3 models
> save /Users/lingxiaobin/Desktop/ROOL:GOLLD/map/R-236-293.pdb models #7
> selectedOnly true relModel #7
> open /Users/lingxiaobin/Desktop/ROOL:GOLLD/map/R-236-293.pdb
Chain information for R-236-293.pdb #8
---
Chain | Description
A | No description available
> hide #7 models
> show #!1 models
> select clear
> select #8/A:269
20 atoms, 21 bonds, 1 residue, 1 model selected
> view matrix models #8,1,0,0,192.21,0,1,0,-9.0856,0,0,1,-5.7085
> view matrix models #8,1,0,0,16.306,0,1,0,216.31,0,0,1,111.54
> view matrix models #8,1,0,0,284.23,0,1,0,180.79,0,0,1,216.37
> view matrix models #8,1,0,0,344.73,0,1,0,270.74,0,0,1,322.77
> ui tool show "Model Panel"
> show #!3 models
> select #3/C:460@P
1 atom, 1 residue, 1 model selected
> select up
20 atoms, 21 bonds, 1 residue, 1 model selected
> select up
768 atoms, 858 bonds, 36 residues, 1 model selected
> select up
10332 atoms, 11566 bonds, 482 residues, 1 model selected
> style sel stick
Changed 10332 atom styles
> cartoon sel
> select #8/A:280
20 atoms, 21 bonds, 1 residue, 1 model selected
> view matrix models #8,1,0,0,258.82,0,1,0,267.25,0,0,1,370.28
> view matrix models #8,1,0,0,246.94,0,1,0,268.93,0,0,1,334.81
> view matrix models #8,1,0,0,196.23,0,1,0,281.45,0,0,1,283.71
> hide #!4 models
> ui mousemode right "rotate selected models"
> view matrix models
> #8,0.78857,0.29009,-0.54223,176.98,-0.56182,0.69835,-0.44346,299.33,0.25002,0.65433,0.71368,242.02
> view matrix models
> #8,0.32664,0.30787,-0.8936,185.61,-0.74607,0.66443,-0.043798,325.88,0.58025,0.68099,0.44673,213.67
> view matrix models
> #8,0.80066,0.31305,-0.51083,177.05,-0.52281,0.78149,-0.34051,299.31,0.29261,0.5397,0.78937,246
> view matrix models
> #8,-0.094414,0.7613,-0.64149,205.16,0.052132,0.64727,0.76048,318.71,0.99417,0.038357,-0.1008,187.39
> view matrix models
> #8,-0.19851,0.85056,-0.48697,214.38,0.61191,0.49568,0.61633,288.58,0.76561,-0.17563,-0.61886,183.47
> view matrix models
> #8,-0.45882,0.35229,-0.8157,227,0.88659,0.24214,-0.39412,239.9,0.058666,-0.90402,-0.42344,246.49
> view matrix models
> #8,-0.67836,-0.05849,-0.7324,252.37,0.56065,0.60306,-0.56744,239.76,0.47487,-0.79555,-0.3763,224.49
> view matrix models
> #8,-0.65926,-0.49016,-0.57019,269.48,0.007876,0.75378,-0.65708,260.06,0.75187,-0.43768,-0.49308,196.19
> view matrix models
> #8,-0.48018,-0.38406,-0.78862,248.72,0.061197,0.8822,-0.46689,261.67,0.87503,-0.27245,-0.40011,189.34
> view matrix models
> #8,-0.36824,-0.36298,-0.85595,239.78,0.53411,0.67098,-0.51431,241.46,0.76101,-0.64656,-0.053212,219.12
> view matrix models
> #8,-0.31773,-0.54964,-0.77262,245.56,0.50595,0.59087,-0.6284,240.35,0.80191,-0.59057,0.090347,221.42
> view matrix models
> #8,-0.22063,-0.73606,-0.63995,250.99,0.56215,0.44021,-0.70014,238.58,0.79706,-0.51422,0.31666,228.86
> view matrix models
> #8,-0.20685,-0.82677,-0.52314,257.47,0.46935,0.3853,-0.79451,240.91,0.85844,-0.40988,0.30834,222.63
> ui mousemode right "translate selected models"
> view matrix models
> #8,-0.20685,-0.82677,-0.52314,254.88,0.46935,0.3853,-0.79451,225.38,0.85844,-0.40988,0.30834,206.79
> view matrix models
> #8,-0.20685,-0.82677,-0.52314,260.91,0.46935,0.3853,-0.79451,234.41,0.85844,-0.40988,0.30834,201.59
> view matrix models
> #8,-0.20685,-0.82677,-0.52314,261.42,0.46935,0.3853,-0.79451,228.66,0.85844,-0.40988,0.30834,199.64
> view matrix models
> #8,-0.20685,-0.82677,-0.52314,267.87,0.46935,0.3853,-0.79451,227.39,0.85844,-0.40988,0.30834,194.26
> ui mousemode right "rotate selected models"
> view matrix models
> #8,-0.11925,-0.88889,-0.44232,268.37,-0.62925,0.41226,-0.65885,287.78,0.768,0.19976,-0.6085,145
> view matrix models
> #8,0.29108,-0.67352,-0.67944,232.25,0.081776,0.72511,-0.68376,242.55,0.9532,0.14347,0.26614,172.8
> view matrix models
> #8,-0.0052948,-0.26057,-0.96544,224.67,0.48503,0.84361,-0.23035,237.62,0.87448,-0.46949,0.12192,186.9
> view matrix models
> #8,0.24026,-0.51403,-0.82343,224.75,0.25428,0.85199,-0.45766,239.66,0.93681,-0.099427,0.33541,182.89
> view matrix models
> #8,0.36463,-0.59247,-0.71835,224.81,0.15346,0.79915,-0.58122,241.1,0.91842,0.10169,0.38231,180.46
> view matrix models
> #8,0.37989,-0.63164,-0.6758,226.81,0.067455,0.74754,-0.66078,243.58,0.92257,0.20544,0.32659,175.23
> ui mousemode right "translate selected models"
> view matrix models
> #8,0.37989,-0.63164,-0.6758,223.7,0.067455,0.74754,-0.66078,246.28,0.92257,0.20544,0.32659,176.75
> ui mousemode right "rotate selected models"
> view matrix models
> #8,0.036155,-0.41938,-0.90709,226.05,0.05444,0.90716,-0.41724,252.72,0.99786,-0.034297,0.05563,168.12
> ui mousemode right "translate selected models"
> view matrix models
> #8,0.036155,-0.41938,-0.90709,225.08,0.05444,0.90716,-0.41724,246.41,0.99786,-0.034297,0.05563,165.12
> view matrix models
> #8,0.036155,-0.41938,-0.90709,222.42,0.05444,0.90716,-0.41724,251.86,0.99786,-0.034297,0.05563,166.19
> view matrix models
> #8,0.036155,-0.41938,-0.90709,225.9,0.05444,0.90716,-0.41724,256.58,0.99786,-0.034297,0.05563,161.91
> view matrix models
> #8,0.036155,-0.41938,-0.90709,223.86,0.05444,0.90716,-0.41724,256.67,0.99786,-0.034297,0.05563,161.1
> ui mousemode right "rotate selected models"
> view matrix models
> #8,-0.21282,-0.62041,-0.75485,247.96,-0.62548,0.68001,-0.38256,298.36,0.75065,0.39073,-0.53278,138.27
> view matrix models
> #8,-0.31161,-0.31247,-0.89736,239,0.20106,0.90132,-0.38367,250.8,0.92869,-0.29998,-0.21803,160.35
> view matrix models
> #8,-0.13148,-0.44762,-0.88451,234.01,0.32176,0.82468,-0.46517,243.38,0.93765,-0.34576,0.035597,171.52
> view matrix models
> #8,-0.1007,-0.48277,-0.86994,233.97,0.35317,0.8001,-0.48489,241.63,0.93012,-0.35607,0.089931,174.41
> ui mousemode right "translate selected models"
> view matrix models
> #8,-0.1007,-0.48277,-0.86994,240.79,0.35317,0.8001,-0.48489,246.12,0.93012,-0.35607,0.089931,178.61
> view matrix models
> #8,-0.1007,-0.48277,-0.86994,240.81,0.35317,0.8001,-0.48489,247.19,0.93012,-0.35607,0.089931,179.37
> view matrix models
> #8,-0.1007,-0.48277,-0.86994,238.62,0.35317,0.8001,-0.48489,236.48,0.93012,-0.35607,0.089931,179.42
> view matrix models
> #8,-0.1007,-0.48277,-0.86994,238.99,0.35317,0.8001,-0.48489,232.44,0.93012,-0.35607,0.089931,180.88
> view matrix models
> #8,-0.1007,-0.48277,-0.86994,240.38,0.35317,0.8001,-0.48489,237.23,0.93012,-0.35607,0.089931,183.61
> view matrix models
> #8,-0.1007,-0.48277,-0.86994,240.68,0.35317,0.8001,-0.48489,235.65,0.93012,-0.35607,0.089931,182.51
> view matrix models
> #8,-0.1007,-0.48277,-0.86994,237.97,0.35317,0.8001,-0.48489,241.27,0.93012,-0.35607,0.089931,185.57
> view matrix models
> #8,-0.1007,-0.48277,-0.86994,239.61,0.35317,0.8001,-0.48489,244.63,0.93012,-0.35607,0.089931,185.31
> view matrix models
> #8,-0.1007,-0.48277,-0.86994,240.99,0.35317,0.8001,-0.48489,240.05,0.93012,-0.35607,0.089931,184.7
> view matrix models
> #8,-0.1007,-0.48277,-0.86994,240.87,0.35317,0.8001,-0.48489,240.8,0.93012,-0.35607,0.089931,184.8
> view matrix models
> #8,-0.1007,-0.48277,-0.86994,239.33,0.35317,0.8001,-0.48489,238.25,0.93012,-0.35607,0.089931,185.03
> view matrix models
> #8,-0.1007,-0.48277,-0.86994,238.46,0.35317,0.8001,-0.48489,239.2,0.93012,-0.35607,0.089931,185.21
> view matrix models
> #8,-0.1007,-0.48277,-0.86994,239.02,0.35317,0.8001,-0.48489,239.92,0.93012,-0.35607,0.089931,186.06
> view matrix models
> #8,-0.1007,-0.48277,-0.86994,238.42,0.35317,0.8001,-0.48489,237.9,0.93012,-0.35607,0.089931,186.15
> view matrix models
> #8,-0.1007,-0.48277,-0.86994,239.05,0.35317,0.8001,-0.48489,236.88,0.93012,-0.35607,0.089931,186.51
> view matrix models
> #8,-0.1007,-0.48277,-0.86994,238.56,0.35317,0.8001,-0.48489,236.37,0.93012,-0.35607,0.089931,186.6
> view matrix models
> #8,-0.1007,-0.48277,-0.86994,238.42,0.35317,0.8001,-0.48489,236.9,0.93012,-0.35607,0.089931,187.04
> select #8/A:240
23 atoms, 25 bonds, 1 residue, 1 model selected
> show #!4 models
> hide #8 models
> hide #!3 models
> hide #!1 models
> select clear
> show #!1 models
> hide #!4 models
> show #8 models
> select #8/A:293
22 atoms, 24 bonds, 1 residue, 1 model selected
> hide #!1 models
> show #!1 models
> show #!3 models
> select add #8/A:292
53 atoms, 48 bonds, 3 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> ui mousemode right "rotate selected models"
> select #8/A:243
20 atoms, 21 bonds, 1 residue, 1 model selected
> view matrix models
> #8,-0.17747,-0.40229,-0.89815,238.89,0.26275,0.86014,-0.43718,242.07,0.9484,-0.31357,-0.046943,178.77
> view matrix models
> #8,-0.13544,-0.59635,-0.79121,246.76,0.037575,0.79491,-0.60557,247.56,0.99007,-0.11175,-0.085253,169.55
> view matrix models
> #8,-0.26224,-0.61682,-0.74213,255.91,0.0053657,0.7681,-0.6403,248.34,0.96499,-0.1719,-0.19812,167.29
> view matrix models
> #8,-0.25959,-0.61355,-0.74577,255.53,0.02228,0.76823,-0.63979,247.51,0.96546,-0.1827,-0.18575,168.11
> ui mousemode right "move picked models"
> ui mousemode right "translate selected models"
> view matrix models
> #8,-0.25959,-0.61355,-0.74577,255.12,0.02228,0.76823,-0.63979,247.63,0.96546,-0.1827,-0.18575,168.06
> view matrix models
> #8,-0.25959,-0.61355,-0.74577,254.78,0.02228,0.76823,-0.63979,247.17,0.96546,-0.1827,-0.18575,167.71
> view matrix models
> #8,-0.25959,-0.61355,-0.74577,254.93,0.02228,0.76823,-0.63979,247.06,0.96546,-0.1827,-0.18575,167.64
> select #8/A:240
23 atoms, 25 bonds, 1 residue, 1 model selected
> select add #8/A:239
45 atoms, 49 bonds, 2 residues, 1 model selected
> select add #8/A:238
67 atoms, 73 bonds, 3 residues, 1 model selected
> ui mousemode right "translate selected atoms"
> hide #!1 models
> select add #8/A:237
89 atoms, 97 bonds, 4 residues, 1 model selected
> select clear
> select add #8/A:237
22 atoms, 24 bonds, 1 residue, 1 model selected
> select add #8/A:236
35 atoms, 36 bonds, 2 residues, 1 model selected
> show #!1 models
> select #1
3 models selected
> hide #!1 models
> select #8/A:238
22 atoms, 24 bonds, 1 residue, 1 model selected
> select #8/A:239
22 atoms, 24 bonds, 1 residue, 1 model selected
> select #8/A:238
22 atoms, 24 bonds, 1 residue, 1 model selected
> select #8/A:239
22 atoms, 24 bonds, 1 residue, 1 model selected
> select #8/A:238
22 atoms, 24 bonds, 1 residue, 1 model selected
> select #8/A:237
22 atoms, 24 bonds, 1 residue, 1 model selected
> select #8/A:236
13 atoms, 12 bonds, 1 residue, 1 model selected
> select #8/A:238
22 atoms, 24 bonds, 1 residue, 1 model selected
> select #8/A:237
22 atoms, 24 bonds, 1 residue, 1 model selected
> select #8/A:238
22 atoms, 24 bonds, 1 residue, 1 model selected
> select #8/A:239
22 atoms, 24 bonds, 1 residue, 1 model selected
> select #8/A:240
23 atoms, 25 bonds, 1 residue, 1 model selected
> show #!1 models
> hide #!1 models
Drag select of 7452 atoms, 537 residues, 3 pseudobonds, 8214 bonds, 165 shapes
> combine #3 #8
Remapping chain ID 'A' in R-236-293.pdb #8 to 'E'
> hide #!3 models
> hide #8 models
> save /Users/lingxiaobin/Desktop/ROOL:GOLLD/map/R-combine-new-5.pdb models #9
> relModel #9
> show #!1 models
> hide #!1 models
[deleted to fit within ticket limits]
> select add #5/O:395
1104 atoms, 1185 bonds, 52 residues, 1 model selected
> select add #5/O:396
1127 atoms, 1210 bonds, 53 residues, 1 model selected
> select add #5/O:397
1150 atoms, 1235 bonds, 54 residues, 1 model selected
> save /Users/lingxiaobin/Desktop/ROOL:GOLLD/map/R14.pdb models #5 relModel #2
> open /Users/lingxiaobin/Desktop/ROOL:GOLLD/map/R14.pdb
Chain information for R14.pdb #6
---
Chain | Description
A B C L M N O | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H | No description available
I | No description available
J | No description available
K | No description available
> close #6
> save /Users/lingxiaobin/Desktop/ROOL:GOLLD/map/R14.pdb models #5
> selectedOnly true relModel #2
> open /Users/lingxiaobin/Desktop/ROOL:GOLLD/map/R14.pdb
Chain information for R14.pdb #6
---
Chain | Description
O | No description available
> delete atoms sel
> delete bonds sel
> show #!1 models
Drag select of 35 residues, 104 shapes
> view matrix models #6,1,0,0,-87.082,0,1,0,84.779,0,0,1,-337.8
> view matrix models #6,1,0,0,-277.96,0,1,0,-236.91,0,0,1,-312.95
> view matrix models #6,1,0,0,-277.17,0,1,0,-241.76,0,0,1,-423.25
> view matrix models #6,1,0,0,-296.88,0,1,0,-228.61,0,0,1,-433.29
> ui mousemode right "rotate selected models"
> view matrix models
> #6,-0.65359,0.61254,0.44454,-2.4025,-0.7485,-0.43617,-0.4995,1216.7,-0.11207,-0.65921,0.74356,123.28
> view matrix models
> #6,-0.81867,0.33738,-0.46471,876.72,0.39562,-0.25521,-0.88224,784.53,-0.41625,-0.90612,0.075455,890.04
> view matrix models
> #6,0.086968,0.018124,-0.99605,917.41,0.97827,-0.19043,0.081952,-263.01,-0.18819,-0.98153,-0.034291,880.52
> view matrix models
> #6,0.31553,-0.074441,-0.94599,799.71,0.86072,0.44217,0.2523,-618.77,0.39951,-0.89384,0.20359,345.42
> ui mousemode right "translate selected models"
> view matrix models
> #6,0.31553,-0.074441,-0.94599,797.93,0.86072,0.44217,0.2523,-614.97,0.39951,-0.89384,0.20359,330.34
> view matrix models
> #6,0.31553,-0.074441,-0.94599,768.9,0.86072,0.44217,0.2523,-617.63,0.39951,-0.89384,0.20359,302.67
> view matrix models
> #6,0.31553,-0.074441,-0.94599,783.24,0.86072,0.44217,0.2523,-656.28,0.39951,-0.89384,0.20359,331.6
> view matrix models
> #6,0.31553,-0.074441,-0.94599,769.08,0.86072,0.44217,0.2523,-676.17,0.39951,-0.89384,0.20359,332.42
> view matrix models
> #6,0.31553,-0.074441,-0.94599,773.29,0.86072,0.44217,0.2523,-673.71,0.39951,-0.89384,0.20359,311.84
> fitmap #6 inMap #1
Fit molecule R14.pdb (#6) to map
cryosparc_P104_J132_8mers_6dot8_map_emready_zflip.mrc (#1) using 1150 atoms
average map value = 3.336, steps = 324
shifted from previous position = 13.4
rotated from previous position = 64.4 degrees
atoms outside contour = 512, contour level = 3.2169
Position of R14.pdb (#6) relative to
cryosparc_P104_J132_8mers_6dot8_map_emready_zflip.mrc (#1) coordinates:
Matrix rotation and translation
0.78611487 0.50113304 -0.36178595 -173.35783027
-0.05037818 0.63534113 0.77058658 -639.19960499
0.61602390 -0.58754346 0.52469729 -194.95154361
Axis -0.77077029 -0.55492976 -0.31299541
Axis point 0.00000000 -282.14893447 300.37046308
Rotation angle (degrees) 61.76580551
Shift along axis 549.34888620
> view matrix models
> #6,0.78611,0.50113,-0.36179,-176.93,-0.050378,0.63534,0.77059,-636.21,0.61602,-0.58754,0.5247,-182.01
> ui mousemode right "rotate selected models"
> view matrix models
> #6,0.4991,-0.25611,-0.82783,673.38,0.6784,0.70986,0.18939,-647.97,0.53914,-0.65613,0.52803,-110.21
> view matrix models
> #6,0.0037117,-0.22257,-0.97491,1035.4,0.99433,0.10447,-0.020065,-384.75,0.10631,-0.9693,0.2217,495.92
> ui mousemode right "translate selected models"
> view matrix models
> #6,0.0037117,-0.22257,-0.97491,1037.6,0.99433,0.10447,-0.020065,-385.8,0.10631,-0.9693,0.2217,496.29
> view matrix models
> #6,0.0037117,-0.22257,-0.97491,1039.4,0.99433,0.10447,-0.020065,-388.24,0.10631,-0.9693,0.2217,495.24
> view matrix models
> #6,0.0037117,-0.22257,-0.97491,1039.9,0.99433,0.10447,-0.020065,-389.45,0.10631,-0.9693,0.2217,493.45
> view matrix models
> #6,0.0037117,-0.22257,-0.97491,1035.4,0.99433,0.10447,-0.020065,-388.34,0.10631,-0.9693,0.2217,491.09
> fitmap #6 inMap #1
Fit molecule R14.pdb (#6) to map
cryosparc_P104_J132_8mers_6dot8_map_emready_zflip.mrc (#1) using 1150 atoms
average map value = 3.159, steps = 492
shifted from previous position = 6.59
rotated from previous position = 34 degrees
atoms outside contour = 537, contour level = 3.2169
Position of R14.pdb (#6) relative to
cryosparc_P104_J132_8mers_6dot8_map_emready_zflip.mrc (#1) coordinates:
Matrix rotation and translation
-0.51531875 -0.29935961 -0.80301333 1228.22541066
0.80658382 0.14722082 -0.57249329 101.77032426
0.28960165 -0.94271409 0.16559297 423.07800135
Axis -0.23166046 -0.68368846 0.69202855
Axis point 663.35099779 697.58854740 0.00000000
Rotation angle (degrees) 126.95965277
Shift along axis -61.32840248
> select #6/O:375
20 atoms, 21 bonds, 1 residue, 1 model selected
> select add #6/O:374
42 atoms, 45 bonds, 2 residues, 1 model selected
> select add #6/O:407
65 atoms, 70 bonds, 3 residues, 1 model selected
> select add #6/O:409
87 atoms, 94 bonds, 4 residues, 1 model selected
> select add #6/O:408
107 atoms, 115 bonds, 5 residues, 1 model selected
> select add #6/O:372
127 atoms, 136 bonds, 6 residues, 1 model selected
> select add #6/O:373
147 atoms, 157 bonds, 7 residues, 1 model selected
> select add #6/O:371
167 atoms, 178 bonds, 8 residues, 1 model selected
> select add #6/O:370
189 atoms, 202 bonds, 9 residues, 1 model selected
> select add #6/O:369
209 atoms, 223 bonds, 10 residues, 1 model selected
> select add #6/O:368
229 atoms, 244 bonds, 11 residues, 1 model selected
> select add #6/O:367
249 atoms, 265 bonds, 12 residues, 1 model selected
> select add #6/O:366
271 atoms, 289 bonds, 13 residues, 1 model selected
> select add #6/O:365
293 atoms, 313 bonds, 14 residues, 1 model selected
> select add #6/O:364
313 atoms, 334 bonds, 15 residues, 1 model selected
> select add #6/O:410
335 atoms, 358 bonds, 16 residues, 1 model selected
> select add #6/O:411
357 atoms, 382 bonds, 17 residues, 1 model selected
> select add #6/O:412
377 atoms, 403 bonds, 18 residues, 1 model selected
> select add #6/O:413
400 atoms, 428 bonds, 19 residues, 1 model selected
> select add #6/O:414
420 atoms, 449 bonds, 20 residues, 1 model selected
> select add #6/O:415
440 atoms, 470 bonds, 21 residues, 1 model selected
> select add #6/O:416
463 atoms, 495 bonds, 22 residues, 1 model selected
> select add #6/O:417
485 atoms, 519 bonds, 23 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> hide #!5 models
> open /Users/lingxiaobin/Desktop/ROOL:GOLLD/map/R13-coot-3.pdb
Chain information for R13-coot-3.pdb #7
---
Chain | Description
A B C L N O | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H | No description available
I | No description available
J | No description available
K | No description available
M | No description available
> select #7/D:39@P
1 atom, 1 residue, 1 model selected
> select up
20 atoms, 21 bonds, 1 residue, 1 model selected
> select up
258 atoms, 288 bonds, 12 residues, 1 model selected
> select up
11378 atoms, 12726 bonds, 530 residues, 1 model selected
> style sel stick
Changed 11378 atom styles
> cartoon sel
> ui mousemode right "rotate selected models"
> view matrix models
> #7,-0.20489,0.83635,0.50846,-18.609,-0.78967,0.16568,-0.59074,442.65,-0.57831,-0.52255,0.6265,295.02
> view matrix models
> #7,-0.31937,0.90406,-0.28403,165.32,-0.3003,-0.38083,-0.87452,504.89,-0.89879,-0.194,0.39312,351.03
> view matrix models
> #7,-0.39399,0.91846,0.034741,108.33,-0.54574,-0.20336,-0.8129,508.98,-0.73955,-0.33924,0.58137,304.09
> ui mousemode right "translate selected models"
> view matrix models
> #7,-0.39399,0.91846,0.034741,134.4,-0.54574,-0.20336,-0.8129,527.21,-0.73955,-0.33924,0.58137,336.32
> view matrix models
> #7,-0.39399,0.91846,0.034741,125.83,-0.54574,-0.20336,-0.8129,539.31,-0.73955,-0.33924,0.58137,333.11
> fitmap #7 inMap #1
Fit molecule R13-coot-3.pdb (#7) to map
cryosparc_P104_J132_8mers_6dot8_map_emready_zflip.mrc (#1) using 11378 atoms
average map value = 3.746, steps = 116
shifted from previous position = 7.43
rotated from previous position = 8.56 degrees
atoms outside contour = 4040, contour level = 3.2169
Position of R13-coot-3.pdb (#7) relative to
cryosparc_P104_J132_8mers_6dot8_map_emready_zflip.mrc (#1) coordinates:
Matrix rotation and translation
-0.48121319 0.86907071 0.11467327 133.11581819
-0.59977259 -0.23101409 -0.76609746 540.42369676
-0.63930173 -0.43743410 0.63241182 318.89861967
Axis 0.19523222 0.44787532 -0.87252053
Axis point 272.94805547 309.73798753 0.00000000
Rotation angle (degrees) 122.67735803
Shift along axis -10.21465917
> view matrix models
> #7,-0.48121,0.86907,0.11467,131.53,-0.59977,-0.23101,-0.7661,541.07,-0.6393,-0.43743,0.63241,320.41
> fitmap #7 inMap #1
Fit molecule R13-coot-3.pdb (#7) to map
cryosparc_P104_J132_8mers_6dot8_map_emready_zflip.mrc (#1) using 11378 atoms
average map value = 3.746, steps = 56
shifted from previous position = 2.29
rotated from previous position = 0.0114 degrees
atoms outside contour = 4034, contour level = 3.2169
Position of R13-coot-3.pdb (#7) relative to
cryosparc_P104_J132_8mers_6dot8_map_emready_zflip.mrc (#1) coordinates:
Matrix rotation and translation
-0.48126089 0.86903487 0.11474470 133.11332712
-0.59966839 -0.23092140 -0.76620697 540.39748174
-0.63936357 -0.43755422 0.63226618 318.95415348
Axis 0.19523340 0.44797167 -0.87247080
Axis point 272.94393536 309.76323318 0.00000000
Rotation angle (degrees) 122.68078347
Shift along axis -10.20725680
> view matrix models
> #7,-0.48126,0.86903,0.11474,133.07,-0.59967,-0.23092,-0.76621,540.43,-0.63936,-0.43755,0.63227,319.1
> view matrix models
> #7,-0.48126,0.86903,0.11474,130.99,-0.59967,-0.23092,-0.76621,543.84,-0.63936,-0.43755,0.63227,319.28
> fitmap #7 inMap #1
Fit molecule R13-coot-3.pdb (#7) to map
cryosparc_P104_J132_8mers_6dot8_map_emready_zflip.mrc (#1) using 11378 atoms
average map value = 3.746, steps = 72
shifted from previous position = 4.07
rotated from previous position = 0.00292 degrees
atoms outside contour = 4038, contour level = 3.2169
Position of R13-coot-3.pdb (#7) relative to
cryosparc_P104_J132_8mers_6dot8_map_emready_zflip.mrc (#1) coordinates:
Matrix rotation and translation
-0.48128698 0.86902432 0.11471518 133.12613712
-0.59966840 -0.23097019 -0.76619226 540.39476018
-0.63934392 -0.43754942 0.63228937 318.95043481
Axis 0.19523135 0.44795128 -0.87248173
Axis point 272.94125914 309.75360698 0.00000000
Rotation angle (degrees) 122.68254272
Shift along axis -10.21750547
> combine #6 #7
Remapping chain ID 'O' in R13-coot-3.pdb #7 to 'P'
> hide #6 models
> hide #!7 models
> select #1
2 models selected
> select clear
> select #8/I:291
22 atoms, 24 bonds, 1 residue, 1 model selected
> fitmap #8 inMap #1
Fit molecule combination (#8) to map
cryosparc_P104_J132_8mers_6dot8_map_emready_zflip.mrc (#1) using 12043 atoms
average map value = 3.728, steps = 48
shifted from previous position = 0.0313
rotated from previous position = 0.0237 degrees
atoms outside contour = 4306, contour level = 3.2169
Position of combination (#8) relative to
cryosparc_P104_J132_8mers_6dot8_map_emready_zflip.mrc (#1) coordinates:
Matrix rotation and translation
-0.51567092 -0.29931553 -0.80280366 1228.27651472
0.80636970 0.14713165 -0.57281775 102.17531133
0.28957107 -0.94274201 0.16548746 423.19143473
Axis -0.23153453 -0.68371423 0.69204523
Axis point 663.23230199 697.66885411 0.00000000
Rotation angle (degrees) 126.97926091
Shift along axis -61.37953069
> save /Users/lingxiaobin/Desktop/ROOL:GOLLD/map/R15.pdb models #8 relModel #1
> open
> /Users/lingxiaobin/Desktop/ROOL:GOLLD/RealSpaceRefine_20/R15_real_space_refined_020.pdb
Chain information for R15_real_space_refined_020.pdb #9
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H | No description available
I | No description available
J | No description available
K | No description available
L | No description available
M | No description available
N | No description available
O | No description available
P | No description available
> hide #!8 models
> select #9/F:2@N7
1 atom, 1 residue, 1 model selected
> select up
22 atoms, 24 bonds, 1 residue, 1 model selected
> select up
1353 atoms, 1517 bonds, 63 residues, 1 model selected
> select up
12043 atoms, 13472 bonds, 561 residues, 1 model selected
> style sel stick
Changed 12043 atom styles
> cartoon sel
> select clear
> ui mousemode right "translate selected atoms"
> select #9/I:287
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #9/I:286
22 atoms, 24 bonds, 1 residue, 1 model selected
> select #9/I:286
22 atoms, 24 bonds, 1 residue, 1 model selected
> select #9/I:287
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #9/I:288
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #9/I:290
22 atoms, 24 bonds, 1 residue, 1 model selected
> select #9/I:289
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #9/I:291
22 atoms, 24 bonds, 1 residue, 1 model selected
> select #9/I:290
22 atoms, 24 bonds, 1 residue, 1 model selected
> select #9/I:288
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #9/I:289
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #9/I:290
22 atoms, 24 bonds, 1 residue, 1 model selected
> select #9/I:291
22 atoms, 24 bonds, 1 residue, 1 model selected
> select #9/I:290
22 atoms, 24 bonds, 1 residue, 1 model selected
> select #9/I:287
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #9/I:286
22 atoms, 24 bonds, 1 residue, 1 model selected
> select #9/I:285
22 atoms, 24 bonds, 1 residue, 1 model selected
> select #9/I:286
22 atoms, 24 bonds, 1 residue, 1 model selected
> select #9/I:287
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #9/I:285
22 atoms, 24 bonds, 1 residue, 1 model selected
> select #9/I:284
22 atoms, 24 bonds, 1 residue, 1 model selected
> select #9/I:284
22 atoms, 24 bonds, 1 residue, 1 model selected
> select #9/I:283
22 atoms, 24 bonds, 1 residue, 1 model selected
> select #9/I:284
22 atoms, 24 bonds, 1 residue, 1 model selected
> select #9/I:286
22 atoms, 24 bonds, 1 residue, 1 model selected
> select #9/I:285
22 atoms, 24 bonds, 1 residue, 1 model selected
> select #9/I:287
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #9/I:290
22 atoms, 24 bonds, 1 residue, 1 model selected
> select #9/I:291
22 atoms, 24 bonds, 1 residue, 1 model selected
> select #9/I:292
22 atoms, 24 bonds, 1 residue, 1 model selected
> select #9/I:289
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #9/I:287
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #9/I:286
22 atoms, 24 bonds, 1 residue, 1 model selected
> select #9/I:285
22 atoms, 24 bonds, 1 residue, 1 model selected
> select #9/I:284
22 atoms, 24 bonds, 1 residue, 1 model selected
> select #1
2 models selected
> select #9/I:283
22 atoms, 24 bonds, 1 residue, 1 model selected
> select #9/I:282
23 atoms, 25 bonds, 1 residue, 1 model selected
> select #9/I:284
22 atoms, 24 bonds, 1 residue, 1 model selected
> select #9/I:287
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #9/I:218
22 atoms, 24 bonds, 1 residue, 1 model selected
> select #9/I:219
22 atoms, 24 bonds, 1 residue, 1 model selected
> select #9/I:220
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #1
2 models selected
> select #1
2 models selected
> select clear
> select #9/I:217
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #9/I:218
22 atoms, 24 bonds, 1 residue, 1 model selected
> select #9/I:220
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #9/I:219
22 atoms, 24 bonds, 1 residue, 1 model selected
> select #9/I:220
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #9/I:221
22 atoms, 24 bonds, 1 residue, 1 model selected
> select #9/I:222
23 atoms, 25 bonds, 1 residue, 1 model selected
> select #9/I:223
22 atoms, 24 bonds, 1 residue, 1 model selected
> select #9/I:221
22 atoms, 24 bonds, 1 residue, 1 model selected
> select #9/I:220
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #9/I:221
22 atoms, 24 bonds, 1 residue, 1 model selected
> select #9/I:222
23 atoms, 25 bonds, 1 residue, 1 model selected
> select #9/I:223
22 atoms, 24 bonds, 1 residue, 1 model selected
> select #9/I:222
23 atoms, 25 bonds, 1 residue, 1 model selected
> select #9/I:223
22 atoms, 24 bonds, 1 residue, 1 model selected
> select #9/I:222
23 atoms, 25 bonds, 1 residue, 1 model selected
> select #9/I:221
22 atoms, 24 bonds, 1 residue, 1 model selected
> select #9/I:220
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #9/I:219
22 atoms, 24 bonds, 1 residue, 1 model selected
> select clear
> select #9/I:219
22 atoms, 24 bonds, 1 residue, 1 model selected
> select #9/I:220
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #9/I:221
22 atoms, 24 bonds, 1 residue, 1 model selected
> select #9/I:222
23 atoms, 25 bonds, 1 residue, 1 model selected
> select #9/I:223
22 atoms, 24 bonds, 1 residue, 1 model selected
> select #9/I:221
22 atoms, 24 bonds, 1 residue, 1 model selected
> select up
1503 atoms, 1682 bonds, 70 residues, 1 model selected
> hide sel target a
Drag select of 171 atoms, 14 residues, 189 bonds
> select clear
Drag select of 231 atoms, 15 residues, 256 bonds
> select subtract #9/L:239
323 atoms, 253 bonds, 15 residues, 1 model selected
> select add #9/L:239
343 atoms, 274 bonds, 16 residues, 1 model selected
> select subtract #9/L:238
321 atoms, 260 bonds, 15 residues, 1 model selected
> select add #9/L:238
343 atoms, 284 bonds, 16 residues, 1 model selected
> save /Users/lingxiaobin/Desktop/ROOL:GOLLD/map/R16.pdb models #9
> selectedOnly true relModel #9
> open /Users/lingxiaobin/Desktop/ROOL:GOLLD/map/R16.pdb
Chain information for R16.pdb #10
---
Chain | Description
L | No description available
> hide #10 models
> show #10 models
> delete atoms sel
> delete bonds sel
> select clear
> select #10/L:232
20 atoms, 21 bonds, 1 residue, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models #10,1,0,0,-8.841,0,1,0,20.743,0,0,1,-38.53
> ui mousemode right "rotate selected models"
> view matrix models
> #10,-0.27824,0.41871,-0.86445,409.08,0.50369,0.82992,0.23986,-112.84,0.81785,-0.36868,-0.44181,327.5
> view matrix models
> #10,-0.9154,0.067985,-0.39676,470.36,0.057601,0.99761,0.038046,-1.6564,0.3984,0.011974,-0.91713,468.9
> view matrix models
> #10,-0.96712,-0.25378,0.016384,427.17,-0.25107,0.96309,0.097106,48.312,-0.040423,0.0898,-0.99514,560.68
> view matrix models
> #10,-0.51314,-0.49228,0.7031,182.54,-0.35094,0.86791,0.35154,11.358,-0.78328,-0.066356,-0.61812,625.09
> view matrix models
> #10,-0.68814,-0.34223,0.6398,201.89,-0.34467,0.93012,0.12681,64.969,-0.63849,-0.13325,-0.75801,654.75
> view matrix models
> #10,-0.54443,-0.53344,0.64734,215,-0.44663,0.83759,0.31458,48.168,-0.71001,-0.11785,-0.69426,645.63
> ui mousemode right "translate selected models"
> view matrix models
> #10,-0.54443,-0.53344,0.64734,213.85,-0.44663,0.83759,0.31458,49.676,-0.71001,-0.11785,-0.69426,639.53
> view matrix models
> #10,-0.54443,-0.53344,0.64734,217.33,-0.44663,0.83759,0.31458,47.816,-0.71001,-0.11785,-0.69426,638.18
> ui mousemode right "rotate selected models"
> view matrix models
> #10,-0.49602,0.092382,0.86338,0.017901,-0.43493,0.83416,-0.33913,246.66,-0.75153,-0.54373,-0.37358,644.84
> view matrix models
> #10,0.065235,0.16175,0.98467,-162.3,-0.51016,0.85347,-0.1064,185.82,-0.8576,-0.4954,0.1382,498.08
> view matrix models
> #10,0.079161,0.16672,0.98282,-165.58,-0.50405,0.85729,-0.10483,183.28,-0.86004,-0.48709,0.1519,492.48
> fitmap #10 inMap #1
Fit molecule R16.pdb (#10) to map
cryosparc_P104_J132_8mers_6dot8_map_emready_zflip.mrc (#1) using 343 atoms
average map value = 5.083, steps = 240
shifted from previous position = 7.56
rotated from previous position = 83.8 degrees
atoms outside contour = 39, contour level = 3.2169
Position of R16.pdb (#10) relative to
cryosparc_P104_J132_8mers_6dot8_map_emready_zflip.mrc (#1) coordinates:
Matrix rotation and translation
-0.97593527 0.07845376 0.20345850 302.69581693
-0.01340369 0.90969021 -0.41507115 175.68009013
-0.21764810 -0.40780967 -0.88674719 663.33902685
Axis 0.01684525 0.97688696 -0.21309176
Axis point 187.27781935 0.00000000 333.96878899
Rotation angle (degrees) 167.55308557
Shift along axis 35.36649348
> hide #10 models
> select #9/B:240
22 atoms, 24 bonds, 1 residue, 1 model selected
> select add #9/B:241
44 atoms, 48 bonds, 2 residues, 1 model selected
> select add #9/B:242
64 atoms, 69 bonds, 3 residues, 1 model selected
> select add #9/B:243
84 atoms, 90 bonds, 4 residues, 1 model selected
> select add #9/B:244
104 atoms, 111 bonds, 5 residues, 1 model selected
> select add #9/B:245
126 atoms, 135 bonds, 6 residues, 1 model selected
> select add #9/B:246
148 atoms, 159 bonds, 7 residues, 1 model selected
> select add #9/B:247
171 atoms, 184 bonds, 8 residues, 1 model selected
> select add #9/B:248
191 atoms, 205 bonds, 9 residues, 1 model selected
> select add #9/B:249
211 atoms, 226 bonds, 10 residues, 1 model selected
> select add #9/B:250
233 atoms, 250 bonds, 11 residues, 1 model selected
> select subtract #9/B:250
211 atoms, 226 bonds, 10 residues, 1 model selected
> select add #9/B:250
233 atoms, 250 bonds, 11 residues, 1 model selected
> select add #9/B:251
256 atoms, 275 bonds, 12 residues, 1 model selected
> select add #9/B:252
279 atoms, 300 bonds, 13 residues, 1 model selected
> select add #9/B:281
301 atoms, 324 bonds, 14 residues, 1 model selected
> select add #9/B:280
321 atoms, 345 bonds, 15 residues, 1 model selected
> select add #9/B:279
341 atoms, 366 bonds, 16 residues, 1 model selected
> select add #9/B:278
361 atoms, 387 bonds, 17 residues, 1 model selected
> show #10 models
> delete atoms sel
> delete bonds sel
Drag select of 394 atoms, 25 residues, 436 bonds
> delete atoms sel
> delete bonds sel
> show #16 models
> hide #16 models
> show #16 models
> hide #16 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!9 models
> hide #10 models
> select #8/C:277
20 atoms, 21 bonds, 1 residue, 1 model selected
> select add #8/C:276
42 atoms, 45 bonds, 2 residues, 1 model selected
> select add #8/C:275
65 atoms, 70 bonds, 3 residues, 1 model selected
> select add #8/C:274
87 atoms, 94 bonds, 4 residues, 1 model selected
> select add #8/C:273
107 atoms, 115 bonds, 5 residues, 1 model selected
> select add #8/C:272
130 atoms, 140 bonds, 6 residues, 1 model selected
> select add #8/C:271
153 atoms, 165 bonds, 7 residues, 1 model selected
> select add #8/C:270
173 atoms, 186 bonds, 8 residues, 1 model selected
> select add #8/C:269
193 atoms, 207 bonds, 9 residues, 1 model selected
> select add #8/C:268
213 atoms, 228 bonds, 10 residues, 1 model selected
> select add #8/C:253
233 atoms, 249 bonds, 11 residues, 1 model selected
> select add #8/C:254
256 atoms, 274 bonds, 12 residues, 1 model selected
> select add #8/C:255
279 atoms, 299 bonds, 13 residues, 1 model selected
> select add #8/C:256
301 atoms, 323 bonds, 14 residues, 1 model selected
> select add #8/C:257
323 atoms, 347 bonds, 15 residues, 1 model selected
> select add #8/C:267
346 atoms, 372 bonds, 16 residues, 1 model selected
> select add #8/C:266
368 atoms, 396 bonds, 17 residues, 1 model selected
> select add #8/C:258
391 atoms, 421 bonds, 18 residues, 1 model selected
> select add #8/C:259
411 atoms, 442 bonds, 19 residues, 1 model selected
> select add #8/C:260
434 atoms, 467 bonds, 20 residues, 1 model selected
> select add #8/C:261
454 atoms, 488 bonds, 21 residues, 1 model selected
> select add #8/C:262
477 atoms, 513 bonds, 22 residues, 1 model selected
> select add #8/C:263
499 atoms, 537 bonds, 23 residues, 1 model selected
> select add #8/C:264
522 atoms, 562 bonds, 24 residues, 1 model selected
> select add #8/C:265
544 atoms, 586 bonds, 25 residues, 1 model selected
> save /Users/lingxiaobin/Desktop/ROOL:GOLLD/map/R17.pdb models #8
> selectedOnly true relModel #8
> open /Users/lingxiaobin/Desktop/ROOL:GOLLD/map/R17.pdb
Chain information for R17.pdb #11
---
Chain | Description
C | No description available
> hide #11 models
> show #11 models
> hide #11 models
> show #11 models
> hide #!8 models
> show #!8 models
> close #11
> save /Users/lingxiaobin/Desktop/ROOL:GOLLD/map/R17.pdb models #8
> selectedOnly true relModel #8
> open /Users/lingxiaobin/Desktop/ROOL:GOLLD/map/R17.pdb
Chain information for R17.pdb #11
---
Chain | Description
C | No description available
> hide #!8 models
> show #!7 models
> hide #!7 models
> show #!5 models
> show #!4 models
> hide #!5 models
> show #!8 models
> hide #!4 models
> show #!9 models
> hide #!8 models
> show #10 models
Drag select of 25 residues, 75 shapes
> ui mousemode right "translate selected models"
> view matrix models #11,1,0,0,-403.92,0,1,0,-263.74,0,0,1,-381.08
> view matrix models #11,1,0,0,-429.44,0,1,0,-222.83,0,0,1,-414.62
> ui mousemode right "rotate selected models"
> view matrix models
> #11,-0.17732,0.13478,0.97488,-463.8,-0.94744,-0.29141,-0.13205,1061.4,0.26629,-0.94706,0.17937,452.51
> view matrix models
> #11,-0.1917,-0.63726,0.74643,67.137,-0.58645,-0.53545,-0.60776,1293.7,0.78697,-0.55425,-0.27107,272.86
> view matrix models
> #11,0.20461,0.13287,0.96978,-698.62,-0.43622,-0.87454,0.21186,760.61,0.87627,-0.46639,-0.12097,67.423
> view matrix models
> #11,-0.12497,0.42174,0.89806,-573.77,-0.72322,-0.65838,0.20854,842.69,0.67922,-0.62344,0.38729,-106.08
> view matrix models
> #11,-0.5418,0.4372,0.71785,-189.27,-0.78257,-0.574,-0.24105,1167.5,0.30666,-0.69237,0.65313,-34.403
> view matrix models
> #11,-0.36306,0.15918,0.91807,-318.18,-0.29305,-0.95481,0.049658,825.92,0.88449,-0.25101,0.39329,-410.8
> ui mousemode right "translate selected models"
> view matrix models
> #11,-0.36306,0.15918,0.91807,-316.19,-0.29305,-0.95481,0.049658,814.62,0.88449,-0.25101,0.39329,-424.69
> view matrix models
> #11,-0.36306,0.15918,0.91807,-315.49,-0.29305,-0.95481,0.049658,813.4,0.88449,-0.25101,0.39329,-420.82
> ui mousemode right "rotate selected models"
> view matrix models
> #11,-0.96988,-0.2181,0.10844,826.66,0.042186,-0.58889,-0.80711,1057.3,0.23989,-0.77823,0.58036,89.855
> view matrix models
> #11,-0.91547,-0.35452,0.19036,796.01,0.070835,-0.60766,-0.79103,1036.3,0.39611,-0.71068,0.5814,-39.764
> fitmap #11 inMap #1
Fit molecule R17.pdb (#11) to map
cryosparc_P104_J132_8mers_6dot8_map_emready_zflip.mrc (#1) using 544 atoms
average map value = 4.401, steps = 72
shifted from previous position = 2.08
rotated from previous position = 8.78 degrees
atoms outside contour = 117, contour level = 3.2169
Position of R17.pdb (#11) relative to
cryosparc_P104_J132_8mers_6dot8_map_emready_zflip.mrc (#1) coordinates:
Matrix rotation and translation
-0.91503739 -0.30392262 0.26521239 717.19325795
-0.06131728 -0.54504771 -0.83615979 1121.55897807
0.39868128 -0.78137957 0.48010332 63.46628582
Axis 0.19407536 -0.47285364 0.85950229
Axis point 311.72581706 610.52157984 0.00000000
Rotation angle (degrees) 171.88668547
Shift along axis -336.59428079
> select clear
> hide #10 models
> show #10 models
> select #10/L:228
20 atoms, 21 bonds, 1 residue, 1 model selected
> view matrix models
> #10,0.79438,-0.54975,-0.25833,240.6,0.14442,0.58403,-0.79878,335.96,0.59001,0.59723,0.54333,-160.4
> view matrix models
> #10,-0.119,0.02072,-0.99268,515.29,-0.96051,0.25087,0.12038,345.83,0.25152,0.9678,-0.0099513,-8.5022
> view matrix models
> #10,-0.78596,-0.18515,0.58991,208.8,0.57182,0.14518,0.80743,-138.81,-0.23514,0.97193,-0.0082362,85.159
> view matrix models
> #10,-0.87198,-0.38663,-0.30028,543.77,-0.28076,-0.10754,0.95374,39.636,-0.40104,0.91594,-0.014777,132.15
> ui mousemode right "translate selected models"
> view matrix models
> #10,-0.87198,-0.38663,-0.30028,536.29,-0.28076,-0.10754,0.95374,46.002,-0.40104,0.91594,-0.014777,164.91
> ui mousemode right "rotate selected models"
> view matrix models
> #10,-0.97085,-0.052813,0.2338,316.75,0.20232,-0.70358,0.6812,170.63,0.12852,0.70865,0.69376,-108.17
> view matrix models
> #10,-0.8923,0.41584,-0.17571,320.9,-0.34215,-0.36906,0.86413,145.31,0.29449,0.83119,0.4716,-100.28
> view matrix models
> #10,-0.81201,-0.010097,-0.58356,527.03,-0.52018,-0.4409,0.73145,237.09,-0.26467,0.8975,0.35276,30.372
> fitmap #10 inMap #1
Fit molecule R16.pdb (#10) to map
cryosparc_P104_J132_8mers_6dot8_map_emready_zflip.mrc (#1) using 343 atoms
average map value = 4.66, steps = 104
shifted from previous position = 6.45
rotated from previous position = 6.55 degrees
atoms outside contour = 53, contour level = 3.2169
Position of R16.pdb (#10) relative to
cryosparc_P104_J132_8mers_6dot8_map_emready_zflip.mrc (#1) coordinates:
Matrix rotation and translation
-0.80868009 -0.08242326 -0.58244563 537.37624213
-0.46500203 -0.51686934 0.71876226 245.29622120
-0.36029102 0.85208713 0.37965497 47.60027346
Axis 0.28854770 -0.48079703 -0.82799423
Axis point 294.24960839 70.78241866 0.00000000
Rotation angle (degrees) 166.64243116
Shift along axis -2.29176567
> select clear
> select #9/I:223
22 atoms, 24 bonds, 1 residue, 1 model selected
> select add #9/I:222
45 atoms, 49 bonds, 2 residues, 1 model selected
> select add #9/I:220
65 atoms, 70 bonds, 3 residues, 1 model selected
> select add #9/I:221
87 atoms, 94 bonds, 4 residues, 1 model selected
> view matrix models
> #9,0.99823,0.033014,-0.049505,4.1855,-0.032354,0.99938,0.014083,4.499,0.049939,-0.012456,0.99867,-8.5345
> fitmap #9 inMap #1
Fit molecule R15_real_space_refined_020.pdb (#9) to map
cryosparc_P104_J132_8mers_6dot8_map_emready_zflip.mrc (#1) using 10795 atoms
average map value = 4.718, steps = 72
shifted from previous position = 0.681
rotated from previous position = 3.6 degrees
atoms outside contour = 1730, contour level = 3.2169
Position of R15_real_space_refined_020.pdb (#9) relative to
cryosparc_P104_J132_8mers_6dot8_map_emready_zflip.mrc (#1) coordinates:
Matrix rotation and translation
0.99999392 0.00128168 0.00324298 -0.97965491
-0.00128490 0.99999868 0.00099188 0.09918452
-0.00324170 -0.00099604 0.99999425 0.95743182
Axis -0.27412273 0.89420323 -0.35391711
Axis point 296.82177089 0.00000000 301.08753510
Rotation angle (degrees) 0.20775223
Shift along axis 0.01838529
> ui mousemode right "translate selected atoms"
> select subtract #9/I:220
67 atoms, 73 bonds, 3 residues, 1 model selected
> select subtract #9/I:221
45 atoms, 49 bonds, 2 residues, 1 model selected
> select subtract #9/I:222
22 atoms, 24 bonds, 1 residue, 1 model selected
> select add #9/I:222
45 atoms, 49 bonds, 2 residues, 1 model selected
> select #9/I:222
23 atoms, 25 bonds, 1 residue, 1 model selected
> select clear
> select #9/I:221
22 atoms, 24 bonds, 1 residue, 1 model selected
> select #9/I:220
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #9/I:219
22 atoms, 24 bonds, 1 residue, 1 model selected
> select #9/I:220
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #9/I:221
22 atoms, 24 bonds, 1 residue, 1 model selected
> select #10/L:224
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #1
3 models selected
> select #9/I:223
22 atoms, 24 bonds, 1 residue, 1 model selected
> select #9/I:282
23 atoms, 25 bonds, 1 residue, 1 model selected
> select add #9/I:283
45 atoms, 49 bonds, 2 residues, 1 model selected
> select add #9/I:284
67 atoms, 73 bonds, 3 residues, 1 model selected
> select add #9/I:285
89 atoms, 97 bonds, 4 residues, 1 model selected
> select add #9/I:286
111 atoms, 121 bonds, 5 residues, 1 model selected
> select #9/I:219
22 atoms, 24 bonds, 1 residue, 1 model selected
> select #9/I:220
20 atoms, 21 bonds, 1 residue, 1 model selected
> select clear
> select #9/I:221
22 atoms, 24 bonds, 1 residue, 1 model selected
> select #9/I:222
23 atoms, 25 bonds, 1 residue, 1 model selected
> select clear
> select #9/I:223
22 atoms, 24 bonds, 1 residue, 1 model selected
> select clear
> select #9/I:222
23 atoms, 25 bonds, 1 residue, 1 model selected
> select #9/I:221
22 atoms, 24 bonds, 1 residue, 1 model selected
> select clear
> select #9/I:220
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #9/I:219
22 atoms, 24 bonds, 1 residue, 1 model selected
> select clear
> select #9/I:218
22 atoms, 24 bonds, 1 residue, 1 model selected
> select #9/I:217
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #9/I:220
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #9/I:221
22 atoms, 24 bonds, 1 residue, 1 model selected
> select #9/I:222
23 atoms, 25 bonds, 1 residue, 1 model selected
> select clear
> select #9/I:223
22 atoms, 24 bonds, 1 residue, 1 model selected
Drag select of 2 residues
> select clear
> select #9/I:282
23 atoms, 25 bonds, 1 residue, 1 model selected
> select add #9/I:283
45 atoms, 49 bonds, 2 residues, 1 model selected
> select add #9/I:284
67 atoms, 73 bonds, 3 residues, 1 model selected
> select add #9/I:285
89 atoms, 97 bonds, 4 residues, 1 model selected
> select add #9/I:286
111 atoms, 121 bonds, 5 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> open
> /Users/lingxiaobin/Downloads/fold_2024_07_25_17_01/fold_2024_07_25_17_01_model_0.cif
Chain information for fold_2024_07_25_17_01_model_0.cif #12
---
Chain | Description
A | .
Drag select of 24 residues, 72 shapes
> select clear
> select #12/A:11
23 atoms, 25 bonds, 1 residue, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models #12,1,0,0,7.5136,0,1,0,-4.0247,0,0,1,-40.988
> fitmap #12 inMap #1
Fit molecule fold_2024_07_25_17_01_model_0.cif (#12) to map
cryosparc_P104_J132_8mers_6dot8_map_emready_zflip.mrc (#1) using 515 atoms
average map value = 2.233, steps = 204
shifted from previous position = 10.7
rotated from previous position = 25.9 degrees
atoms outside contour = 327, contour level = 3.2169
Position of fold_2024_07_25_17_01_model_0.cif (#12) relative to
cryosparc_P104_J132_8mers_6dot8_map_emready_zflip.mrc (#1) coordinates:
Matrix rotation and translation
0.90998473 0.28243019 -0.30358027 43.37191687
-0.32366630 0.94145785 -0.09432521 105.91167205
0.25916774 0.18409321 0.94812540 -111.81552989
Axis 0.31904159 -0.64485683 -0.69453015
Axis point 374.87094210 -7.88305823 0.00000000
Rotation angle (degrees) 25.87031208
Shift along axis 23.19883662
> view matrix models
> #12,0.90998,0.28243,-0.30358,47.604,-0.32367,0.94146,-0.094325,99.179,0.25917,0.18409,0.94813,-119.71
> ui mousemode right "rotate selected models"
> view matrix models
> #12,0.62958,0.57379,0.52383,-249.48,-0.7365,0.65543,0.16725,166.17,-0.24737,-0.4911,0.83524,191.22
> view matrix models
> #12,0.93206,0.16303,-0.32356,82.699,-0.13235,0.98453,0.11484,-14.332,0.33728,-0.064214,0.93921,-63.05
> view matrix models
> #12,0.57198,-0.64028,-0.51272,427.11,0.70449,0.70362,-0.092776,-19.766,0.42016,-0.30814,0.85353,16.399
> view matrix models
> #12,-0.039102,-0.91177,-0.40885,576.49,0.91136,0.13524,-0.38876,194.09,0.40975,-0.38781,0.82566,48.996
> view matrix models
> #12,-0.21688,-0.94344,-0.25076,565.69,0.9125,-0.10465,-0.39546,261.47,0.34685,-0.31459,0.88359,21.505
> ui mousemode right "translate selected models"
> view matrix models
> #12,-0.21688,-0.94344,-0.25076,569.17,0.9125,-0.10465,-0.39546,253.63,0.34685,-0.31459,0.88359,19.043
> fitmap #12 inMap #1
Fit molecule fold_2024_07_25_17_01_model_0.cif (#12) to map
cryosparc_P104_J132_8mers_6dot8_map_emready_zflip.mrc (#1) using 515 atoms
average map value = 4.22, steps = 212
shifted from previous position = 11.6
rotated from previous position = 33.1 degrees
atoms outside contour = 135, contour level = 3.2169
Position of fold_2024_07_25_17_01_model_0.cif (#12) relative to
cryosparc_P104_J132_8mers_6dot8_map_emready_zflip.mrc (#1) coordinates:
Matrix rotation and translation
-0.03803875 -0.77789953 -0.62723630 608.12177743
0.99776040 -0.06412757 0.01902193 83.89783465
-0.05502029 -0.62510797 0.77859668 205.26448093
Axis -0.32636446 -0.28992749 0.89968233
Axis point 306.90390707 356.21869543 0.00000000
Rotation angle (degrees) 99.31050867
Shift along axis -38.12079565
> ui mousemode right "rotate selected models"
> view matrix models
> #12,-0.80312,-0.028016,-0.59515,529.66,-0.57382,-0.23249,0.78529,162.14,-0.16037,0.9722,0.17064,-14.826
> view matrix models
> #12,0.30121,-0.89982,-0.31558,480.08,-0.60986,-0.4362,0.66167,264.1,-0.73304,-0.0068395,-0.68015,629.44
> view matrix models
> #12,0.59293,-0.80493,-0.022878,307.52,-0.52871,-0.41058,0.74289,216.37,-0.60737,-0.42839,-0.66902,718.39
> view matrix models
> #12,0.60038,-0.79946,-0.020343,303.88,-0.52459,-0.4129,0.74453,215.74,-0.60362,-0.43632,-0.66728,719.32
> ui mousemode right "translate selected models"
> view matrix models
> #12,0.60038,-0.79946,-0.020343,304.66,-0.52459,-0.4129,0.74453,210.92,-0.60362,-0.43632,-0.66728,711.67
> view matrix models
> #12,0.60038,-0.79946,-0.020343,304.67,-0.52459,-0.4129,0.74453,210.84,-0.60362,-0.43632,-0.66728,711.7
> view matrix models
> #12,0.60038,-0.79946,-0.020343,303.92,-0.52459,-0.4129,0.74453,210.92,-0.60362,-0.43632,-0.66728,710.33
> fitmap #12 inMap #1
Fit molecule fold_2024_07_25_17_01_model_0.cif (#12) to map
cryosparc_P104_J132_8mers_6dot8_map_emready_zflip.mrc (#1) using 515 atoms
average map value = 4.212, steps = 608
shifted from previous position = 7.82
rotated from previous position = 75.8 degrees
atoms outside contour = 133, contour level = 3.2169
Position of fold_2024_07_25_17_01_model_0.cif (#12) relative to
cryosparc_P104_J132_8mers_6dot8_map_emready_zflip.mrc (#1) coordinates:
Matrix rotation and translation
0.90397762 -0.38220667 -0.19168336 191.18917880
-0.42755140 -0.80283465 -0.41551934 684.02055907
0.00492422 0.45757467 -0.88915756 432.74909801
Axis 0.97432130 -0.21940244 -0.05060204
Axis point 0.00000000 310.91356393 304.75974623
Rotation angle (degrees) 153.38120315
Shift along axis 14.30592447
> view matrix models
> #12,0.90398,-0.38221,-0.19168,189.8,-0.42755,-0.80283,-0.41552,685.92,0.0049242,0.45757,-0.88916,438.32
> view matrix models
> #12,0.90398,-0.38221,-0.19168,189.38,-0.42755,-0.80283,-0.41552,685.07,0.0049242,0.45757,-0.88916,437.44
> ui mousemode right "rotate selected models"
> view matrix models
> #12,0.90066,-0.31278,0.30165,11.471,-0.22782,-0.93102,-0.28514,642.25,0.37002,0.18809,-0.90978,452.51
> view matrix models
> #12,0.81541,-0.51487,0.2646,93.76,-0.42958,-0.84458,-0.31959,665.79,0.38803,0.14693,-0.90986,460.55
> ui mousemode right "translate selected models"
> view matrix models
> #12,0.81541,-0.51487,0.2646,93.966,-0.42958,-0.84458,-0.31959,666.46,0.38803,0.14693,-0.90986,455.71
> fitmap #12 inMap #1
Fit molecule fold_2024_07_25_17_01_model_0.cif (#12) to map
cryosparc_P104_J132_8mers_6dot8_map_emready_zflip.mrc (#1) using 515 atoms
average map value = 4.212, steps = 284
shifted from previous position = 2.63
rotated from previous position = 28.7 degrees
atoms outside contour = 132, contour level = 3.2169
Position of fold_2024_07_25_17_01_model_0.cif (#12) relative to
cryosparc_P104_J132_8mers_6dot8_map_emready_zflip.mrc (#1) coordinates:
Matrix rotation and translation
0.90545048 -0.37894547 -0.19120605 189.87514167
-0.42442710 -0.80345731 -0.41751405 684.27329384
0.00458916 0.45919133 -0.88832554 432.12172669
Axis 0.97470891 -0.21768241 -0.05056584
Axis point 0.00000000 310.59358823 304.74887743
Rotation angle (degrees) 153.27384504
Shift along axis 14.26813495
> open
> /Users/lingxiaobin/Downloads/fold_2024_07_25_17_09/fold_2024_07_25_17_09_model_0.cif
Chain information for fold_2024_07_25_17_09_model_0.cif #13
---
Chain | Description
A | .
Drag select of 35 residues, 105 shapes
> view matrix models #13,1,0,0,-113.49,0,1,0,198.03,0,0,1,131.07
> view matrix models #13,1,0,0,161.28,0,1,0,373.42,0,0,1,127.77
> view matrix models #13,1,0,0,135.5,0,1,0,226.73,0,0,1,254.5
> view matrix models #13,1,0,0,244.98,0,1,0,303.37,0,0,1,239.11
> view matrix models #13,1,0,0,244.79,0,1,0,293.01,0,0,1,270.46
> ui mousemode right "rotate selected models"
> view matrix models
> #13,0.96994,0.14254,-0.19725,244.96,0.077175,0.58853,0.80478,294.6,0.2308,-0.79581,0.55984,266.32
> view matrix models
> #13,-0.37423,-0.24711,-0.89381,245.57,0.069492,0.95366,-0.29275,291.75,0.92473,-0.17167,-0.33971,262.66
> view matrix models
> #13,-0.55277,-0.814,0.17843,248.47,-0.75053,0.39325,-0.5311,291.97,0.36215,-0.4275,-0.82831,262.01
> view matrix models
> #13,-0.014737,-0.98965,-0.14275,245.61,-0.71755,0.10989,-0.68778,290.64,0.69635,0.092296,-0.71175,262.78
> view matrix models
> #13,0.1022,-0.88143,-0.46112,244.3,-0.67942,0.27673,-0.67956,290.8,0.72659,0.38275,-0.57058,263.77
> ui mousemode right "translate selected models"
> view matrix models
> #13,0.1022,-0.88143,-0.46112,241.12,-0.67942,0.27673,-0.67956,290.31,0.72659,0.38275,-0.57058,285.45
> view matrix models
> #13,0.1022,-0.88143,-0.46112,236.08,-0.67942,0.27673,-0.67956,296.95,0.72659,0.38275,-0.57058,270.41
> view matrix models
> #13,0.1022,-0.88143,-0.46112,208.94,-0.67942,0.27673,-0.67956,281.36,0.72659,0.38275,-0.57058,270.6
> view matrix models
> #13,0.1022,-0.88143,-0.46112,182.4,-0.67942,0.27673,-0.67956,257.68,0.72659,0.38275,-0.57058,248.77
> view matrix models
> #13,0.1022,-0.88143,-0.46112,171.43,-0.67942,0.27673,-0.67956,247.96,0.72659,0.38275,-0.57058,275.62
> ui mousemode right "rotate selected models"
> view matrix models
> #13,-0.023879,-0.83834,-0.54463,171.53,-0.99547,0.070118,-0.064287,250.24,0.092082,0.54062,-0.83621,276.57
> view matrix models
> #13,-0.2218,-0.50285,-0.83543,172.05,-0.92649,0.37581,0.019781,250.95,0.30401,0.7784,-0.54924,277.3
> ui mousemode right "translate selected models"
> view matrix models
> #13,-0.2218,-0.50285,-0.83543,171.56,-0.92649,0.37581,0.019781,253.81,0.30401,0.7784,-0.54924,277.87
> ui mousemode right "rotate selected models"
> view matrix models
> #13,0.079305,-0.97407,-0.21189,171.44,-0.99515,-0.06496,-0.073831,252.8,0.058152,0.21672,-0.9745,276.16
> fitmap #13 inMap #1
Fit molecule fold_2024_07_25_17_09_model_0.cif (#13) to map
cryosparc_P104_J132_8mers_6dot8_map_emready_zflip.mrc (#1) using 756 atoms
average map value = 2.88, steps = 168
shifted from previous position = 18.7
rotated from previous position = 23.3 degrees
atoms outside contour = 413, contour level = 3.2169
Position of fold_2024_07_25_17_09_model_0.cif (#13) relative to
cryosparc_P104_J132_8mers_6dot8_map_emready_zflip.mrc (#1) coordinates:
Matrix rotation and translation
-0.01030827 -0.99919963 0.03865009 188.38153792
-0.93099516 -0.00451408 -0.36500359 250.98922731
0.36488593 -0.03974561 -0.93020349 267.39460428
Axis 0.69843146 -0.70053121 0.14645650
Axis point 196.71699661 0.00000000 176.10562897
Rotation angle (degrees) 166.53514368
Shift along axis -5.09251618
> view matrix models
> #13,0.098521,-0.99492,-0.020559,187.9,-0.91181,-0.081977,-0.40235,250.65,0.39862,0.058386,-0.91526,267.56
> view matrix models
> #13,0.82887,-0.47286,-0.29895,186.31,-0.55207,-0.60498,-0.57378,248.06,0.09046,0.64063,-0.7625,269.88
> view matrix models
> #13,0.78439,-0.48733,-0.38372,186.15,-0.62017,-0.60514,-0.4992,248.54,0.011072,0.62954,-0.77689,270.04
> ui mousemode right "translate selected models"
> view matrix models
> #13,0.78439,-0.48733,-0.38372,183.78,-0.62017,-0.60514,-0.4992,253.39,0.011072,0.62954,-0.77689,276.66
> fitmap #13 inMap #1
Fit molecule fold_2024_07_25_17_09_model_0.cif (#13) to map
cryosparc_P104_J132_8mers_6dot8_map_emready_zflip.mrc (#1) using 756 atoms
average map value = 2.877, steps = 180
shifted from previous position = 9.85
rotated from previous position = 38 degrees
atoms outside contour = 395, contour level = 3.2169
Position of fold_2024_07_25_17_09_model_0.cif (#13) relative to
cryosparc_P104_J132_8mers_6dot8_map_emready_zflip.mrc (#1) coordinates:
Matrix rotation and translation
0.56167713 -0.82368662 -0.07784056 184.93179875
-0.82733135 -0.55990253 -0.04507766 256.54840213
-0.00645326 0.08971902 -0.99594621 266.82454863
Axis 0.88346972 -0.46787885 -0.02388786
Axis point 0.00000000 171.45581661 141.83279582
Rotation angle (degrees) 175.62475557
Shift along axis 36.97420623
> view matrix models
> #13,0.56168,-0.82369,-0.077841,183.44,-0.82733,-0.5599,-0.045078,256.86,-0.0064533,0.089719,-0.99595,273.25
> view matrix models
> #13,0.56168,-0.82369,-0.077841,182.97,-0.82733,-0.5599,-0.045078,256.62,-0.0064533,0.089719,-0.99595,274.38
> ui mousemode right "rotate selected models"
> view matrix models
> #13,0.89689,0.044281,-0.44003,182.9,-0.23284,-0.79864,-0.55494,252.88,-0.376,0.60018,-0.70598,277.47
> view matrix models
> #13,0.96917,0.2063,-0.13474,183.91,0.063394,-0.73718,-0.67271,251.71,-0.23811,0.64343,-0.72753,277.06
> view matrix models
> #13,0.99219,0.013343,0.12406,184.15,0.089723,-0.76722,-0.63507,251.65,0.086704,0.64124,-0.76242,276.06
> fitmap #13 inMap #1
Fit molecule fold_2024_07_25_17_09_model_0.cif (#13) to map
cryosparc_P104_J132_8mers_6dot8_map_emready_zflip.mrc (#1) using 756 atoms
average map value = 3.619, steps = 176
shifted from previous position = 9.94
rotated from previous position = 70.1 degrees
atoms outside contour = 267, contour level = 3.2169
Position of fold_2024_07_25_17_09_model_0.cif (#13) relative to
cryosparc_P104_J132_8mers_6dot8_map_emready_zflip.mrc (#1) coordinates:
Matrix rotation and translation
0.37387590 0.78774355 0.48956808 189.81446087
0.75875227 0.04378830 -0.64990582 248.24521258
-0.53339647 0.61444501 -0.58133082 268.46591042
Axis 0.77728901 0.62889119 -0.01782306
Axis point 0.00000000 -43.21840887 156.34770341
Rotation angle (degrees) 125.57959159
Shift along axis 298.87503790
> ui mousemode right "translate selected models"
> ui mousemode right "rotate selected models"
> view matrix models
> #13,0.71198,-0.68439,-0.15714,183.8,-0.69908,-0.7119,-0.066975,252.4,-0.066029,0.15754,-0.9853,264.97
> view matrix models
> #13,0.0073824,-0.98767,-0.15639,185.19,-0.95902,-0.051292,0.27865,255.42,-0.28324,0.14793,-0.94757,265.69
> view matrix models
> #13,-0.33104,-0.87958,0.34169,188.85,-0.73133,0.01033,-0.68195,252.55,0.5963,-0.47564,-0.64668,263.05
> ui mousemode right "translate selected models"
> view matrix models
> #13,-0.33104,-0.87958,0.34169,187.4,-0.73133,0.01033,-0.68195,250.06,0.5963,-0.47564,-0.64668,268.81
> view matrix models
> #13,-0.33104,-0.87958,0.34169,185.17,-0.73133,0.01033,-0.68195,251.23,0.5963,-0.47564,-0.64668,270.23
> view matrix models
> #13,-0.33104,-0.87958,0.34169,185.53,-0.73133,0.01033,-0.68195,251.95,0.5963,-0.47564,-0.64668,270.15
> fitmap #13 inMap #1
Fit molecule fold_2024_07_25_17_09_model_0.cif (#13) to map
cryosparc_P104_J132_8mers_6dot8_map_emready_zflip.mrc (#1) using 756 atoms
average map value = 2.962, steps = 96
shifted from previous position = 10.2
rotated from previous position = 8.92 degrees
atoms outside contour = 385, contour level = 3.2169
Position of fold_2024_07_25_17_09_model_0.cif (#13) relative to
cryosparc_P104_J132_8mers_6dot8_map_emready_zflip.mrc (#1) coordinates:
Matrix rotation and translation
-0.26116929 -0.94056935 0.21707119 188.12179132
-0.72608812 0.04323850 -0.68624083 256.45066996
0.63607126 -0.33683784 -0.69422880 261.39024662
Axis 0.59603417 -0.71475735 0.36587593
Axis point 174.52654602 0.00000000 214.52297138
Rotation angle (degrees) 162.95596959
Shift along axis 24.46341217
> view matrix models
> #13,-0.26117,-0.94057,0.21707,186.39,-0.72609,0.043238,-0.68624,249.98,0.63607,-0.33684,-0.69423,268.68
> view matrix models
> #13,-0.26117,-0.94057,0.21707,186.35,-0.72609,0.043238,-0.68624,250.15,0.63607,-0.33684,-0.69423,268.69
> view matrix models
> #13,-0.26117,-0.94057,0.21707,186.36,-0.72609,0.043238,-0.68624,249.89,0.63607,-0.33684,-0.69423,269.8
> ui mousemode right "rotate selected models"
> view matrix models
> #13,0.78842,-0.020661,-0.61479,182.96,-0.59167,-0.29889,-0.74873,248.69,-0.16828,0.95406,-0.24787,276.33
> view matrix models
> #13,0.49584,-0.66928,-0.55336,182.27,-0.86315,-0.44988,-0.2293,250.94,-0.095481,0.59133,-0.80076,273.77
> view matrix models
> #13,0.81259,-0.50308,-0.2943,182.54,-0.5827,-0.71214,-0.39155,249.15,-0.012606,0.48966,-0.87182,273.12
> view matrix models
> #13,0.99425,-0.061789,-0.087486,183.65,-0.09748,-0.86046,-0.5001,247.1,-0.044377,0.50575,-0.86154,273.27
> ui mousemode right "translate selected models"
> view matrix models
> #13,0.99425,-0.061789,-0.087486,186.02,-0.09748,-0.86046,-0.5001,252.32,-0.044377,0.50575,-0.86154,273.89
> view matrix models
> #13,0.99425,-0.061789,-0.087486,183.77,-0.09748,-0.86046,-0.5001,256.42,-0.044377,0.50575,-0.86154,278.12
> select #13/A:15
22 atoms, 24 bonds, 1 residue, 1 model selected
> select add #13/A:14
44 atoms, 48 bonds, 2 residues, 1 model selected
> select add #13/A:13
67 atoms, 73 bonds, 3 residues, 1 model selected
> select add #13/A:12
89 atoms, 97 bonds, 4 residues, 1 model selected
> select add #13/A:11
112 atoms, 122 bonds, 5 residues, 1 model selected
> select add #13/A:10
135 atoms, 147 bonds, 6 residues, 1 model selected
> view matrix models
> #13,0.99425,-0.061789,-0.087486,184.09,-0.09748,-0.86046,-0.5001,255.88,-0.044377,0.50575,-0.86154,277.18
> view matrix models
> #13,0.99425,-0.061789,-0.087486,183.81,-0.09748,-0.86046,-0.5001,254.92,-0.044377,0.50575,-0.86154,276.28
> view matrix models
> #13,0.99425,-0.061789,-0.087486,183.98,-0.09748,-0.86046,-0.5001,254.15,-0.044377,0.50575,-0.86154,276.41
> view matrix models
> #13,0.99425,-0.061789,-0.087486,183.58,-0.09748,-0.86046,-0.5001,254.47,-0.044377,0.50575,-0.86154,276.61
> select add #13/A:9
155 atoms, 168 bonds, 7 residues, 1 model selected
> select add #13/A:8
178 atoms, 193 bonds, 8 residues, 1 model selected
> select add #13/A:7
200 atoms, 217 bonds, 9 residues, 1 model selected
> select add #13/A:6
220 atoms, 238 bonds, 10 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> hide #12 models
> open
> /Users/lingxiaobin/Downloads/fold_2024_07_25_17_20/fold_2024_07_25_17_20_model_0.cif
Chain information for fold_2024_07_25_17_20_model_0.cif #14
---
Chain | Description
A | .
> hide #14 models
> show #14 models
Drag select of 64 residues, 192 shapes
> view matrix models #14,1,0,0,303.43,0,1,0,276.43,0,0,1,333.47
> view matrix models #14,1,0,0,355.11,0,1,0,350.41,0,0,1,213.87
> view matrix models #14,1,0,0,198.08,0,1,0,282.38,0,0,1,313.99
> ui mousemode right "rotate selected models"
> view matrix models
> #14,-0.28824,0.77815,-0.55803,201.09,0.14199,0.61106,0.77875,283.02,0.94697,0.14523,-0.28662,309.36
> view matrix models
> #14,-0.20073,0.79873,-0.56722,200.71,0.14197,0.59661,0.78987,283.06,0.96931,0.07802,-0.23315,309.46
> ui mousemode right "translate selected models"
> view matrix models
> #14,-0.20073,0.79873,-0.56722,209.6,0.14197,0.59661,0.78987,237.28,0.96931,0.07802,-0.23315,303.32
> view matrix models
> #14,-0.20073,0.79873,-0.56722,209.54,0.14197,0.59661,0.78987,237.77,0.96931,0.07802,-0.23315,301.62
> view matrix models
> #14,-0.20073,0.79873,-0.56722,192.16,0.14197,0.59661,0.78987,238.25,0.96931,0.07802,-0.23315,295.49
> view matrix models
> #14,-0.20073,0.79873,-0.56722,191.67,0.14197,0.59661,0.78987,232.17,0.96931,0.07802,-0.23315,296.63
> fitmap #14 inMap #1
Fit molecule fold_2024_07_25_17_20_model_0.cif (#14) to map
cryosparc_P104_J132_8mers_6dot8_map_emready_zflip.mrc (#1) using 1380 atoms
average map value = 2.695, steps = 332
shifted from previous position = 9.39
rotated from previous position = 15.2 degrees
atoms outside contour = 765, contour level = 3.2169
Position of fold_2024_07_25_17_20_model_0.cif (#14) relative to
cryosparc_P104_J132_8mers_6dot8_map_emready_zflip.mrc (#1) coordinates:
Matrix rotation and translation
-0.42533717 0.66963453 -0.60883322 199.74140872
0.07312258 0.69594541 0.71436201 235.67971597
0.90207615 0.25932526 -0.34497685 300.50345968
Axis -0.26974255 -0.89565635 -0.35360805
Axis point 12.54193374 0.00000000 134.23896512
Rotation angle (degrees) 122.49216720
Shift along axis -371.22723480
> select #14/A:20
20 atoms, 21 bonds, 1 residue, 1 model selected
> select add #14/A:19
40 atoms, 42 bonds, 2 residues, 1 model selected
> select add #14/A:18
62 atoms, 66 bonds, 3 residues, 1 model selected
> select add #14/A:17
84 atoms, 90 bonds, 4 residues, 1 model selected
> select add #14/A:16
104 atoms, 111 bonds, 5 residues, 1 model selected
> select add #14/A:15
126 atoms, 135 bonds, 6 residues, 1 model selected
> select add #14/A:14
148 atoms, 159 bonds, 7 residues, 1 model selected
> select add #14/A:13
171 atoms, 184 bonds, 8 residues, 1 model selected
> select add #14/A:12
193 atoms, 208 bonds, 9 residues, 1 model selected
> select add #14/A:11
216 atoms, 233 bonds, 10 residues, 1 model selected
> select add #14/A:10
239 atoms, 258 bonds, 11 residues, 1 model selected
> select add #14/A:9
259 atoms, 279 bonds, 12 residues, 1 model selected
> select add #14/A:8
282 atoms, 304 bonds, 13 residues, 1 model selected
> select add #14/A:7
304 atoms, 328 bonds, 14 residues, 1 model selected
> select add #14/A:6
324 atoms, 349 bonds, 15 residues, 1 model selected
> select add #14/A:5
344 atoms, 370 bonds, 16 residues, 1 model selected
> select add #14/A:4
364 atoms, 391 bonds, 17 residues, 1 model selected
Drag select of 4 residues, 3 shapes
> select clear
> select add #14/A:20
20 atoms, 21 bonds, 1 residue, 1 model selected
> select add #14/A:19
40 atoms, 42 bonds, 2 residues, 1 model selected
> select add #14/A:17
71 atoms, 66 bonds, 4 residues, 1 model selected
> select add #14/A:16
91 atoms, 87 bonds, 5 residues, 1 model selected
> select add #14/A:15
113 atoms, 111 bonds, 6 residues, 1 model selected
> select add #14/A:14
135 atoms, 135 bonds, 7 residues, 1 model selected
> select add #14/A:13
158 atoms, 160 bonds, 8 residues, 1 model selected
> select add #14/A:11
181 atoms, 185 bonds, 9 residues, 1 model selected
> select add #14/A:12
203 atoms, 209 bonds, 10 residues, 1 model selected
> select add #14/A:10
226 atoms, 234 bonds, 11 residues, 1 model selected
> select add #14/A:9
246 atoms, 255 bonds, 12 residues, 1 model selected
> select add #14/A:8
269 atoms, 280 bonds, 13 residues, 1 model selected
> select add #14/A:7
291 atoms, 304 bonds, 14 residues, 1 model selected
> select add #14/A:6
311 atoms, 325 bonds, 15 residues, 1 model selected
> select add #14/A:5
331 atoms, 346 bonds, 16 residues, 1 model selected
> select add #14/A:4
351 atoms, 367 bonds, 17 residues, 1 model selected
> select add #14/A:3
371 atoms, 388 bonds, 18 residues, 1 model selected
> select add #14/A:2
394 atoms, 413 bonds, 19 residues, 1 model selected
> select add #14/A:1
415 atoms, 435 bonds, 20 residues, 1 model selected
> save /Users/lingxiaobin/Desktop/ROOL:GOLLD/map/R18.pdb models #14
> selectedOnly true relModel #14
> open /Users/lingxiaobin/Desktop/ROOL:GOLLD/map/R18.pdb
Chain information for R18.pdb #15
---
Chain | Description
A | No description available
> delete atoms sel
> delete bonds sel
Drag select of 6 atoms, 20 residues, 6 bonds, 57 shapes
> view matrix models #15,1,0,0,117.38,0,1,0,295.02,0,0,1,78.053
> view matrix models #15,1,0,0,198.16,0,1,0,202.18,0,0,1,226.95
> view matrix models #15,1,0,0,216.58,0,1,0,230.1,0,0,1,238.73
> view matrix models #15,1,0,0,208.37,0,1,0,242.14,0,0,1,288.63
> view matrix models #15,1,0,0,198.79,0,1,0,246.39,0,0,1,281.86
> view matrix models #15,1,0,0,201.76,0,1,0,240.27,0,0,1,283.67
> fitmap #15 inMap #1
Fit molecule R18.pdb (#15) to map
cryosparc_P104_J132_8mers_6dot8_map_emready_zflip.mrc (#1) using 415 atoms
average map value = 3.624, steps = 132
shifted from previous position = 6.9
rotated from previous position = 43.3 degrees
atoms outside contour = 151, contour level = 3.2169
Position of R18.pdb (#15) relative to
cryosparc_P104_J132_8mers_6dot8_map_emready_zflip.mrc (#1) coordinates:
Matrix rotation and translation
0.74611491 -0.06069773 -0.66304474 198.79300612
0.19503053 0.97207963 0.13047711 240.55695095
0.63661262 -0.22666488 0.73712102 289.96146065
Axis -0.26033022 -0.94735452 0.18640707
Axis point -375.00743927 0.00000000 354.83722215
Rotation angle (degrees) 43.30960452
Shift along axis -225.59367449
> view matrix models
> #15,0.74611,-0.060698,-0.66304,199.24,0.19503,0.97208,0.13048,238.16,0.63661,-0.22666,0.73712,297.46
> ui mousemode right "rotate selected models"
> view matrix models
> #15,0.57703,-0.61551,0.53683,197.85,0.50688,0.78528,0.35554,243.96,-0.6404,0.066955,0.76512,275.16
> view matrix models
> #15,0.87453,-0.31385,0.36972,201.1,0.3699,0.9247,-0.089997,241.76,-0.31363,0.21546,0.92478,279.02
> ui mousemode right "translate selected models"
> view matrix models
> #15,0.87453,-0.31385,0.36972,200.69,0.3699,0.9247,-0.089997,245.58,-0.31363,0.21546,0.92478,278.88
> fitmap #15 inMap #1
Fit molecule R18.pdb (#15) to map
cryosparc_P104_J132_8mers_6dot8_map_emready_zflip.mrc (#1) using 415 atoms
average map value = 3.704, steps = 124
shifted from previous position = 4.66
rotated from previous position = 41.2 degrees
atoms outside contour = 143, contour level = 3.2169
Position of R18.pdb (#15) relative to
cryosparc_P104_J132_8mers_6dot8_map_emready_zflip.mrc (#1) coordinates:
Matrix rotation and translation
0.92039512 -0.38731503 -0.05347789 204.17294026
0.27480251 0.73810508 -0.61618542 246.84011553
0.27813018 0.55243819 0.78578346 279.41494457
Axis 0.84469246 -0.23968953 0.47858497
Axis point 0.00000000 -85.15521515 532.87605653
Rotation angle (degrees) 43.76840156
Shift along axis 247.02214642
> hide #10 models
> hide #!9 models
> show #!9 models
> hide #!13 models
> hide #11 models
> select #14/A:47
20 atoms, 21 bonds, 1 residue, 1 model selected
> ui mousemode right "rotate selected models"
> view matrix models
> #14,-0.80674,0.4763,0.34972,201.39,0.36897,-0.056247,0.92774,232.4,0.46155,0.87748,-0.13036,304.27
> view matrix models
> #14,-0.81784,0.56802,0.092177,201.46,0.20032,0.13087,0.97095,233.67,0.53946,0.81254,-0.22081,303.68
> ui mousemode right "translate selected models"
> view matrix models
> #14,-0.81784,0.56802,0.092177,203.58,0.20032,0.13087,0.97095,227.52,0.53946,0.81254,-0.22081,302.35
> ui mousemode right "rotate selected models"
> view matrix models
> #14,-0.88928,0.31483,0.33175,203.33,0.36004,0.034585,0.9323,226.56,0.28204,0.94852,-0.14411,303.87
> ui mousemode right "translate selected models"
> view matrix models
> #14,-0.88928,0.31483,0.33175,204.51,0.36004,0.034585,0.9323,223.67,0.28204,0.94852,-0.14411,306.6
> ui mousemode right "rotate selected models"
> view matrix models
> #14,-0.30928,0.49844,-0.80988,201.88,-0.10065,0.8297,0.54907,227.65,0.94563,0.25133,-0.20644,301.75
> view matrix models
> #14,0.39262,-0.24999,-0.88507,197.09,0.26419,0.95245,-0.15182,226.11,0.88094,-0.17422,0.44,301.28
> ui mousemode right "translate selected models"
> view matrix models
> #14,0.39262,-0.24999,-0.88507,187.84,0.26419,0.95245,-0.15182,231.98,0.88094,-0.17422,0.44,293.82
> ui mousemode right "rotate selected models"
> view matrix models
> #14,0.20169,0.022969,-0.97918,189.32,0.29553,0.9517,0.083199,232.16,0.9338,-0.30616,0.18516,293.13
> view matrix models
> #14,0.26403,-0.25307,-0.93072,188.39,0.23492,0.95278,-0.19242,232.12,0.93547,-0.16784,0.31102,293.76
> ui mousemode right "translate selected models"
> view matrix models
> #14,0.26403,-0.25307,-0.93072,190.38,0.23492,0.95278,-0.19242,230.56,0.93547,-0.16784,0.31102,294.84
> fitmap #14 inMap #1
Fit molecule fold_2024_07_25_17_20_model_0.cif (#14) to map
cryosparc_P104_J132_8mers_6dot8_map_emready_zflip.mrc (#1) using 965 atoms
average map value = 3.772, steps = 280
shifted from previous position = 5.42
rotated from previous position = 78.8 degrees
atoms outside contour = 368, contour level = 3.2169
Position of fold_2024_07_25_17_20_model_0.cif (#14) relative to
cryosparc_P104_J132_8mers_6dot8_map_emready_zflip.mrc (#1) coordinates:
Matrix rotation and translation
-0.47310798 0.67656046 -0.56430026 200.57236931
0.05613124 0.66236593 0.74707473 235.62532479
0.87921449 0.32177215 -0.35134678 300.58908837
Axis -0.26128351 -0.88681944 -0.38115904
Axis point 19.92203616 0.00000000 129.36248048
Rotation angle (degrees) 125.52403482
Shift along axis -375.93561872
> select #15/A:10
23 atoms, 25 bonds, 1 residue, 1 model selected
> ui mousemode right "rotate selected models"
> view matrix models
> #15,0.85047,-0.5144,-0.10992,204.17,0.49563,0.85365,-0.16011,248.85,0.17619,0.081689,0.98096,280.37
> ui mousemode right "translate selected models"
> view matrix models
> #15,0.85047,-0.5144,-0.10992,201.53,0.49563,0.85365,-0.16011,248.44,0.17619,0.081689,0.98096,287.94
> view matrix models
> #15,0.85047,-0.5144,-0.10992,201.36,0.49563,0.85365,-0.16011,248.79,0.17619,0.081689,0.98096,288.26
> fitmap #15 inMap #1
Fit molecule R18.pdb (#15) to map
cryosparc_P104_J132_8mers_6dot8_map_emready_zflip.mrc (#1) using 415 atoms
average map value = 3.704, steps = 120
shifted from previous position = 4.99
rotated from previous position = 30.8 degrees
atoms outside contour = 144, contour level = 3.2169
Position of R18.pdb (#15) relative to
cryosparc_P104_J132_8mers_6dot8_map_emready_zflip.mrc (#1) coordinates:
Matrix rotation and translation
0.92036470 -0.38720869 -0.05475630 204.16253752
0.27392308 0.73825947 -0.61639200 246.81242552
0.27909670 0.55230643 0.78553335 279.42572719
Axis 0.84466615 -0.24128922 0.47782697
Axis point 0.00000000 -85.67296838 533.25375559
Rotation angle (degrees) 43.77362560
Shift along axis 246.41315436
> select clear
> delete atoms sel
> delete bonds sel
Drag select of 1 atoms
> delete atoms sel
> delete bonds sel
> select clear
No visible atoms or bonds selected
> select clear
> select #9/I:223
22 atoms, 24 bonds, 1 residue, 1 model selected
> select up
1392 atoms, 1556 bonds, 65 residues, 1 model selected
> show sel target ab
> select #15/A:18
9 atoms, 9 bonds, 1 residue, 1 model selected
> select add #15/A:17
31 atoms, 33 bonds, 2 residues, 1 model selected
> select add #15/A:20
51 atoms, 54 bonds, 3 residues, 1 model selected
> select add #15/A:19
71 atoms, 75 bonds, 4 residues, 1 model selected
> view matrix models
> #15,0.92036,-0.38721,-0.054756,204.1,0.27392,0.73826,-0.61639,246.74,0.2791,0.55231,0.78553,278.92
> fitmap #15 inMap #1
Fit molecule R18.pdb (#15) to map
cryosparc_P104_J132_8mers_6dot8_map_emready_zflip.mrc (#1) using 415 atoms
average map value = 3.704, steps = 64
shifted from previous position = 0.524
rotated from previous position = 0.0343 degrees
atoms outside contour = 143, contour level = 3.2169
Position of R18.pdb (#15) relative to
cryosparc_P104_J132_8mers_6dot8_map_emready_zflip.mrc (#1) coordinates:
Matrix rotation and translation
0.92032283 -0.38722463 -0.05534414 204.16134066
0.27363920 0.73844650 -0.61629404 246.80670170
0.27951292 0.55204515 0.78556902 279.44037841
Axis 0.84452173 -0.24204792 0.47769849
Axis point 0.00000000 -85.90603644 533.60916697
Rotation angle (degrees) 43.76613679
Shift along axis 246.16788865
> ui mousemode right "translate selected atoms"
> select #15/A:17
22 atoms, 24 bonds, 1 residue, 1 model selected
> select #15/A:18
9 atoms, 9 bonds, 1 residue, 1 model selected
> select add #15/A:19
29 atoms, 30 bonds, 2 residues, 1 model selected
> select add #15/A:20
49 atoms, 51 bonds, 3 residues, 1 model selected
> select #1
2 models selected
> select clear
> select #15/A:18
9 atoms, 9 bonds, 1 residue, 1 model selected
> select #9/I:223
22 atoms, 24 bonds, 1 residue, 1 model selected
> select #15/A:18
9 atoms, 9 bonds, 1 residue, 1 model selected
> select clear
> select #15/A:19
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #15/A:20
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #14/A:21
20 atoms, 21 bonds, 1 residue, 1 model selected
> select clear
> select #15/A:16
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #15/A:17
22 atoms, 24 bonds, 1 residue, 1 model selected
> select #15/A:18@C1'
1 atom, 1 residue, 1 model selected
> select up
9 atoms, 9 bonds, 1 residue, 1 model selected
> select #14/A:64
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #14/A:63
22 atoms, 24 bonds, 1 residue, 1 model selected
> select add #14/A:64
42 atoms, 45 bonds, 2 residues, 1 model selected
> select add #14/A:62
64 atoms, 69 bonds, 3 residues, 1 model selected
> select add #14/A:61
86 atoms, 93 bonds, 4 residues, 1 model selected
> select subtract #14/A:61
64 atoms, 69 bonds, 3 residues, 1 model selected
> select subtract #14/A:63
42 atoms, 45 bonds, 2 residues, 1 model selected
> select subtract #14/A:62
20 atoms, 21 bonds, 1 residue, 1 model selected
> select add #14/A:63
42 atoms, 45 bonds, 2 residues, 1 model selected
> select subtract #14/A:63
20 atoms, 21 bonds, 1 residue, 1 model selected
> select add #14/A:61
42 atoms, 45 bonds, 2 residues, 1 model selected
> select add #14/A:62
64 atoms, 69 bonds, 3 residues, 1 model selected
> select add #14/A:63
86 atoms, 93 bonds, 4 residues, 1 model selected
> select add #14/A:60
108 atoms, 117 bonds, 5 residues, 1 model selected
> select subtract #14/A:60
86 atoms, 93 bonds, 4 residues, 1 model selected
> select subtract #14/A:61
64 atoms, 69 bonds, 3 residues, 1 model selected
> select subtract #14/A:64
44 atoms, 48 bonds, 2 residues, 1 model selected
> select add #14/A:64
64 atoms, 69 bonds, 3 residues, 1 model selected
> select subtract #14/A:62
42 atoms, 45 bonds, 2 residues, 1 model selected
> select subtract #14/A:63
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #15/A:19
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #15/A:18@C1'
1 atom, 1 residue, 1 model selected
> select clear
> select #15/A:17
22 atoms, 24 bonds, 1 residue, 1 model selected
> select #15/A:18
9 atoms, 9 bonds, 1 residue, 1 model selected
> select #15/A:19
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #15/A:20
20 atoms, 21 bonds, 1 residue, 1 model selected
> select clear
> select #15/A:17
22 atoms, 24 bonds, 1 residue, 1 model selected
> select #15/A:18
9 atoms, 9 bonds, 1 residue, 1 model selected
> select #15/A:19
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #15/A:20
20 atoms, 21 bonds, 1 residue, 1 model selected
> select clear
> select #15/A:1
21 atoms, 22 bonds, 1 residue, 1 model selected
> select #15/A:2
23 atoms, 25 bonds, 1 residue, 1 model selected
> select #9/I:216
22 atoms, 24 bonds, 1 residue, 1 model selected
> select #9/I:217
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #9/I:219
22 atoms, 24 bonds, 1 residue, 1 model selected
> select #9/I:218
22 atoms, 24 bonds, 1 residue, 1 model selected
> select #9/I:220
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #9/I:221
22 atoms, 24 bonds, 1 residue, 1 model selected
> select #9/I:223
22 atoms, 24 bonds, 1 residue, 1 model selected
> select #9/I:222
23 atoms, 25 bonds, 1 residue, 1 model selected
> select #9/I:220
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #9/I:219
22 atoms, 24 bonds, 1 residue, 1 model selected
> select #9/I:216
22 atoms, 24 bonds, 1 residue, 1 model selected
> select #9/I:218
22 atoms, 24 bonds, 1 residue, 1 model selected
> select #9/I:220
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #9/I:221
22 atoms, 24 bonds, 1 residue, 1 model selected
> select #9/I:222
23 atoms, 25 bonds, 1 residue, 1 model selected
> select #9/I:223
22 atoms, 24 bonds, 1 residue, 1 model selected
> select #9/I:222
23 atoms, 25 bonds, 1 residue, 1 model selected
> select #9/I:223
22 atoms, 24 bonds, 1 residue, 1 model selected
> select #9/I:221
22 atoms, 24 bonds, 1 residue, 1 model selected
> select #9/I:222
23 atoms, 25 bonds, 1 residue, 1 model selected
> select #9/I:221
22 atoms, 24 bonds, 1 residue, 1 model selected
> select #15/A:18
9 atoms, 9 bonds, 1 residue, 1 model selected
> select #15/A:19
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #15/A:20
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #9/I:289@N4
1 atom, 1 residue, 1 model selected
> select #9/I:289@C1'
1 atom, 1 residue, 1 model selected
> select #9/I:289@C4'
1 atom, 1 residue, 1 model selected
Drag select of 8 atoms, 11 bonds
> select clear
Drag select of 12 atoms, 13 bonds
> select clear
> select #9/I:289
20 atoms, 21 bonds, 1 residue, 1 model selected
> select clear
> select #9/I:289@N1
1 atom, 1 residue, 1 model selected
> select #9/I:219@N6
1 atom, 1 residue, 1 model selected
> select #9/I:219
22 atoms, 24 bonds, 1 residue, 1 model selected
===== Log before crash end =====
Log:
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 Metal - 76.3
OpenGL renderer: Apple M1 Pro
OpenGL vendor: Apple
Python: 3.11.2
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro18,3
Chip: Apple M1 Pro
Total Number of Cores: 8 (6 performance and 2 efficiency)
Memory: 16 GB
System Firmware Version: 7429.81.3
OS Loader Version: 7429.81.3
Software:
System Software Overview:
System Version: macOS 12.2.1 (21D62)
Kernel Version: Darwin 21.3.0
Time since boot: 7 days 9:27
Graphics/Displays:
Apple M1 Pro:
Chipset Model: Apple M1 Pro
Type: GPU
Bus: Built-In
Total Number of Cores: 14
Vendor: Apple (0x106b)
Metal Family: Supported, Metal GPUFamily Apple 7
Displays:
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3024 x 1964 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: No
Connection Type: Internal
Installed Packages:
alabaster: 0.7.16
appdirs: 1.4.4
appnope: 0.1.3
asttokens: 2.4.1
Babel: 2.14.0
backcall: 0.2.0
beautifulsoup4: 4.11.2
blockdiag: 3.0.0
blosc2: 2.0.0
build: 0.10.0
certifi: 2022.12.7
cftime: 1.6.3
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.13
ChimeraX-AddH: 2.2.5
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.4.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.2
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.49.1
ChimeraX-AtomicLibrary: 12.1.5
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: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.10.5
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: 1.1
ChimeraX-CheckWaters: 1.3.2
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-Clipper: 0.22.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.5
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.7.1
ChimeraX-CoreFormats: 1.2
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: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ISOLDE: 1.7.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-Label: 1.1.8
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.1.4
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.1.2
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.6.1
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.12.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.14
ChimeraX-ModelPanel: 1.4
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.1
ChimeraX-NRRD: 1.1
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.1
ChimeraX-PDB: 2.7.3
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBImages: 1.2
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-QScore: 1.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.2
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.11
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.2
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StarMap: 1.2.15
ChimeraX-StdCommands: 1.12.4
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: 2.2.2
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.33.3
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.3.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.3
ChimeraX-XMAS: 1.1.3
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.1
contourpy: 1.2.0
cxservices: 1.2.2
cycler: 0.12.1
Cython: 0.29.33
debugpy: 1.8.0
decorator: 5.1.1
docutils: 0.19
et-xmlfile: 1.1.0
executing: 2.0.1
filelock: 3.9.0
fonttools: 4.47.2
funcparserlib: 2.0.0a0
glfw: 2.6.4
grako: 3.16.5
h5py: 3.10.0
html2text: 2020.1.16
idna: 3.6
ihm: 0.38
imagecodecs: 2023.9.18
imagesize: 1.4.1
ipykernel: 6.23.2
ipython: 8.14.0
ipython-genutils: 0.2.0
ipywidgets: 8.1.1
jedi: 0.18.2
Jinja2: 3.1.2
jupyter-client: 8.2.0
jupyter-core: 5.7.1
jupyterlab-widgets: 3.0.9
kiwisolver: 1.4.5
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.4
matplotlib: 3.7.2
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.6.0
netCDF4: 1.6.2
networkx: 3.1
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.8.8
numpy: 1.25.1
openpyxl: 3.1.2
openvr: 1.23.701
packaging: 21.3
pandas: 2.2.2
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pexpect: 4.9.0
pickleshare: 0.7.5
pillow: 10.2.0
pip: 23.0
pkginfo: 1.9.6
platformdirs: 4.1.0
prompt-toolkit: 3.0.43
psutil: 5.9.5
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.16.1
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.2801
pyparsing: 3.0.9
pyproject-hooks: 1.0.0
PyQt6-commercial: 6.3.1
PyQt6-Qt6: 6.3.2
PyQt6-sip: 13.4.0
PyQt6-WebEngine-commercial: 6.3.1
PyQt6-WebEngine-Qt6: 6.3.2
pyqtgraph: 0.13.7
python-dateutil: 2.8.2
pytz: 2023.3.post1
pyzmq: 25.1.2
qtconsole: 5.4.3
QtPy: 2.4.1
QtRangeSlider: 0.1.5
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.11.1
seaborn: 0.13.2
setuptools: 67.4.0
setuptools-scm: 7.0.5
sfftk-rw: 0.7.3
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 6.1.3
sphinx-autodoc-typehints: 1.22
sphinxcontrib-applehelp: 1.0.8
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.6
sphinxcontrib-htmlhelp: 2.0.5
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.7
sphinxcontrib-serializinghtml: 1.1.10
stack-data: 0.6.3
superqt: 0.5.0
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2023.7.18
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.4
traitlets: 5.9.0
typing-extensions: 4.9.0
tzdata: 2023.4
urllib3: 2.1.0
wcwidth: 0.2.13
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.9
![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Crashed in threaded C++ implementation of find_group. Not too much else to go on.